1H NMR study of the hetero‐association of non‐symmetrical diols with pyridine; GIAO/DFT calculations on diols

The ¹H NMR titration method is used to investigate the association of non‐symmetrical 1,2‐ and 1,3‐diols with pyridine in benzene. These diols give well‐defined titration curves for the two non‐equivalent OH protons, but it is not possible to determine individual association constants. Only the sum of the first association constants for the two protons and the product of the first and second association constants are accessible. The sum is significantly higher than that of the association constants of the corresponding primary and secondary alcohols, but close to an estimate based on symmetrical diols. The product leads to second association constants similar to those found for symmetrical diols. The sum of the chemical shifts of the associated and non‐associated OH protons in either 1:1 pyridine complex is higher than that of the shifts in the free diol and the 2:1 complex. These features are consistent with small cooperative effects, amounting to an average increase in the reaction free energy of 1.3 kJ mol^?1 compared to monohydric alcohols. Infrared (IR) spectra of non‐symmetrical diols and quantum mechanical (QM) calculation of the energies and ¹H NMR shifts of the OH protons in several conformers of propan‐1,2‐ and butan‐1,3‐diols indicate that both the primary and the secondary OH groups act as “donor” or “acceptor” in the free molecule. Gauche interactions in propan‐1,2‐diol enhance chemical shifts considerably less than does the intramolecular hydrogen bond in butan‐1,3‐diol. Copyright © 2011 John Wiley & Sons, Ltd.     

Cooperative and diminutive interplay between the sodium bonding with hydrogen and dihydrogen bondings in ternary complexes of NaC3N with HMgH and HCN (HNC)

Ternary complexes of NaC₃N with HMgH and HCN (HNC) are connected by sodium, hydrogen and dihydrogen bonds. Molecular geometries and interaction energies of dyads and triads are investigated at the MøllerPlesset perturbation theory of the second order/aug-cc-pVDZ computational level. Particular attention is paid to parameters, such as cooperative energies and many-body interaction energies. Triads with the HMgH molecule located at the end of the chain show an energetic cooperativity ranging between ?2.13 and ?10.53 kJ mol^?1. When the HMgH molecule is located in the middle, the obtained cluster is diminutive with an energetic effect with values 4.39 and 6.77 kJ mol^?1. The electronic properties of the complexes are analysed using parameters derived from the atoms in molecules methodology. Based on the energy decomposition analysis, it can be seen that the stabilities of the complexes are predicted to be attributable mainly to electrostatic effects.     

Visible absorbing symmetrical squaraine and croconine dye derivatives: A comparative computational study

Visible absorbing C–N bonding squaraines (SQ1‐SQ5) and croconines (CR1‐CR5) with an increase in conjugation at donor groups and heteroaromatic donor substituents have been studied by density functional theory and time‐dependent density functional theory methodologies. In these molecules, croconines always have absorption nearly 100‐nm red shift than its corresponding squaraines (it is in consistent with C–C bonding, near infrared absorbing squaraine and croconines). The reason behind this drastic red shift, by changing the central acceptor of 4‐membered squarate ring with 5‐membered croconate ring, has been analyzed by considering the concept of diradical character and variation in central C–C–C angle. It is also observed that within the same series of molecules (either in squaraine or in croconines), with an increase in donor capacity (conjugation), absorption increases towards longer wavelength region because of destabilization of HOMO and stabilization of LUMO levels. A small blue shift was observed for heteroaromatic donor groups when compared with aromatic donor group.     

Tuning of pnicogen and chalcogen bonds by an aerogen-bonding interaction: a comparative ab initio study

Using high-level ab initio calculations, the cooperativity effects between an aerogen-bonding and a pnicogen- or chalcogen-bonding interactions are studied in ternary Y···PH₂CN···ZO₃ and Y···SHCN···ZO₃ complexes (Y?=?NH₃, N₂ and Z?=?Ar, Kr, Xe). A detailed analysis of the structures, interaction energies and bonding properties is performed on these systems. For each set of the complexes, a favourable cooperativity is observed between Z···N and P/S···N interactions, especially in complexes involving NH₃ and XeO₃ molecules. It is found that for a given Y or Z, the amount of cooperativity effects in Y···PH₂CN···ZO₃ complexes are important than Y···SHCN···ZO₃ ones. For each ternary complex considered, the effect of a Z···N aerogen bond on a P/S···N bond is more pronounced than that of a P/S···N bond on a Z···N bond. The mechanism of the cooperativity effects in the ternary complexes is studied by electron density difference, quantum theory of atoms in molecules and natural bond orbital analyses. The solvent effects are also studied on the interaction energy and cooperativity of Z···N and P/S···N bonds in the ternary systems.     

An ab initio study on substituent and cooperative effects in bifurcated fluorine bonds

Bifurcated fluorine bond (BFB) interactions are studied in model binary complexes pairing N-formyl formamide derivatives and FX molecules (X = F, CN, NC, CF₃ and CCH) by means of ab initio calculations. The calculated F···O binding distances in these complexes are in the range of 2.813–3.048 Å. The corresponding interaction energies lie in a narrow range, from?2.25 to ?16.49 kJ/mol. The nature of BFBs is analysed by a vast number of methods including molecular electrostatic potential, quantum theory of atoms in molecules, non-covalent interaction index and natural bond orbital methods. According to the energy decomposition analysis, the electrostatic and dispersion effects have a dominant role in the formation of these complexes. The formation of a hydrogen- and lithium-bonding interaction tends to increase the strength of BFBs in the ternary XF:NFF-H:NH₃ and XF:NFF-Li:NH₃ complexes, respectively.     

Molecular alignment of biphenyl derivatives -a computational analysis

Molecular alignment of some biphenyl derivatives likes 4'-Nitro-2-biphenylamine (NBPA), 4-Acetyl-3'-chlorobiphenyl (ACBP) and 4-Acetyl-3'-florobiphenyl (AFBP) has been examined. The CNDO/2 method has been employed to compute the net atomic charge and atomic dipole-moment components at each atomic centre. Configurational energy has been computed using a modified Rayleigh- Schrodinger perturbation method at an interval of 0.1 A° in translation and 1° in rotation, and corresponding probabilities have been calculated using MB-statistics. A comparative study of molecular parameters like the total energy, the binding energy and the total dipole moment etc., has been made. On the basis of the stacking and the in-plane interaction energy calculations, all the possible geometrical arrangements between molecular pairing have been obtained. The investigation suggests that a strong intermolecular interaction energy between a pair of NBPA molecules, and the specific minimum energy configuration, determines the alignment of molecules with respect to one another. An attempt has been made to correlate the liquid crystalline properties exhibited by this class of molecules, and thereby develop a molecular model for the liquid crystallinity.     

Ab initio study of the structure,cooperativity, and vibrational properties of HNC ternary complexes with two HF molecules

MP2/aug-cc-pVDZ calculations have been used to provide information on the three ternary systems comprising one HNC and two HF molecules. The binding distances, frequency shifts, and interaction energies in these systems have been analysed to study the cooperativity of hydrogen bond in these systems. The cooperativity of hydrogen bond in HNC–HF–HF trimer is larger than that in HF–HF–HNC trimer. The result indicates that the proton acceptor HNC plays a more important role in enhancing the cooperativity of hydrogen bond. Many-body interaction analyses have also been performed for these ternary systems.     

1H NMR study of through‐bond and through‐space effects in the hetero‐association of pyridine with alkane diols

The ¹H NMR titration method is used to investigate through‐space and through‐bond effects on the association of diols with pyridine in benzene. Alkan‐1,n‐diols (n goes from 2 to 10), DL and meso isomers of butan‐2,3‐, pentan‐2,4‐ and hexan‐2,5‐diols, two adamantane diols and a bicyclo[2.2.2]octane diol are compared with alkanols. The –CH₂OH groups of the tri‐ and bicyclic compounds behave as if they were independent, with limiting OH proton shifts (at very low concentration) and both the first and the second association constants similar to those of a primary alcohol. In contrast, the alkane diols, with n = 2–4, display unusually high limiting shifts, ranging from 1.0 to 1.5 ppm (2.1 ppm for one methyl‐substituted diol). For these diols the first dissociation constant and the sum of the OH proton shifts in the 1:1 pyridine: diol complex are enhanced. This may be attributed to small cooperative effects, implying intramolecular hydrogen bonding, for n = 3 and 4, but for n = 2 a through‐bond effect accounts for most of the increase. Substituent interaction falls off sharply for n = 5 and is practically negligible for n = 10, for which the second association constant is close to the first. A sterically hindered BiEDOT diol, 2,2′‐bis{(3,4‐ethylenedioxythienyl)‐5‐[3‐(2,2,4,4‐tetramethylpentan‐3‐ol)]} behaves like the polycyclic compounds, with the two ? C(t‐Bu)₂OH groups independent. Copyright © 2010 John Wiley & Sons, Ltd.     

光谱法在分子间非共价相互作用中的应用及进展

对光谱法在分子间非共价相互作用中的应用作了较详细的评述。重点介绍了紫外、荧光、圆二色、红外、激光拉曼、共振散射等方法在分子间相互作用研究中的应用及进展,总结了这些方法的优缺点。紫外-可见吸收光谱简便、快速,荧光光谱法可获得分子间作用的结合常数、结合位点数及作用方式等信息,圆二色谱法是测定作用前后生物大分子构象变化的有效方法,红外光谱法可提供蛋白质二级结构及构象变化的谱学信息,拉曼光谱法是研究溶液中生物大分子构象变化的有效技术,表面等离子共振(SPR)技术能在保持生物分子天然活性的条件下实时检测分子间的相互作用。     

13C NMR relaxation and computational study of anisole and derivatives in the solution state

¹³C NMR spin–lattice relaxation times and nuclear Overhauser effects were measured at several temperatures for the methoxyl methyl carbon and the phenyl ring carbons in neat samples and in dilute cyclohexane solution for anisole, 4‐methylanisole, and 4‐chloroanisole. Similar measurements were made for 2‐methylanisole, 2‐methyl‐4‐bromoanisole, and 2,4,6‐trimethylanisole in dilute cyclohexane solution. Density functional theory (DFT) computations were performed on anisole, 4‐chloroanisole and 2,4,6‐trimethylanisole to obtain the minimum energy structures and the potential energy barriers to the internal rotations of the methoxyl group. The shortest distance between a methoxyl methyl hydrogen and the ortho hydrogen in anisole is 1.920 Å. The DFT results point to steric interactions that arise thereof as the principal source of the energy barriers to the internal rotation of the methyl or of the methoxyl group. The carbon relaxation data are consistent with the existence of noncovalent intermolecular interaction, especially π ? π stacking interaction. The nuclear magnetic resonance and DFT results are discussed with reference to the rotational characteristics of the methoxyl methyl and the anisotropy in the reorientational motion of anisole and its derivatives in dilute cyclohexane solution. Copyright © 2012 John Wiley & Sons, Ltd.     

Gibbs energy of cooperative hydrogen‐bonding interactions in aqueous solutions of amines and pyridines

A method to determine the Gibbs energy of specific (hydrogen bonding) interactions of a solute with water is proposed. The energies of hydrogen bonding in bulk water are very difficult to determine by any method. The Gibbs energy of hydration of substances forming hydrogen bonds with water is considered as the sum of contributions due to non‐specific interactions, the hydrophobic effect, and specific interactions. The first two terms were found to be rather accurately described by empirical equations. The Gibbs energies of hydrogen bonding of aliphatic amines and pyridines in bulk water are determined, and the results are compared with the energies of their complexes with one molecule of water. The cooperativity of hydrogen bonding is proved in aqueous solutions of amines and pyridines. To use our equations, experimental values of the Gibbs energies of solvation in 'standard' solvents need to be known. The Gibbs energies of solvation of ten amines and pyridines in dimethyl sulfoxide are determined experimentally using chromatographic head space analysis. The tendencies observed for the series of amines and pyridines are in agreement with other studies. Copyright © 2009 John Wiley & Sons, Ltd.     

Hydrogen bonding in oxalic acid and its complexes: A database study of neutron structures

The basic result of carboxylic group that the oxygen atom of the -OH never seems to be a hydrogen bond acceptor is violated in the cases, namely urea oxalic acid and bis urea oxalic acid complexes, where the hydroxyl oxygen atom is an acceptor of a weak N—H… O hydrogen bond. The parameters of this hydrogen bond, respectively in these structures are: hydrogen acceptor distance 2.110 Å and 2.127 Å and the bending angle at hydrogen, 165.6° and 165.8°. The bond strength around the hydroxyl oxygen is close to 1.91 valence units, indicating that it has hardly any strength left to form hydrogen bonds. These two structures being highly planar, force the formation of this hydrogen bond. As oxalic acid is the common moiety, the structures of the two polymorphs, α-oxalic acid and β-oxalic acid, also were looked into in terms of hydrogen bonding and packing.     

Anisotropic charge transport properties of chrysene derivatives as organic semiconductor: A computational study

We used density functional theory to calculate the angular resolution anisotropic charge mobility of the substituted chrysene molecules, viz, 4,10‐diphenoxychrysene (DPC), 4,10‐bis(phenylsulfanyl)chrysene (BPSC), and ethyl 8,9,12‐trimethoxychrysene‐6‐carboxylate (ETCC). The highest occupied molecular orbital–lowest unoccupied molecular orbital gap for DPC, BPSC, and ETCC was calculated to be 3.92, 3.83, and 3.81 eV, respectively, which inferred the compounds to be wide‐band‐gap semiconductors indicating that the compounds should have high stability in atmospheric conditions. The fact is also supported by electronic band‐structure calculation. In addition, higher electron affinity of studied compounds as compared with the bare chrysene molecule imparts enhancement of n‐type character in the compounds. The maximum hole ( ) and electron mobilities ( ) for DPC compound were found to be 0.739 cm²V^?1s^?1 and 0.319 cm²V^?1s^?1, respectively, at Φ = 0°. On the other hand, in the case of BPSC crystal, comparatively larger anisotropic electron mobility (0.709 cm²V^?1s^?1 at Φ = 0° and Φ = 179.90°) than the hole mobility (0.208 cm²V^?1s^?1 at Φ = 127.19° and Φ = 307.10°) was noted. Similarly, in ETCC, the parallel dimers were found to contribute maximum and of 0.052 and 0.102 cm²V^?1s^?1, respectively, at Φ = 0°. The substitution of ‐SPh in BPSC and ‐OCH₃ and ‐CO₂CH₂CH₃ in ETCC have relatively more impact on band reduction than ‐OPh in DPC, thus facilitating electron transport in BPSC and ETCC.     

Cooperativity effects of intramolecular OH…O interactions on pKa values of polyolalkyl sulfonic acids in the gas phase and solution: a density functional theory study

Density functional theory method and B3LYP/6‐311++G(d,p) level of theory were used to determine the acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution (H₂O, DMSO, and CH₃CN) phase. Polarized continuum model was applied to calculate pK_a values of alkyl sulfonic acids and polyolalkyl sulfonic acids. A comparison between acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution phase indicates that the acidity strength of polyolalkyl sulfonic acids enhances with the increase of the cooperativity effect of intramolecular hydrogen bonds in polyolalkyl sulfonic acids. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of cooperativity effect on the acidity of polyolalkyl sulfonic acids. Copyright © 2014 John Wiley & Sons, Ltd.     

Hydrogen bonding in amylose/DMSO complexes studied by vibrational spectroscopy and density functional theory calculations

The intermolecular interactions in amylose/dimethyl sulfoxide (DMSO) complexes are discussed both experimentally and theoretically by means of Raman and infrared spectroscopies. The study is based on a preliminary analysis of well known systems such as pure liquid DMSO or DMSO in mixture with water: for such systems, an analysis of the CS stretching region is carried out both by means of Raman and infrared spectra. In particular, Raman spectra reveal a high sensitivity to the strength and to the type of interaction involving the DMSO molecules. These results, applied to the investigation of amylose‐DMSO complexes, show the presence of different hydrogen‐bonded complexes which coexist in this compound. In particular, DMSO molecules are identified both on the external surface of the V‐amylose helix, where they can interact via one hydrogen bond and in the inner channel of the helix where they can interact via two hydrogen bonds. The present findings open the possibility of applying vibrational spectroscopy to the characterization of inclusion compounds of amylose which are currently being involved in many fields of nanosciences. Copyright © 2009 John Wiley & Sons, Ltd.     

Visible to NIR absorbing C–N and C–C bonding squaraines: A computational study

We report a comparative computational study of 2 series of molecules with C–N bonding squaraines (NSQ) and C–C bonding squaraines (CSQ), having absorption from visible to near infrared region (350‐800 nm). The NSQ are considered as molecules with break‐in conjugation, and CSQ are considered as molecules with complete conjugation in molecular backbone. The lowest electronic excitations in CSQ molecules are always having around 200 nm red shifted absorption than its corresponding NSQ molecules. The reason for this drastic red shift in CSQ series than NSQ has been systematically studied by density functional theory, time‐dependent density functional theory, and symmetry adopted cluster configuration interaction methods. The CSQ series are showing less charge transfer than NSQ, but having small diradical character. This study may be helpful in design and synthesis of new squaraine dyes, which are useful in materials applications.     

A study of the headgroup motion of sphingomyelin using 31P NMR and an analytically soluble model

A 31P NMR investigation has been carried out of the headgroup dynamics of sphingomyelin molecules in bilayers for the L alpha and L beta' phases. The resulting line shapes have been analysed in terms of a reduced-parameter model, using van Faassen's method for obtaining an analytic solution to first-order stochastic differential equations to simulate the line shapes of oriented and non-oriented samples. Our treatment results in good fits to measured data but using fewer parameters than traditional methods. Angles and correlation times (tau parallel and tau perpendicular) describing the geometry and dynamics of the headgroup are obtained by optimising the agreement between simulated and experimental data. The results are contrasted with those obtained for the lecithins DMPC and DPPC using a similar analysis. Not only are tau parallel and tau perpendicular now equal in value for the L alpha phase, but this value is also found to be nearly four times larger than the longest correlation time for the lecithins. We interpret this as evidence of inter- and intramolecular hydrogen bonding in the L(alpha) phase of sphingomyelin. In the L beta' phase of sphingomyelin, however, although tau(parallel) and tau(perpendicular) remain equal their value is now 32% smaller than that of the lecithins in the same phase. This indicates less difference between the fluidities in the headgroup region of the two phases of sphingomyelin as compared to that of the lecithins. Another significant difference between the L beta' phases is that the tilt angle for sphingomyelin is found to be nearly twice as large as for the lecithins. We argue that these combined observations point to the existence of hydrogen bonding in this phase also. Again in contrast to our previous work on lecithins, our results provide evidence of a negative diamagnetic anisotropy in sphingomyelin molecules, even in the L beta' phase. This is provided for in our model by the assumption that our unoriented samples consist of prolate ellipsoidal liposomes whose major axes are oriented parallel to the static magnetic field. The apparently different diamagnetic behaviour of sphingomyelin in the present work is due to the higher static field used rather than any intrinsic difference in this respect between sphingomyelin and the lecithins DMPC and DPPC.     

Effect of material stiffness on hardness: A computational study based on model potentials

We investigate the dependence of the hardness of materials on their elastic stiffness. This is possible by constructing a series of model potentials of Morse type; starting with modelling natural Cu, the model potentials exhibit an increased elastic modulus, while keeping all other potential parameters (lattice constant, bond energy) unchanged. Using molecular-dynamics simulation, we perform nanoindentation experiments on these model crystals. We find that the crystal hardness scales with the elastic stiffness. Also the load drop, which is experienced when plasticity sets in, increases in proportion to the elastic stiffness, while the yield point, i.e. the indentation at which plasticity sets in, is independent of the elastic stiffness.