Ab initio study of the structure,cooperativity, and vibrational properties in the mixed hydrogen‐bonded trimers of hydrogen isocyanide and water

The five trimers of H₂O···HNC···H₂O, H₂O···H₂O···HNC, HNC···H₂O···H₂O, H₂O···HNC···HNC, and HNC···HNC···H₂O have been studied with quantum chemical calculations. Their structures, harmonic vibrational frequencies and interaction energies have been calculated at the B3LYP and MP2 levels with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets. The cooperative effect on these properties has also been studied quantitatively. For HNC:(H₂O)₂ systems, the cyclic H₂O···H₂O···HNC trimer is most stable with an interaction energy of ?16.01 kcal/mol and a large cooperative energy of ?3.25 kcal/mol at the MP2/aug‐cc‐pVTZ level. For H₂O:(HNC)₂ systems, the interaction energy and cooperative energy in the H₂O···HNC···HNC trimer are larger than those in the HNC···HNC···H₂O trimer. The NH stretch frequency has a blue shift for the terminal HNC molecule in the HNC···H₂O···H₂O and HNC···HNC···H₂O trimers and a red shift in other cases. A many‐body analysis has also been performed to understand the interaction energies in these hydrogen‐bonded clusters. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical Study of the Interplay between Lithium Bond and Hydrogen Bond in Complexes Involved with HLi and HCN

The lithium‐ and hydrogen‐bonded complex of HLi? NCH? NCH is studied with ab initio calculations. The optimized structure, vibrational frequencies, and binding energy are calculated at the MP2 level with 6‐311++G(2d,2p) basis set. The interplay between lithium bonding and hydrogen bonding in the complex is investigated with these properties. The effect of lithium bonding on the properties of hydrogen bonding is larger than that of hydrogen bonding on the properties of lithium bonding. In the trimer, the binding energies are increased by about 19 % and 61 % for the lithium and hydrogen bonds, respectively. A big cooperative energy (?5.50 kcal mol^?1) is observed in the complex. Both the charge transfer and induction effect due to the electrostatic interaction are responsible for the cooperativity in the trimer. The effect of HCN chain length on the lithium bonding has been considered. The natural bond orbital and atoms in molecules analyses indicate that the electrostatic force plays a main role in the lithium bonding. A many‐body interaction analysis has also been performed for HLi? (NCH)_N (N=2–5) systems.     

New equation for calculating total interaction energy in one noncyclic ABC triad and new insights into cooperativity of noncovalent bonds

In this work, a new equation consist of A???B, B???C, A???BC, and AB???C interactions is proposed for calculating the total interaction energy of noncyclic ABC triads. New equations are also proposed for calculating the changes in values of A???B and B???C interactions on the formation of triad from the corresponding dyads. The advantages of equations proposed here in comparison with many‐body interaction energy approach are discussed. All proposed equations were tested in F₃MLi???NCH???HLH and F₃MLi???HLH???HCN (M = C, Si; L = Be, Mg) as well as H₃N???XY???HF (X, Y = F, Cl, Br) noncyclic A???B???C triads. The data show that the total cooperativity of triad correlates well with the sum of the changes in values of A???B and B???C interactions calculated through new equations proposed here. © 2016 Wiley Periodicals, Inc.     

Influence of hydrogen bonds between sidechains and cooperativity on self‐assembly of the cyclopeptides

The self‐assembly of four cyclic D,L‐octapeptides, [‐(D‐Ala‐Gln)₄‐], [‐(D‐Val‐Gln)₄‐], [‐(D‐Leu‐Gln)₄‐], and [‐(D‐Phe‐Gln)₄‐], was investigated on the theory level in detail. Based on these cyclic peptides, which contain L‐Gln residues and possess C₄ symmetry, a series of oligomers were constructed according to different stacking modes as well as interaction patterns. We employed the semiempirical molecular orbital method AM1 to optimize the structures of all the oligomers, some of which were further studied using density functional method B3PW91/6‐31G to calculate the interaction energies. The studies indicate that when these cyclopeptides aggregate to form oligomers, or even nanotubes, four more hydrogen bonds could form between the sidechains of L‐Gln residues in addition to eight hydrogen bonds formed between the backbones of adjacent two cyclic peptides, a result that would clearly affect the self‐assembling process of cyclic peptides. The main effects can be summarized as follows. First, the dimers of these cyclic peptides with C₄ symmetry are more stable than those with D₄ symmetry due to their additional H‐bonds between Gln sidechains. Second, for the self‐assembly of the cyclopeptides, there is a competition between parallel and antiparallel stacking modes in lower oligomers such as dimers. However, with an increasing degree of oligomerization, energetically there is an increased possibility for the cyclic peptides to take the parallel stacking mode in assembly. Finally, the synergetic effect of weak interactions is the fundamental driving force for cyclic peptides to form stable nanotubes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Cooperativity of conventional and unconventional hydrogen bonds involving imidazole

Correlated ab initio calculations are used to investigate the cooperativity of H‐bonds between imidazole and a pair of water molecules. H‐bonds comprise not only the conventional NH … O and OH … N types, but also CH … O and OH … φ (wherein a proton is donated to the delocalized π cloud lying above the aromatic ring). Conventional and OH … φ H‐bonds obey the normal principles of cooperativity, wherein these bonds are strengthened when a central molecule serves simultaneously as both proton donor and acceptor. In contrast, CH … O bonds do not appear to be amenable to such positive cooperativity. When placed in a polarizable medium, all H‐bonds weaken as the dielectric constant of the solvent grows. The qualitative aspects of the cooperativity are not affected by the medium, although some weakening is observed. Calculations also consider the effects of cooperativity on other aspects of the complexes, including the intermolecular distance, the effect on the covalent X‐H bond length, and IR and NMR spectral data. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Interstitial water and the formation of low barrier hydrogen bonds: A computational model study

The B3LYP/D95+(d,p) analysis of the uncharged low barrier hydrogen bond (LBHB) between 4‐methyl‐1H‐imidazole (Mim) and acetic acid (HAc) shows that uncharged LBHBs can be formed either by adding three water molecules around the cluster or by placing the Mim–HAc pair in a dielectric environment created by a polarizable continuum model with a permittivity larger than 20.7. The permittivity of environment around uncharged LBHB can be lowered significantly by including water molecules into the system. A Mim–HAc LBHB stabilized with one water molecule observed in diethyl ether (ε = 4.34), with two water molecules in toluene (ε = 2.38), and with three water molecules in vacuo (ε = 1). Solvation models with different numbers of water molecules predict average differences in the proton affinities of the hydrogen bonded bases (ΔPA) for stable uncharged LBHB systems in vacuo to be 91.5 kcal/mol being different from the ΔPA values close to zero in charge‐assisted LBHB systems. The results clearly indicate that small amounts of interstitial water molecules at the active site of enzymes do not preclude the existence of LBHBs in biological catalysis. Our results also show that interstitial water molecules provide a useful clue in the search for uncharged LBHBs in an enzymatic environment and the number of water molecules can be used as a relative measure for the polarity around the direct environment of LBHBs. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Properties of the network of the hydrogen bonds of water

Networks of the hydrogen bonds and those consisting of lines connecting nearby molecules were constructed using configurations of water molecules obtained by the Monte-Carlo method. The concentrations of closed cycles of hydrogen bonds were established to be determined only by the probability of hydrogen bond formation. Characteristics of a model ideal water network were determined. Topological properties of the Polk model and those of the network of nearest neighbors substantially differ from the properties of the ideal network. The totality of the hydrogen bonds in pure water was proposed to be considered as a hierarchical system. Three topologically different structures of water associates were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 928–931, May, 1997.     

Theoretical study of chiral discrimination in the hydrogen bonding complexes of the hydrazine dimer

In this work, the discrimination of different chiral forms of the hydrazine dimer were investigated using Density Functional Theory (DFT) and second‐order Moller–Plesset Perturbation (MP2) theory at basis set levels from 6‐31g to 6‐31++g(d,p). Four chiral structures were studied. The optimized geometric parameters, interaction energies, and chirodiastatic energy for various isomers at different levels were estimated. Finally, the solvent effects on the geometries of the hydrazine dimers were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐31++g(d,p) level. The results indicate that the polarity of the solvent has played an important role in the structures and relative stabilities of different isomers. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study on the interactions of halogen‐bonds and pnicogen‐bonds in phosphine derivatives with Br2, BrCl,and BrF

The MP2 ab initio quantum chemistry methods were utilized to study the halogen‐bond and pnicogen‐bond system formed between PH₂X (X = Br, CH₃, OH, CN, NO₂, CF₃) and BrY (Y = Br, Cl, F). Calculated results show that all substituent can form halogen‐bond complexes while part substituent can form pnicogen‐bond complexes. Traditional, chlorine‐shared and ion‐pair halogen‐bonds complexes have been found with the different substituent X and Y. The halogen‐bonds are stronger than the related pnicogen‐bonds. For halogen‐bonds, strongly electronegative substituents which are connected to the Lewis acid can strengthen the bonds and significantly influenced the structures and properties of the compounds. In contrast, the substituents which connected to the Lewis bases can produce opposite effects. The interaction energies of halogen‐bonds are 2.56 to 32.06 kcal·mol^?1; The strongest halogen‐bond was found in the complex of PH₂OH???BrF. The interaction energies of pnicogen‐bonds are in the range 1.20 to 2.28 kcal·mol^?1; the strongest pnicogen‐bond was found in PH₂Br???Br₂ complex. The charge transfer of lp(P) ? σ*(Br? Y), lp(F) ? σ*(Br? P), and lp(Br) ? σ*(X? P) play important roles in the formation of the halogen‐bonds and pnicogen‐bonds, which lead to polarization of the monomers. The polarization caused by the halogen‐bond is more obvious than that by the pnicogen‐bond, resulting in that some halogen‐bonds having little covalent character. The symmetry adapted perturbation theory (SAPT) energy decomposition analysis showes that the halogen‐bond and pnicogen‐bond interactions are predominantly electrostatic and dispersion, respectively.     

Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case

Hydrogen bonding is not well described by available semiempirical theories. This is an important restriction because hydrogen bonds represent a key feature in many chemical and biochemical processes, besides being responsible for the singular properties of water. In this study, we describe a possible solution to this problem. The basic idea is to replace the nonphysical gaussian correction functions (GCF) appearing in the core–core repulsion terms of most MNDO‐based semiempirical methods by a simple function exhibiting the correct physical behavior in the whole range of intermolecular separation distances. The parameterized interaction function (PIF) is the sum of atom‐pair contributions, each one having five adjustable parameters. In this work, the approach is used to study water–water interactions. The parameters are optimized to reproduce a reference ab initio intermolecular energy surface for the water–water dimer obtained at the MP2/aug‐cc‐pVQZ level. OO, OH, and HH parameters are reported for the PM3 method. The results of PM3‐PIF calculations remarkably improve qualitatively and quantitatively those obtained at the standard PM3 level, both for water–dimer properties and for water clusters up to the hexamer. For example, the root‐mean‐square deviation of the PM3‐PIF interaction energies, with respect to ab initio values obtained using 700 points of the water dimer surface, is only 0.47 kcal/mol. This value is much smaller than that obtained using the standard PM3 method (4.2 kcal/mol). The PM3‐PIF water dimer energy minimum (−5.0 kcal/mol) is also much closer to ab initio data (−5.0±0.01 kcal/mol) than PM3 (−3.50 kcal/mol). The method is therefore promising for the development of new semiempirical approaches as well as for application of combined quantum mechanics and molecular mechanics techniques to investigate chemical processes in water. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 572–581, 2000     

Photochromism of diarylethenes linked by hydrogen bonds in the single-crystalline phase

Photochromic diarylethenes, which bear carboxyl groups at the ortho, meta, or para positions of both terminal phenyl groups, have been synthesized. The diarylethenes adopt linear chain structures as a result of hydrogen bonding in the crystalline phase, and the crystals exhibit photochromic properties. The absorption maximum of the photogenerated closed-ring isomer of the para-substituted derivative shows an 80 nm bathochromic shift in comparison with that of the ortho-substituted derivative. The maximum of the closed-ring isomer of the meta-substituted derivative is located in between those of the para- and ortho-substituted derivatives. The shifts can be attributed to the differences in conformation among the derivatives, arising from the restrictions imposed by the hydrogen-bonded chains.     

A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides,acetamides, and N‐methylformamides

A scheme is proposed in this article to predict the cooperativity in hydrogen bond chains of formamides, acetamides, and N‐methylformamides. The parameters needed in the scheme are derived from fitting to the hydrogen bonding energies of MP2/6‐31+G** with basis set superposition error (BSSE) correction of the hydrogen bond chains of formamides containing from two to eight monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in the chains of formamides containing 9 and 12 monomeric units, in the chains of acetamides containing from two to seven monomeric units, in the chains of N‐methylformamides containing from two to seven monomeric units. The calculation results show that the cooperativity predicted by the scheme proposed in this paper is in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, demonstrating that the scheme proposed in this article is reasonable. Based on our scheme, a cooperativity effect of almost 240% of the dimer hydrogen bonding energy in long hydrogen bond formamide chains, a cooperativity effect of almost 190% of the dimer hydrogen bonding energy in long hydrogen bond acetamide chains, and a cooperativity effect of almost 210% of the dimer hydrogen bonding energy in long hydrogen bond N‐methylformamide chains are predicted. The scheme is further applied to some heterogeneous chains containing formamide, acetamide, and N‐methylformamide. The individual hydrogen bonding energies in these heterogeneous chains predicted by our scheme are also in good agreement with those obtained from Møller‐Plesset calculations including BSSE correction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical study of salicylaldehyde conformal isomers and their intramolecular oxygen and hydrogen relations

To verify the semiempirical‐type localized hydrogen bonding analysis methods introduced by us several years ago, the intramolecular oxygen and hydrogen relations within salicylaldehyde are selected as the major topic in this theoretical study. The B3LYP/6‐31G** density functional method is chosen for both the full‐optimization and frequency‐type calculations. Four ortho‐type planar conformal isomers are proven to be local minima, and four internal rotation transition states are found by QST3‐type calculation. The special interpretations of  CHO and  OH characteristic frequencies, energy barriers, and thermal chemical results are discussed. In the semiempirical scheme, both local hydrogen bonding population analysis and localized hydrogen bond energy breaking procedures are applied to five pairs of related oxygen and hydrogen atoms in each isomer. The explanations for the strong or weak hydrogen bonds and intra‐CHO repulsion relationships are discussed. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 395–404, 1999     

Insights into the cooperativity between multiple interactions of dimethyl sulfoxide with carbon dioxide and water

Interactions of dimethyl sulfoxide with carbon dioxide and water molecules which induce 18 significantly stable complexes are thoroughly investigated. An addition of CO₂ or H₂O molecules into the DMSO⋯1CO₂ and DMSO⋯1H₂O systems leads to an increase in the stability of the resulting complexes, in which it is larger for a H₂O addition than a CO₂. The overall stabilization energy of the DMSO⋯1,2CO₂ is mainly contributed by the S=O⋯C Lewis acid–base interaction, whereas the O − H⋯O hydrogen bond plays a significant role in stabilizing complexes of DMSO⋯1,2H₂O and DMSO⋯1CO₂⋯1H₂O. Remarkably, the complexes of DMSO⋯2H₂O are found to be more stable than DMSO⋯1CO₂⋯1H₂O and DMSO⋯2CO₂. The level of the cooperativity of multiple interactions in ternary complexes tends to decrease in going from DMSO⋯2H₂O to DMSO⋯1CO₂⋯1H₂O and finally to DMSO⋯2CO₂. It is generally found that the red shift of the O − H bond involved in an O − H⋯O hydrogen bond increases while the blue shift of a C − H bond in a C − H⋯O hydrogen bond decreases when a cooperative effect occurs in ternary complexes as compared to those of the corresponding binary complexes. © 2018 Wiley Periodicals, Inc.     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Cu(100)表面吸附HCN和HNC的密度泛函研究

采用密度泛函方法，以原子簇Cul4为模拟表面，对氢氰酸(HCN)和异氰酸(HNC) 在Cu(100)表面上不同吸附位的吸附情况进行了研究．结果表明：HCN和HNC分别通 过原子N和C垂直吸附在表面上时，顶位是其最佳吸附位，且是吸附能为18．5kJ· mol^-1和42．6kJ·mol^-1的弱吸附，计算结果与实验相符．C—N(HCN)键或N—C (NHC)键偏离垂直的分子轴线的吸附体系均不稳定．顶位吸附时HCN和HNC分子的C- N键振动频率均发生蓝移．     

Theoretical study of the interaction of fluorinated dimethyl ethers and the ClF and HF molecules. Comparison between halogen and hydrogen bonds

A theoretical study of the halogen‐bonded complexes formed between fluorinated dimethyl ethers (n_F = 0–4) and ClF is carried out using the wB97XD method combined with the 6‐311++G(d,p) basis set. The properties of the complexes are compared with the corresponding properties of the hydrogen‐bonded complexes formed between the same electron donors and HF. The optimized geometries, the interaction energies, relevant natural bonding orbital characteristics along with some vibrational data are calculated. The analyzed properties also include the symmetry adapted perturbation theory decomposition of the energies along with the atoms‐in molecule analysis. For both the halogen and hydrogen bonds, the interaction energies are ruled by the intermolecular hyperconjugation energies. In contrast, the correlations between the binding energies and the basic properties of the ethers or the charge transfer are different for the halogen and hydrogen bonds. The applicability of the Bent's rule to these systems is discussed. © 2016 Wiley Periodicals, Inc.