Intramolecular Hydrogen Bonding Involving

molecules Review

Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations Sandeep Kumar Mishra and N. Suryaprakash * NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India; [email protected] * Correspondence: [email protected]; Tel.: +80-2293-7344 or +80-2293-3300 or +91-9845124802; Fax: +91-2360-1550 Academic Editor: Steve Scheiner Received: 31 January 2017; Accepted: 2 March 2017; Published: 7 March 2017

Abstract: The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established. Keywords: NMR spectroscopy; intramolecular hydrogen bond; organic fluorine

1. Introduction 1.1. Weak Molecular Interactions The presence of molecular interactions in Nature cannot be ignored. The existence of various forms of matter, such as, solids and liquids is mainly due to the presence of intermolecular interactions. One can safely make a statement that the world would be a uniform ideal gas in the absence of intermolecular interactions. The existence of intermolecular interactions is reflected at the molecular level, viz., the thermodynamic non-ideal-gas behavior arising due to vapor pressure, viscosity, virial coefficients, absorption, and superficial tension [1]. The molecular interactions are non-covalent and are inherently electrostatic in nature. These forces could be attractive, repulsive or the combination of attractive as well as repulsive between or within the molecules. They could also be between non-bonded atoms. Intermolecular interactions play predominant role in many fields, such as, conformation of biomolecules, drug design, etc. Kaplan classified the intermolecular interactions on the basis of distance between the interacting objects [2]. In the classification, there are three main ranges for molecular forces depending on the

Molecules 2017, 22, 423; doi:10.3390/molecules22030423

www.mdpi.com/journal/molecules

Molecules 2017, 22, 423

2 of 44

interatomic distances Molecules 2017, 22, 423

(R) for an interatomic potential (V). For range I the short distances are defined 2 of 41 where the potential is repulsive in nature and the electronic exchange is due to the overlapped molecular electronic shells. The rangeand II represents theexchange intermediate with themolecular van der where the potential is repulsive in nature the electronic is due distances to the overlapped Waals minimum, which arises due to the between repulsive and forces.minimum, Range III electronic shells. The range II represents thebalance intermediate distances with theattractive van der Waals represents the large distances negligible electronic exchangeforces. whereRange the intermolecular are which arises due to the balancewith between repulsive and attractive III representsforces the large predominantly attractive. electronic The representation rangethe of molecular forcesforces is illustrated in Figure 1a. distances with negligible exchangeofwhere intermolecular are predominantly Depending on the nature, the various molecular interactions can also be classified as given in the attractive. The representation of range of molecular forces is illustrated in Figure 1a. Depending on Figure 1b. the various molecular interactions can also be classified as given in the Figure 1b. the nature,

Figure of intermolecular intermolecular interactions interactionson onthe thebasis basisofofinteratomic interatomicdistances distancesfor fora Figure 1. 1. (a) (a) The The classification classification of atypical typicalinteratomic interatomicpotential. potential.Where WhereRRisisthe the distance distance between between the the centers of masses of the molecules, centers of masses of the molecules, V and thethe graph of VofasVthe of R isofcalled model V isisthe theLennard-Johns Lennard-Johnspotential potential and graph asfunction the function R is Lennard-Johns called Lennard-Johns potential graph; (b) Schematic illustration of some of known molecular interactions. Some model potential graph; (b) Schematic illustration of some of known molecular interactions. Some other other molecular molecular interactions interactions that that are are not not listed listed in in the the scheme scheme may may also also be be possible. possible. This This review review is is mainly mainly focused the scheme. scheme. focused on on the the intramolecular intramolecular HB HB hence hence hydrogen hydrogen bonding bonding is is highlighted highlighted in in the

The change in molecular interactions are reflected in physical, chemical and biological phenomenon, such as, phase transitions of water (ice to water to vapor or vice versa), protein folding and unfolding and separation of DNA strands, RNA unfolding, etc. Such processes do not fall under chemical reactions. All the weak molecular interactions have their specific significance and govern the properties of a substrate it may be pointed out that the intermolecular interactions cannot be measured directly by any experiment.

Molecules 2017, 22, 423

3 of 44

The change in molecular interactions are reflected in physical, chemical and biological phenomenon, such as, phase transitions of water (ice to water to vapor or vice versa), protein folding and unfolding and separation of DNA strands, RNA unfolding, etc. Such processes do not fall under chemical reactions. All the weak molecular interactions have their specific significance and govern the properties of a substrate it may be pointed out that the intermolecular interactions cannot be measured directly 2017, by any experiment. Molecules 22, 423 3 of 41 Among all the weak molecular interactions described in Figure 1, except for the hydrogen bond (HB),Among usually tomolecular intermolecular interactions. the other hand, HB can be detected allpertain the weak interactions describedOn in Figure 1, except forthe the hydrogen bond (HB), within the molecule or between the two or more molecules. Thisthe review is focused on the studies usually pertain to intermolecular interactions. On the other hand, HB can be detected within the carried out by authors’ laboratory on the rare type of intramolecular hydrogen bonding (HB) involving molecule or between the two or more molecules. This review is focused on the studies carried out by organic fluorine. authors’ laboratory on the rare type of intramolecular hydrogen bonding (HB) involving organic fluorine. 1.2. Hydrogen Hydrogen Bond Bond 1.2. The idea idea of of HB HB was was first first suggested by Huggins Huggins [3–6] [3–6] in in 1919, 1919, and and was was further further described described by by The suggested by Larimer and and Rodebush Rodebush in in 1920 1920 [7]. [7]. HB HB is is an an interaction interaction which which occurs occurs between between an an atom atom containing containing aa Larimer lone pair of electrons (a Lewis base) and a hydrogen atom which is bonded to an electronegative atom lone pair of electrons (a Lewis base) and a hydrogen atom which is bonded to an electronegative atom (e.g., N, the Lewis base plays thethe rolerole of aofHB acceptor (A) (e.g., N, O, O, SS or orF) F)through throughaacovalent covalentbond. bond.InIna aHB, HB, the Lewis base plays a HB acceptor and the electronegative atom bonded to proton is called the HB donor (D). The hydrogen bonding (A) and the electronegative atom bonded to proton is called the HB donor (D). The hydrogen bonding interaction is is schematically schematically depicted depicted in interaction in Figure Figure 2. 2.

Figure where HB acceptor/donor cancan be F, Figure 2. 2. The Thepictorial pictorialillustration illustrationofofhydrogen hydrogenbond bondinteraction, interaction, where HB acceptor/donor beO, F, N, or S atom in the molecule. Polarization of electron and exposure of positive proton on either side is O, N, or S atom in the molecule. Polarization of electron and exposure of positive proton on either side shown schematically. is shown schematically.

Hydrogen is the only atom that easily participate in the HB. This is due to the fact that hydrogen Hydrogen is the only atom that easily participate in the HB. This is due to the fact that hydrogen atom can form covalent sigma bonds with electronegative atoms like F, N, O and S, etc., where the atom can form covalent sigma bonds with electronegative atoms like F, N, O and S, etc., where the electron of 1s shells participates in the covalent bond. Since the more electronegative atom has tendency electron of 1s shells participates in the covalent bond. Since the more electronegative atom has tendency to pull the shared electron pair towards it, in the covalent bond between hydrogen and electronegative to pull the shared electron pair towards it, in the covalent bond between hydrogen and electronegative atom the bonding electrons moves away from hydrogen nucleus. Due to this the positive charge gets atom the bonding electrons moves away from hydrogen nucleus. Due to this the positive charge gets exposed from the back side (the opposite side to the bonded partner). This exposed positive nucleus exposed from the back side (the opposite side to the bonded partner). This exposed positive nucleus attracts the partial negative charge of lone pair of the other nucleus. On the other hand, the atoms attracts the partial negative charge of lone pair of the other nucleus. On the other hand, the atoms other than proton having non-bonding electrons in the inner shell shields the nucleus precluding it other than proton having non-bonding electrons in the inner shell shields the nucleus precluding it from getting exposed in this manner. from getting exposed in this manner. Importance of Hydrogen Bond Importance of Hydrogen Bond Hydrogen bonding is an important non-covalent interaction encountered most often in Hydrogen bonding is an important non-covalent interaction encountered most often in chemistry chemistry and biology [8–11]. Voluminous information is available on the self-assembly of molecules and biology [8–11]. Voluminous information is available on the self-assembly of molecules driven driven by HB [12–24]. HB interaction is responsible for the three-dimensional conformation of proteins, synthetic foldamers [25–33], peptide catalysis, peptidomimetic design [34–39], double helical structure of DNA [40,41], unique properties of water [42], etc. Thus, in-depth knowledge of HB interaction aids in understanding the chemical properties of many organic and bio-macromolecules [43–53].

Molecules 2017, 22, 423

4 of 44

by HB [12–24]. HB interaction is responsible for the three-dimensional conformation of proteins, synthetic foldamers [25–33], peptide catalysis, peptidomimetic design [34–39], double helical structure of DNA [40,41], unique properties of water [42], etc. Thus, in-depth knowledge of HB interaction aids in understanding the chemical properties of many organic and bio-macromolecules [43–53]. 1.3. Organic Fluorine in the HB A large fraction of the information available in the literature on intramolecular HB pertains to the motifs of the type O···H-N and N···H-N [54–58]. It is well known that organic fluorine hardly ever accepts HB. Dunitz and co-workers have even published a paper entitled “organic fluorine hardly ever accepts hydrogen bonds” [59–62]. Nevertheless, a few reports are available on the participation of organic fluorine in the HB in the solution state [63,64]. In foldamers and benzanilides, NMR and X-ray crystallographic studies have also been reported on the N-H···F-C HB [65,66]. Recently DFT theoretical studies have been carried out on organofluorine systems and through space J couplings have been also reported [67,68]. The first NMR spectroscopic observation of through space (1h JFH ) coupling revealed the information about the involvement of organic fluorine in the HB in the solution state [69]. The Limbach group have reported numerous examples where not only organic fluorine but other halogens also participate in the intermolecular HB [70–73]. Subsequently this field of research has seen phenomenal growth. Furthermore, the utility of organofluorine molecules as drugs, agrochemicals, biomaterials and also in molecular imaging is well documented [74,75]. Organic fluorine also has enormous importance in molecular association applications, such as crystal engineering [76–78] and in the design of the functional materials [79]. Consequent to the binding nature of fluorinated molecules with enzyme active sites, intermolecular hydrogen bonds of the type X-H···F-C (X = O, N) are highly significant, especially in bio-inorganic and medicinal chemistry [80–84]. Despite all its importance in various branches of chemistry and biology, there is limited exploration of organic fluorine-involved HBs, attributed mainly to the fact flourine hardly ever accepts intramolecular HB [85–89]. The present review summarizes the work carried out by authors’ laboratory in recent years, taken directly from their published work. 1.4. NMR Spectroscopic Techniques for the Detection of Hydrogen Bond NMR spectroscopy has proven as a powerful tool in deriving information about HB. Monitoring of the chemical shift as a function of variation in the physical parameters, such as, dilution, temperature is a general technique adopted for gathering information about the HB. The other important parameter that can provide the unambiguous evidence about the existence of HB is through space coupling between two NMR active nuclei mediated by HB. Many of these parameters can be measured by various one and two dimensional NMR experiments. 1.5. Theoretical Calculations The information derived by NMR spectroscopic analysis will conclusively evident if it is also corroborated by theoretical calculations. For such a purpose, various DFT-based theoretical calculations can be carried out. The commonly employed theoretical methods are briefly introduced below. 1.5.1. Non-Covalent Interaction (NCI) Calculations For the detection of non-covalent interactions in real space, which is dependent on the electron density and its derivatives, NCI [90] calculations are performed. They provide a strong representation of the steric repulsion, van der Waals interactions and the HBs. The calculations yield a large positive gradient of the reduced density gradient (RDG), and the RDG values will be small and approach to zero in the density tail (i.e., regions far from the molecule, where the electron density exponentially decays to zero). This is the condition for both the covalent and non-covalent bonding regions respectively. There will be a strong correlation of electron density (ρ(r) ) with the weak interactions in the corresponding regions. The correlations for the HB are negative and positive for the steric effect. On the other hand,

Molecules 2017, 22, 423

5 of 44

for van der Waals interaction the ρ(r) values are always small [90] (near to zero). The calculated grid points are plotted for a defined real space function, sign(λ2(r) )ρ(r) , as function 1 and reduced density gradient (RDG) as function 2. 1.5.2. Atoms in Molecules (AIM) Calculations For in depth understanding of the molecular properties influenced by weak HBs the interaction energy must be known. The topology analysis technique has been reported and is cited as “atoms in molecules” (AIM) theory. It is also cited as “the quantum theory of atoms in molecules” (QTAIM) [91–95] which is dependent on the quantum observables (electron density ρ(r) and the energy densities). In topology analysis, the critical points (CPs) are those points where gradient norm of function value is zero (except at infinity). According to the negative eigenvalues of the Hessian matrix of the real space function [91–95] CPs can be of four types. Out of these the (3, −1) CP is called the bond critical point (BCP). The value of the real space function at the BCP has a great significance. For example, the bond strength and bond type respectively are related closely to the value of electron density (ρ(r) ) and the sign of Laplacian of electron density (∇2 ρ(r) ) at BCPs [91–95]. The sign of (∇2 ρ(r) ) at BCP is important in discriminating shared-shell (covalent bond (−ve)) and closed-shell (ionic, van der Waals interaction, and HB (+ve)). AIM calculations yield the magnitudes of ρ(r) and signs of ∇2 ρ( r ) for BCP of HBs of interest. At corresponding (3, −1) critical points (rcp ) the gradients of electron density (ρ(r) ) gets vanished. The energy of HB (EHB ) is directly related to potential energy density (V (r) ) by straightforward relationship EHB = V(rbcp )/2 [96]. The EHB of X···HX type HB can be calculated. 1.5.3. Natural Bond Orbitals (NBO) Per-Olov Löwdin introduced the concept of natural orbitals in 1955, to describe the unique set of orthonormal 1-electron functions which are intrinsic to the N-electron wavefunction. NBO is calculated where the electron density could be the maximum. The general sequence of localized orbital is: (1) natural atomic orbitals (NAO); (2) natural hybrid orbitals (NHO); (3) natural bonding orbitals (NBO) and (4) natural (semi-) localized molecular orbitals (NLMO). These localized sets are considered as intermediate between basic atomic orbitals (AO) and molecular orbitals (MO). For the calculation of the electron density distribution in individual atoms and in bonds formed between atoms, NBOs are frequently utilized in computational chemistry. NBOs provide the percentage of highest possible electron density and most possibility for “natural Lewis structure” of ψ. During the formation of HB, the electron transfer from the HB acceptor (lone pairs (lp)) to the anti-bonding orbital (σ*) of the H atom takes place. NBO analysis is proved to be a powerful technique to obtain the detailed information of lp transfer. 1.5.4. Molecular Dynamics (MD) The idea of molecular dynamics (MD) was first proposed in the 1950s [97]. MD is a computational method for studying the motion of atoms, groups, or molecules. MD studies give dynamic information about the atoms or group of atoms or molecules that interact for a period of time. During MD simulations, mostly the trajectories of atoms/molecules are stabilized where forces and potential energies among the particles are calculated by molecular mechanics force fields or interatomic potentials. MD is also called statistical mechanics by numbers and Laplace’s vision of Newtonian mechanics of predicting the dynamics by animating nature's forces and revealing the information of molecular motion at an atomic scale. MD simulations are also found be very powerful in the detection and quantification of the percentage of different conformers of a molecule where there exists a freely rotating group.

Molecules 2017, 22, 423

6 of 44

2. Studies on Benzanilides Isomers of fluorinated benzanilides belong to the class of molecules where the cooperative interplay of weak interactions is highly significant in building their higher analogues, called driven foldamers, supra-molecular clusters and bulk moieties such as dendrimers [86,98,99]. Hence these molecules have drawn great attention in structural chemistry. Furthermore, the C-F bond is longer, has opposite bond polarity, stronger than C-H bond and makes the molecule more resistant towards metabolic degradation. As a consequence, the families of these molecules have important biological applications as voltage dependent potassium channel openers [100–103]. Especially while modeling the higher analogs of benzanilides, three centered N-H···F HBs provide a new approach for the formation of structural features via strong binding effects and induced chirality upon complexation with chiral L-tyrosine-derived ammonium ions [86]. Hence extensive studies have been carried out on the intramolecular HB interactions in the fluorine-substituted derivatives of benzanilides [104]. 2.1. NMR Spectroscopic Experimental Findings Molecules 2017, 22, 423

6 of 41

NMR 2.1. spectroscopy can be used to distinguish between labile free and hydrogen bonded protons, NMR Spectroscopic Experimental Findings possessing different exchangecan rates, even in complex molecules if their exchange rates are within NMR spectroscopy be used to distinguish between labile free and hydrogen bonded protons, the NMR time scaledifferent [105–110]. Hence about hydrogen bondingrates canare bewithin derived possessing exchange rates,information even in complex molecules if their exchange the from the NMRparameters time scale [105–110]. Hence information about hydrogen bonding be derived from theon NMR NMR spectral [70,72,111–114]. Investigations have thuscan been carried out a set of four spectral parameters [70,72,111–114]. Investigations have thus been carried out on a set of four derivatives of fluorinated benzanilides, whose chemical structures are reported in Figure 3, where derivatives of fluorinated benzanilides, whose chemical /structures are reported in Figure 3, where there there the fluorine substitution atpositions positions X and/or X has been systematically altered. the fluorine substitution at X and/or X/ has been systematically altered.

Figure 3. Chemical structures with numbering of interacting spins of fluorine-substituted benzanilides.

Figure 3. Chemical structures with numbering of interacting spins of fluorine-substituted benzanilides. The 400 MHz 1H-NMR spectra of molecules 1, 2, 3 and 4 respectively (top trace to bottom trace) in the 1 The 400 MHz spectra of molecules 2, 3 made and 4based respectively (top trace (MQ)-single to bottom trace) in peak assignments have1,been on multiple quantum solventH-NMR CDCl3. The experiments.have The expansions forbased amide on protons in each molecule (MQ)-single are the solventquantum CDCl3 .(SQ) Thecorrelation peak assignments been made multiple quantum depicted by arrowsexperiments. (reproduced from quantum (SQ) correlation The[103]). expansions for amide protons in each molecule are depicted by arrows Unambiguous (reproduced from [103]). assignment of aromatic 1H resonances have also been made employing the higher quantum correlation experiments for filtering of spectrum corresponding to different spin systems [115–117]. The systematic study by employing diverse one and two dimensional NMR experiments revealed information about the weak interactions in all the investigated fluorine-substituted derivatives of benzanilides at ambient conditions. 2.1.1. Detection of Spin-Spin Couplings Mediated by Hydrogen Bonds NH proton signals are either singlets (in molecules 1, 2) or a partially resolved doublet (in molecules

Molecules 2017, 22, 423

7 of 44

Unambiguous assignment of aromatic 1 H resonances have also been made employing the higher quantum correlation experiments for filtering of spectrum corresponding to different spin systems [115–117]. The systematic study by employing diverse one and two dimensional NMR experiments revealed information about the weak interactions in all the investigated fluorine-substituted derivatives of benzanilides at ambient conditions. 2.1.1. Detection of Spin-Spin Couplings Mediated by Hydrogen Bonds NH proton signals are either singlets (in molecules 1, 2) or a partially resolved doublet (in molecules Hz. Molecules 2017, 22, 3 423and 4). The peak separation of the partially resolved doublet is about 16 7 of 41 These partially resolved doublets might be due to the proton exchange between two distinguishable chemical orlong due to the existence of long range scalar couplings. The particular type of or due to environments the existence of range scalar couplings. The particular type of interaction responsible 1 19 19 interaction responsible this can be identified by either two-dimensional exchange for this can be identified for by either two-dimensional exchange spectroscopy (EXSY), or H-{ spectroscopy F} or F-{1H} 1 19 19 1 1 H-{19 F} or 1H-{19F} of 19F-{NH 1H} spectra (EXSY), or H-{ F} or F-{ H} NH experiments. doublets in both experiments. The collapse of the doublets inThe bothcollapse or the in the molecules 3 and 19 F-{1 H} spectra in the molecules 3 and 4, is conclusively evident from Figure 4. This unambiguously 4, is conclusively evident from Figure 4. This unambiguously established that the doublet detected for 19F.to established doublet detected for NH proton protonand is due theacoupling between NH and NH proton isthat duethe to the coupling between Such large coupling value ofproton NH proton 19 F. Such a large coupling 5J 4JH(11)H(10) value of NH protonand is very unlikely for 5 JF(5)H(11) , 4 Jthus , is very unlikely for 5JF(5)H(11) , 4JF(6)H(11) , 5JH(11)H(1) [115–117] and has been attributed to F(6)H(11) H(11)H(1) and 4J 19 19 [115–117] thus been to the coupling NH proton and between F atom the coupling betweenand NHhas proton and attributed F atom mediated throughbetween hydrogen bond bridges H(11)H(10) 19F and 1H. mediated through hydrogen bond bridges between 19 F and 1 H.

19F, 19 19 F, 1919 Figure 4. The MHz F-{1 1H} H}and and 11H-{ 2, 32,and 4 in4 CDCl 3. Figure 4. The 400400 MHz F-{ H-{19F} F}NMR NMRspectra spectraofofmolecules molecules 3 and in CDCl 3.

2.1.2. Simultaneous through Space Space Couplings Couplings 2.1.2. Simultaneous Detection Detection of of Two Two through In the the molecules molecules where where X X and and X X// are In are fluorine, fluorine, the the coupling coupling of of NH NH proton proton with with both both the the fluorine fluorine 1 atoms, even not bebe detected in the oneone dimensional H spectrum. The excessively broad 1 H spectrum. atoms, evenififititexists, exists,could could not detected in the dimensional The excessively 14N nucleus prevented the visualization of small couplings, if any. The NH peak due to quadrupolar 14 broad NH peak due to quadrupolar N nucleus prevented the visualization of small couplings, if any. 14N decoupling achieved by systematic variation of the power and frequency of second irradiating RF 14 N decoupling achieved by systematic variation of the power and frequency of second irradiating The over a wide range circumvented thisthis problem of quadrupolar broadening and and resulted in sharp NH RF over a wide range circumvented problem of quadrupolar broadening resulted in sharp signals as reported in Figure 5A. NH signals as reported in Figure 5A. Nearly eight-fold reduction in line width of NH peak in 4 (reduced from 16 Hz to 2 Hz), resulted in a distinct doublet of doublet (dd) with measurable couplings of 17.7 Hz (1hJN-H…F(X/)) and 3.7 Hz. Similarly, a doublet for molecules 3, (16 Hz), and a doublet (3.6 Hz pertaining to 1hJN-H…F(X/)) for the NH proton of molecule 2 were detected at ambient temperature. Another interesting feature observed was the significant narrowing of NH signal on lowering the temperature (Figure 5B, molecule 4). This is because of self-decoupling of NH proton with 14N, at very low temperatures. However, this fact is not clearly obvious from the 1H-{14N} spectrum reported in Figure 5B as the decoupling at very low

Molecules 2017, 22, 423

Molecules 2017, 22, 423

Molecules 2017, 22, 423

8 of 44

8 of 41

8 of 41

1 14N} (right side) NMR spectrum of NH proton for the molecules 2, 3 and Figure5.5.(A) (A)The The11H H (left (left side) Figure side) 1H-{ H-{14 N} (right side) NMR spectrum of NH proton for the molecules 2, 1H and 1H-{14N} NMR spectrum of NH proton for molecule 4 at 230 K. 4 respectively at 298 K. (B) The 3 and 4 respectively at 298 K. (B) The 1 H and 1 H-{14 N} NMR spectrum of NH proton for molecule 4 at 230 K.

2.1.3. Temperature and Solvent Induced Perturbations

The investigated moleculesinwere subjected to temperature variation over of 320–220 Nearly eight-fold reduction line width of NH peak in 4 (reduced from 16 the Hz range to 2 Hz), resultedK / ) andand 1hJNH…F1h CDCl 3 solvent. The chemical shiftmeasurable of NH protons (δNH) of and monitored their inina the distinct doublet of doublet (dd) with couplings 17.7 Hz ( were JN-H ··· 3.7 Hz. F(X ) 1h / dependency on the temperature is plotted in Figure 6A for all the investigated molecules. Similarly, a doublet for molecules 3, (16 Hz), and a doublet (3.6 Hz pertaining to JN-H ···F(X ) ) for the NH proton of molecule 2 were detected at ambient temperature. Another interesting feature observed was the significant narrowing of NH signal on lowering the temperature (Figure 5B, molecule 4). This is because of self-decoupling of NH proton with 14 N, at very low temperatures. However, this fact is not clearly obvious from the 1 H-{14 N} spectrum reported in Figure 5B as the decoupling at very low temperatures has very little effect on the line width due to the strengthening of the bifurcated HB at this temperature. Due to the slightly perturbed structural conformation, X/ (F) is not in close 1H (leftproton. 14N} (right Figurewith 5. (A)the Theamide side) 1H-{ side) NMR of NH proton fornot thebe molecules 2, 3by and proximity Thus in this case thespectrum hydrogen bond could detected NMR 1H and 1H-{14N} NMR spectrum of NH proton for molecule 4 at 230 K. 4 respectively at 298 K. (B) The as predicted by single crystal X-ray diffraction studies. 2.1.3. 2.1.3. Temperature Temperatureand andSolvent SolventInduced InducedPerturbations Perturbations The The investigated investigated molecules molecules were were subjected subjected to to temperature temperature variation variation over over the the range range of of 320–220 320–220 K K 1h 1h … in solvent. The chemical shift of NH protons (δ ) and J ··· were and their inthe theCDCl CDCl 3 solvent. The chemical shift of NH protons (δ NH ) and J NH F were monitored and their 3 NH NH F Figure 6. (A) Variation of chemical shift of NH protons (δNH) with temperature for all the investigated dependency on isisplotted in for the molecules. dependency onthe thetemperature temperature plotted inFigure Figure 6A forall alltriangles theinvestigated investigated molecules. molecules. The squares, circles, upper triangles and6A inverted correspond to molecules 1, 2, 3 and 4 respectively; (B) The variation of 1hJN-H...F(5), with temperature for molecules 3 and 4. Squares pertain to molecules 3 and triangles correspond to molecule 4.

HB gets strengthened on lowering the temperature and hence results in deshielding in the 1H-NMR peaks as reported in Figure 6A. Another interesting observation is the change in 1hJN-H…F(X). It varied from 17.03 (220 K) to 15.72 (320 K) Hz and 17.71 Hz (220 K) to 15.94 Hz (320 K) respectively for molecules 3 and 4, as reported in Figure 6B, which provides clear and straightforward evidence in the favor of HB. 2.2. Theoretical Calculations For the fluorinated oligomers ground state geometry optimizations, have been carried out. The geometry optimization was performed to enumerate the intramolecular N-H…F distances by employing the B3LYP/6-311+G** basis set [118]. Self-Consistent Isodensity Polarized Continuum Model (SCI-PCM) Figure6. 6. (A) (A) Variation Variation ofchemical chemical shiftof ofNH NHprotons protons NH) with temperature for all the investigated Figure of shift (δ(δNH ) with temperature for all the investigated has molecules. been utilized to create the uniform CHCl 3 solvent environment [119]. toOptimized The squares, squares,circles, circles,upper uppertriangles trianglesand andinverted invertedtriangles trianglescorrespond correspond molecules1,1,molecular molecules. The to molecules 2,2,33 1h geometries along with(B) HBs are reported inJN-H...F(5) Figure 7. temperature for molecules 3 and 4. Squares , with and 4 respectively; The variation of 1h and 4 respectively; (B) The variation of JN-H...F(5) , with temperature for molecules 3 and 4. Squares …F(X/) are in close agreement with the The theoretically HB correspond distances involving pertain tomolecules molecules3observed 3and andtriangles triangles moleculeN-H pertain to correspond totomolecule 4.4. X-ray structures [104]. HB gets strengthened on lowering the temperature and hence results in deshielding in the 1H-NMR peaks as reported in Figure 6A. Another interesting observation is the change in 1hJN-H…F(X). It varied from 17.03 (220 K) to 15.72 (320 K) Hz and 17.71 Hz (220 K) to 15.94 Hz (320 K) respectively for molecules 3 and 4, as reported in Figure 6B, which provides clear and straightforward evidence in the favor of HB. 2.2. Theoretical Calculations

Molecules 2017, 22, 423

9 of 44

HB gets strengthened on lowering the temperature and hence results in deshielding in the N-H . . . F(X) . It varied from 17.03 (220 K) to 15.72 (320 K) Hz and 17.71 Hz (220 K) to 15.94 Hz (320 K) respectively for molecules 3 and 4, as reported in Figure 6B, which provides clear and straightforward evidence in the favor of HB.

1 H-NMR peaks as reported in Figure 6A. Another interesting observation is the change in 1h J

2.2. Theoretical Calculations For the fluorinated oligomers ground state geometry optimizations, have been carried out. The geometry optimization was performed to enumerate the intramolecular N-H···F distances by employing the B3LYP/6-311+G** basis set [118]. Self-Consistent Isodensity Polarized Continuum Model (SCI-PCM) has been utilized to create the uniform CHCl3 solvent environment [119]. Optimized molecular geometries along with HBs are reported in Figure 7. Molecules 2017, 22, 423 9 of 41

Molecules 2017, 22, 423

9 of 41

Optimized structures structures of fluorinated benzanilides visualized using Molden-4.7: HB parameters Figure 7. Optimized were measured measuredbyby their optimization (Molden Control) in the vicinity ofHB F···distances H-N HBand distances their optimization (Molden Control) in the vicinity of F…H-N angles. and angles.

3. CF3 Substituted Benzanilides The theoretically observed distances involving benzanilides N-H···F(X/ ) have are inbeen close agreement[120]. withThe the Extending the study anotherHB series of CF3 substituted investigated X-ray structures [104]. chemical structures of the investigated molecules are reported in Figure 8. In this series of molecules, the Figure 7. Optimized of fluorinated using Molden-4.7: unambiguous evidence forstructures the engagement ofbenzanilides CF3 groupvisualized in N-H···F-C type HB,HB in parameters the different CF3 3. CF3 Substituted Benzanilides measured byhas theirbeen optimization (Molden the vicinity of F…H-N HB distances substitutedwere derivatives observed in Control) a low in polarity solvent CDCl 3. It is and wellangles. known that 3 2 Extending the study another series of CF substituted benzanilides have been investigated C(Sp )-F fluorine is a better acceptor than C(Sp3 )-F and C(Sp)-F fluorine [121]. To understand the[120]. role 3. CF3 Substituted Benzanilides The the investigated areutility reported in Figure 8. In this series of of CFchemical 3 group instructures HB and inof structural chemistrymolecules an extensive of NMR experimental techniques, Extending the study another series of CFthe 3 substituted benzanilides have been investigated [120]. The HB, molecules,variable the unambiguous evidence for engagement of CF group in N-H F-C type including temperature and dilution studies, has been made. The example of ··· the engagement 3 first chemical structures of the investigated molecules are reported in Figure 8. In this series of molecules, in the different CFin derivatives been observed in ahas lowbeen polarity solvent CDClthe It is of CF3 group the intramolecular HB has of the type C-F···H-N reported [121–127]. 3 substituted 3 . The unambiguous evidence for the engagement of CF3 group in N-H···F-C type HB, in the different CF3 3 2 well that C(Sp fluorine is substantiated a better acceptor than C(Sp )-F and(MD) C(Sp)-F fluorine [121]. NMRknown findings have been)-F additionally by molecular dynamics simulations. substituted derivatives has been observed in a low polarity solvent CDCl3. It is well known that To understand the role of CF3 group in HB and in structural chemistry an extensive utility of C(Sp3)-F fluorine is a better acceptor than C(Sp2)-F and C(Sp)-F fluorine [121]. To understand the role NMR of experimental techniques, including variable temperature and dilution studies, has been made. CF3 group in HB and in structural chemistry an extensive utility of NMR experimental techniques, The first example of the engagement the CF themade. intramolecular HB ofofthe C-F···H-N 3 group including variable temperature andof dilution studies, hasin been The first example thetype engagement has been reported [121–127]. The NMR findings have been additionally substantiated by molecular of the CF3 group in the intramolecular HB of the type C-F···H-N has been reported [121–127]. The dynamics simulations. NMR(MD) findings have been additionally substantiated by molecular dynamics (MD) simulations.

Figure 8. Chemical structure of benzanilide (1) and its trifluoromethyl derivatives 5–8.

3.1. NMR Experimental Findings In the 1H-NMR spectrum the NH proton of molecule 5 displayed a doublet with a separation of 1hJFH (coupling Figure 8. Chemical structure benzanilide (1)and and its its trifluoromethyl derivatives 5–8.5–8. mediated through HB) between NH proton and the 16.7 Hz [120]. This attributed to Figure 8.isChemical structure of of benzanilide (1) trifluoromethyl derivatives 1 19 fluorine of ring a. Collapsing of this doublet to a singlet in the H{ F} experiment unambiguously 3.1. NMR Experimental Findings established that it is mediated through HB, confirming the involvement of F in HB. Analogous to 1H-NMR spectrum the NH proton of molecule 5 displayed a doublet with a separation of In the benzanilides discussed in the previous section, even in this molecule the excessive broadening of NH HB) between NH proton and the of 16.7 Hz [120]. This is to 1hJFH (coupling signal was observed, dueattributed to quadrupole relaxationmediated by 14N, through may prevent the precise measurement fluorine of ring a. Collapsing of this doublet to a singlet in the 1H{19F} experiment unambiguously small couplings, if any, that may be hidden within the line width. In circumventing such problems, established that it is mediated through HB, confirming the 15involvement of F in HB. Analogous to 1

15

Molecules 2017, 22, 423

10 of 44

3.1. NMR Experimental Findings In the 1 H-NMR spectrum the NH proton of molecule 5 displayed a doublet with a separation of 16.7 Hz [120]. This is attributed to 1h JFH (coupling mediated through HB) between NH proton and the fluorine of ring a. Collapsing of this doublet to a singlet in the 1 H{19 F} experiment unambiguously established that it is mediated through HB, confirming the involvement of F in HB. Analogous to benzanilides discussed in the previous section, even in this molecule the excessive broadening of NH signal was observed, due to quadrupole relaxation by 14 N, may prevent the precise measurement of small couplings, if any, that may be hidden within the line width. In circumventing such problems, a 2D 15 N-1 H HSQC experiment has been carried out where 15 N is present in its natural abundance. Molecules 2017, 22, 423 spectrum is reported in Figure 9. 10 of 41 The corresponding

1 H-HSQC 1H-HSQC Figure two-dimensional1515NNspectrum molecule 5 the in the CDCl Figure 9. 9. 400 MHz two-dimensional spectrum of of molecule 5 in CDCl 3, depicting the 3 , depicting the through-space couplings. The measured couplingstrengths strengthsare areidentified identified by by a−d a−d and and their values through-space couplings. The measured coupling values have have also also been been reported. reported.

3.2. Theoretical The two Calculations types of couplings mediated through HB, 1h JFH and 2h JFN are reflected in the 15 N-1 H-HSQC spectrum. The signs of couplings decided on the basis of the relative slopes of the To ascertain the presence of weak molecular interactions established by NMR experiments in 1h J displacement vectors assuming [104]. FH to be negative these molecules, the DFT based theoretical calculations have been carried out. Gaussian09 has been used at B3LYP/6-311+g (d,p) level of theory [118] for full-geometry optimizations of the molecules 5–8. 3.2. Theoretical Calculations With the presence of three fluorine atoms in the CF3 group there are various possible ways of To ascertain of weak molecular interactions established byderive NMR the experiments in interactions, suchthe as, presence two centered, three-centered, or four-centered HBs. To quantitative these molecules, theHBs, DFTquantum based theoretical beensimulations carried out.have Gaussian09 has been information about chemicalcalculations calculations have and MD been carried out. used at B3LYP/6-311+g (d,p) level of theory criteria [118] forhave full-geometry of represented the molecules For calculation, the geometry measurement been usedoptimizations in which HB is as 5–8. Withwhere the presence threeatom fluorine in acceptor the CF3 group various possible N ways N-H···F, N is theofdonor andatoms F is the atom. there If the are distance, r between andofF interactions, such3.5 as,Åtwo or four-centered HBs.an ToHB derive the quantitative atom is less than andcentered, the anglethree-centered, ∠NHF (θ) is greater than 120°, then exists between the N information HBs,probable quantumdistance, chemicalP(r), calculations and MDangle, simulations have been carried and F atoms.about The most and appropriate P(θ), are calculated for allout. the For calculation, geometry criteria have beenofused in which is represented as fluorine atoms inthe each of thesemeasurement four molecules. The percentage occurrence ofHB various types of HBs N-H ···F, where N isfrom the donor atom and F is the acceptorofatom. If the distance, r between N and F has been calculated the MD simulations. A snapshot the formation of HB and their percentage of theisoccurrence forÅthe molecule 6 is reported Figure than 10. 120◦ , then an HB exists between the N atom less than 3.5 and the angle ∠NHF (θ) isingreater and F atoms. The most probable distance, P(r), and appropriate angle, P(θ), are calculated for all the fluorine atoms in each of these four molecules. The percentage of occurrence of various types of HBs has been calculated from the MD simulations. A snapshot of the formation of HB and their percentage of the occurrence for the molecule 6 is reported in Figure 10.

N-H···F, where N is the donor atom and F is the acceptor atom. If the distance, r between N and F atom is less than 3.5 Å and the angle ∠NHF (θ) is greater than 120°, then an HB exists between the N and F atoms. The most probable distance, P(r), and appropriate angle, P(θ), are calculated for all the fluorine atoms in each of these four molecules. The percentage of occurrence of various types of HBs has been2017, calculated Molecules 22, 423 from the MD simulations. A snapshot of the formation of HB and their percentage 11 of 44 of the occurrence for the molecule 6 is reported in Figure 10.

Figure Figure 10. 10. (a,b) (a,b) Snapshot Snapshot of of HB HB formation formationin in molecule molecule6,6, along alongwith withtheir theirpercentage percentageof ofoccurrence, occurrence, obtained from MD simulations. Blue colored dashed lines show H-bonds; (c,d) Probability obtained from MD simulations. Blue colored dashed lines show H-bonds; (c,d) Probabilitydistributions distributions of of angles angles and and distances, distances, respectively. respectively.

The calculations reveal that the percentage of occurrence in a situation when there is no HB is The2017, calculations reveal that the percentage of occurrence in a situation when there is no11 HB is Molecules 22, 423 of 41 56.27%, whereas the occurrence of a two-centered HB is 42.60% (Figure 10a), and the occurrence of a 56.27%, whereas the occurrence of a two-centered HB is 42.60% (Figure 10a), and the occurrence of bifurcated HB geometrical a bifurcated HBisismuch muchless lessand andisis 1.13% 1.13% (Figure (Figure 10b). 10b). Figure Figure 10c,d 10c,d contain contain the HB geometrical parameters obtained It has been observed thatthat all the F atoms in thein CFthe 3 group parameters obtainedby byMD MDsimulations. simulations. It has been observed allthree the three F atoms CF3 have equal of forming HBs, as P(r)as and P(θ) same three atoms (Figure 10c,d).10c,d). group have probability equal probability of forming HBs, P(r) andare P(θ) are for same for F three F atoms (Figure For molecule 5, 5, where a single fluorine is substituted on ring “a” and the CF CF33 group on the ring “b”, there there are are five five different different possibilities possibilities of of fluorine fluorine getting getting involved involved in the HB formation and also a “b”, possibility when there is no HB. All such possibilities with their percentage of occurrence determined Figure 11. 11. by MD simulations are reported in Figure

Figure 11. Various possibilities of HB formation for molecule 5, with their % of occurrence obtained Figure 11. Various possibilities of HB formation for molecule 5, with their % of occurrence obtained from the MD simulations (HB is shown by blue line). from the MD simulations (HB is shown by blue line).

A very interesting result has been derived from the 19F{1H} NMR spectrum of this molecule, A very interesting result has been derived from the 19 F{1 H} NMR spectrum of this molecule, which exhibited doublet and quartet patterns for CF3 and CF groups, respectively. The corresponding which exhibited doublet and quartet patterns for CF3 and CF groups, respectively. The corresponding spectrum is reported in Figure 12. Fluorine atoms of CF and CF3 groups in molecule 5 are separated by eight covalent bonds and the observed doublet peak with separation of 5.7 Hz is quite large. Thus the scalar couplings between the fluorine atoms, mediated through covalent bonds is quite unlikely. It can be safely attributed to the interaction between CF and CF3 groups mediated through HB of the type F…H…F (2hJFF).

Figure 11. Various possibilities of HB formation for molecule 5, with their % of occurrence obtained from the MD simulations (HB is shown by blue line). Molecules 2017, 22, 423

12 of 44

A very interesting result has been derived from the 19F{1H} NMR spectrum of this molecule, which exhibited doublet and quartet patterns for CF3 and CF groups, respectively. The corresponding spectrum is is reported reported in inFigure Figure12. 12. Fluorine Fluorine atoms atoms of of CF CF and andCF CF33 groups groups in in molecule molecule 55 are are separated separated spectrum by eight covalent doublet peak with separation of 5.7 quite large.large. Thus by covalent bonds bondsand andthe theobserved observed doublet peak with separation ofHz 5.7isHz is quite the scalar couplings between the fluorine atoms, mediated through covalent bonds is quite unlikely. Thus the scalar couplings between the fluorine atoms, mediated through covalent bonds is quite 3 groups through HB of the It can be It safely attributed to the interaction between CF and CF unlikely. can be safely attributed to the interaction between CF and CFmediated through 3 groups mediated …H…F (2hJFF). typeofFthe HB type F···H···F (2h JFF ).

19F{1H} NMR spectrum of molecule 5 showing 2hJFF through-space coupling. Figure Figure12. 12.376.7 376.7MHz MHz 19 F{1 H} NMR spectrum of molecule 5 showing 2h JFF through-space coupling.

19F-19F COSY and J-resolved experiments also reflected the cross peaks pertaining to The 2D-19 The 2DF-19 F COSY and J-resolved experiments also reflected the cross peaks pertaining 2hJFF [120]. The strengths of HB for each fluorine atom present in all the molecules have also been to 2h JFF [120]. The strengths of HB for each fluorine atom present in all the molecules have also calculated using atomistic molecular dynamics. The histogram of the HB formation H(r,θ) i.e., as a been calculated using atomistic molecular dynamics. The histogram of the HB formation H(r,θ) function of the distance, r between donor and acceptor atoms and θ the angle between donor-hydrogeni.e., as a function of the distance, r between donor and acceptor atoms and θ the angle between acceptor atoms, reported in Figure 13, have been calculated at 300 K for molecule 7, from the 50 ns donor-hydrogen-acceptor atoms, reported in Figure 13, have been calculated at 300 K for molecule 7, molecular dynamics simulation trajectory. Molecules 2017, 22, 423 12 of 41 from the 50 ns molecular dynamics simulation trajectory.

Figure ···F1-C H-bond Figure 13. 13. F(r,θ) F(r,θ)for forN-H N-H···F1-C H-bond occurring occurring in in molecule molecule 7. 7.

The The free free energy energy landscape landscape of of each each atom atom involved involved in in the the HB HB calculation calculation can can be be performed performed from from this histogram histogram using using formulae formulae given given in in the the Equation Equation (1): (1): this

F(r,θ) = −kBT ln(2πr2sinθH(r, θ)) (1) F(r,θ) = −kB T ln(2πr2 sinθH(r, θ)) (1) For any fluorine atom participating in the HB with N atom, F(r,θ) has two minima corresponding Forstates, any fluorine atom in the N free atom, F(r,θ) landscape has two minima corresponding to two one with HBparticipating and other with no HB HB.with In the energy for molecule 7 given to states, with HB and withon nothe HB. In the free energy forr molecule 7 given in two Figure 13, one for N-H···F 1-C theother minima left-hand side is forlandscape HB (where and θ satisfy the in Figure 13, for N-H ··· F -C the minima on the left-hand side is for HB (where r and θ satisfy the 1 conditions for HB) and the other minima belongs to a situation where there is no HB. The strength of conditions HB)calculated and the other minima belongs a situation where there HB has alsofor been for the molecules 2–5to[120] using Equation (2): is no HB. The strength of HB has also been calculated for the molecules 2–5 [120] using Equation (2): Ehb = Fhbmin (r, θ) − Fno−hbmax (r, θ) (2) −hb Fhb min (r,bonded θ) − Fnostate no−hbmax (r, θ) is the maxima for (2) max where Fhbmin (r, θ) is the minimaEhb of = hydrogen and(r,Fθ) no hydrogen bonded state.

4. Studies on Hydrazides Hydrazides are organic compounds that share a common functional group with a N-N covalent

Molecules 2017, 22, 423

13 of 44

where Fhb min (r, θ) is the minima of hydrogen bonded state and Fno−hb max (r, θ) is the maxima for no hydrogen bonded state. 4. Studies on Hydrazides Hydrazides are organic compounds that share a common functional group with a N-N covalent bond where at least one of the four substituents should be an acyl group [128]. Different derivatives of hydrazides have proven to be extremely important as, reagents in organic synthesis [129], anti-tumor medicine [130,131], and also in the cytotoxic functioning [132]. In combination with other cmedicines, the derivatives of hydrazides are utilized for the treatment or prevention of tuberculosis [133]. 4.1. N,N-Diacyl Substituted Derivatives of Hydrazides The hydrazides provide a possibility to synthesize a variety of derivatives with different combinations of substituted acyl group(s) of interest. The different derivatives of hydrazides have been synthesized and characterized using one and two dimensional multinuclear NMR experiments, and ESI mass spectrometry. The procedure for synthesis of these molecules and the NMR spectral analysis have been reported [134]. The NMR experiments reveal the existence of weak intramolecular interactions in all the investigated derivatives of hydrazides [134]. The NMR derived HB information has been further ascertained by DFT [135,136] based NCI [90], and QTAIM [91–95] calculations. 4.1.1. NMR Spectroscopic Detection One of the NMR spectral parameters that provides information on the HB is the variation of chemical shift under different experimental conditions. In the reported work [134] the different derivatives of hydrazide, 9–18, generically named 2-X-N-(2-X’)benzohydrazides, whose basic chemical structures and their site specific substituents, reported in Figure 14, have been investigated. The disubstituted molecules are classified into two categories, one where X = X’ (9–11 and 18) and the Molecules 2017, 22, 423X’ (12–17). 13 of 41 other where X 6=

Figure 14. The The chemical chemical structures structures of 2-X-N-(2-X’) benzohydrazide benzohydrazide derivatives; derivatives; (a) symmetrically symmetrically substituted molecules and (b) asymmetrically substituted molecules.

For discarding any possibility of dimerization or self-aggregation, if any, 2D DOSY [137,138] For discarding any possibility of dimerization or self-aggregation, if any, 2D DOSY [137,138] experiments, ESI-MS analysis and dilution studies have been carried out. Solvent titration experiments, ESI-MS analysis and dilution studies have been carried out. Solvent titration experiment [63,64,139] has been employed to understand the weak interactions, such as, intra- and experiment [63,64,139] has been employed to understand the weak interactions, such as, intra- and inter- molecular HB, to compare their relative strengths of interaction and also to evaluate the effect of inter- molecular HB, to compare their relative strengths of interaction and also to evaluate the effect monomeric water on HB, which is absorbed from the atmosphere. The variation in the chemical shift of of monomeric water on HB, which is absorbed from the atmosphere. The variation in the chemical NH proton as a function of temperature (300–220 K) is compared for all the investigated molecules shift of NH proton as a function of temperature (300–220 K) is compared for all the investigated in Figure 15b. On lowering the temperature, the NH peak of all investigated molecules except one molecules in Figure 15b. On lowering the temperature, the NH peak of all investigated molecules NH proton peak of molecule 13 is showed downfield shift due to the strengthening of HB. The except one NH proton peak of molecule 13 is showed downfield shift due to the strengthening of HB. unusual behaviour of this NH proton of the molecule 13 has been attributed to the switching of this The unusual behaviour of this NH proton of the molecule 13 has been attributed to the switching of molecule to another possible conformer on lowering the temperature. The possibility of such a this molecule to another possible conformer on lowering the temperature. The possibility of such a switching phenomenon is illustrated in Scheme 1. switching phenomenon is illustrated in Scheme 1.

Scheme 1. Two different possible stable conformations of molecule 13, (a) at higher temperature; and

NH proton as a function of temperature (300–220 K) is compared for all the investigated molecules in Figure 15b. On lowering the temperature, the NH peak of all investigated molecules except one NH proton peak of molecule 13 is showed downfield shift due to the strengthening of HB. The unusual behaviour of this NH proton of the molecule 13 has been attributed to the switching of this molecule to 22, another possible conformer on lowering the temperature. The possibility of such a Molecules 2017, 423 14 of 44 switching phenomenon is illustrated in Scheme 1.

Scheme 1. 1. Two different possible possible stable stable conformations conformations of of molecule molecule 13, 13, (a) (a) at at higher and Scheme Two different higher temperature; temperature; and (b) at at lower lower temperature. temperature. (b)

The relative strength of intramolecular HBs has been qualitatively derived by titration with The relative strength of intramolecular HBs has been qualitatively derived by titration with dimethylsulphoxide (DMSO) solvent [134]. The observed variation in the chemical shifts as a function dimethylsulphoxide (DMSO) solvent [134]. The observed variation in the chemical shifts as a function of the incremental addition of DMSO-d6 is plotted for the molecules 9–17, in Figure 15c. Disruption of the incremental addition of DMSO-d6 is plotted for the molecules 9–17, in Figure 15c. Disruption of intramolecular HB [104] by the solvent DMSO results in the deshielding of NH protons. On the of intramolecular HB [104] by the solvent DMSO results in the deshielding of NH protons. On the contrary for the NH protons of molecule 11, and one of the two NH protons of asymmetric molecules, contrary for the NH protons of molecule 11, and one of the two NH protons of asymmetric molecules, 15–17 the high field shift was detected on addition of DMSO-d6. This is due to the fact that these NH 15–17 the high field shift was detected on addition of DMSO-d6 . This is due to the fact that these protons involved in HB with OMe group are relatively stronger than the DMSO interaction. The high NH protons involved in HB with OMe group are relatively stronger than the DMSO interaction. field shift of these protons is attributed to an equilibrium which is stabilized between intra- and interThe high field shift of these protons is attributed to an equilibrium which is stabilized between intramolecular hydrogen bonded species. and inter- molecular hydrogen bonded species. Another strong evidence in the favour of organic fluorine involved intramolecular HB is the Another strong evidence in the favour of organic fluorine involved intramolecular HB is the 19F detection of through space couplings between the NH proton and fluorine [40,140–142]. The 19 detection of through space couplings between the NH proton and fluorine [40,140–142]. The F coupled and decoupled 1H spectrum of molecule 9 in the solvent CDCl3, and the 19F coupled spectrum coupled and decoupled 1 H spectrum of molecule 9 in the solvent CDCl3 , and the 19 F coupled spectrum in the solvent DMSO-d6 are given in Figure 16. The NH peak of the molecule 9 is a doublet with a in the solvent DMSO-d6 are given in Figure 16. The NH peak of the molecule 9 is a19doublet with a F) experiment separation of 12.75 Hz (Figure 16a). This doublet collapsed into a singlet in the11H{19 separation of 12.75 Hz (Figure 16a). This doublet1collapsed into a singlet in the H{ F) experiment 19F (Figure 16c). The doublet also collapsed confirming the presence of the coupling between 1 H and 19 confirming the presence of the coupling between H and F (Figure 16c). The doublet also collapsed to a singlet in a high polarity solvent DMSO-d6 (Figure 16b). to a singlet high polarity solvent DMSO-d6 (Figure 16b). Molecules 2017,in 22,a 423 14 of 41

Figure Figure 15. 15. (a, b) b) Variation Variation in in the the chemical chemical shifts shifts of of NH NH proton proton as as aa function function of of temperature temperature and the volume of DMSO-d respectively for the molecules 9–17. The initial concentration was 10 10 mM mM in in the the volume of DMSO-d66 respectively for the molecules 9–17. The initial concentration was solvent CDCl . (a) The DMSO-d was incrementally added to an initial volume of 450 µL in CDCl 3, solvent CDCl33. (a) The DMSO-d6 6was incrementally added to an initial volume of 450 µL in CDCl3, at at The temperaturewas wasvaried variedfrom from300 300toto220 220K. K.The Themolecules molecules 9–17 9–17 are are identified identified by 298298 K;K; (b)(b) The temperature by the the symbols symbols given given in in the the inset. inset.

1

1

Figure 15. (a, b) Variation in the chemical shifts of NH proton as a function of temperature and the volume of DMSO-d6 respectively for the molecules 9–17. The initial concentration was 10 mM in the solvent CDCl3. (a) The DMSO-d6 was incrementally added to an initial volume of 450 µL in CDCl3, at 2982017, K; (b) Molecules 22,The 423 temperature was varied from 300 to 220 K. The molecules 9–17 are identified by the 15 of 44 symbols given in the inset.

Figure 16. of molecule molecule 9, 9, (a) (a) in in CDCl CDCl33;; (b) (b) 11H-NMR spectrum in in DMSO-d DMSO-d66 Figure 16. 400 400 MHz MHz 11H-NMR H-NMR spectrum spectrum of H-NMR spectrum 1 19 1 19 and (c) and (c) H{ H{ F} F}NMR NMRspectrum spectrumin inCDCl CDCl33. .

The 3JHH and 4hJFH couplings, if any, are not detectable due to the symmetry of the molecule. For The 3 JHH and 4h JFH couplings, if any, are not detectable due to the symmetry of the molecule. For detection of these couplings the symmetry of the molecule has to be broken. For such a purpose 2D detection of these couplings the symmetry of the molecule has to be broken. For such a purpose 2D 1 15N HSQC experiment has been carried out for the molecule 9, where 15N is present in its natural 1HH-15 N HSQC experiment has been carried out for the molecule 9, where 15 N is present in its natural abundance. The HSQC spectrum is reported Figure 17A where all the possible seven couplings, 1JNH, abundance. The HSQC spectrum is reported Figure 17A where all the possible seven couplings, 1 JNH , 2hJFN, 2JNH, 3hJFN, 1hJFH, 4hJFH and 3JHH has been measured from this spectrum. The observation of through 2h J , 2 J 3h J , 1h J , 4h J 3 this spectrum. The observation FN NH , FN FH FH and J HH has been measured from 4h space couplings of significant strengths, such as 1hJFH, 2hJFN 3hJFN and JFH, provided strong and direct of through space couplings of significant strengths, such as 1h JFH , 2h JFN 3h JFN and 4h JFH , provided evidence for the involvement of organic fluorine in the intramolecular HB. In the solvent DMSO, strong and direct evidence for the involvement of organic fluorine in the intramolecular HB. In the except for 1JNH, all the other couplings mediated through HB disappeared as reported in Figure 17B. solvent DMSO, except for 1 JNH , all the other couplings mediated through HB disappeared as reported The relative signs of all the couplings were determined with respect to coupling c marked in in Figure2017, 17B.22, 423 Molecules 15 of 41 Figure 17B. From this it was inferred that 1hJFH is negative. The comparison of 1JNH [143,144] of molecules 9–17 with unsubstituted molecule 18, provided ample evidence that the nature of HBs in derivatives of hydrazides are predominantly covalent in nature. The close proximity of NH proton with the fluorine in fluorinated molecules is detected by 2D HOESY (hetero-nuclear Overhauser effect spectroscopy) experiment. This also provided evidence in favor of intramolecular HB.

1 15N-HSQC (NH-coupled) spectrum of molecule 9 in CDCl3; (B) the chemical Figure 17. 17. (A) 15 N-HSQC (NH-coupled) spectrum of molecule 9 in CDCl ; (B) the Figure (A)800 800MHz MHzH-1 H3 structure of the molecule 9 with marking couplings and their magnitudes; (C) 400 MHz chemical structure of the molecule 9 withofmarking ofdetermined couplings determined and their magnitudes; 1H-15N-HSQC spectrum (NH-coupled) in DMSO-d6. (C) 400 MHz 1 H-15 N-HSQC spectrum (NH-coupled) in DMSO-d6 .

4.1.2. NCI Plot The relative signs of all the couplings were determined with respect to coupling c marked in 1h J The weak molecular interactions established by NMR studies have also been1 corroborated by Figure 17B. From this it was inferred that FH is negative. The comparison of J NH [143,144] of theoretical DFT [135,136] optimized structure based calculations. The calculation of noncovalent molecules 9–17 with unsubstituted molecule 18, provided ample evidence that the nature of HBs in interaction (NCI) has been shown to be very useful technique for the visualization of weak interactions [90]. The calculated grid points are plotted for a defined real space function, sign(λ2(r))ρ(r), as function 1 and reduced density gradient (RDG) as function 2 and also the color filed isosurfaces for all the investigated molecules. Figure 18 gives these plots for the molecule 9.

Molecules 2017, 22, 423

16 of 44

derivatives of (A) hydrazides covalent in nature. The close proximity ofchemical NH proton Figure 17. 800 MHz 1are H-15predominantly N-HSQC (NH-coupled) spectrum of molecule 9 in CDCl 3; (B) the with the fluorine in molecule fluorinated molecules 2D HOESY structure of the 9 with marking is of detected couplingsby determined and(hetero-nuclear their magnitudes;Overhauser (C) 400 MHzeffect 1H-15N-HSQC spectrum (NH-coupled) in DMSO-d6. spectroscopy) experiment. This also provided evidence in favor of intramolecular HB. 4.1.2. NCI Plot The weak weak molecular molecular interactions established by NMR studies have also been corroborated by theoretical DFT DFT [135,136] [135,136] optimized optimized structure structure based based calculations. calculations. The calculation calculation of of noncovalent noncovalent interaction (NCI) has been shown to be very useful technique for the visualization very useful technique the visualization of weak interactions interactions [90]. [90]. The The calculated calculated grid grid points points are areplotted plottedfor foraadefined definedreal realspace spacefunction, function,sign(λ sign(λ2(r) 2(r))ρ )ρ(r) (r), as asas function 2 and also thethe color filed isosurfaces for as function function11and andreduced reduceddensity densitygradient gradient(RDG) (RDG) function 2 and also color filed isosurfaces all investigated molecules. Figure 18 gives these plots for the 9. 9. forthe all the investigated molecules. Figure 18 gives these plots for molecule the molecule

Figure 18. 18. (a) (a) The The plot plot of of sign(λ sign(λ2(r) 2(r))*ρ )*ρ(r) (r) as v/s the and (b) (b) coloured coloured Figure as function function 11 v/s the RDG RDG as as function function 2; 2; and isosurface plot plot (green (green color color denotes isosurface denotes weak weak H-bond H-bond and and red red color color stands stands for for steric steric effect) effect) for formolecule molecule9.9.

There are three spikes on the left hand side of Figure 18a (i.e., sign(λ2(r))*ρ(r) is negative) denoting There are three spikes on the left hand side of Figure 18a (i.e., sign(λ2(r) )*ρ(r) is negative) denoting three HBs, viz., N-H···F, N-H···O and C-H···O. These three HBs can be observed in Figure 18b as green three HBs, viz., N-H···F, N-H···O and C-H···O. These three HBs can be observed in Figure 18b as green coloured isosurfaces. The red colour in isosurface plot (Figure 18b) represents the steric hindrance coloured isosurfaces. The red colour in isosurface plot (Figure 18b) represents the steric hindrance arising from phenyl ring of the molecule and other HB mediated rings. This is seen as four spikes on arising from phenyl ring of the molecule and other HB mediated rings. This is seen as four spikes on the right hand side (i.e., sign(λ2(r))*ρ(r) is positive) of Figure 18a. Similar results have been derived for the right hand side (i.e., sign(λ2(r) )*ρ(r) is positive) of Figure 18a. Similar results have been derived for all other investigated molecules [134]. all other investigated molecules [134]. 4.1.3. Atoms in Molecules (AIM) Calculations The magnitudes of ρ(r) , signs of ∇2 ρ(r) and potential energy density (V (r) ) at corresponding (3, −1) BCP (bond critical points) (rcp ) for HBs of interest have been calculated using QTAIM calculations [91– 95]. The value of (V (r) ) used in the EHB = V(rbcp )/2 [96] for the calculation of energy of HB (EHB ) of X···HX type. The calculated EHB of different HBs in all investigated molecules ranged between −3 to −8.6 Kcal/mol [134]. The 1 H-NMR spectra were simulated using the GIAO [145] and CSGT [145] methods. It is observed that in most of the cases there are more than one conformers for the molecules. Thus the calculated chemical shift values of NH protons are not in complete agreement with the experimental data. The values observed from CSGT method are comparable with the experimental results. 4.2. N, N Acyl-Phenyl Substituted Derivatives of Hydrazides In this work another series of hydrazide derivatives has also been synthesized and investigated, where the formation of five and six membered rings mediated through HBs is possible. The general chemical structure is given in the Figure 19.

data. The values observed from CSGT method are comparable with the experimental results. data. The values observed from CSGT method are comparable with the experimental results. 4.2. N, N Acyl-Phenyl Substituted Derivatives of Hydrazides 4.2. N, N Acyl-Phenyl Substituted Derivatives of Hydrazides In this work another series of hydrazide derivatives has also been synthesized and investigated, In this work another series of hydrazide derivatives has also been synthesized and investigated, where the of five and six membered rings mediated through HBs is possible. The general Molecules 2017,formation 22, 423 17 of 44 where the formation of five and six membered rings mediated through HBs is possible. The general chemical structure is given in the Figure 19. chemical structure is given in the Figure 19.

Figure19. 19.The Thechemical chemicalstructures structuresofofNN′-phenylbenzohydrazide andits itshalo haloderivatives. derivatives.The Thedotted dotted 0 -phenylbenzohydrazide and Figure Figure 19. The chemical structures of N′-phenylbenzohydrazide and its halo derivatives. The dotted lines indicate the HB. lines indicate indicate the the HB. HB. lines

The main focus of this work is to determine the conformations of the fluorinated hydrazide The main main focus focus of of this this work is to determine the conformations conformations of the fluorinated hydrazide hydrazide The derivatives and thereby understanding the effect of HB of the type F/CF3…H (N). derivatives and and thereby thereby understanding the effect of HB of the type F/CF (N). derivatives F/CF33…··· HH(N). 4.2.1. Spectroscopic Experimental Observations 4.2.1. Spectroscopic Spectroscopic Experimental Experimental Observations Observations 4.2.1. 1 For initiating the study, the H-119F HOESY experiments have been carried out for all the investigated 19 F HOESY Forinitiating initiatingthethe study, experiments have been outinvestigated for all the For study, the 1the H-19FHHOESY experiments have been carried outcarried for all the molecules and the strong correlation in 1H-19F HOESY spectrum is observed where fluorine (X’) in the 1 H-19 F HOESY investigated molecules and the strong correlation in spectrum is observed 1 19 molecules and the strong correlation in H- F HOESY spectrum is observed where fluorine (X’) where in the phenyl ring B established correlation with NH(1) proton whereas fluorine in the phenyl ring A (X) fluorinering (X’)Binestablished the phenylcorrelation ring B established correlation with NHfluorine fluorine in (X) the (1) proton phenyl with NH (1) proton whereas inwhereas the phenyl ring A established correlation with NH(2) proton. From the obtained correlations, the conformations of all the phenyl ring A (X) established correlation with NH proton. From the obtained correlations, the (2) established correlation with NH(2) proton. From1the19obtained correlations, the conformations of all the synthesized molecules have been derived and H- F HOESY spectrum for the molecule 20 is reported 1 19 19F HOESY conformations of all the synthesized molecules been derived andforHF HOESY20 spectrum for synthesized molecules have been derived and 1H-have spectrum the molecule is reported in Figure 20. the molecule 20 is reported in Figure 20. in Figure 20.

Figure 20. 400 MHz two dimensional 1H-19F HOESY spectrum of molecule 20. The detection of strong 1H-19F HOESY spectrum of molecule 20. The detection of strong Figure 20. MHz 1 19 HOESY spectrum of molecule 20. The detection of strong Figure 20. 400 400convincingly MHz two two dimensional dimensional cross peaks establishedHtheFcorrelations between NH(1) proton and F and also NH(2) and FF and also NH NH(2) cross peaks convincingly established the correlations between NH(1) proton cross peaks established theobserved correlations between NH and also 1 and b1and . The mixing time used proton and convincingly F. The cross peaks were also for phenyl protons (1)aproton (2) and b b1.. The mixing time used proton and F. The cross cross peaks peaks were were also also observed observed for for phenyl phenyl protons protons aa1 and proton F. The 1 1 The mixing time used in the and experiment was 450 ms. in in the the experiment experiment was was 450 450 ms. ms.

After arriving at the conformations of the molecules, the further studies were directed to derive the information about the weak molecular interactions (HB) that validate the proposed conformations. The titration experiment with CDCl3 did not show any significant change in the chemical shift of NH protons confirming the absence of any intermolecular interactions. The peak at 1.54 ppm corresponding to monomeric water remain constant indicating the absence of hydrizide-water interaction [146]. For discarding the possibility of dimerization or aggregation, if any, DOSY experiment has been carried out with the mixture of 1:1 molar ratio of molecules 20 and 25 in the solvent CDCl3 , which have different diffusion coefficients. The 1 H-NMR spectra for the investigated molecules have been acquired at different temperatures where the HB gets strengthened on lowering of temperature and results in deshielding of the NH proton participating in HB. The corresponding plots of temperature dependent variation of chemical

discarding the possibility of dimerization or aggregation, if any, DOSY experiment has been carried out with the mixture of 1:1 molar ratio of molecules 20 and 25 in the solvent CDCl3, which have different diffusion coefficients. The 1H-NMR spectra for the investigated molecules have been acquired at different temperatures Molecules 2017, 22, 423 18 of 44 where the HB gets strengthened on lowering of temperature and results in deshielding of the NH proton participating in HB. The corresponding plots of temperature dependent variation of chemical shifts Figure 21A,B. 21A,B. In In addition addition to this the the incremental incremental additions shifts of of NH NH protons protons are are reported reported in in the the Figure to this additions of DMSO-d 6 resulted in the deshielding of NH proton providing information about the strength of of DMSO-d6 resulted in the deshielding of NH proton providing information about the strength of HB. perturbation on the chemical chemical shifts shifts of of NH NH proton proton (δ (δNH)) induced by DMSO-d6 are given in HB. The The perturbation on the NH induced by DMSO-d6 are given in Figure 21C,D. The temperature coefficient is directly proportional to the strength Figure 21C,D. The temperature coefficient is directly proportional to the strength of of HB. HB. On On the the other other hand, /ΔV DMSO has inverse relation to the strength of HB. Hence mere visual inspection of hand, the the Δδ ∆δNH /∆V has inverse relation to the strength of HB. Hence mere visual inspection DMSO NH the graphs given in in Figure 2121provides of the graphs given Figure providesinformation informationabout aboutthe thecomparative comparativestrengths strengthsof ofHB HB in in the the studied molecules. studied molecules.

The variation variation of of the chemical shift of; (A) NH protons with with temperature; temperature; Figure 21. The NH(1) (1);; (B) NH(2) (2) protons (C) NH(1) and (D) NH protons with the incremental addition of DMSO-d for the molecules in (1) and (D) NH(2) (2)protons with the incremental addition of DMSO-d66 for the molecules 19–25 in 21C, and is The color color code code for forthe themolecules moleculesare aregiven givenasasananinset insetininFigure Figure 21C, and the solvent CDCl33 at 298 K. The same forfor Figure 21A–D. is same Figure 21A–D.

The The direct direct evidence evidence about about the the presence presence of of HB HB can can be be obtained obtained by by deriving deriving the the coupling coupling between between two two NMR NMR active active nuclei nuclei which which are are participating participating in in the the formation formation of of HB. HB. In In order order to to overcome overcome the the 14N nucleus) in the NMR spectrum, the 2D 15 15N-1 1H HSQC spectra 14 broadening (due to quadrupolar broadening (due to quadrupolar N nucleus) in the NMR spectrum, the 2D N- H HSQC spectra 15N is in natural abundance. The 15 N is in have beenrecorded recorded all investigated the investigated molecules have been forfor all the molecules wherewhere natural abundance. The expanded 15 1 1 expanded NH (2) 15 region of NH HSQC spectrum of molecule 20 in CDCl is Figure given in which NH(2) region of N- H HSQC spectrum of molecule 20 in CDCl3 is given 3in 22Figure which 22 provides 1hJ2h 1hJFH and 2hJNF detected in the solvent CDCl3, disappeared in 1h 1h 2h FH and 2hJNF. These provides values of values of JFH and JNF . These JFH and JNF detected in the solvent CDCl3 , disappeared in the the solvent solvent DMSO-d DMSO-d66.. This This unequivocally unequivocally established established that that these these are are coupling coupling arising arising from from through through space interactions. space interactions.

Molecules 2017, 22, 423 Molecules 2017, 22, 423

19 of 44 18 of 41

15N-1H-HSQC spectra of molecule 20 in the solvents (A) CDCl3 and (B) Figure Figure 22. 22. 400 400MHz MHzcoupled coupled 15 N-1 H-HSQC spectra of molecule 20 in the solvents (A) CDCl3 and 6. The measured couplings and their signs are reported in the Figure 22A. DMSO-d (B) DMSO-d . The measured couplings and their signs are reported in the Figure 22A.

6

Furthermore, in the 2D 1515N-1H HSQC spectrum of molecule 25, the NH(2) peak appeared as a Furthermore, in the 2D N-1 H HSQC spectrum of molecule 25, the NH peak appeared as quartet in CDCl3 while it appeared as a singlet in DMSO solvent indicating that the(2)couplings observed a quartet in CDCl3 while it appeared as a singlet in 1DMSO solvent indicating that the couplings in CDCl3 are the through space contribution [134]. The JNH scalar coupling is another important NMR observed in CDCl3 are the through space contribution [134]. The 1 JNH scalar coupling is another parameter for extracting the information about the nature of HB [40,144,147]. There is a significant important NMR parameter for extracting the information about the nature of HB [40,144,147]. There is increase in 1JNH(1) and 11JNH(2) values in halo/methoxy substituted molecules compared to the a significant increase in JNH(1) and 1 JNH(2) values in halo/methoxy substituted molecules compared unsubstituted molecule of hydrazide, confirming that the corresponding HBs are predominantly to the unsubstituted molecule of hydrazide, confirming that the corresponding HBs are predominantly electrostatic in nature. electrostatic in nature. 4.2.2. Theoretical Calculations 4.2.2. Theoretical Calculations The observed NMR experimental results have been corroborated by IR and QTAIM [91–95], The observed NMR experimental results have been corroborated by IR and QTAIM [91–95], NCI [90] and the conformational study by using relaxed potential energy scan. The chemical structures NCI [90] and the conformational study by using relaxed potential energy scan. The chemical structures of all the synthesized molecules have been optimized using G09 program with B3LYP/6-311G** level of of all the synthesized molecules have been optimized using G09 program with B3LYP/6-311G** level of theory by taking chloroform as a solvation medium. The molecular structures were also optimized with theory by taking chloroform as a solvation medium. The molecular structures were also optimized with larger basis set like aug-cc-pVTZ and 11H-NMR spectra were simulated using GIAO [145] method for larger basis set like aug-cc-pVTZ and H-NMR spectra were simulated using GIAO [145] method for optimized structures (both by 6-311G** and aug-cc-pVTZ basis sets) in chloroform solvation medium. optimized structures (both by 6-311G** and aug-cc-pVTZ basis sets) in chloroform solvation medium. Additional information has been derived by IR and QTAIM an NCI analysis. The C=O and N-H Additional information has been derived by IR and QTAIM an NCI analysis. The C=O and N-H stretching frequencies in the IR spectra of all the investigated molecules showed blue shift, providing stretching frequencies in the IR spectra of all the investigated molecules showed blue shift, providing an evidence for the existence of HB [148]. Positive sign for Laplacian of electron density (∇22ρ) at the an evidence for the existence of HB [148]. Positive sign for Laplacian of electron density (∇ ρ) at the NH(1)…X’ [148] indicates that in all the molecules the type of interaction is HB. NH(1) ···X’ [148] indicates that in all the molecules the type of interaction is HB. The NCI index detects the weak interactions in real space based on the electron density and its The NCI index detects the weak interactions in real space based on the electron density and its derivatives. Using Multiwfn program, the grid points have been calculated and plotted for the two derivatives. Using Multiwfn program, the grid points have been calculated and plotted for the two functions: sign(λ2)*ρ as function 1, and reduced density gradient (RDG) as function 2. Both these functions: sign(λ2)*ρ as function 1, and reduced density gradient (RDG) as function 2. Both these functions have the information about HB. The color filled isosurface graphs show the presence of functions have the information about HB. The color filled isosurface graphs show the presence of H(N)…X–C and C=O…H(N)…X–C type HBs in the investigated molecules. These calculations further H(N)···X–C and C=O···H(N)···X–C type HBs in the investigated molecules. These calculations further supported the NMR observations. supported the NMR observations. Relaxed Relaxed Potential Potential Energy Energy Scan Scan In the NH NH(2) proton of molecule 25 appeared as a quartet in 11H-1515N HSQC spectrum. In NMR NMR study, study, the (2) proton of molecule 25 appeared as a quartet in H- N HSQC spectrum. To understand the thereason reasonbehind behindthe the observation quartet relaxed potential energy has To understand observation of of quartet thethe relaxed potential energy scan scan has been been performed using B3LYP/6-311G** level of theory at ambient temperature for the F28–C27–C5–H12 performed using B3LYP/6-311G** level of theory at ambient temperature for the F28–C27–C5–H12 dihedral rotation of the CF3CF group was confirmed (Figure 23). The dihedral angle anglethrough throughwhich whichthe theinternal internal rotation of the 3 group was confirmed (Figure 23). calculated energy barrier for the rotation is about 2.31 2.31 kcal/mol. Because of such a lowa The calculated energy barrier forCF the3 internal CF3 internal rotation is about kcal/mol. Because of such energy barrier CF 3 group appeared as a quartet in NMR spectrum. low energy barrier CF group appeared as a quartet in NMR spectrum. 3

Molecules 2017, 22, 423 Molecules Molecules2017, 2017,22, 22,423 423

20 of 44 19 19of of41 41

Figure Relaxedpotential potentialenergy internalrotation rotationof ofthe the CF CF333group. Figure23. 23.Relaxed Relaxed potential energysurface surfaceScan Scanfor forthe theinternal group.The Thescan scan ◦ was performed in 28 steps with increments of 5° in the dihedral angle. was performed in 28 steps with increments of 55° in the dihedral angle.

The relaxed potential energy surface scan has also been carried out for the molecule 20 using The The relaxed relaxed potential potential energy energy surface surface scan scan has has also also been been carried carried out out for for the the molecule molecule 20 20 using using B3LYP/6-311G** level of theory at ambient temperature in 36 steps with 10° increment in the dihedral ◦ B3LYP/6-311G** level of theory at ambient temperature in 36 steps with 10° increment in the dihedral B3LYP/6-311G** level of theory at ambient temperature in 36 steps with 10 increment in the dihedral angle (−180° ◦to +180°)◦in order to get the information about the internal rotation of the phenyl ring angle angle (−180° (−180 toto+180°) +180 )ininorder ordertotoget getthe theinformation informationabout aboutthe the internal internal rotation rotation of of the the phenyl phenyl ring ring through a single bond. From Figure 24 itit isis clear that the proposed conformation has lower energy through through aa single single bond. bond. From From Figure Figure 24 24 it is clear clear that that the the proposed proposed conformation conformation has has lower lower energy energy over the other. over over the the other. other.

Figure24. 24. Relaxed Relaxedpotential potentialenergy energysurface surfacescan scanfor forthe theinternal internalrotation rotationof ofphenyl phenylring ringthrough throughaaa Figure Figure 24. Relaxed potential energy surface scan for the internal rotation of phenyl ring through single bond in molecule 20. Selected dihedral angles; (A) N26–C10–C13–H14 (B) N26–N27–C4–C5. single bond in molecule 20. Selected dihedral angles; (A) N26–C10–C13–H14 (B) N26–N27–C4–C5. single bond in molecule 20. Selected dihedral angles; (A) N26–C10–C13–H14 (B) N26–N27–C4–C5.

5. 5.Studies Studieson onDerivatives Derivativesof ofImides Imides 5. Studies on Derivatives of Imides The derivatives of ammonia or the primary amines [128]. The importance Theimides imides are are the amines [128]. The importance of The imides arethe thediacyl diacylderivatives derivativesof ofammonia ammoniaor orthe theprimary primary amines [128]. The importance of imide derivatives isis found in daily as, strength imide derivatives is found in many field offield dailyof such as, such high conductive of imide derivatives found in many many field ofinterest daily interest interest suchstrength as, high highelectrically strength electrically electrically conductive polymers [149–151], synthetic applications [152], medicinal activity [153], polymers [149–151], synthetic applications [152], medicinal activity [153], as ionic fluids [154], conductive polymers [149–151], synthetic applications [152], medicinal activity [153], as as ionic ionic fluids [154], in pharmacology [155] and as synthetic precursors [156] are well documented. The in pharmacology [155] and as[155] synthetic [156] are well The NH linker of fluids [154], in pharmacology and asprecursors synthetic precursors [156]documented. are well documented. The NH NH linker of an imide provides ample scope to synthesize different derivatives with the desired an imide provides ample scope to synthesize different derivatives with the desired substitution on linker of an imide provides ample scope to synthesize different derivatives with the desired substitution on acyl Several derivatives whose structures are in acyl group(s). derivatives of imides whose of chemical are given in the Figure 25 have substitution onSeveral acyl group(s). group(s). Several derivatives of imides imidesstructures whose chemical chemical structures are given given in the Figure 25 have been synthesized by using microwave assisted method [157] and characterized by been synthesized using microwave method [157] and characterized extensive utilityby of the Figure 25 haveby been synthesized byassisted using microwave assisted method [157]by and characterized extensive utility of NMR techniques and ESI-HRMS spectrometry [158]. NMR techniques and ESI-HRMS spectrometry [158]. extensive utility of NMR techniques and ESI-HRMS spectrometry [158].

Molecules 2017, 22, 423

20 of 41

Molecules 2017, 22, 423 Molecules 2017, 22, 423

21 of 44 20 of 41

Figure 25. The chemical structures of the derivatives of 2-X-N-(2-X’-benzoyl)benzamide.

5.1. Information Derived by NMR Spectroscopy The NMR spectroscopic derived information on intramolecular HB in these molecules has Figure 25. The chemicalby structures the of the derivatives derivatives of 2-X-N-(2-X’-benzoyl)benzamide. 2-X-N-(2-X’-benzoyl)benzamide. been unequivocally supported DensityofFunction Theory DFT [135,136] based NCI [90,159], and QTAIM [91–95] calculations. 5.1. Information Derived by NMR Spectroscopy Spectroscopy The solvent titration experiments [62,63,140] have been performed on the molecules 26–32 in the solvent CDCl 3 to distinguish the intraand inter- molecular HB and to monitor thethese effect molecules of atmospheric The NMR on intramolecular HB in has NMR spectroscopic spectroscopic derived derived information information intramolecular these molecules has monomeric water onsupported HB. It is observed thatFunction there is no change in the chemical shiftNCI of NH proton as been unequivocally by Density Theory DFT [135,136] based [90,159], and and well as the residual water peak position in the deuterated solvent [158]. These observations discarded QTAIM [91–95] calculations. QTAIM [91–95] calculations. any possibility of titration intermolecular HB, aggregation, dimerization or water-imide interaction. The solvent titration experiments [62,63,140]have havebeen been performed molecules 26–32 in solvent experiments [62,63,140] performed onon thethe molecules 26–32 in the DMSO-d solvent titration has been employed to derive the qualitative information on the the solvent to distinguish the intraand intermolecular HB and to monitor the effect of solvent CDClCDCl 36to distinguish the intraand intermolecular HB and to monitor the effect of atmospheric 3 relative strengths of intramolecular on the molecules 26–32. Thechemical excessive deshielding of NH atmospheric monomeric on HB.HB It is observed there is in nothe change in theshift chemical shift monomeric water on HB.water It is observed that there isthat no change of NH proton as proton is well observed as a peak consequence the deuterated disruption of intramolecular HB These due to the strong proton as thewater residual water peakof in the deuterated solvent [158]. observations well as as the residual position inposition the solvent [158]. These observations discarded interaction with The upfield shiftHB, for aggregation, NH peak with addition of DMSO [158] in the discarded any possibility of intermolecular dimerization or water-imide interaction. any possibility of DMSO. intermolecular HB, aggregation, dimerization orthe water-imide interaction. molecule 6, indicated that in this particular molecule, the intramolecular HB formed between oxygen DMSO-d been employed to derive the qualitative information on the relative DMSO-d66 solvent solventtitration titrationhas has been employed to derive the qualitative information on the atom of the and proton to be stronger than itsexcessive interactiondeshielding with DMSO strengths ofmethoxy intramolecular HB NH on the molecules 26–32. The excessive deshielding of NH proton is relative strengths of group intramolecular HB onmight the molecules 26–32. The of[134]. NH The strength HB gets on lowering the temperature. Excessive deshielding of the NH observed a of consequence of the disruption of disruption intramolecular HB due to the strong interaction with proton is as observed as a increased consequence of the of intramolecular HB due to the strong proton isThe observed on lowering the temperature due to the displacement of the hydrogen bonded proton DMSO. upfield shift for peak with ofwith DMSO in 6, indicated interaction with DMSO. TheNH upfield shift the for addition NH peak the[158] addition ofmolecule DMSO [158] in the towards the HB acceptor. isthe anintramolecular evidence in favor of intramolecular [160–162]. chemical that in this molecule, HBthe formed between oxygen atombetween ofThe the methoxy molecule 6,particular indicated that This in this particular molecule, HB formed oxygen shift NH protons as a function temperature (over the range of its 298–220 K) forwith molecules 26–32 group proton might toNH beofstronger than to itsbe interaction with DMSO [134]. TheDMSO strength of atomof ofand the NH methoxy group and proton might stronger than interaction [134]. are contained in HB Figure 26A. HB increased ongets lowering the temperature. deshielding of the NH proton isofobserved Thegets strength of increased on lowering Excessive the temperature. Excessive deshielding the NH The inon FHlowering coupling value lowering theof temperature hasofalso been detected. Such on lowering the temperature due totemperature theon displacement hydrogen bonded proton towards HBa proton is change observed the due to the displacement hydrogen bondedthe proton variation is possible only when the spin polarization is transmitted between two NMR active nuclei acceptor. This an evidence favor of intramolecular HB [160–162].HB The chemicalThe shift of NH towards the HBisacceptor. This in is an evidence in favor of intramolecular [160–162]. chemical mediated The variation in the range coupling constant (through space) as a function of shift of NH as function of (over temperature (over the range K) for molecules 26–32 protons as through a protons functionHB. of atemperature of 298–220 K) of for298–220 molecules 26–32 are contained temperature in the Figure 26B, for the molecules 26 and 29–32. areFigure contained Figure 26A. in 26A.isinreported The change in FH coupling value on lowering the temperature has also been detected. Such a variation is possible only when the spin polarization is transmitted between two NMR active nuclei mediated through HB. The variation in the coupling constant (through space) as a function of temperature is reported in the Figure 26B, for the molecules 26 and 29–32.

(a)

(b)

Figure 26. 26. Variation of (a) (a) chemical chemical shifts shifts of of NH NH protons protons as as aa function function of of temperature temperature for for the the molecules molecules Figure Variation of 26–32 and and (b) (b) through through space space mediated mediated HF HF coupling coupling constant constant as as aa function function of of temperature temperature for for the the 26–32 molecules 26 and 29–32. The molecules are identified by the symbols given in the inset. The initial molecules 26 and 29–32. The molecules are identified by the symbols given in the inset. The initial (a) in CDCl3. (b) concentration was was 10 10 mM mM concentration in CDCl . 3

Figure 26. Variation of (a) chemical shifts of NH protons as a function of temperature for the molecules 26–32change and (b)inthrough space mediated coupling the constant as a function of temperature for theSuch The FH coupling value onHFlowering temperature has also been detected. molecules 26 and 29–32. molecules are polarization identified by the symbols givenbetween in the inset. initial a variation is possible onlyThe when the spin is transmitted twoThe NMR active was 10 mM CDCl 3. nucleiconcentration mediated through HB.inThe variation in the coupling constant (through space) as a function of

temperature is reported in the Figure 26B, for the molecules 26 and 29–32.

Molecules 2017, 22, 423

22 of 44

22, 423 of 41 TheMolecules GIAO2017, [145] and CSGT [145], DFT methods of NMR simulation have been used 21 for chemical shifts Molecules calculation and it has been observed that the CSGT method is giving the values that are 2017,GIAO 22, 423[145] and CSGT [145], DFT methods of NMR simulation have been used for chemical 21 ofin41close The agreement with the experimentally observedthat values. shifts calculation and it has been observed the CSGT method is giving the values that are in close The GIAO [145] and CSGT [145], DFT methods It isagreement obvious that the molecule 2-methoxy-N’-(2-methoxybenzoyl)benzohydrazide labelled as with the experimentally observed values.of NMR simulation have been used for chemical shiftschemical calculation and it the hasmolecule been observed that the is giving the values that are as in 11 close or It is obvious that 2-methoxy-N’-(2-methoxybenzoyl)benzohydrazide labelled 11 whose structure is given in Figure 27,CSGT doesmethod not show any type of self-dimerization agreement with thestructure experimentally observed values. 1 whose chemical is given in Figure 27, does not show any type of self-dimerization or aggregation [134], even in 20 mM solution. The H-DOSY [137,138] NMR experiment has therefore It is obvious that the in molecule as 11 aggregation [134], even 20 mM 2-methoxy-N’-(2-methoxybenzoyl)benzohydrazide solution. The 1H-DOSY [137,138] NMR experiment haslabelled therefore been carried out for a mixture of 1:1 molar ratio (20 mM final solution) of molecules 11 and 26 in the whose is given Figure not show anyoftype of self-dimerization been chemical carried outstructure for a mixture of 1:1in molar ratio27, (20does mM final solution) molecules 11 and 26 in the or solvent CDCl3 and the corresponding spectrum is reported in Figure 27. aggregation [134], even in 20 mM solution. The 1H-DOSY [137,138] NMR experiment has therefore

solvent CDCl3 and the corresponding spectrum is reported in Figure 27.

been carried out for a mixture of 1:1 molar ratio (20 mM final solution) of molecules 11 and 26 in the solvent CDCl3 and the corresponding spectrum is reported in Figure 27.

Figure 27. 500 MHz 1H-DOSY NMR spectrum of 20 mM solution of the mixture of molecules 11 and

Figure 27. 500 MHz 1 H-DOSY NMR spectrum of 20 mM solution of the mixture of molecules 11 and 26 at a 1:1 molar ratio in CDCl3. 26 at a 1:1 molar ratio in CDCl3 . 1H-DOSY The different diffusion coefficients detected thesesolution two molecules discarded the possibility Figure 27. 500 MHz NMR spectrum offor 20 mM of the mixture of molecules 11 andof self or cross dimerization. The triplet pattern was detected for the NH peak of the molecule 26 with 3 . 26 at a 1:1 molar ratio in CDCl The different diffusion coefficients detected for these two molecules discarded the possibility the separation of 13.03 Hz between adjacent peaks. This triplet collapses into a singlet in 1H{19F} of self or cross dimerization. The triplet pattern was detected for the NH peak of the molecule 26 experiment confirming the presence detected of coupling between H and 19F.discarded This has the been further of The different diffusion coefficients for these two 1molecules possibility 1 H{19 F} with theascertained separationbyofacquiring 13.03 Hzthe between adjacent peaks. This triplet collapses into a singlet in in a high polarity solvent 6 which self or cross dimerization. The spectrum triplet pattern was detected for the DMSO-d NH peak of the resulted moleculein26the with 1 H and 19 F. This has been further ascertained experiment confirming the presence of coupling between collapsing of triplet to a singlet confirming that this coupling is mediated through HB. the separation of 13.03 Hz between adjacent peaks. This triplet collapses into a singlet in 1H{19F} 1H-15N HSQC NMR experiment The visualization coupling became prominent in the1H by acquiring the spectrumofin a high polarity solvent DMSO-d which resulted in the 19F. 62D experiment confirming the presence of more coupling between and This has beencollapsing further of 1H-15N HSQC spectrum and the corresponding spectrum for molecule 26 is reported in Figure 28. The tripletascertained to a singletbyconfirming thatspectrum this coupling is mediated through HB. 6 which resulted in the acquiring the in a high polarity solvent DMSO-d of the same molecule in the solvent DMSO-d6 is reported in Figure 28c. 1In the solvent DMSO, except 15 N collapsing of triplet to a singlet confirming that this coupling is mediated HB.NMR experiment The visualization of coupling became more prominent in the 2D H-through HSQC for 1JNH, all the other couplings disappeared, giving strong and unambiguous evidence that the 1 15 1 H15 The visualization of coupling became more prominent in the 2D HN HSQC NMR experiment and the measured corresponding spectrum for molecule 26 is reported in Figure 28. The N HSQC spectrum couplings 1hJFH and 2hJFN in the solvent CDCl3 are mediated through HB. The 1H-15N HSQC 1 15 and the corresponding spectrum for molecule 26 is reported in Figure 28. The HN HSQC spectrum of the same molecule in the solvent DMSO-d reported in molecules Figure 28c. In exhibited the solvent DMSO, except for 6 is investigated spectra of all the other fluorine containing also through space of the same molecule in the solvent DMSO-d 6 is reported in Figure 28c. In the solvent DMSO, except 1J , all the other couplings disappeared, giving strong and unambiguous evidence that the measured couplings of different magnitudes. NH

for 1JNH, all the other couplings disappeared, giving strong and unambiguous evidence that the

couplings 1h JFH and 2h JFN in the solvent CDCl3 are mediated through HB. The 1 H-15 N HSQC spectra measured couplings 1hJFH and 2hJFN in the solvent CDCl3 are mediated through HB. The 1H-15N HSQC of all the other fluorine containing investigated molecules also exhibited through space couplings of spectra of all the other fluorine containing investigated molecules also exhibited through space different magnitudes. couplings of different magnitudes.

Figure 28. Cont.

Figure 28. Cont.

Figure 28. Cont.

Molecules 2017, 22, 423

23 of 44

Molecules 2017, 22, 423 Molecules 2017, 22, 423

22 of 41 22 of 41

1 15N-HSQC 15 Figure 28. 3 (a) 1H(NH-coupled) spectrum; (b) Figure 28. 800 800MHz MHzspectrum spectrumofofmolecule molecule2626ininCDCl CDCl 3 (a) H- N-HSQC (NH-coupled) spectrum; Figure 28. 800structure MHz spectrum of molecule 26 in CDClcouplings 3 (a) 1H-15N-HSQC (NH-coupled) spectrum; 1 15(b) Nthe chemical of molecule 1 and measured with their 400 MHz (b) the chemical structure of molecule 1 and measured couplings withsigns; their (c) signs; (c) 4001HMHz 15NHthe chemical structure of molecule 1 and measured couplings with their signs; (c) 400 MHz 1HSQC 6. spectrum (NH-coupled) in DMSO-d H-15 N-HSQC spectrum (NH-coupled) in DMSO-d 6. HSQC spectrum (NH-coupled) in DMSO-d6.

The 11JNH values of the molecules 26, 27 and 29–32 are substantially smaller than the molecule 28, The valuesof ofthe themolecules molecules26, 26,27 27and and 29–32 29–32 are substantially substantially smaller than than the the molecule molecule 28, 28, NHvalues The 1JJNH providing strong and unambiguous evidence that the are nature of HBs insmaller the derivatives of imides is providing strong and unambiguous evidence that the nature of HBs in the derivatives of imides providing strong andcovalent unambiguous evidence that the nature of HBs in the of [163–165] imides is is 19F HOESY H-19 predominantly of the type [143,144] The strong correlations in the 2D11derivatives 1 19 predominantly of the covalent type [143,144] The strong correlations in the 2D HF HOESY [163–165] HF HOESY [163–165] predominantly of the covalent type [143,144] The strong correlations in the 2D experiments for the molecules 26 and 29–32 established the close proximity between NH and F atoms experiments for molecules 26 and established the close close proximity proximity between NH and atoms experiments for the theThe molecules and 29–32 29–32 established the between NH and F F29. atoms in these molecules. 2D 11H-1926 F HOESY spectrum of the molecule 26 is reported in the Figure 19 1 19 in these molecules. The 2D HF HOESY spectrum of the molecule 26 is reported in the Figure in these molecules. The 2D H- F HOESY spectrum of the molecule 26 is reported in the Figure 29.29.

Figure 29. 376.5 MHz 2D 1H-19F HOESY spectrum of the molecule 26 in CDCl3. 19F HOESY spectrum of the molecule 26 in CDCl3. Figure29. 29. 376.5 376.5 MHz MHz2D 2D11HH-19 Figure F HOESY spectrum of the molecule 26 in CDCl3 .

5.2. Theoretical Calculations 5.2. Theoretical Calculations 5.2. Theoretical Calculations The DFT [135,136] optimized structure calculations have been carried out to ascertain the NMR The DFT DFT The [135,136] optimized structure structure calculations have been carried out out to to(d,p) ascertain thetheory NMR observations. DFT optimized calculations have been performed with B3LYP/6-311+g level the of The [135,136] calculations have been carried ascertain NMR observations. The DFT calculations have been performed with B3LYP/6-311+g (d,p) level of theory with the chloroform as calculations the solvationhave medium. energy with minimized structures(d,p) werelevel confirmed by observations. The DFT been The performed B3LYP/6-311+g of theory with the chloroform as the solvation medium. The energy minimized structures were confirmed by harmonic vibrationalas frequency. The wave function files forminimized QTAIM, and NCI studies simulated with the chloroform the solvation medium. The energy structures wereand confirmed by harmonic vibrational frequency. The wave function files for QTAIM, and NCI studies and simulated 1 H-NMR spectra usingfrequency. CSGT [145] were generated optimized harmonic vibrational The wave functionfrom files for QTAIM,coordinates. and NCI studies and simulated spectra using CSGT [145] were generated from optimized coordinates. 11H-NMR H-NMR spectra using CSGT [145] were generated from optimized coordinates. 5.2.1. Conformational Study 5.2.1. Conformational Study 5.2.1. Conformational Study For all the investigated imides maximum of 3–4 major conformations are possible due to ring For all the the investigated imidesmaximum maximumofof 3–4 major conformations possible to ring For all imides 3–4 major conformations areare possible duedue to ring flip flip as shown ininvestigated the Figure 30. flip as shown in the Figure 30. as shown in the Figure 30.

Molecules 2017, 22, 423

24 of 44

Molecules 2017, 22, 423

23 of 41

Molecules 2017, 22, 423

23 of 41

Figure 30. The possible conformersofofthe theinvestigated investigated imide arising duedue to the flip. flip. Figure 30. The possible conformers imidemolecules, molecules, arising to ring the ring Figure 30. four The possible of the the cis-cis investigated imide molecules, arisingwere due to the ring flip. Out of the possibleconformers conformers and trans-trans conformers optimized and the

Out of the four possible conformers the cis-cis and trans-trans conformers were optimized and the difference {(cis-cis) – (trans-trans)} of minimum energy has been taken. The energy difference ΔEcis-trans difference {(cis-cis) –four (trans-trans)} of−11 minimum energy taken. Theimide energy difference ∆E Out of the possible−2 conformers the cis-cis andhas trans-trans conformers weremolecules optimized and cis-trans varied from approximately to Kcal/mol among all been the investigated and itthe is varied from approximately − 2 to − 11 Kcal/mol among all the investigated imide molecules and difference {(cis-cis) – (trans-trans)} of minimum energy has been taken. The energy difference ΔE cis-trans also found that the energy of cis-cis conformers is always lower than the trans-trans that are due to it is varied fromthe approximately −2 to conformers −11 Kcal/molisamong alllower the investigated imide molecules and it isto the also found that energy of cis-cis always than the trans-trans that are due the presence of HB. also found that the energy of cis-cis conformers is always lower than the trans-trans that are due to presence of HB. the presence of HB. Relaxed Potential Energy Scan

Relaxed Potential Energy Scan

The Potential findings of cis-cisScan and trans-trans energies of the conformers has been further supported by Relaxed Energy relax potential energy scans. potential energy surface for the internal rotation of the phenyl by The findings of cis-cis and Relaxed trans-trans energies of the conformers has been further supported The findings ofbond cis-cis and trans-trans energies of the conformers has been further supported by ring through single has been performed. The rotation of 360° (−180–0–+180) through single bond relax potential energy scans. Relaxed potential energy surface for the internal rotation of the phenyl relaxscanned potentialinenergy scans. potential energy surface the ◦internal of the phenyl was 20 steps withRelaxed 18° of rotational segments. The for scanned graphrotation of energy (kcal/mol) ring through single bond has been performed. The rotation of 360 ( − 180–0–+180) through single ring through single bond been performed. The of 360° (−180–0–+180) through singleofbond versus dihedral angle (θ°)has is reported in Figure 31.rotation From the graph, it is clear that the energy the ◦ bond was wasscanned scannedinin20 20steps stepswith with18° 18 ofofrotational rotational segments. The scanned graph of energy (kcal/mol) segments. Thethe scanned graph of energy (kcal/mol) cis conformer is lower than the other, and the maximum is for trans conformation. ◦ ) is reported in Figure 31. From the graph, it is clear that the energy of the cis versus dihedral angle (θ versus dihedral angle (θ°) is reported in Figure 31. From the graph, it is clear that the energy of the conformer is loweris than other, and the is for thethe trans cis conformer lowerthe than the other, andmaximum the maximum is for transconformation. conformation.

Figure 31. Relaxed potential energy surface for the internal rotation of the phenyl ring through single bond. The dihedral angle and rotation direction are highlighted in the structure of molecule 26. Figure 31. Relaxed potential energy surfacefor for the the internal internal rotation thethe phenyl ringring through single Figure 31. Relaxed potential energy surface rotationofof phenyl through single The dihedral angle and(NCI) rotation direction are highlighted in the structure of molecule 26. 5.2.2. bond. Non Covalent Interaction Calculations

bond. The dihedral angle and rotation direction are highlighted in the structure of molecule 26.

pointsInteraction based on (NCI) NCI [90] calculations have been plotted for a defined real space 5.2.2.The Nongrid Covalent Calculations

sign(λ2(r)Interaction )ρ(r), as function 1 and reduced density gradient (RDG) as function 2 and color filed 5.2.2.function, Non Covalent (NCI) Calculations

The grid based [90] calculations haveThe been plotted for provided a defined the real visual space isosurfaces arepoints plotted for on theNCI investigated molecules. NCI studies

The grid points based on NCI [90] calculations have been plotted forasafunction defined2real function, function, sign(λ2 (r), as function 1 and density (RDG) andspace color filed information about(r))ρ weak interactions andreduced repulsions in thegradient molecules [158]. sign(λ2 )ρ , as function 1 and reduced density gradient (RDG) as function 2 and color filed isosurfaces isosurfaces are plotted for the investigated molecules. The NCI studies provided the visual (r) (r) information about weak interactions and repulsions the molecules [158]. are plotted for the investigated molecules. The NCIinstudies provided the visual information about 5.2.3. Atoms in Molecules (AIM) Calculations weak interactions and repulsions in the molecules [158]. 2 The magnitudes of ρ(r), signs of ∇ ρ(r) and potential energy density (V(r)) at corresponding (3, −1)

5.2.3. Atoms in Molecules (AIM) Calculations BCP (bond critical points) (rcp) for HBs of interest have been calculated using QTAIM calculations 5.2.3. Atoms in Moleculesof(AIM) Calculations 2 (r) and potential energy density (V(r)) at corresponding (3, −1) TheThe magnitudes , signs [91–95]. value of (V(r)ρ)(r)used in of the∇ EρHB = V(rbcp)/2 [96] for the calculation of energy of HB (EHB) of BCP (bond critical points) (r cp ) for HBs of interest been calculated using) at QTAIM 2 X···HX type. The calculated E HB of different HBs in have all the investigated variedcalculations from −2 to The magnitudes of ρ(r) , signs of ∇ ρ(r) and potential energy densitymolecules (V corresponding (3, −1) (r) [91–95]. The value of The (V(r))bond usedpaths in theforEHB =−1) V(rBCPs bcp)/2were [96] for the calculation of energy of HB (EHB)for of −8.56 Kcal/mol [158]. (3, generated for the investigated molecules BCP (bond critical points) (rcp ) for HBs of interest have been calculated using QTAIM calculations [91– X···HX type. and Thethe calculated EHB of different HBs in all investigated varied from −2 to visualization molecular model 26the containing BCPsmolecules and bond path is reported 95]. The value of (V (r) ) used in the EHBfor = the V(rmolecule )/2 [96] for the calculation of energy of HB (EinHB ) of bcpBCPs −8.56 Kcal/mol [158]. The bond paths for (3, −1) were generated for the investigated molecules for Figure 32. X···HX type. Theand calculated EHB of different in all26the investigated molecules varied fromin−2 to visualization the molecular model for theHBs molecule containing BCPs and bond path is reported −8.56Figure Kcal/mol [158]. The bond paths for (3, − 1) BCPs were generated for the investigated molecules 32.

for visualization and the molecular model for the molecule 26 containing BCPs and bond path is reported in Figure 32.

Molecules 2017, 22, 423

25 of 44

Molecules 2017, 22, 423

24 of 41

Molecules 2017, 22, 423

24 of 41

Molecules 2017, 22, 423

24 of 41

Figure 32. The visualization of BCPs and bond paths of HB for the molecule 26 plotted using the Figure 32. The visualization of BCPs and bond paths of HB for the molecule 26 plotted using the Multiwfn software. Dots represent the CPs and thin bar represents the HB interactions. Multiwfn software. Dots represent the CPs and thin bar represents the HB interactions. Figure 32. The visualization of BCPs and bond paths of HB for the molecule 26 plotted using the

6. Studies on Diphenyloxamides Multiwfn software. Dots represent the CPs and thin bar represents the HB interactions.

6. Studies on Diphenyloxamides

Figure 32. The visualization of BCPs C=O and … bond HB involving for the molecule 26 plotted using theother …X-CofHB H(N)paths organic fluorine, and The existence of three centered 6. Studies on Diphenyloxamides

Multiwfn software. Dotscentered represent the CPs thin··· bar represents the HB by interactions. The existence of three C=O ···and H(N) X-C HBexplored involving organic fluorine, and halogens in the derivatives of diphenyloxamide has been NMR spectroscopy andother …H(N)…X-C HB involving organic fluorine, and other The existence of three centered C=O quantum theoretical studies. The diphenyloxamide are the of foldamers, where halogens in the derivatives of diphenyloxamide has derivatives been explored by basic NMRunits spectroscopy and quantum 6. Studies in onthe Diphenyloxamides halogens derivatives ofHB diphenyloxamide been explored by NMR spectroscopy and the formation of three centered contributes to thehas stable rigid structure. The possible mode of the theoretical studies. The diphenyloxamide derivatives areand the basic units of foldamers, where … … … … quantum theoretical studies. The diphenyloxamide derivatives are the basic units of foldamers, where H(N) X-CX HB involving organic and other The existence of three C=O three-centered HB formation C=O H(N) X-C (where = and CF 3, F, Cl, Br and I)fluorine, in thepossible investigated formation of three centered HBcentered contributes to the stable rigid structure. The mode of the formation of three centered contributes to thegiven stable rigid structure. The possible mode of halogens inalong the derivatives ofHB diphenyloxamide has been explored byBr NMR and molecules, with their chemical structures inand Figure three-centered HB formation C=O ···…H(N) ···X-Care (where X = CF3 , 33. F, Cl, and spectroscopy I) in the investigated …X-C (where X = CF3, F, three-centered HB formation C=O H(N) Cl, Br and I) in the investigated quantum theoretical studies. The diphenyloxamide derivatives are the basic units of foldamers, where molecules, along with their chemical structures are given in Figure 33. molecules, along with their chemical structures are given in Figure 33.

the formation of three centered HB contributes to the stable and rigid structure. The possible mode of three-centered HB formation C=O…H(N)…X-C (where X = CF3, F, Cl, Br and I) in the investigated molecules, along with their chemical structures are given in Figure 33.

Figure 33. Chemical structures of N,N-diphenyloxamide (33) and its derivatives 34–40. The dotted line3 indicate the HBs. Figure 33. Chemical structures of N,N-diphenyloxamide (33) and its derivatives 34–40. The dotted Figure 33. Chemical structures of N,N-diphenyloxamide (33) and its derivatives 34–40. The dotted line3 indicateObservation the HBs. 6.1. Experimental by NMR Spectroscopy

line3 indicate the HBs. Figure studies 33. Chemical of N,N-diphenyloxamide (33) and itsofderivatives 34–40.shift The(δ dotted Initial werestructures focused on the concentration dependence NH chemical NH) for all 6.1. Experimental Observation by NMR Spectroscopy line3 indicate the HBs. the molecules and it was observed that δNH remained unaltered for all the molecules, discarding the 6.1. Experimental Observation by NMR Spectroscopy Initial were focused on the interactions concentration dependence of to NHthe chemical shift (δNH ) for all presence ofstudies any type of intermolecular [166]. Compared unsubstituted molecule 6.1. Experimental Observation by NMR Spectroscopy the molecules and it was observed that δ NH remained unaltered for all the molecules, discarding 33 the chemical shifts of NH protons areconcentration observed to bedependence more deshielded for the different substituted Initial studies were focused on the of NH chemical shift (δNHthe ) for all presence anyittype of intermolecular interactions [166]. Compared to the unsubstituted molecule Initialofand studies were focused on theδNH concentration dependence of NH chemical shift (δdiscarding NH ) forThe all the molecules, 34–38, indicating the participation of NH proton in weakfor molecular interactions [166]. the molecules was observed that remained unaltered all the molecules, 33 the chemical shifts of NH protons areδobserved to beunaltered more deshielded for the different substituted the molecules was observed NH remained for to allto thethe molecules, discarding deshielding of and NH shift onthat lowering the temperature due the strengthening in the HBthe is 33 presence of any type ofitchemical intermolecular interactions [166]. Compared unsubstituted molecule molecules, indicating the participation of NH proton in weak molecular interactions [166]. The presence of34–38, any type of intermolecular interactions [166]. Compared to the unsubstituted molecule evident from Figure 34A. the chemical shifts of NH protons are observed to be more deshielded for the different substituted deshielding of NH chemical shift on are lowering the to temperature due to thefor strengthening the HB is 33 the chemical shifts of NH protons observed be more deshielded the different in substituted molecules, indicating participation of NH proton in weak molecular interactions [166]. evident34–38, from Figure 34A. the molecules, 34–38, indicating the participation of NH proton in weak molecular interactions [166]. The

The deshielding of NH chemical shift on lowering the temperature due to the strengthening in the HB deshielding of NH chemical shift on lowering the temperature due to the strengthening in the HB is is evident from Figure evident from Figure34A. 34A.

Figure 34. The variation of the chemical shift of NH proton (A) with temperature; (B) with the incremental addition of DMSO-d6 to the solution containing 200 µL of CDCl3. The 10 mM concentration Figure variation of the has chemical shift oftaken NH proton temperature; (B) with the at 298 K34. for The the molecules, 33–38 been initially for both(A) the with studies. incremental addition of DMSO-d6 to the solution containing 200 µL of CDCl3. The 10 mM concentration at 298 K34. forThe the molecules, been initially for both(A) thewith studies. Figure variation of33–38 the has chemical shift of taken NH proton temperature; (B) with the

Figure 34. The variation of the chemical shift of NH proton (A) with temperature; (B) with the incremental addition of DMSO-d6 to the solution containing 200 µL of CDCl3. The 10 mM concentration incremental addition of DMSO-d6 to the solution containing 200 µL of CDCl3 . The 10 mM concentration at 298 K for the molecules, 33–38 has been initially taken for both the studies. at 298 K for the molecules, 33–38 has been initially taken for both the studies.

Molecules 2017, 22, 423 Molecules 2017, 2017, 22, 22, 423 423 Molecules

26 of 44 25 of of 41 41 25

The high high polarity solvent solvent DMSO-d66 induced induced perturbation of of δδNH NH is is reported in in Figure 34B. 34B. The The The The high polarity polarity solvent DMSO-d DMSO-d6 inducedperturbation perturbation of δNHreported is reportedFigure in Figure 34B. larger value of Δδ NH /ΔV DMSO in molecule 33 compared to the molecules, 34–38, is giving an indication larger value of Δδof NH/ΔVDMSO in molecule 33 compared to the molecules, 34–38, is giving an indication The larger value ∆δNH /∆VDMSO in molecule 33 compared to the molecules, 34–38, is giving an that the the probable probable three three centered centered H-bond is is relatively relatively stronger stronger than the the two centered centered one. that indication that the probable threeH-bond centered H-bond is relativelythan strongertwo than the twoone. centered one. 15 1 The 2D 2D 15NN-1 1H H HSQC HSQC experiments experiments for all all the investigated investigated molecules molecules have have been been carried carried out, out, The The 2D 15 NH HSQC experiments forfor all the the investigated molecules have been carried out, where 15N is in natural abundance. The 15 15N-11H HSQC spectrum of molecule 38 in CDCl3 yielded a 15 where 15 1 H HSQC where is in natural abundance. N- H spectrum HSQC spectrum of molecule 38 inyielded CDCl3 ayielded N is in N natural abundance. The 15 N-The of molecule 38 in CDCl quarteta 3 group is is very very quartet for for the the NH NH proton proton (reported (reported in in Figure Figure 35B) 35B) implying implying that that the the rotation rotation of of CF CF33 group quartet for the NH proton (reported in Figure 35B) implying that the rotation of CF3 group is very fast unlike 15N-11H HSQC spectrum of molecule 34 in the fast unlike unlike in in the the earlier earlier reported reported studies studies [79]. The 15 15 1 fast [79]. The NH HSQC spectrum of molecule 34 in the, in the earlier reported studies [79]. The N- H HSQC spectrum of molecule 34 in the solvent CDCl 3 3 , reported in Figure 35A, yielded a doublet for the NH proton. solvent CDCl 3, reported in Figure 35A, yielded a doublet for the NH proton. solvent CDCl reported in Figure 35A, yielded a doublet for the NH proton.

15 15 N-111H-HSQC Figure H-HSQCspectra spectra of of the the molecules molecules 34 Figure35. 35. (A,B) (A,B) 15 spectra of 34 and 38 respectively, respectively,in inCDCl CDCl333... The Themolecular molecular Figure 35. (A,B) N- H-HSQC 34 and 38 38 respectively, in CDCl The molecular structures and the measured couplings have also been reported. structures and the measured couplings have also been reported. structures and the measured couplings have also been reported. 15N-111H HSQC spectrum of molecule 38 which was observed in the solvent CDCl3 Thequartet quartetin in1515 The N- H HSQC spectrum of molecule The quartet in molecule 38 38 which which was was observed observedin inthe thesolvent solventCDCl CDCl33 reported in36B. Figure 36B. This This unambiguously unambiguously collapsedtoto tothethe the singlet insolvent the solvent solvent DMSO-d collapsed singlet in the DMSO-d in Figurein This unambiguously established 66 reported Figure 36B. collapsed singlet in the DMSO-d 6 reported established the existence of HB in in the the molecule 38. 38. the existencethe of HB in the of molecule 38.molecule established existence HB

15N-11H HSQC spectra of the molecules 34 and 38 respectively, in DMSO-d6. 15 Figure 36. (A,B) (A,B) 1 H HSQC Figure 36. N- 15 HNHSQC spectra of the of molecules 34 and34 38and respectively, in DMSO-d 6. Figure 36. (A,B) spectra the molecules 38 respectively, in DMSO-d 6.

The molecule molecule 34 34 in in solvent solvent DMSO-d DMSO-d6 yielded yielded aa doublet doublet as as reported reported in in Figure Figure 36A, 36A, with with the the The The molecule 34 in solvent DMSO-d66 yielded a doublet as reported in Figure 36A, with the JJHF HF = = 0.85 0.85 Hz Hz and and JJNF NF = = 1.25 1.25 Hz, Hz, whereas whereas in in CDCl CDCl33 these these values values were were JJHF HF = = 2.9 2.9 Hz Hz and and JJNF NF = = 0.4 0.4 Hz, Hz, JHF = 0.85 Hz and JNF = 1.25 Hz, whereas in CDCl3 these values were JHF = 2.9 Hz and JNF = 0.4 Hz, respectively. But But it it is is observed observed that that the the relative relative slopes slopes of of the the displacement displacement vectors vectors of of the the cross cross sections sections respectively. in the solvents (DMSO-d 6 or CDCl 3 ) are opposite (Figures 35A and 36A). As the HB gets ruptured in in the solvents (DMSO-d6 or CDCl3) are opposite (Figures 35A and 36A). As the HB gets ruptured in

couplings and the observed coupling in the solvent CDCl3 is considered as through space coupling. Hence the contribution from the HB alone turns out to be −3.75 Hz. As far as signs of JNF is concerned, it has to be negative. These observations gave a strong evidence for the presence of HB in the molecule 34. The close proximity between fluorine atom and Molecules 2017, 22, 423 27 of 44 NH protons has also been confirmed by the detection of cross peak in the 2D 1H-19F HOESY spectra of molecules 34 and 38. This is additional support for the presence of intramolecular HB between F and NH proton [166]. An increase in the 1JNH relative to molecule 33, is observed in molecules 34–36 respectively. But it is observed that the relative slopes of the displacement vectors of the cross sections and 38, indicating that the HB in these molecules is predominantly an electrostatic in nature [143,144]. in the solvents (DMSO-d ) are opposite (Figures 35A and 36A). As the HB gets ruptured 6 or CDCl On the other hand, 1JNH decreases in3 molecule 37, hence the nature of HB is predominantly covalent in the high polar solvents, the couplings observed in the DMSO-d6 are considered as through bond in this molecule [40]. couplings and the observed coupling in the solvent CDCl3 is considered as through space coupling. Hence the contribution 6.2. Theoretical Studies from the HB alone turns out to be −3.75 Hz. As far as signs of JNF is concerned, it has to be negative. These observations gave a strong The for observed experimental have been also corroborated by DFT fluorine based theoretical evidence the presence of HB inresults the molecule 34. The close proximity between atom and 1 19 calculations, such as, QTAIM [91–95], Natural Bond Orbital (NBO) [159] and NCI [90]. NH protons has also been confirmed by the detection of cross peak in the 2D H- F HOESY spectra of molecules 34 and 38. This is additional support for the presence of intramolecular HB between F 6.2.1.NH QTAIM Calculations and proton [166]. An increase in the 1 JNH relative to molecule 33, is observed in molecules 34–36 and 38, thatoftheelectron HB in these molecules is predominantly an electrostatic nature [143,144]. Theindicating magnitude density (ρ) and sign of Laplacian of electron indensity (∇2ρ) are 1 On the other JNH decreases molecule 37,a hence theBCPs nature of bond HB is paths predominantly covalent examined forhand, the determination of in HB. For such purpose and for intramolecular in this molecule [40]. HBs are detected for the investigated molecules and are reported in Figure 37. The observed electron density values fall in the expected range (0.0102–0.0642 a.u.) for HBs [167]. 6.2. Studies The Theoretical positive sign of Laplacian of electron density (∇2ρ) at the (3, −1) BCPs indicates the type of interactions that belong to the HBs.results On thehave basisbeen of electron density, the proton acceptance trend for The observed experimental also corroborated by DFT based theoretical ...X follows the pattern Br > Cl > I, as organic halogens in the intramolecular five membered N-H calculations, such as, QTAIM [91–95], Natural Bond Orbital (NBO) [159] and NCI [90]. detected from the chemical shift difference between the molecules 34–37 [166] compared to that of 6.2.1. QTAIM Calculations molecule 33. This trend is further supported by the ρ(NH...X) values [166]. The obtained electron ...X, NH...O and CH...O, respectively. density are about 0.015,density 0.020 and 0.017 forofNH By using Thevalues magnitude of electron (ρ) and sign Laplacian of electron density (∇2 ρ) are examined these in the bonding (BE) equation;BCPs {BE (kj/mol) = 777 × ρfor (inintramolecular a.u.) − 0.4}, the HBs BEs are are for thevalues determination of HB.energy For such a purpose and bond paths ...X, NH...O and CH...O HB interactions, respectively. estimated to be around 11, 15 and 13 kJ for NH detected for the investigated molecules and are reported in Figure 37.

Figure 37. Molecular graphs, contour plots and AIM calculated bond paths for the molecules 33–38. Figure 37. Molecular graphs, contour plots and AIM calculated bond paths for the molecules 33–38. Dotted lines indicate the intramolecular HBs. Green and red dots are bond critical points (BCP) and Dotted lines indicate the intramolecular HBs. Green and red dots are bond critical points (BCP) and ring critical points (RCP), respectively. Electron density is plotted as contours in the blue curves in ring critical points (RCP), respectively. Electron density is plotted as contours in the blue curves in the the plane of molecules. plane of molecules.

6.2.2. NBO Analysis The observed electron density values fall in the expected range (0.0102–0.0642 a.u.) for HBs [167]. For HB formation, electronoftransfer the electron region HB indicates acceptor to antiThe positive sign of Laplacian electronfrom density (∇2 ρ) at rich the (3, −1) of BCPs thethe type of bonding orbital (σ*) of the HB donor takes place. This has been studied by the Natural Bond Orbital interactions that belong to the HBs. On the basis of electron density, the proton acceptance trend for organic halogens in the intramolecular five membered N-H... X follows the pattern Br > Cl > I, as detected from the chemical shift difference between the molecules 34–37 [166] compared to that of molecule 33. This trend is further supported by the ρ(NH... X) values [166]. The obtained electron density values are about 0.015, 0.020 and 0.017 for NH... X, NH... O and CH... O, respectively. By using these values in the bonding energy (BE) equation; {BE (kj/mol) = 777 × ρ (in a.u.) − 0.4}, the BEs are estimated to be around 11, 15 and 13 kJ for NH... X, NH... O and CH... O HB interactions, respectively.

Molecules 2017, 22, 423

28 of 44

6.2.2. NBO Analysis Molecules 423 For2017, HB22,formation,

41 electron transfer from the electron rich region of HB acceptor 27 toofthe anti-bonding orbital (σ*) of the HB donor takes place. This has been studied by the Natural Bond Orbital (NBO) (NBO) analysis analysis and and found found that that the the values values of of lp(O) lp(O) → → σ*(N-H) σ*(N-H) were were always always greater greater than than the the lp(O) lp(O) → → …O bonds are concluded to be stronger than the C-H…O bonds. σ*(C-H) values. Hence the N-H σ*(C-H) values. Hence the N-H···O bonds are concluded to be stronger than the C-H···O bonds.

6.2.3. 6.2.3. NCI NCIAnalysis Analysis …F QTAIM the intramolecular intramolecular BCP BCP for for N-H N-H··· QTAIM calculations calculations and and NBO analysis did not show the F interaction interaction in in molecule molecule 22 which which contradicts contradicts the the NMR NMR observations. observations. Another Another powerful powerful method, method, NCI NCI index index has has been been used used to to visualize visualize the the weak weak interaction interaction which which showed showed the the presence presence of of HB HB in in molecule molecule 34, 34, which which is is in in agreement agreement with with NMR NMR observations. observations. In In Figure Figure 38 38 (left (left side), side), the the calculated calculated grid grid points points are are plotted plotted for for the the two two functions: functions: sign(λ sign(λ22)*ρ )*ρ as as function function 11 and and reduced reduced density density gradient gradient (RDG) (RDG) as as function 2 by Multiwfn program. Color filled isosurface graphs are plotted using these grid points function Multiwfn program. Color filled isosurface graphs are plotted using these grid points and and are reported in right the right ofFigure the Figure are reported in the side side of the 38. 38.

Figure 38. 38. The The plot plot of of function function 11 (sign(λ (sign(λ22)*ρ )*ρ values) values) on on X-axis X-axis vs vs function function 2, 2, the the reduced reduced density density Figure gradient (RDG) (RDG) on on Y-axis. Y-axis. (left (lefthand handside), side), colored colored isosurface isosurfaceplots plots in in which which Green Green colour colour denotes denotes gradient weak HB HB and and red red color color stands stands for for steric steric effect. effect. Labels Labels 33–38 33–38 represent represent molecules molecules 33–38, 33–38, respectively. respectively. weak

For For the the molecules molecules 35, 35, 36, 36, and and 37, 37, there there are are three three spikes spikes on on the left-hand left-hand side side which which denote denote three three …X, N-H…O and C-H…O (where X = Cl, Br, and I), these three bonds can be also seen HBs namely N-H HBs namely N-H···X, N-H···O and C-H···O (where X = Cl, Br, and I), these three bonds can be also in thein colored isosurface plots plots reported on theon right side of theof Figure 38. For = F,Xall=three bondsbonds exist seen the colored isosurface reported the right side the Figure 38.XFor F, all three and corresponds to two thesethese threethree HBs HBs also also are clearly seenseen in the existthe andspikes the spikes corresponds toHBs two are HBsoverlapped, are overlapped, are clearly in isosurfaces plot 2. For X = CF 3 , the four spikes have been seen that are also visible in isosurfaces plot 6. the isosurfaces plot 2. For X = CF3 , the four spikes have been seen that are also visible in isosurfaces plot 6. 6.2.4. Relaxed Potential Energy Scan 6.2.4. Relaxed Potential Energy Scan 15 1 It may be pointed out that in the N- H-HSQC NMR spectrum of molecule 38 the NH group It may pointed outtothat the 15 NH-HSQC spectrumtemperature. of moleculeRelaxed 38 the NH group appeared as be a quartet due fast in rotation of 1CF 3 group NMR at the ambient potential appeared as for a quartet due to fast rotation of CF group at the ambient temperature. Relaxed potential energy scan the H9–C5–C16–F2 dihedral angle was performed to derive the information about 3 energy scanbarrier for theofH9–C5–C16–F2 dihedral performed to in derive the information about the the energy internal rotation of CF3 angle group.was This is reported the Figure 39. energy barrier of internal rotation of CF3 group. This is reported in the Figure 39.

Figure 39. Relaxed potential energy surface for the internal rotation of CF3 group at B3LYP/6-311G** level of calculation. The dihedral angle H9–C5–C16–F2 has been selected for the scan.

The barrier for this internal rotation was calculated as 2.15 kcal/mol using B3LYP/6-311G** level of theory and the energy barriers that can be observed in NMR is in between the 7–24 kcal/mol. This was the reason for observation of quartet for NH group.

6.2.4. Relaxed Potential Energy Scan It may be pointed out that in the 15N-1H-HSQC NMR spectrum of molecule 38 the NH group appeared as a quartet due to fast rotation of CF3 group at the ambient temperature. Relaxed potential energy for423 the H9–C5–C16–F2 dihedral angle was performed to derive the information 29 about Moleculesscan 2017, 22, of 44 the energy barrier of internal rotation of CF3 group. This is reported in the Figure 39.

Figure of CF CF33 group Figure 39. 39. Relaxed Relaxed potential potential energy energy surface surface for for the the internal internal rotation rotation of group at at B3LYP/6-311G** B3LYP/6-311G** level level of of calculation. calculation. The The dihedral dihedral angle angle H9–C5–C16–F2 H9–C5–C16–F2 has has been been selected selected for for the the scan. scan.

The barrier for this internal rotation was calculated as 2.15 kcal/mol using B3LYP/6-311G** level The barrier for this internal rotation was calculated as 2.15 kcal/mol using B3LYP/6-311G** level of theory and the energy barriers that can be observed in NMR is in between the 7–24 kcal/mol. This of theory and the energy barriers that can be observed in NMR is in between the 7–24 kcal/mol. This was the reason for observation of quartet for NH group. was the reason for observation of quartet for NH group. 7. Utility of H/D Exchange for Study of HB The presence of HBs affects the release rate of labile hydrogen(s) which is/are participating in the reaction. There are number of chemical reactions in which the transfer of one or more protons (viz., hydride ions or hydrogen atoms) takes place in the rate determining step [40,42–45] The reaction kinetics depend on several factors, which also include the strength of intramolecular HB and the electronic effects caused by the substituents. The NMR spectroscopy is found to be a powerful technique which is widely employed for understanding the protein conformation, and dynamics [46–52] in aqueous media can be utilized to monitored by hydrogen/deuterium (H/D) exchange. 7.1. Factors Affecting the H/D Exchange The rate of H/D exchange in a particular molecule can be affected by the inter- and the intra- molecular HBs. There will be a rapid exchange of the proton attached to nitrogen with the labile protons of the solvent. The mechanism of H/D exchange has been reported earlier in the derivatives of amides [53]. In the non-deuterated solvents, the proton exchange does not reflect in the NMR spectrum. On the other hand, in the presence of a labile deuterium-containing solvent the exchange takes place with the deuterium of the solvent molecules. This will have significant effect on the time dependent variation in the NMR signals intensities and permits the determination of H/D exchange rate. If the deuterated solvent is used in excess compared to the substrate, then the rate of exchange follows the pseudo first order kinetics. It is well known that the rate of H/D exchange is not only dependent on the strength of the intramolecular hydrogen bond, but also dependent on the electronic effect of the substituents. The amides and amines are the basic building blocks for the synthesis of heterocyclic and linear nitrogen containing compounds. Consequent to significant difference in electronegativity (EN) and size among halogens, the strength of hydrogen bonds, steric hindrance and electronic effects [168] by these groups would also be substantially different. Hence the electronic effect, size effect and the effect of organic fluorine involved intramolecular HB on H/D exchange using 1 H-NMR spectroscopic techniques has also been explored in the different halo substituted anilines and benzamides [169]. The chemical structures of all the investigated molecules are reported in Figure 40.

nitrogen containing compounds. Consequent to significant difference in electronegativity (EN) and size among halogens, the strength of hydrogen bonds, steric hindrance and electronic effects [168] by these groups would also be substantially different. Hence the electronic effect, size effect and the effect of organic fluorine involved intramolecular HB on H/D exchange using 1H-NMR spectroscopic techniques has also been explored in the different halo substituted anilines and benzamides [169]. Molecules 2017, 22, 423 30 of 44 The chemical structures of all the investigated molecules are reported in Figure 40.

Figure Figure40. 40.The Thegeneral generalchemical chemicalstructures structuresof ofinvestigated investigatedhalo halosubstituted substitutedbenzamides benzamidesand andanilines. anilines. For (a) and (b) X = F, Cl, Br, I and H and for (c), (d), (e), and (f) X = F, Cl and H. For (a) and (b) X = F, Cl, Br, I and H and for (c), (d), (e), and (f) X = F, Cl and H.

For all investigated molecules the 5 mM stock solution was prepared on the volume scale of 5 mL in For all investigated molecules the 5 mM stock solution was prepared on the volume scale of the fresh CDCl3 solvent and the 1H-NMR spectra have been obtained using 450 µL of this stock solution. 5 mL in the fresh CDCl3 solvent and the 1 H-NMR spectra have been obtained using 450 µL of To this solution 50 µL of CD3OD was added with the marking time as zero, resulting in the final this stock solution. To this solution 50 µL of CD OD was added with the marking time as zero, substrate concentration of less than 5 mM. This 3was well below the concentrations where the resulting in the final substrate concentration of less than 5 mM. This was well below the concentrations possibility of any aggregation and intermolecular interaction is observable. The added methanol where the possibility of any aggregation and intermolecular interaction is observable. The added created a 10% methanol:chloroform solution, with the final methanol concentration of 2.47 M, which methanol created a 10% methanol:chloroform solution, with the final methanol concentration of 2.47 M, ensured pseudo-first-order kinetics. The NMR spectra were acquired at every two minutes’ interval which ensured pseudo-first-order kinetics. The NMR spectra were acquired at every two minutes’ until the amino proton signal intensity submerged within the baseline noise. A distinct noninterval until the amino proton signal intensity submerged within the baseline noise. A distinct exchangeable aromatic proton peak was used as an internal integration reference. Rate constants and non-exchangeable Molecules 2017, 22, 423 aromatic proton peak was used as an internal integration reference. Rate constants 29 of 41 corresponding half-lives were determined from the slope of a nonlinear least squares fit to the graph and corresponding half-lives were determined from the slope of a nonlinear least squares fit to the ( − kt)than (−kt),exp of A(t)of = A(o) rather estimating the values the extended time. Thetime. absolute graph A(t) =exp A(o) , rather than estimating theatvalues at the extended The intensity absolute of Y intercept was taken 1 at zero1time, and thisand value used normalize with respect to the intensity of Y intercept was taken at zero time, thiswas value wastoused to normalize with respect remaining hydrogen. The X-intercept was the time. ensure reproducibility the experiments have to the remaining hydrogen. The X-intercept was the To time. To ensure reproducibility the experiments been been repeated on a different sample at different time.time. have repeated on a different sample at different 7.2. Exchange Mechanism On addition of CD3 OD the labile protons undergo exchange with the hydroxy deuterium of the solvent molecule. This time dependent phenomenon followed the first order reaction kinetics and the intensity of the labile protons was systematically reduced. The mechanism of exchange is pictorially illustrated in Figure 41.

Figure 41. The Themechanism mechanism H/D exchange of labile protons with the hydroxy cdeuterium of the Figure 41. ofof H/D exchange of labile protons with the hydroxy cdeuterium of the solvent solvent molecule. The rate of deuteration is fast due to the high concentration of CD OD compared 3 molecule. The rate of deuteration is fast due to the high concentration of CD3OD compared to substrate. to substrate.

To get qualitative information about the strength of intramolecular HBs, and electronic effect the To get qualitative information about the strength of intramolecular HBs, and electronic effect different halo substituted benzamide molecules were also investigated. The intensity of the peak at the halo substituted benzamide molecules were alsoafter investigated. peak zerodifferent time is taken as 100%. The other spectra were acquired adding 50The µL intensity of CD3ODoftothe 450 µL solution. The plot of integral areas of NH2 peaks as a function of time, for unsubstituted and orthohalosubstituted benzamides (2-fluoro, 2-chloro, 2-bromo, 2-iodo) are compared in Figure 42. Similar results for meta- and para-substituted derivatives have also been obtained [169].

Figure 41. The mechanism of H/D exchange of labile protons with the hydroxy cdeuterium of the solvent molecule. The rate of deuteration is fast due to the high concentration of CD3OD compared to substrate. Molecules 2017, 22, 423

31 of 44

To get qualitative information about the strength of intramolecular HBs, and electronic effect the different halo substituted benzamide molecules were also investigated. The intensity of the peak at zero time is taken as 100%. The other spectra were were acquired after adding 50 µL 50 of CD ODCD to 3450 at zero time is taken as 100%. The other spectra acquired after adding µL 3of ODµL to solution. The plotThe of plot integral areas ofareas NH2ofpeaks a function of time, unsubstituted and ortho450 µL solution. of integral NH2 as peaks as a function offor time, for unsubstituted and halosubstituted benzamides (2-fluoro, 2-chloro, 2-bromo, 2-iodo)2-iodo) are compared in Figure Similar ortho-halosubstituted benzamides (2-fluoro, 2-chloro, 2-bromo, are compared in42. Figure 42. results for meta-for and para-substituted derivatives have also been obtained [169]. [169]. Similar results metaand para-substituted derivatives have also been obtained

of integral integral intensities intensities of of the the NH NH22 peaks peaks v/s v/s time Figure 42. The plot of time (in mins) for unsubstituted and by the the symbols symbols given given in in inset. inset. ortho-halosubstituted benzamides. The molecules are identified by

The nature natureofofthethe substituents dictated the H/D rate constants andwere theydifferent were different for The substituents dictated the H/D rate constants and they for different different substituents. It has been observed that when all the physical parameters were kept substituents. It has been observed that when all the physical parameters were kept unchanged for any unchanged for anymolecules, of the investigated the results with couldhigh be reproduced with high degree of the investigated the resultsmolecules, could be reproduced degree of accuracy within the of accuracy within the experimental error match [169]. There is a perfect of from graphical plots obtained experimental error [169]. There is a perfect of graphical plots match obtained integral intensity of from integral intensity labile protons a function of time, carried out for times different the labile protons peaksof as the a function of time, peaks carriedasout for different samples at different for samples at different This timesisfor 2-fluorobenzamide. This 43. is clearly evident from Figure 43. 2-fluorobenzamide. clearly evident from Figure Molecules 2017, 22, 423

30 of 41

Figure 43. The integral intensity of NH2 peaks v/s time (in minutes) for 2-fluorobenzamide plotted Figure 43. The integral intensity of NH2 peaks v/s time (in minutes) for 2-fluorobenzamide plotted from two experiments carried out at different times intervals are represented by two different from two experiments carried out at different times intervals are represented by two different symbols, symbols, in the inset. shown in shown the inset.

8. Multiple Quantum (MQ) NMR for the Detection of Intramolecular HBs 8. Multiple Quantum (MQ) NMR for the Detection of Intramolecular HBs In deriving the evidence for C-F…H-N HB it is very important to know the precise magnitudes In deriving the evidence for C-F···H-N HB it is very important to know the precise magnitudes and also the relative signs of 1hJFH, 3hJFH, 2hJFN and 1JNH [65,69,170]. When three or more NMR active and also the relative signs of 1h JFH , 3h JFH , 2h JFN and 1 JNH [65,69,170]. When three or more NMR active spins are coupled among themselves the magnitudes and signs of the couplings between the passive spins are coupled among themselves the magnitudes and signs of the couplings between the passive spins cannot be determined from the one-dimensional spectrum of any one of the coupled nuclei. spins cannot be determined from the one-dimensional spectrum of any one of the coupled nuclei. Consequently, to obtain 2hJFN in organofluorine molecules several experimental strategies have been Consequently, to15obtain 2h JFN in organofluorine molecules several experimental strategies have been reported where N is either isotopically labelled [111,170,171] or unlabelled [69]. reported where 15 N is either isotopically labelled [111,170,171] or unlabelled [69]. 8.1. The Pulse Sequence The utilization of two dimensional 15N-1H correlation (HSQC) type experiments [172,173] gives information on the magnitudes of 1hJFH, 3hJFH, 2hJFN and 1JNH but fails to provide the signs of the passive couplings. Hence the multiple quantum NMR experimental methodology has been employed [174,175]. The application of two dimensional heteronuclear 15N-1H double quantum-single quantum

8.1. The Pulse Sequence The utilization of two dimensional 15N-1H correlation (HSQC) type experiments [172,173] gives information on the magnitudes of 1hJFH, 3hJFH, 2hJFN and 1JNH but fails to provide the signs of the passive couplings. Hence the multiple quantum NMR experimental methodology has been employed Molecules 2017, 22, 423 32 of 44 [174,175]. The application of two dimensional heteronuclear 15N-1H double quantum-single quantum (DQ-SQ) and zero quantum-single quantum (ZQ-SQ) correlation experiment, where 15N is present in its natural abundance has been exploited for the determination of relative signs and magnitudes of 8.1. The Pulse Sequence the couplings among 1H, 19F and 15N, involved in hydrogen bonding [169]. The pulse sequence 15 N-1 H correlation (HSQC) type experiments [172,173] gives The utilization of two dimensional utilized for DQ-SQ and ZQ-SQ experiments is well known and is reported in the Figure 44. 1h The on MQthe experiments haveofbeen carried fluorine substituted derivatives of of information magnitudes JFH , 3h JFHout , 2hon JFNdifferent and 1 JNH but fails to provide the signs benzamide in solution state in a low polarity solvent CDCl 3 . The magnitudes and signs of through the passive couplings. Hence the multiple quantum NMR experimental methodology has been space [174,175]. and long range coupling interactions among fluorine, hydrogen and1 H nitrogen in its 15 Nemployed The application of two dimensional heteronuclear doublenuclei quantum-single natural abundance have been used to extract direct evidence for the existence of non-linear and/or 15 quantum (DQ-SQ) and zero quantum-single quantum (ZQ-SQ) correlation experiment, where N three centered intra-molecular C-F...H-N type HB. The chemical structures and 1D 1H-NMR spectra is present in its natural abundance has been exploited for the determination of relative signs and obtained for the investigated molecules are given in the Figure 45. 1 H, 19 F and 15 N, involved in hydrogen bonding [169]. The pulse magnitudes of the couplings among derived Subsequently the theoretically results [63] have been employed in conjunction with NMR sequence utilized forthe DQ-SQ andunambiguous ZQ-SQ experiments ison well and is reported in the Figure 44. findings to draw direct and conclusions the known intra-molecular C-F…H-N type HB.

Figure 44. The pulse Sequence DQ-SQand and ZQ-SQ ZQ-SQ experiments. DQDQ andand ZQZQ excitation, I andI Sand S Figure 44. The pulse Sequence forforDQ-SQ experiments.For For excitation, 15N of NH group. And the pulses were selective on these two spins. The phases of the spins1are 1H and 15 spins are H and N of NH group. And the pulses were selective on these two spins. The phases of pulses φ1 and φR are x, −x, −x, x. The phase of all the remaining pulses are x. The gradients ratio G1:G2 the pulses φ1 and φR are x, −x, −x, x. The phase of all the remaining pulses are x. The gradients ratio employed are 50:55 for DQ-SQ and 50:45 for ZQ-SQ experiments. The τ delay for all the DQ-SQ and ZQG1 :G2 employed are 50:55 for DQ-SQ and 50:45 for ZQ-SQ experiments. The τ delay for all the DQ-SQ SQ experiments and also 15N-1H HSQC experiments was optimized for 1/2JNH (JNH is taken to be 90 Hz). and ZQ-SQ experiments and also 15 N-1 H HSQC experiments was optimized for 1/2JNH (JNH is taken to be 90 Hz).

The MQ experiments have been carried out on different fluorine substituted derivatives of benzamide in solution state in a low polarity solvent CDCl3 . The magnitudes and signs of through space and long range coupling interactions among fluorine, hydrogen and nitrogen nuclei in its natural abundance have been used to extract direct evidence for the existence of non-linear and/or three centered intra-molecular C-F... H-N type HB. The chemical structures and 1D 1 H-NMR spectra obtained Molecules 2017, 22, 423molecules are given in the Figure 45. 31 of 41 for the investigated

Figure 45. Chemical structures and expanded NH regions of the 1D 1H-NMR spectra in CDCl3 of 2-

Figure 45. Chemical structures and expanded NH regions of the 1D 1 H-NMR spectra in fluorobenzamide (41) 2-fluoro-N-(2-fluorophenyl)benzamide (42) and 2-fluoro-N-phenyl-benzamide (43). CDCl3 of 2-fluorobenzamide (41) 2-fluoro-N-(2-fluorophenyl)benzamide (42) and 2-fluoro-N-phenylbenzamide (43). 8.2. C-F…N-H Hydrogen Bond in 2-Fluorobenzamide

The two broad singlets with a separation of nearly 145 Hz observed in 1H-NMR spectrum of molecule 41, are attributed to two non-equivalent protons (δNH(1) > δNH(2)) [111]. The excessive broadening of the 1H spectrum due to quadrupolar 14N relaxation prevented the determination of through space and through bond couplings, if any. For visualization of such couplings if present, the heteronuclear 15N-1H DQ-SQ correlation experiments have been carried out using the pulse sequence given in Figure 36 [176,177]. The 15N-1H DQ-SQ correlated spectrum is reported in Figure 37, where DQ coherence evolve at the 1

15

19

1

Molecules 2017, 22, 423

33 of 44

Subsequently the theoretically derived results [63] have been employed in conjunction with NMR 1H-NMR spectra in findings the direct and and unambiguous conclusions C-F ···H-N Figureto 45.draw Chemical structures expanded NH regions of on thethe 1D intra-molecular CDCl 3 of type 2- HB. fluorobenzamide (41) 2-fluoro-N-(2-fluorophenyl)benzamide (42) and 2-fluoro-N-phenyl-benzamide (43).

8.2. C-F···N-H Hydrogen Bond in 2-Fluorobenzamide

…N-H Hydrogen Bond in 2-Fluorobenzamide 8.2. C-FThe two broad singlets with a separation of nearly 145 Hz observed in 1 H-NMR spectrum of

molecule are singlets attributed two non-equivalent protons (δNH(1) δNH(2) )spectrum [111]. The excessive The two41, broad withtoa separation of nearly 145 Hz observed in 1>H-NMR of molecule 1 14 of the H non-equivalent spectrum due to quadrupolar N )relaxation the determination 41,broadening are attributed to two protons (δNH(1) > δNH(2) [111]. Theprevented excessive broadening of the 1Hof 14 through space and through bond couplings, if any. For visualization of such couplings if present, the spectrum due to quadrupolar N relaxation prevented the determination of through space and through 15 1 15 1 heteronuclear HFor DQ-SQ correlation have been carried out using the pulse bond couplings, ifNany. visualization of experiments such couplings if present, the heteronuclear N- H sequence DQ-SQ given in Figure 36 [176,177]. The 15 N-1 H out DQ-SQ correlated reported in Figure 37, where correlation experiments have been carried using the pulsespectrum sequenceisgiven in Figure 36 [176,177]. 1 H, 15 N) and passive (19 F) DQ15coherence evolve at the algebraic of the couplings active The N-1H DQ-SQ correlated spectrumsum is reported in Figurebetween 37, where DQ( coherence evolve at the 1J 15N) and passive 1JNHdetection spins. Nearly amide proton the simultaneous excitation NH of each algebraic sum ofequal the couplings between active (1H, permitted (19F) spins. Nearly equaland of each 15 N-1 H DQ spectra and are identified by the groups marked N-H(1) 15 1 of two different and N-H(2) amide proton permitted the simultaneous excitation and detection of two different N- H DQ spectrain Figure 46. and are identified by the groups marked N-H(1) and N-H(2) in Figure 46.

15 N1 DQ-SQ spectrum of molecule 41 in the solvent CDCl . Figure46. 46.500 500MHz MHz15N1H H Figure DQ-SQ spectrum of molecule 41 in the solvent CDCl3. 3

15 N For are the active spins and H(2) passive spins, ForN-H(1) N-H(1)DQ DQexcitation, excitation,H(1) H(1)and and15N are the active spins and H(2)and and19F19are F are passive spins, 15 19 while NNare F Fare whilefor forN-H(2) N-H(2)DQ, DQ,H(2) H(2)and and 15 arethe theactive activespins spinsand andH(1) H(1)and and 19 arepassive passivespins. spins.The TheSQ SQ 15N, 15 19F and 19 dimension yields the normal spectrum of four coupled spins, viz., two NH protons. The dimension yields the normal spectrum of four coupled spins, viz., N, F and two NH protons. nuclei involved in theinDQ flip simultaneously andand cancan be treated as as a single spin, The nuclei involved thecoherence DQ coherence flip simultaneously be treated a single spin,also also 19 1 called as super spin [178]. The F and H being passive spins, the four possible spin states yield four transitions. The 15 N-1 H(1) DQ coherence gives the parameters 1h JFH(1) , 2h JFN , 2 JH(1)H(2) and 1 JNH(2) while 15 N-1 H(2) DQ coherence yields 3h JFH(2) , 2h JFN , 2 JH(1)H(2) and 1 JNH(1) . The marked separations in the SQ dimensions of Figure 37 yield couplings (in Hz); a = 1 JNH(1) (90.5), c = 1 JNH(2) (89.2) and i = 2 JH(1)H(2) (3.05 Hz). The separations in DQ dimension provide magnitudes of the couplings (in Hz), g = 1 JNH(1) + 2 JH(1)H(2) (93.5), e = 1 JNH(2) + 2 JH(1)H(2) (92.2), f = 1h JFH(1) + 2h JFN (3.8) and h = 3h JFH(2) + 2h J 1h FN (10.4). The displacement of F2 cross sections yield respectively (in Hz), b = J FH(1) (11.2) and 3h d = JFH(2) (3.0). Opposite directions of F1 displacement vectors at δH(1) and δH(2) , denoted by tilted arrows, confirm opposite signs of 1h JFH(1) and 3h JFH(2) [177,179]. The signs of 1 JNH(1) and 1 JNH(2) are negative because of the convention that one bond scalar coupling between two nuclei of opposite signs of magnetic moments is negative. The algebraic combination of parameters obtained from the DQ spectrum established that the relative signs of 1h JFH(1) and 3h JFH(2) are opposite, that of 1h JFH(1) , 2h J 1 2 FN and J NH are same (negative), J H(1)H(2) is positive. Thus, the magnitudes and relative signs of the couplings among all the three nuclei could be obtained from a single 2D NMR experiment. This information can be utilized for ascertaining the existence of C-F···H-N hydrogen bonding, if any,

opposite signs of 1hJFH(1) and 3hJFH(2) [177,179]. The signs of 1JNH(1) and 1JNH(2) are negative because of the convention that one bond scalar coupling between two nuclei of opposite signs of magnetic moments is negative. The algebraic combination of parameters obtained from the DQ spectrum established that the relative signs of 1hJFH(1) and 3hJFH(2) are opposite, that of 1hJFH(1), 2hJFN and 1JNH are same (negative), 2JH(1)H(2) is positive. Thus, the magnitudes and relative signs of the couplings among all the three nuclei Molecules 2017, 22, 423 34 of 44 could be obtained from a single 2D NMR experiment. This information can be utilized for ascertaining the existence of C-F…H-N hydrogen bonding, if any, utilizing the theoretical results [63]. utilizing the for theoretical results [63]. Nevertheless, for unequivocally ascertaining signs of 2hJrelative Nevertheless, unequivocally ascertaining the relative signs of 1hJFH(1) , 3hJFH(2) andthe FN, the 15N-1H 1h J 3h J 2h J , the 15 N-1 H zero quantum 15 N-1 H ZQ-SQ correlation experiment has also , and 15 1 FN FH(2)N- H ZQ-SQ zero FH(1) quantum correlation experiment has also been carried out using the identical beensequence carried out using the identical pulseratio sequence with appropriate gradient ratio and phases of the pulse with appropriate gradient and phases of the pulses. The ZQ coherence evolves 1 H, 15 N) pulses. The ZQ coherence evolves at the algebraic difference of the couplings between active ( 1 15 19 at the algebraic difference of the couplings between active ( H, N) and passive ( F) spins. and passiveto(19 F) spins. Consequent to the opposite signs magnetic moments of excited spinsas the Consequent the opposite signs of magnetic moments of of excited spins the coherence evolved coherence evolved algebraic sums [180]. This resulted in the enhanced along the ZQ algebraic sums [180].as This resulted in the enhanced separation along the ZQseparation dimension of ZQ-SQ dimension of ZQ-SQ spectrum given in Figure 47. spectrum given in Figure 47.

15 N-1 H ZQ-SQ spectrum of 41 in CDCl . Figure47. 47.500 500MHz MHz15N1H ZQ-SQ spectrum of 41 in CDCl3. 3 Figure 1hJ1h 2hJFN2h evident that signs JFH(1) JFNopposite are opposite to 3h JFH(2) . The similar have also It It is is evident that signs ofof FH(1) andand are to 3hJFH(2) . The similar studiesstudies have also been been carried out for other molecules and the obtained results established theofpresence fluorine carried out for other molecules and the obtained results established the presence fluorine of involved involved intramolecular HB. intramolecular HB.

Conclusions 9.9. Conclusions The combined NMR experimental observations and various DFTbased basedtheoretical theoreticalcalculations calculations The combined NMR experimental observations and various DFT revealed the existence of intramolecular HBs in different organofluorine-substituted derivatives revealed the existence of intramolecular HBs in different organofluorine-substituted derivatives of of different classes molecules,viz. viz.benzanilides, benzanilides, hydrazides,imides, imides,benzamides, benzamides,and and different classes of of molecules, hydrazides, diphenyloxamides. The existence more than one conformer has alsobeen beenestablished establishedininseveral several diphenyloxamides. The existence of of more than one conformer has also molecules by adopting diverse NMR experimental strategies. In many examples the solvent titration molecules by adopting diverse NMR experimental strategies. In many examples the solvent titration 1 and DOSY techniques employed to discount any possibility ofor selfor cross-dimerization. 1H H and DOSY techniques are are employed to discount any possibility of selfcross-dimerization. The The variable temperature and solvent titration studies provided the valuable information about the variable temperature and solvent titration studies provided the valuable information about the 1 19 existence HB, and their relative strengths. F HOESY experiment is utilized to extract 1H-19Hexistence ofof HB, and their relative strengths. TheThe F HOESY experiment is utilized to extract the the information about the spatial proximity and possibility of intramolecular HB, as well as for the information about the spatial proximity and possibility of intramolecular HB, as well as for the determination of different conformers. Through space coupling between two NMR active nuclei, where the spin polarization is transmitted through HB of diverse strengths has been detected in several fluorine containing molecules. The 2D 1 H-15 N HSQC experiment aided in the measurement of coupling strengths and their relative signs. The weak molecular interactions established by NMR studies have also been corroborated by theoretical DFT based structure calculations. The NCI analysis served as a very sensitive tool for the detection of non-covalent interactions. NCI analysis provides the visual evidence for the presence of bi and trifurcated HBs in some of the molecules. For the calculation of strengths of different HBs in the investigated molecules the QTAIM calculation is found to be very powerful tool. The Laplacian of electron density sign is used to discriminate the HBs from the covalent bonds. The relaxed potential energy scan has been performed for some of the molecules to determine the free rotation energy of CF3 group and the energies of different possible conformers for a molecule. The quantum calculations and classical MD simulations have supported the various possible ways of intramolecular HB formation with fluorine atom. The use of H/D exchange rates obtained by

Molecules 2017, 22, 423

35 of 44

conventional 1 H-NMR spectroscopic studies confirms the presence or absence of intramolecular HBs, and permitted the calculation of their relative strengths. The effect of inherent electronic and steric effects is also successfully correlated with the relative rates of H/D exchange in the various halo substituted derivatives of anilines and benzamides. The utilization of heteronuclear 15 N-1 H DQ-SQ and ZQ-SQ correlation experiment, in isotopically unlabeled systems for the detection of organic fluorine involved intramolecular HB and unequivocal determination of relative signs and magnitudes of both hydrogen bond and covalent bond mediated through scalar couplings such as 1h JFH , 2h JFN and 3h J FH has been convincingly demonstrated. 10. Computational Methods and the Employed Programs For DFT calculations Gaussian G09 [181] suite of programs has been used. The B3LYP/6-311G** and aug-cc-pVTZ level of theories and basis sets were used to optimize the structures of the molecules. To ensure that all optimized structures are global minima, harmonic vibrational frequency calculation has been performed at the same level of theories and all the real frequencies indicated that optimized geometry is minimum at potential energy surface. The MD simulations were performed using NAMD simulation package [182]. The general AMBER force field (GAFF) along with torsion parameters and partial charges obtained from quantum calculations in vacuum. The long range electrostatic interactions were calculated with the Particle Mesh Ewald (PME) method [183]. Constant pressure-temperature (NPT) simulation is performed followed by constant volume-temperature (NVT) simulation. AIMAll [184] and multiwfn programs were used for QTAIM calculations. Multiwfn [185] program was used for NCI plots. Colour filled isosurface graphs have been plotted by VMD [186] program. Specific combination of methods for theoretical calculations was used for particular and individual series of molecules, the specific information is available with the native articles. Molden 4.7 has been used as a visualization software for Gaussian outputs [187]. Acknowledgments: NS gratefully acknowledges the generous financial support by the Science and Engineering Research Board (SERB), New Delhi (Grant Number: EMR/2015/002263). Conflicts of Interest: The authors declare no conflict of interest.

References 1. 2. 3. 4. 5. 6. 7. 8.

9.

10.

Müller-Dethlefs, K.; Hobza, P. Noncovalent Interactions: A Challenge for Experiment and Theory. Chem. Rev. 2000, 100, 143–167. [CrossRef] [PubMed] Kaplan, I.G. Intermolecular Interactions: Physical Picture, Computational Methods and Model Potentials; John Wiley & Sons, Ltd.: New York, NY, USA, 2006. Huggins, M.L. Quantum Mechanics of the Interaction of Gravity with Electrons: Theory of a Spin-two Field Coupled to Energy. PhD. Thesis, University of California, Oakland, CA, USA, 1919. Huggins, M.L. Atomic structure. Science 1922, 55, 459–460. [CrossRef] Huggins, M.L. Electronic Structures of Atoms. J. Phys. Chem. 1921, 26, 601–625. [CrossRef] Huggins, M.L. Atomic radii. Phys. Rev. 1922, 19, 346–353. [CrossRef] Latimerand, W.M.; Rodebush, W.H. Polarity and ionization from the standpoint of the Lewis theory of valence. J. Am. Chem. Soc. 1920, 42, 1419–1433. [CrossRef] Hu, W.H.; Huang, K.-W.; Chiou, C.W.; Kuo, S.W. Complementary Multiple Hydrogen Bonding Interactions Induce the Self-Assembly of Supramolecular Structures from Heteronucleobase-Functionalized Benzoxazine and Polyhedral Oligomeric Silsesquioxane Nanoparticles. Macromolecules 2012, 45, 9020–9028. [CrossRef] Saccone, M.; Dichiarante, V.; Forni, A.; Goulet-Hanssens, A.; Cavallo, G.; Vapaavuori, J.; Terraneo, G.; Barrett, C.J.; Resnati, G.; Metrangolo, P.; Priimagi, A. Supramolecular hierarchy among halogen and hydrogen bond donors in light-induced surface patterning. J. Mater. Chem. C 2015, 3, 759–768. [CrossRef] Teunissen, A.J.P.; Nieuwenhuizen, M.M.L.; Rodríguez-Llansola, F.; Palmans, A.R.A.; Meijer, E.W. Mechanically Induced Gelation of a Kinetically Trapped Supramolecular Polymer. Macromolecules 2014, 47, 8429–8436. [CrossRef]

Molecules 2017, 22, 423

11.

12.

13. 14. 15. 16. 17. 18. 19. 20. 21.

22. 23. 24. 25.

26. 27. 28.

29.

30. 31. 32. 33. 34.

36 of 44

Xiao, T.; Feng, X.; Ye, S.; Guan, Y.; Li, S.L.; Wang, Q.; Ji, Y.; Zhu, D.; Hu, X.; Lin, C.; Pan, Y.; Wang, L. Highly Controllable Ring−Chain Equilibrium in Quadruply Hydrogen Bonded Supramolecular Polymers. Macromolecules 2012, 45, 9585–9594. [CrossRef] Ajayaghosh, A.; George, S.J.; Schenning, A.P.H.J. Hydrogen-Bonded Assemblies of Dyes and Extended π-Conjugated Systems. In Topics in Current Chemistry; Würthner, F., Ed.; Springer: Berlin/Heidelberg, Germany, 2005; Volume 258, pp. 83–118. Archer, E.A.; Gong, H.; Krische, M.J. Hydrogen bonding in noncovalent synthesis: selectivity and the directed organization of molecular strands. Tetrahedron 2001, 57, 1139–1159. [CrossRef] Brunsveld, L.; Folmer, B.J.B.; Meijer, E.W.; Sijbesma, R.P. Supramolecular Polymers. Chem. Rev. 2001, 101, 4071–4098. [CrossRef] Conn, M.M.; Rebek, J. Self-Assembling Capsules. Chem. Rev. 1997, 97, 1647–1668. [CrossRef] [PubMed] Huang, F.; Gibson, H.W. Polypseudorotaxanes and polyrotaxanes. Prog. Polym. Sci. 2005, 30, 982–1018. [CrossRef] Lawrence, D.S.; Jiang, T.; Levett, M. Self-Assembling Supramolecular Complexes. Chem. Rev. 1995, 95, 2229–2260. [CrossRef] Lukin, O.; Vögtle, F. Knotting and Threading of Molecules: Chemistry and Chirality of Molecular Knots and Their Assemblies. Angew. Chem. Int. Ed. 2005, 44, 1456–1477. [CrossRef] [PubMed] Nowick, J.S. Chemical Models of Protein β-Sheets. Acc. Chem. Res. 1999, 32, 287–296. [CrossRef] Prins, L.J.; Reinhoudt, D.N.; Timmerman, P. Noncovalent Synthesis Using Hydrogen Bonding. Angew. Chem. Int. Ed. 2001, 40, 2382–2426. [CrossRef] Schmuck, C.; Wienand, W. Self-Complementary Quadruple Hydrogen-Bonding Motifs as a Functional Principle: From Dimeric Supramolecules to Supramolecular Polymers. Angew. Chem. Int. Ed. 2001, 40, 4363–4369. [CrossRef] Shenhar, R.; Rotello, V.M. Polymers Nanoparticles: Scaffolds and Building Blocks. Acc. Chem. Res. 2003, 36, 549–561. [CrossRef] [PubMed] Sijbesma, R.P.; Meijer, E.W. Quadruple hydrogen bonded systems. Chem. Commun. 2003, 5–16. [CrossRef] Zeng, F.; Zimmerman, S.C. Dendrimers in Supramolecular Chemistry: From Molecular Recognition to Self-Assembly. Chem. Rev. 1997, 97, 1681–1712. [CrossRef] [PubMed] Liu, X.-H.; Wang, D.; Wan, L.J. Surface Tectonics of Nanoporous Networks of Melamine-Capped Molecular Building Blocks formed through Interface Schiff-Base Reactions. Chem. Asian J. 2013, 8, 2466–2470. [CrossRef] [PubMed] Rotondi, K.S.; Gierasch, L.M. Natural Polypeptide Scaffolds: β-Sheets, β-Turns, and β-Hairpins. Pept. Sci. 2006, 84, 13–22. [CrossRef] [PubMed] Seebach, D.; Hook, D.F.; Glättli, A. Helices and Other Secondary Structures of β- and γ-Peptides. Pept. Sci. 2006, 84, 23–37. [CrossRef] [PubMed] ˇ Užarevi´c, K.; Ðilovi´c, I.; Bregovi´c, N.; Tomiši´c, V.; Matkovi´c-Calogovi´ c, D.; Cindri´c, M. Anion-Templated Supramolecular C3 Assembly for Efficient Inclusion of Charge-Dispersed Anions into Hydrogen-Bonded Networks. Chem. Eur. J. 2011, 17, 10889–10897. [CrossRef] [PubMed] Venugopalan, P.; Kishore, R. Unusual Folding Propensity of an Unsubstituted β,γ-Hybrid Model Peptide: Importance of the C_ H···O Intramolecular Hydrogen Bond. Chem. Eur. J. 2013, 19, 9908–9915. [CrossRef] [PubMed] Cougnon, F.B.L.; Sanders, J.K.M. Evolution of Dynamic Combinatorial Chemistry. Acc. Chem. Res. 2011, 45, 2211–2221. [CrossRef] [PubMed] Goodman, C.M.; Choi, S.; Shandler, S.; DeGrado, W.F. Hydrothermal contribution to the oceanic dissolved iron inventory. Nat. Chem. Biol. 2007, 3, 252–256. [CrossRef] [PubMed] Nowick, J.S. What I have learned by using chemical model systems to study biomolecular structure and interactions. Org. Biomol. Chem. 2006, 4, 3869–3885. [CrossRef] [PubMed] Altintas, O.; Lejeune, E.; Gerstel, P.; Barner-Kowollik, C. Bioinspired dual self-folding of single polymer chains via reversible hydrogen bonding. Polym. Chem. 2012, 3, 640–651. [CrossRef] Moure, A.; Sanclimens, G.; Bujons, J.; Masip, I.; Alvarez-Larena, A.; Pérez-Payá, E.; Alfonso, I.; Messeguer, A. Chemical Modulation of Peptoids: Synthesis and Conformational Studies on Partially Constrained Derivatives. Chem. Eur. J. 2011, 17, 7927–7939. [CrossRef] [PubMed]

Molecules 2017, 22, 423

35.

36. 37. 38. 39. 40.

41. 42.

43. 44.

45.

46. 47. 48.

49.

50. 51.

52.

53.

54. 55. 56.

37 of 44

Mingozzi, M.; Dal Corso, A.; Marchini, M.; Guzzetti, I.; Civera, M.; Piarulli, U.; Arosio, D.; Belvisi, L.; Potenza, D.; Pignataro, L.; Gennari, C. Cyclic isoDGR Peptidomimetics as Low-Nanomolar αv β3 Integrin Ligands. Chem. Eur. J. 2013, 19, 3563–3567. [CrossRef] [PubMed] Rufo, C.M.; Moroz, Y.S.; Moroz, O.V.; Stöhr, J.; Smith, T.A.; Hu, X.; DeGrado, W.F.; Korendovych, I.V. Short peptides self-assemble to produce catalytic amyloids. Nat. Chem. 2014, 6, 303–309. [CrossRef] [PubMed] Wennemers, H. Asymmetric catalysis with peptides. Chem. Commun. 2011, 47, 12036–12041. [CrossRef] [PubMed] Vagner, J.; Qu, H.; Hruby, V.J. Peptidomimetics, a synthetic tool of drug discovery. Curr. Opin. Chem. Biol. 2008, 12, 292–296. [CrossRef] [PubMed] Ripka, A.S.; Rich, D.H. Peptidomimetic design. Curr. Opin. Chem. Biol. 1998, 2, 441–452. [CrossRef] Dingley, A.J.; Masse, J.E.; Peterson, R.D.; Barfield, M.; Feigon, J.; Grzesiek, S. Internucleotide Scalar Couplings Across Hydrogen Bonds in Watson-Crick and Hoogsteen Base Pairs of a DNA Triplex. J. Am. Chem. Soc. 1999, 121, 6019–6027. [CrossRef] Fonseca-Guerra, C.; Bickelhaupt, F.M.; Snijders, J.G.; Baerends, E.J. Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment. J. Am. Chem. Soc. 2000, 122, 4117–4128. [CrossRef] Smith, J.D.; Cappa, C.D.; Wilson, K.R.; Cohen, R.C.; Geissler, P.L.; Saykally, R.J. Unified description of temperature-dependent hydrogen-bond rearrangements in liquid water. Proc. Natl. Acad. Sci. USA 2005, 102, 14171–14174. [CrossRef] [PubMed] Liskamp, R.M.J.; Rijkers, D.T.S.; Kruijtzer, J.A.; Kemmink, W.J. Peptides and Proteins as a Continuing Exciting Source of Inspiration for Peptidomimetics. Chembiochem 2011, 12, 1626–1653. [CrossRef] [PubMed] Panciera, M.; Amorín, M.; Castedo, L.; Granja, J.R. Design of Stable b-Sheet-Based Cyclic Peptide Assemblies Assisted by Metal Coordination: Selective Homo- and Heterodimer Formation. Chem. Eur. J. 2013, 19, 4826–4834. [CrossRef] [PubMed] Tremey, E.; Bonnot, F.; Moreau, Y.; Berthomieu, C.; Desbois, A.; Favaudon, V.; Blondin, G.; Houée-Levin, C.; Nivière, V. Hydrogen bonding to the cysteine ligand of superoxide reductase: Acid–base control of the reaction intermediates. J. Biol. Inorg. Chem. 2013, 18, 815–830. [CrossRef] [PubMed] Wang, D.; Chen, K.; Kulp, J.L.; Arora, P.S. Evaluation of Biologically Relevant Short r-Helices Stabilized by a Main-Chain Hydrogen-Bond Surrogate. J. Am. Chem. Soc. 2006, 128, 9248–9256. [CrossRef] [PubMed] Ko, E.; Liu, J.; Perez, L.M.; Lu, G.; Schaefer, A.; Burgess, K. Universal Peptidomimetics. J. Am. Chem. Soc. 2010, 133, 462–477. [CrossRef] [PubMed] Jo, H.; Meinhardt, N.; Wu, Y.; Kulkarni, S.; Hu, X.; Low, K.E.; Davies, P.L.; DeGrado, W.F.; Greenbaum, D.C. Development of α-Helical Calpain Probes by Mimicking a Natural Protein−Protein Interaction. J. Am. Chem. Soc. 2012, 134, 17704–17713. [CrossRef] [PubMed] Gross, E.; Liu, J.H.; Alayoglu, S.; Marcus, M.A.; Fakra, S.C.; Toste, F.D.; Somorjai, G.A. Asymmetric Catalysis at the Mesoscale: Gold Nanoclusters Embedded in Chiral Self-Assembled Monolayer as Heterogeneous Catalyst for Asymmetric Reactions. J. Am. Chem. Soc. 2013, 135, 3881–3886. [CrossRef] [PubMed] Hammond, M.C.; Bartlett, P.A. Synthesis of Amino Acid-Derived Cyclic Acyl Amidines for Use in β-Strand Peptidomimetics. J. Org. Chem. 2007, 72, 3104–3107. [CrossRef] [PubMed] Emenike, B.U.; Liu, A.T.; Naveo, E.P.; Roberts, J.D. Substituent Effects on Energetics of Peptide-Carboxylate Hydrogen Bonds as Studied by 1 H NMR Spectroscopy: Implications for Enzyme Catalysis. J. Org. Chem. 2013, 78, 11765–11771. [CrossRef] [PubMed] Linton, B.R.; Reutershan, M.H.; Aderman, C.M.; Richardson, E.A.; Brownell, K.R.; Ashley, C.W.; Evans, C.A.; Miller, S.J. Asymmetric Michael addition of α-nitro-ketones using catalytic peptides. Tetrahedron Lett. 2007, 48, 1993–1997. [CrossRef] Ghorai, A.; Padmanaban, E.; Mukhopadhyay, C.; Achari, B.; Chattopadhyay, P. Design and synthesis of regioisomeric triazole based peptidomimetic macrocycles and their dipole moment controlled self-assembly. Chem. Commun. 2012, 48, 11975–11977. [CrossRef] [PubMed] Gong, B. Crescent Oligoamides: From Acyclic “Macrocycles” to Folding Nanotubes. Chem. Eur. J. 2001, 7, 4336–4342. [CrossRef] Huc, I. Aromatic Oligoamide Foldamers. Eur. J. Org. Chem. 2004, 1, 17–29. [CrossRef] Li, Z.T.; Hou, J.L.; Li, C.; Yi, H.P. Shape-Persistent Aromatic Amide Oligomers: New Tools for Supramolecular Chemistry. Chem. Asian J. 2006, 1, 766–778. [CrossRef] [PubMed]

Molecules 2017, 22, 423

57.

58.

59. 60. 61. 62. 63.

64.

65.

66.

67. 68. 69. 70.

71.

72.

73.

74. 75. 76. 77.

38 of 44

Lockman, J.W.; Paul, N.M.; Parquette, J.R. The role of dynamically correlated conformational equilibria in the folding of macromolecular structures. A model for the design of folded dendrimers. Prog. Polym. Sci. 2005, 30, 423–452. [CrossRef] Sanford, A.R.; Yamato, K.; Yang, X.; Yuan, L.; Han, Y.; Gong, B. Well-defined secondary structures, Information-storing molecular duplexes and helical foldamers based on unnatural peptide backbones. Eur. J. Biochem. 2004, 271, 1416–1425. [CrossRef] [PubMed] Chopra, D. Is Organic Fluorine Really “Not” Polarizable? Cryst. Growth Des. 2012, 12, 541–546. [CrossRef] Dunitz, J.D. Organic Fluorine: Odd Man Out. ChemBioChem 2004, 5, 614–621. [CrossRef] [PubMed] Dunitz, J.D.; Taylor, R. Organic Fluorine Hardly Ever Accepts Hydrogen Bonds. Chem. Eur. J. 1997, 3, 89–98. [CrossRef] Howard, J.A.K.; Hoy, V.J.; O’Hagan, D.; Smith, G.T. How Good is Fluorine as a Hydrogen Bond Acceptor? Tetrahedron 1996, 52, 12613–12622. [CrossRef] Alkorta, I.; Elguero, J.; Limbach, H.H.; Shenderovich, I.G.; Winkler, T. A DFT and AIM analysis of the spin–spin couplings across the hydrogen bond in the 2-fluorobenzamide and related compounds. Magn. Reson. Chem. 2009, 47, 585–592. [CrossRef] [PubMed] Bartolome, C.; Espinet, P.; Martin-Alvarez, J.M. Is there any bona fide example of O–H···F–C bond in solution? The cases of HOC(CF3 )2 (4-X-2,6-C6 H2 (CF3 )2 ) (X = Si(i-Pr)3 , CF3 ). Chem. Commun. 2007, 4384–4386. [CrossRef] [PubMed] Kareev, I.E.; Quiñones, G.S.; Kuvychko, I.V.; Khavrel, P.A.; Ioffe, I.N.; Goldt, I.V.; Lebedkin, S.F.; Seppelt, K.; Strauss, S.H.; Boltalina, O.V. Variable-Temperature 19 F NMR and Theoretical Study of 1,9- and 1,7-C60 F(CF3 ) and CS - and C1 -C60 F17 (CF3 ): Hindered CF3 Rotation and Through-Space JFF Coupling. J. Am. Chem. Soc. 2005, 127, 11497–11504. [CrossRef] [PubMed] Prakash, G.K.S.; Wang, F.; Rahm, M.; Shen, J.; Ni, C.; Haiges, R.; Olah, G.A. On the Nature of C-H···F-C Interactions in Hindered CF-C(sp3) Bond Rotations. Angew. Chem. Int. Ed. 2011, 50, 11761–11764. [CrossRef] [PubMed] Ledbetter, M.P.; Saielli, G.; Bagno, A.; Tran, N.; Romalis, M.V. Observation of scalar nuclear spin–spin coupling in van der Waals complexes. Proc. Natl. Acad. Sci. USA 2012, 109, 12393–12397. [CrossRef] Saielli, G.; Bini, R.; Bagno, A. Computational 19 F-NMR. 2. Organic compounds. RSC. Adv. 2014, 4, 41605–41611. [CrossRef] Rae, I.D.; Weigold, J.A.; Contreras, R.H.; Biekofsky, R.R. Analysis of Long-Range Through-Space Couplings via an Intramolecular Hydrogen Bond. Magn. Reson. Chem. 1993, 31, 836–840. [CrossRef] Benedict, H.; Shenderovich, I.G.; Malkina, O.L.; Malkin, V.G.; Denisov, G.S.; Golubev, N.S.; Limbach, H.H. Nuclear Scalar Spin-Spin Couplings and Geometries of Hydrogen Bonds. J. Am. Chem. Soc. 2000, 122, 1979–1988. [CrossRef] Golubev, N.S.; Shenderovich, I.G.; Smirnov, S.N.; Denisov, G.S.; Limbach, H.-H. Nuclear Scalar Spin ± Spin Coupling Reveals Novel Properties of Low-Barrier Hydrogen Bonds in a Polar Environment. Chem. Eur. J. 1999, 5, 492–497. [CrossRef] Shenderovich, I.G.; Smirnov, S.N.; Denisov, G.S.; Gindin, V.A.; Golubev, N.S.; Dunger, A.; Reibke, R.; Kirpekar, S.; Malkina, O.L.; Limbach, H.H. Nuclear Magnetic Resonance of Hydrogen Bonded Clusters between F- and (HF)n: Experiment and Theory. Ber. Bunsenges. Phys. Chem. 1998, 102, 422–428. [CrossRef] Shenderovich, I.G.; Tolstoy, P.M.; Golubev, N.S.; Smirnov, S.N.; Denisov, G.S.; Limbach, H.H. Low-Temperature NMR Studies of the Structure and Dynamics of a Novel Series of Acid-Base Complexes of HF with Collidine Exhibiting Scalar Couplings Across Hydrogen Bonds. J. Am. Chem. Soc. 2003, 125, 11710–11720. [CrossRef] [PubMed] Muegge, I.; Heald, S.L.; Brittelli, D. Simple Selection Criteria for Drug-like Chemical Matter. J. Med. Chem. 2001, 44, 1841–1846. [CrossRef] [PubMed] Smart, B.E. Fluorine substituent effects (on bioactivity). J. Fluor. Chem. 2001, 109, 3–11. [CrossRef] Chopra, D.; Row, T.N.G. Role of organic fluorine in crystal engineering. CrystEngComm 2011, 13, 2175–2186. [CrossRef] Desiraju, G.R. Crystal Engineering: From Molecule to Crystal. J. Am. Chem. Soc. 2013, 135, 9952–9967. [CrossRef] [PubMed]

Molecules 2017, 22, 423

78.

39 of 44

Reichenbacher, K.; Suss, H.I.; Hulliger, J. Fluorine in crystal engineering—“the little atom that could”. Chem. Soc. Rev. 2005, 34, 22–30. [CrossRef] [PubMed] 79. Berger, R.; Resnati, G.; Metrangolo, P.; Weber, E.; Hulliger, J. Organic fluorine compounds: a great opportunity for enhanced materials properties. Chem. Soc. Rev. 2011, 40, 3496–3508. [CrossRef] [PubMed] 80. Abeles, R.H.; Alston, T.A. A Rationale for the Design of an Inhibitor of Tyrosyl Kinase*. J. Biol. Chem. 1990, 265, 16705–16708. [PubMed] 81. Chapeau, M.C.; Frey, P.A. Synthesis of UDP-4-deoxy-4-fluoroglucose and UDP-4-deoxy-4-fluorogalactose and Their Interactions with Enzymes of Nucleotide Sugar Metabolism. J. Org. Chem. 1994, 59, 6994–6998. [CrossRef] 82. Kovacs, T.; Pabuccuoglu, A.; Lesiak, K.; Torrence, P.F. Fluorodeoxy Sugar Analogues of 20 ,50 -Oligoadenylates as Probes of Hydrogen Bonding in Enzymes of the 2-5A System. Bioorg. Chem. 1993, 21, 192–208. [CrossRef] 83. O’Hagan, D.; Rzepa, H.S. Some influences of fluorine in bioorganic chemistry. Chem. Commun. 1997, 645–652. [CrossRef] 84. Takahashi, L.H.; Radhakrishnan, R.; Rosenfield, R.E.; Meyer, E.F.; Trainor, D.A. Crystal Structure of the Covalent Complex Formed by a Peptidyl α,α-Difluoro-β-keto Amide with Porcine Pancreatic Elastase at 1.78-Å Resolution. J. Am. Chem. Soc. 1989, 111, 3368–3374. [CrossRef] 85. Banerjee, R.; Desiraju, G.R.; Mondal, R.; Howard, J.A.K. Organic Chlorine as a Hydrogen-Bridge Acceptor: Evidence for the Existence of Intramolecular O-H···Cl-C Interactions in Some gem-Alkynols. Chem. Eur. J. 2004, 10, 3373–3383. [CrossRef] [PubMed] 86. Li, C.; Ren, S.F.; Hou, J.L.; Yi, H.P.; Zhu, S.Z.; Jiang, X.K.; Li, Z.T. F···H-N Hydrogen Bonding Driven Foldamers: Efficient Receptors for Dialkylammonium Ions**. Angew. Chem. Int. Ed. 2005, 44, 5725–5729. [CrossRef] [PubMed] 87. Mido, Y.; Okuno, T. The Intramolecular NH···Cl Hydrogen Bond in Urea Derivatives Containing the O-Chlorophenyl Group. J. Mol. Struct. 1982, 82, 29–34. [CrossRef] 88. Johnson, E.R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A.J.; Yang, W. Revealing Noncovalent Interactions. J. Am. Chem. Soc. 2010, 132, 6498–6506. [CrossRef] [PubMed] 89. Lu, T.; Chen, F. Multiwfn: A Multifunctional Wavefunction Analyzer. J. Comput. Chem. 2012, 33, 580–592. [CrossRef] [PubMed] 90. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graph. 1996, 14, 33–38. [CrossRef] 91. Bader, R.F.W. Atoms in Molecules: A Quantum Theory; Oxford University Press: Oxford, UK, 1990. 92. Bader, R.F.W.; Anderson, S.G.; Duke, A.J. Quantum Topology of Molecular Charge Distributions, 1. J. Am. Chem. Soc. 1979, 101, 1389–1395. [CrossRef] 93. Bader, R.F.W.; Essén, H. The characterization of atomic interactions. J. Chem. Phys. 1984, 80, 1943–1960. [CrossRef] 94. Bader, R.F.W.; Nguyen-Dang, T.T.; Tal, Y. A topological theory of molecular structure. Rep. Prog. Phys. 1981, 44, 893–948. [CrossRef] 95. Runtz, G.R.; Bader, R.F.W.; Messer, R.R. Definition of bond paths and bond directions in terms of the molecular charge distribution. Can. J. Chem. 1977, 55, 3040–3045. [CrossRef] 96. Espinosa, E.; Molins, E.; Lecomte, C. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chem. Phys. Lett. 1998, 285, 170–173. [CrossRef] 97. Fermi, E.; Pasta, J.; Ulam, S. Studies of Nonlinear Problems. I, Los Alamos Report LA-1940. Los Alamos Scientific Laboratory of the University of California: Oakland, CA, USA, 1955. 98. Chopra, D.; Guru Row, T.N. Evaluation of the interchangeability of C–H and C–F groups: insights from crystal packing in a series of isomeric fluorinated benzanilides. Cryst. Eng. Comm. 2008, 10, 54–67. [CrossRef] 99. Böhm, H.J.; Banner, D.; Bendels, S.; Kansy, M.; Kuhn, B.; Müller, K.; Obst-Sander, U.; Stahl, M. Fluorine in Medicinal Chemistry. Chem. Biochem. 2004, 5, 637–643. [CrossRef] [PubMed] 100. Wickenden, O.; Gross, M.F.; Smith, G.A.M. Benzanilides as Potassium Channel Openers. U.S. Patent 6,989,398, 24 January 2006. 101. Calderone, V.; Fiamingo, F.L.; Giorgi, I.; Leonardi, M.; Livi, O.; Martelli, A.; Martinotti, E. Heterocyclic analogs of benzanilide derivatives as potassium channel activators, IX. Eur. J. Med. Chem. 2006, 41, 761–767. [CrossRef] [PubMed]

Molecules 2017, 22, 423

40 of 44

102. Biagi, G.; Giorgi, I.; Livi, O.; Nardi, A.; Calderone, V.; Martelli, A.; Martinotti, E.; Salerni, O.L. Synthesis and biological activity of novel substituted benzanilides as potassium channel activators, V. Eur. J. Med. Chem. 2004, 39, 491–498. [CrossRef] [PubMed] 103. Bondiwell, W.E.; Chan, J.A. Substituted Benzanilides as CCR5 Receptors Ligands, Anti-inflammatory Agents and Antiviral Agents. U.S. Patent 6,515,027, 4 February 2003. 104. Reddy, G.N.M.; Vasantha Kumar, M.V.; Guru Row, T.N.; Suryaprakash, N. N–H···F hydrogen bonds in fluorinated benzanilides: NMR and DFT study. Phys. Chem. Chem. Phys. 2010, 12, 13232–13237. [CrossRef] [PubMed] 105. Smirnov, S.N.; Golubev, N.S.; Denisov, G.S.; Benedict, H.; Schah-Mohammedi, P.; Limbach, H.H. Hydrogen/Deuterium Isotope Effects on the NMR Chemical Shifts and Geometries of Intermolecular Low-Barrier Hydrogen-Bonded Complexes. J. Am. Chem. Soc. 1996, 118, 4094–4101. [CrossRef] 106. Golubev, N.S.; Smirnov, S.N.; Gindin, V.A.; Denisov, G.S.; Benedict, H.; Limbach, H.H. Formation of Charge Relay Chains between Acetic Acid and Pyridine Observed by Low-Temperature Nuclear Magnetic Resonance. J. Am. Chem. Soc. 1994, 116, 12055–12056. [CrossRef] 107. Golubev, N.S.; Denisov, G.S.; Smirnov, S.N.; Shchepkin, D.N.; Limbach, H.H. Evidence by NMR of Temperature-dependent Solvent Electric Field Effects on Proton Transfer and Hydrogen Bond Geometries. Z. Phys. Chem. 1996, 196, 73–84. [CrossRef] 108. Borman, S. Speedy Route to Folded DNA. Chem. Eng. News 1999, 77, 36–38. [CrossRef] 109. Dingley, A.J.; Grzesiek, S. Direct Observation of Hydrogen Bonds in Nucleic Acid Base Pairs by Internucleotide 2 JNN Couplings. J. Am. Chem. Soc. 1998, 120, 8293–8297. [CrossRef] 110. Pervushin, K.; Ono, A.; Fernández, C.; Szyperski, T.; Kainosho, M.; Wüthrich, K. NMR scalar couplings across Watson–Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc. Natl. Acad. Sci. USA 1998, 95, 14147–14151. [CrossRef] [PubMed] 111. Fritz, H.; Winkler, T.; Küng, W. Weitreichende Kernspin-Kopplungen in 2-Fluorbenzamiden II. [15 N]-2-Fluorbenzamid. Helv. Chim. Acta 1975, 58, 1822–1824. [CrossRef] 112. Hennig, L.; Ayala-Leon, K.; Angulo-Cornejo, J.; Richter, R.; Beyer, L. Fluorine hydrogen short contacts and hydrogen bonds in substituted benzamides. J. Fluor. Chem. 2009, 130, 453–460. [CrossRef] 113. Pople, J.A.; Schneider, W.G.; Bernstein, H.J. High Resolution Nuclear Magnetic Resonance; McGraw Hill: New York, NY, USA, 1959. 114. Günther, H. NMR Spectroscopy: Basic Principles, Concepts and Applications in Chemistry; John Wiley & Sons: New York, NY, USA, 1995. 115. Reddy, G.N.M.; Row, T.N.G.; Suryaprakash, N. Discerning the degenerate transitions of scalar coupled 1 H NMR spectra: Correlation and resolved techniques at higher quantum. J. Magn. Reson. 2009, 196, 119–126. [CrossRef] [PubMed] 116. Bikash, B.; Reddy, G.N.M.; Uday, R.P.; Row, T.N.G.; Suryaprakash, N. Simplifying the Complex 1 H-NMR Spectra of Fluorine-Substituted Benzamides by Spin System Filtering and Spin-State Selection: Multiple-Quantum-Single-Quantum Correlation. J. Phys. Chem. A 2008, 112, 10526–10532. 117. Reddy, G.N.M.; Caldarelli, S. Demixing of Severely Overlapping NMR Spectra through Multiple-Quantum NMR. Anal. Chem. 2010, 82, 3266–3269. 118. Becke, A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648–5652. [CrossRef] 119. Foresman, J.B.; Keith, T.A.; Wiberg, K.B.; Snoonian, J.; Frisch, M.J. Solvent Effects. 5. Influence of Cavity Shape, Truncation of Electrostatics, and Electron Correlation on ab Initio Reaction Field Calculations. J. Phys. Chem. 1996, 100, 16098–16104. [CrossRef] 120. Chaudhari, S.R.; Mogurampelly, S.; Suryaprakash, N. Engagement of CF3 Group in N−H···F−C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies. J. Phys. Chem. B 2013, 117, 1123–1129. [CrossRef] [PubMed] 121. Schneider, H.J. Hydrogen bonds with fluorine. Studies in solution, in gas phase and by computations, conflicting conclusions from crystallographic analyses. Chem. Sci. 2012, 3, 1381–1394. [CrossRef] 122. Jiang, J.C.; Tsa, M.H. Ab Initio Study of the Hydrogen Bonding between Pyrrole and Hydrogen Fluoride: A Comparison of NH···F and FH···π Interactions. J. Phys. Chem. A 1997, 101, 1982–1988. [CrossRef]

Molecules 2017, 22, 423

41 of 44

123. Wu, X.; Wang, S. Folding Studies of a Linear Pentamer Peptide Adopting a Reverse Turn Conformation in Aqueous Solution through Molecular Dynamics Simulation. J. Phys. Chem. B 2000, 104, 8023–8034. [CrossRef] 124. Pophristic, V.; Vemparala, S.; Ivanov, I.; Liu, Z.; Klein, M.L.; DeGrado, W.F. Controlling the Shape and Flexibility of Arylamides: A Combined ab Initio, ab Initio Molecular Dynamics, and Classical Molecular Dynamics Study. J. Phys. Chem. B 2006, 110, 3517–3526. [CrossRef] [PubMed] 125. Schnabel, T.; Srivastava, A.; Vrabec, J.; Hasse, H. Hydrogen Bonding of Methanol in Supercritical CO2 : Comparison between 1 H NMR Spectroscopic Data and Molecular Simulation Results. J. Phys. Chem. B 2007, 111, 9871–9878. [CrossRef] [PubMed] 126. Liu, Z.; Remsing, R.C.; Liu, D.; Moyna, G.; Pophristic, V. Hydrogen Bonding in ortho-Substituted Arylamides: The Influence of Protic Solvents. J. Phys. Chem. B 2009, 113, 7041–7044. [CrossRef] [PubMed] 127. Galan, J.F.; Brown, J.; Wildin, J.L.; Liu, Z.; Liu, D.; Moyna, G.; Pophristic, V. Intramolecular Hydrogen Bonding in ortho-Substituted Arylamide Oligomers: A Computational and Experimental Study of ortho-Fluoro- and ortho-Chloro-N-methylbenzamides. J. Phys. Chem. B. 2009, 113, 12809–12815. [CrossRef] [PubMed] 128. International Union of Pure and Applied Chemistry (IUPAC). Compendium of Chemical Terminology, 2nd ed.; The “Gold Book”; McNaught, A.D., Wilkinson, A., Eds.; Blackwell Scientific Publications: Oxford, UK, 1997. 129. Friedman, L.; Litle, R.L.; Reichle, W.R. p-Toluenesulphonylhydrazide [p-Toluenesulphonic acid, hydrazide]. Org. Synth. 1960, 40, 93–96. 130. Mohareb, R.M.; Fleita, D.H.; Sakka, O.K. Novel Synthesis of Hydrazide-Hydrazone Derivatives and Their Utilization in the Synthesis of Coumarin, Pyridine, Thiazole and Thiophene Derivatives with Antitumor Activity. Molecules 2011, 16, 16–27. [CrossRef] [PubMed] 131. Wadrdakhan, W.W.; El-saeed, N.N.E.; Mohereb, R.M. Development of coated beads for oral controlled delivery of cefaclor: In vitro evaluation. Acta Pharm. 2013, 63, 45–57. 132. Swietlinska, ´ Z.; Zuk, J. Cytotoxic Effects of Maleic Hydrazide. Mutat. Res. Rev. Gen. Toxicol. 1978, 55, 15–30. [CrossRef] 133. Kaplancikli, Z.A.; Turan-Zitouni, G.; Ozdemir, A.; Teulade, J.C. Synthesis and Antituberculosis Activity of New Hydrazide Derivatives. Arch. Pharm. 2008, 341, 721–724. [CrossRef] [PubMed] 134. Mishra, S.K.; Suryaprakash, N. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations. Phys. Chem. Chem. Phys. 2015, 17, 15226–15235. [CrossRef] [PubMed] 135. Kohn, W.; Sham, L.J. Self-Consistent Equations Including Exchange and Correlation Effects. Phys. Rev. 1965, 140, A1133–A1138. [CrossRef] 136. Parr, R.G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: New York, NY, USA, 1989. 137. Morris, K.F.; Johnson, C.S. Diffusion-Ordered Two-Dimensional Nuclear Magnetic Resonance Spectroscopy. J. Am. Chem. Soc. 1992, 114, 3139–3141. [CrossRef] 138. Morris, K.F.; Johnson, C.S. Resolution of Discrete and Continuous Molecular Size Distributions by Means of Diffusion-Ordered 2D NMR Spectroscopy. J. Am. Chem. Soc. 1993, 115, 4291–4299. [CrossRef] 139. Reed, A.E.; Curtiss, L.A.; Weinhold, F. Intermolecular Interactions from a Natural Bond Orbital, Donor-Acceptor Viewpoint. Chem. Rev. 1988, 88, 899–926. [CrossRef] 140. Axenrod, T.; Pregosin, P.S.; Wieder, M.J.; Becker, E.D.; Bradley, R.B.; Milne, G.W.A. Nitrogen- 15 Nuclear Magnetic Resonance Spectroscopy. Substituent Effects on 15 N-H Coupling Constants and Nitrogen Chemical Shifts in Aniline Derivatives. J. Am. Chem. Soc. 1971, 93, 6536–6541. [CrossRef] 141. Dunger, A.; Limbach, H.-H.; Weisz, K. Geometry and Strength of Hydrogen Bonds in Complexes of 2’-Deoxyadenosine with 2’-Deoxyuridine. J. Am. Chem. Soc. 2000, 122, 10109–10114. [CrossRef] 142. Grzesiek, S.; Cordier, F.; Jaravine, V.; Barfield, M. Insights into biomolecular hydrogen bonds from hydrogen bond scalar couplings. Prog. Nucl. Magn. Reson. Spectrosc. 2004, 45, 275–300. [CrossRef] 143. Afonin, A.V.; Ushakov, I.A.; Sobenina, L.N.; Stepanova, Z.V.; Petrova, O.G.V.; Trofimov, B.A. Different types of hydrogen bonds in 2-substituted pyrroles and 1-vinyl pyrroles as monitored by 1 H, 13 C and 15 N NMR spectroscopy and ab initio calculations. Magn. Reson. Chem. 2006, 44, 59–65. [CrossRef] [PubMed] 144. King, M.M.; Yeh, H.J.C.; Dudek, G.O. Nitrogen NMR Spectroscopy: Application to some Substituted Pyrroles. Org. Magn. Reson. 1976, 8, 208–212. [CrossRef] 145. Cheeseman, J.R.; Trucks, G.W.; Keith, T.A.; Frisch, M.J. A comparison of models for calculating nuclear magnetic resonance shielding tensors. J. Chem. Phys. 1996, 104, 5497–5509. [CrossRef]

Molecules 2017, 22, 423

42 of 44

146. Nakahara, M.; Wakai, C. Monomeric and Cluster States of Water Molecules in Organic Solvent. Chem. Lett. 1992, 21, 809–812. [CrossRef] 147. Vizioli, C.; de Azua, M.C.R.; Giribet, C.G.; Contreras, R.H.; Turi, L.; Dannenberg, J.J.; Rae, I.D.; Weigold, J.A.; Malagoli, M. Proximity Effects on Nuclear Spin-Spin Coupling Constants. 1. 1 J(CH) Couplings in the Vicinity of an Atom Bearing Lone Pairs. J. Phys. Chem. 1994, 98, 8858–8861. [CrossRef] 148. Lakshmipriya, A.; Suryaprakash, N. Two- and Three-Centered Hydrogen Bonds Involving Organic Fluorine Stabilize Conformations of Hydrazide Halo Derivatives: NMR, IR, QTAIM, NCI, and Theoretical Evidence. J. Phys. Chem. A 2016, 120, 7810–7816. [CrossRef] [PubMed] 149. Walter, W.W.; Michael, H.A. “Polyimides” in Ullmann’s Encyclopedia of Industrial Chemistry; Wiley-VCH: Weinheim, Germany, 2002. 150. Prinos, J.; Tselios, C.; Bikiaris, D.; Panayiotou, C. Properties of miscible blends of polyglutarimide with poly(styrene-co-maleic anhydride). Polymer 1997, 38, 5921–5930. [CrossRef] 151. Luo, L.; Zheng, Y.; Huang, J.; Li, K.; Wang, H.; Feng, Y.; Wang, X.; Liu, X. High-performance copoly(benzimidazole-benzoxazole-imide) fibers: Fabrication, structure, and properties. J. Appl. Polym. Sci. 2015, 132. [CrossRef] 152. Kanaoka, Y. Photoreactions of Cyclic Imides. Examples of Synthetic Organic Photochemistry. Acc. Chem. Res. 1978, 11, 407–413. [CrossRef] 153. Stec, J.; Huang, Q.; Pieroni, M.; Kaiser, M.; Fomovska, A.; Mui, E.; Witola, W.H.; Bettis, S.; McLeod, R.; Brun, R.; Kozikowski, A.P. Synthesis, Biological Evaluation, and Structure−Activity Relationships of N-Benzoyl-2-hydroxybenzamides as Agents Active against P. falciparum (K1 strain), Trypanosomes, and Leishmania. J. Med. Chem. 2012, 55, 3088–3100. [CrossRef] [PubMed] 154. Wang, H.; Kelley, S.P.; Brantley, J.W.; Chatel, G.; Shamshina, J.; Pereira, J.F.B.; Debbeti, V.; Myerson, A.S.; Rogers, R.D. Ionic Fluids Containing Both Strongly and Weakly Interacting Ions of the Same Charge Have Unique Ionic and Chemical Environments as a Function of Ion Concentration. ChemPhysChem 2015, 16, 993–1002. [CrossRef] [PubMed] 155. Sprecher, D.; Maxwell, M.; Goodman, J.; White, B.; Tang, C.M.; Boullay, V.; de Gouville, A.C. Discovery and characterization of GSK256073, a non-flushing hydroxy-carboxylic acid receptor 2 (HCA2) agonist. Eur. J. Pharmacol., 2015, 756, 1–7. [CrossRef] [PubMed] 156. Mhidia, R.; Boll, E.; Fécourt, F.; Ermolenko, M.; Ollivier, N.; Sasaki, K.; Crich, D.; Delpech, B.; Melnyk, O. Exploration of an imide capture/N,N-acyl shift sequence for asparagine native peptide bond formation. Bioorg. Med. Chem. 2013, 21, 3479–3485. [CrossRef] [PubMed] 157. Li, Y.; Wang, Y.; Wang, J. Microwave-Assisted Synthesis of Amides from Various Amines and Benzoyl Chloride under Solvent-Free Conditions: A Rapid and Efficient Method for Selective Protection of Diverse Amines. Russ. J. Organ. Chem. 2008, 44, 358–361. [CrossRef] 158. Mishra, S.K.; Suryaprakash, N. Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations. RSC Adv. 2015, 5, 86013–86022. [CrossRef] 159. Contreras-García, J.; Yang, W.; Johnson, E.R. Analysis of Hydrogen-Bond Interaction Potentials from the Electron Density: Integration of Noncovalent Interaction Regions. J. Phys. Chem. A 2011, 115, 12983–12990. [CrossRef] [PubMed] 160. Gellman, S.H.; Adams, B.R.; Dado, G.P. Temperature-Dependent Changes in the Folding Pattern of a Simple Triamide. J. Am. Chem. Soc. 1990, 112, 460–461. [CrossRef] 161. Gellman, S.H.; Dado, G.P.; Liang, G.B.; Adams, B.R. Conformation-Directing Effects of a Single Intramolecular Amide-Amide Hydrogen Bond: Variable-Temperature NMR and IR Studies on a Homologous Diamide Series. J. Am. Chem. Soc. 1991, 113, 1164–1173. [CrossRef] 162. Martinez-Martinez, F.J.; Ariza-Castolo, A.; Tlahuext, H.; Tlahuextl, M.; Contreras, R. 1 H, 13 C, 15 N, 2D and Variable Temperature NMR Study of the Role of Hydrogen Bonding in the Structure and Conformation of Oxamide Derivatives. J. Chem. Soc. Perkin Trans. 2 1993, 1481–1485. [CrossRef] 163. Rinaldi, P.L. Heteronuclear 2D-NOE Spectroscopy. J. Am. Chem. Soc. 1983, 105, 5167–5168. [CrossRef] 164. Yu, C.; Levy, G.C. Solvent and Intramolecular Proton Dipolar Relaxation of the Three Phosphates of ATP: A Heteronuclear 2D NOE Study. J. Am. Chem. Soc. 1983, 105, 6994–6996. [CrossRef] 165. Yu, C.; Levy, G.C. Two-Dimensional Heteronuclear NOE (HOESY) Experiments: Investigation of Dipolar Interactions between Heteronuclei and Nearby Protons. J. Am. Chem. Soc. 1984, 106, 6533–6537. [CrossRef]

Molecules 2017, 22, 423

43 of 44

166. Lakshmipriya, A.; Chaudhari, S.R.; Shahi, A.; Arunan, E.; Suryaprakash, N. Three centered hydrogen bonds of the type C-O···H(N)···X–C in diphenyloxamide derivatives involving halogens and a rotating CF3 group: NMR, QTAIM, NCI and NBO studies. Phys. Chem. Chem. Phys. 2015, 17, 7528–7536. [CrossRef] [PubMed] 167. Shahi, A.; Arunan, E. Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding. Phys. Chem. Chem. Phys. 2014, 16, 22935–22952. [CrossRef] [PubMed] 168. Brotherhood, P.R.; Luck, I.J.; Blake, I.M.; Jensen, P.; Turner, P.; Crossley, M.J. Regioselective Reactivity of an Asymmetric Tetravalent Di[dihydroxotin(IV)] Bis-Porphyrin Host Driven by Hydrogen-Bond Templation. Chem. Eur. J. 2008, 14, 10967–10977. [CrossRef] [PubMed] 169. Mishra, S.K.; Suryaprakash, N. Study of H/D exchange rates to derive the strength of intramolecular hydrogen bonds in halo substituted organic building blocks: An NMR spectroscopic investigation. Chem. Phys. Letts. 2015, 639, 254–260. [CrossRef] 170. Pietrzak, M.; Limbach, H.H.; Torralba, M.P.; Sanz, D.; Claramunt, R.M.; Elguero, J. Scalar Coupling Constants Across the Intramolecular NHN-Hydrogen Bond of Symmetrically and Non-symmetrically substituted 6-Aminofulvene-1-aldimines. Magn. Reson. Chem. 2001, 39, S100–S108. [CrossRef] 171. Shenderovich, I.G.; Burtsev, A.P.; Denisov, G.S.; Golubev, N.S.; Limbach, H.H. Influence of the temperature-dependent dielectric constant on the H/D isotope effects on the NMR chemical shifts and the hydrogen bond geometry of the collidine–HF complex in CDF3 /CDClF2 solution. Magn. Reson. Chem. 2001, 39, S91–S99. [CrossRef] 172. Wang, Y.X.; Marquardt, J.L.; Wingfield, P.; Stahl, S.J.; Huang, S.L.; Torchia, D.; Bax, A. Simultaneous Measurement of 1 H-15 N, 1 H-13 C’, and 15 N-13 C’ Dipolar Couplings in a Perdeuterated 30 kDa Protein Dissolved in a Dilute Liquid Crystalline Phase. J. Am. Chem. Soc. 1998, 120, 7385–7386. [CrossRef] 173. Cornilescu, G.; Hu, J.S.; Bax, A. Identification of the Hydrogen Bonding Network in a Protein by Scalar Couplings. J. Am. Chem. Soc. 1999, 121, 2949–2950. [CrossRef] 174. Norwood, T.J. Multiple-Quantum NMR Methods. Prog. NMR Spect. 1992, 24, 295–375. [CrossRef] 175. Bodenhausen, G. Multiple-Quantum NMR. Prog. NMR Spect. 1981, 14, 137–173. [CrossRef] 176. Divya, K.; Hebbar, S.; Suryaprakash, N. Intra-molecular hydrogen bonding with organic fluorine in the solution state: Deriving evidence by a two dimensional NMR experiment. Chem. Phys. Lett. 2012, 525–526, 129–133. [CrossRef] 177. Hebbar, S.; Suryaprakash, N. Spin-selective multiple quantum excitation: Relative signs of the couplings and ambiguous situations. J. Magn. Reson. 2008, 194, 192–201. [CrossRef] [PubMed] 178. Munowitz, M.; Pines, A. Homogeneous NMR spectra in inhomogeneous fields. Science 1986, 233, 525–531. [CrossRef] [PubMed] 179. Bikash, B.; Suryaprakash, N. Spin selective multiple quantum NMR for spectral simplification, determination of relative signs, and magnitudes of scalar couplings by spin state selection. J. Chem. Phys. 2007, 127, 214510–214521. 180. Griffey, R.H.; Poulter, C.D.; Bax, A.; Hawkins, B.L.; Yamaizumi, Z.; Nishimura, S. Multiple quantum two-dimensional 1 H- 15 N nuclear magnetic resonance spectroscopy: Chemical shift correlation maps for exchangeable imino protons of Escherichia coli tRNAf Met in water. Proc. Nat. Acad. Sci. USA 1983, 80, 5895–5897. [CrossRef] [PubMed] 181. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G.A.; et al. Gaussian G09; Gaussian, Inc.: Wallingford, CT, USA, 2009. 182. Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781–1802. [CrossRef] [PubMed] 183. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089–10092. [CrossRef] 184. Keith, T.A. AIMAll (Version 13.11.04); TK Gristmill Software: Overland Park, KS, USA, 2013. 185. Takemura, H.; Kon, N.; Yasutake, M.; Nakashima, S.; Shinmyozu, T.; Inazu, T. The C-F···Cation Interaction: An Ammonium Complex of a Hexafluoro Macrocyclic Cage Compound. Chem. Eur. J. 2000, 6, 2334–2337. [CrossRef]

Molecules 2017, 22, 423

44 of 44

186. Zhao, X.; Wang, X.Z.; Jiang, X.K.; Chen, Y.Q.; Li, Z.T.; Chen, G.J. Hydrazide-Based Quadruply Hydrogen-Bonded Heterodimers. Structure, Assembling Selectivity, and Supramolecular Substitution. J. Am. Chem. Soc. 2003, 125, 15128–15139. [CrossRef] [PubMed] 187. Schaftenaar, G.; Noordik, J.H. Molden: A pre- and post-processing program for molecular and electronic structures. J. Comput. Aided Mol. Des. 2000, 14, 123–134. [CrossRef] [PubMed] © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).