H2O, H2S与双卤分子间相互作用的电子密度拓扑研究

运用量子化学微扰理论MP2和密度泛函B3LYP方法, 采用6-311＋＋G(d,p)基组, 对H₂O, H₂S与双卤分子XY (XY＝F₂, Cl₂, Br₂, ClF, BrF, BrCl)形成的卤键复合物进行构型全优化, 并计算得到了这些体系的分子间相互作用能. 利用电子密度拓扑分析方法对卤键复合物的拓扑性质进行了分析研究, 探讨了该类分子间卤键的作用本质. 结果表明, 形成卤键后, 作为电子受体的双卤分子X—Y键长增长, 振动频率减小. 复合物体系中的卤键介于共价键与离子键之间, 偏于静电作用成分为主.     

Halogen bonding with the halogenabenzene bird structure,halobenzene, and halocyclopentadiene

The ability of the “bird-like” halogenabenzene molecule, referred to as X-bird (XCl to At), to form halogen-bonded complexes with the nucleophiles H₂O and NH₃ was investigated using double-hybrid density functional theory and the aug-cc-pVTZ/aug-cc-pVTZ-PP basis set. The structures and interaction energies were compared with 5-halocyclopenta-1,3-diene (halocyclopentadiene; an isomer of halogenabenzene) and halobenzene, also complexed with H₂O and NH₃. The unusual structure of the X-bird, with the halogen bonded to two carbon atoms, results in two distinct σ-holes, roughly at the extension of the C-X bonds. Based on the behavior of the interaction energy (which increases for heavier halogens) and van der Waals (vdW) ratio (which decreases for heavier halogens), it is concluded that the X-bird forms proper halogen bonds with H₂O and NH₃. The interaction energies are larger than those of the halogen-bonded complexes involving halobenzene and halocyclopentadiene, presumably due to the presence of a secondary interaction. © 2019 Wiley Periodicals, Inc.     

3-硝基-1,2,4-三唑-5-酮与NH3及H2O分子间相互作用的理论研究

在DFT-B3LYP/6-311＋＋G**水平上, 求得3-硝基-1,2,4-三唑-5-酮(NTO)/NH₃和NTO/H₂O两种超分子体系势能面上5种全优化构型. 经基组叠加误差(BSSE)和零点能(ZPE)校正, 求得NTO与NH₃和H₂O的分子间最大相互作用能依次为－37.58和－30.14 kJ/mol, 表明NTO与NH₃的分子间相互作用强于与H₂O的作用. 超分子体系中电子均由NH₃或H₂O向NTO转移, 相互作用能主要由强氢键所贡献, 由自然键轨道分析揭示了相互作用的本质. 对优化构型进行振动分析, 并基于统计热力学求得200.0～800.0 K温度范围从单体形成超分子的热力学性质变化. 发现由NTO和NH₃形成超分子II和III在常温下可自发进行; 而NTO和H₂O只在低温下才能自发形成IV, V和VI超分子.     

Treatment of hydrogen bonding within CNDO/2 and MINDO/3: CNDO/2H and MINDO/3H

A formalism has been developed to treat hydrogen-bonded A—H…?B systems within the CNDO /2 and the MINDO /3 methodologies. In this formalism the interactions are divided into three distinct classes; those between (a) two hydrogen-bonded atoms, (b) one hydrogen-bonded and non-hydrogen-bonded atom, and (c) two non-hydrogen-bonded atoms. The last class of interactions is treated solely by the existing CNDO /2 or MINDO /3 method. For A –H…?B systems, the core resonance integrals are individually parametrized depending upon the class of the interaction. Three types of A—H…?B systems have been thus far parametrized. Nine hydrogen-bonded dimers have been studied using the new formalism and the current CNDO /2 and the MINDO /3 methods. MINDO /3 predicts very large interatomic (A –B) distances for the equilibrium geometry, and relatively small stabilization values for the hydrogen-bond energies. CNDO/2 predicts the reverse. The new formalism for both CNDO /2 and MINDO /3 predicts accurate geometries as well as energies for all nine dimers. The new formalisms are called CNDO /2H and MINDO /3H. A general discussion of the nature of hydrogen bonding as exhibited by CNDO /2H and MINDO /3H is presented.     

Theoretical study on intermolecular interactions between furan and dihalogen molecules XY(X,Y=F,Cl,Br)

Equilibrium geometries, interaction energies, atomic charge, and charge transfer for the intermolecular interactions between furan and dihalogen molecules XY(X; Y=F,Cl,Br) were studied at the MP2aug-cc-pVDZ level. Three types of geometry are observed in these interactions: the pi-type geometry (I), in which the XY lies above the furan ring and almost perpendicularly to the C4-C5 bond of furan; the sigma-type geometry (II), where the X atom is pointed toward the nonbonding electron pair (n pair) of oxygen atom in furan; and the chi-type geometry (III), describing a blueshift hydrogen bond formed between the hydrogen atom of furan and dihalogen molecules XY. The calculated interaction energies show that the pi-type structures are more stable than the corresponding sigma-type and chi-type structures. To study the nature of the intermolecular interactions, an energy decomposition analysis was carried out and the results indicate that both the pi-type and sigma-type interactions are dominantly inductive energy in nature, while dispersion energy governs the chi-type interactions.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

Time-Dependent Density Functional Theory Study on Excited-State Hydrogen Bonding Dynamics of Acetic Acid Hydrates

The time-dependent density functional theory (TDDFT) method was performed to investigate the hydrogen-bonding dynamics of acetic acid (AA) hydrates in aqueous solution. For AA, it tends to be both active hydrogen acceptor and donor and denote double H-bonds as O_A···H_W and H_A···O_W, resulting in ring structure hydrates. The ground-state geometry optimizations and electronic transition energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated AA monomer and the hydrogen-bonded ring structure hydrates are calculated by the density functional theory and TDDFT methods, respectively. Different types of intermolecular hydrogen bonds are formed between one AA molecule and water molecules. According to Zhao’s rule on the excited-state hydrogen bonding dynamics, it can be found that the intermolecular hydrogen bonds O_A···H_W and H_A···O_W are strengthened in electronically excited states of the hydrogen-bonded ring structure hydrates, with the excitation energy of a related excited state being lowered and electronic spectral redshifts being induced. Moreover, the hydrogen bond strengthening in the electronically excited state is crucial to the photophysics and photochemistry of hydrates with AA in aqueous solution.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.     

Density Functional Theory Studies on Intermolecular Interactions of 4‐Amino‐3,5‐dinitropyrazole with NH3 and H2O

Density functional theory (DFT) method with 6‐311++G** basis set was applied to study intermolecular interactions of 4‐amino‐3,5‐dinitropyrazole (LLM‐116)/NH₃ and LLM‐116/H₂O supermolecules. Four optimized stable supermolecules were found on the potential energy surface. The intermolecular interaction energy was calculated with basis set superposition error (BSSE) correction and zero point energy (ZPE) correction. The greatest corrected intermolecular interaction energies of LLM‐116/NH₃ and LLM‐116/H₂O supermolecules are –42.75 and –19.09 kJ×mol^‐1 respectively, indicating that the intensity of interaction between LLM‐116 and NH₃ is stronger than that of LLM‐116/H₂O. The intermolecular interaction is an exothermic process accompanied by a decrease in the probability of supermolecules formation, and the interactions become weak as temperature increase. Natural bond orbital (NBO) analysis was performed to reveal the origin of interaction. The IR spectra were obtained and assigned by vibrational analysis. Based on vibrational analysis, the changes of thermodynamic properties from LLM‐116 to supermolecules with temperature ranging from 200.0 to 400.0 K were obtained using statistical thermodynamic method.     

The energy parameters of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane polymorphs and their phase transitions

The calculated dispersion and electrostatic intermolecular interaction energies in crystals of γ, α(H₂O), and ? polymorphs of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazawurtzitane (HNIW) were compared. Preliminarily, nonempirical quantum-chemical calculations of the three compounds with complete geometry optimization were performed using the GAUSSIAN-03 package and density functional theory. The dispersion intermolecular interaction energy was calculated with the “6-exp” potential. The van der Waals and dipole-dipole interaction energies were substantially different in crystals of different HNIW polymorphs, but total energy changes in phase transitions were close to zero. The calculated ? > γ and α(H₂O) > γ phase transition energies were close to the experimental values determined using a differential calorimeter. Dehydration substantially influenced the kinetics and heat effects of polymorphic transitions.     

Analysis of the structures,energetics, and vibrational frequencies for the hydrogen-bonded interaction of nucleic acid bases with Carmustine pharmaceutical agent: a detailed computational approach

In the present study, it is attempted to scrutinize the hydrogen bonding interaction between Carmustine drug and DNA pyrimidine bases by means of density functional theory calculations regarding their geometries, binding energies, vibrational frequencies, and topological features of the electron density in the gas phase and the water solution. Based on the density functional theory results, it is found that the process of intermolecular interaction between Carmustine drug and nucleobases is exothermic and all of the optimized configurations are stable. Furthermore, the negative stability energy represented by a polarizable continuum model shows the significant increase in the solubility of the nucleobase after hydrogen bonding intermolecular interaction in the presence of water solvent. It is also found that the intermolecular hydrogen bonds between drug and the nucleobases play the significant role in the stability of the physisorption configurations. Hydrogen bond energies for hydrogen-bonded complexes are obtained from Espinosa method and the atoms-in-molecules theory are also applied to get a more precise insight into the nature of the intermolecular hydrogen bond interactions.     

Coupling Interactions between Sulfurous Acid and the Hydroperoxyl Radical

Radical–molecule complexes associated with the hydroperoxyl radical (HOO) play an important role in atmospheric chemistry. Herein, the nature of the coupling interactions between sulfurous acid (H₂SO₃) and the HOO radical is systematically investigated at the B3LYP/6‐311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, the natural bond orbital (NBO) method, and energy decomposition analyses (EDA). Eight stable stationary points possessing double H‐bonding features were located on the H₂SO₃???HOO potential energy surface. The largest binding energies of ?12.27 and ?11.72 kcal mol^?1 are observed for the two most stable complexes, where both of them possess strong double intermolecular H‐bonds of partially covalence. Moreover, the characteristics of the IR spectra for the two most stable complexes are discussed to provide some help for their possible experimental identification.     

How does halogen bonding behave in solution? A theoretical study using implicit solvation model

A systematic study of halogen bonding interactions in gas phase and in solution was carried out by means of quantum chemical DFT/B3LYP method. Three solvents with different polarities (chloroform, acetone, and water) were selected, and solvation effects were considered using the polarized continuum model (PCM). For charged halogen-bonded complexes, the strength of the interactions tends to significantly weaken in solution, with a concomitant elongation of intermolecular distances. For neutral systems, halogen bond distances are shown to shorten and the interaction energies change slightly. Computations also reveal that in the gas phase the binding affinities decrease in the order Cl(-) > Br(-) > I(-), while in solution the energy gaps of binding appear limited for the three halide anions. According to free energy results, many systems under investigation are stable in solution. Particularly, calculated free energies of formation of the complexes correlate well with halogen-bonding association constants determined experimentally. The differences of the effects of solvent upon halogen and hydrogen bonding were also elucidated. This study can establish fundamental characteristics of halogen bonding in media, which would be very helpful for applying this noncovalent interaction in medicinal chemistry and material design.     

π-Complexation and C—H hydrogen bonding in the formation of colored cocrystals

The present study evaluates the potential combination of charge-transfer electron-donor–acceptor π–π complexation and C—H hydrogen bonding to form colored cocrystals. The crystal structures of the red 1:1 cocrystals formed from the isomeric pyridines 4- and 3-{2-[4-(dimethylamino)phenyl]ethynyl}pyridine with 1-[2-(3,5-dinitrophenyl)ethynyl]-2,3,5,6-tetrafluorobenzene, both C₁₄H₄F₄N₂O₄·C₁₅H₁₄N₂, are reported. Intermolecular interaction energy calculations confirm that π-stacking interactions dominate the intermolecular interactions within each crystal structure. The close contacts revealed by Hirshfeld surface calculations are predominantly C—H interactions with N, O, and F atoms.     

Theoretical Investigations on the Interaction Nature of Br2 with HF, H2O and NH3

The interactions of HF, H2O and NH3 with Br2 are investigated at the MP2(full)/ aug-cc-pVDZ level. It is found that two kinds of stable complexes, halogen-bonded and hydrogen- bonded complexes, exist between Br2 and HF and between Br2 and H2O. The interaction energy analysis and natural population analysis (NPA) are conducted to these two kinds of complexes, indicating the halogen-bonded complexes are more stable than the corresponding hydrogen-bonded ones, and the binding energies of the former increase in the order HFH2O for the latter.     

Polymorphism of 3‐(5‐phenyl‐1,3,4‐oxadiazol‐2‐yl)‐ and 3‐[5‐(pyridin‐4‐yl)‐1,3,4‐oxadiazol‐2‐yl]‐2H‐chromen‐2‐ones

This study of 3‐(5‐phenyl‐1,3,4‐oxadiazol‐2‐yl)‐2H‐chromen‐2‐one, C₁₇H₁₀N₂O₃, 1 , and 3‐[5‐(pyridin‐4‐yl)‐1,3,4‐oxadiazol‐2‐yl]‐2H‐chromen‐2‐one, C₁₆H₉N₃O₃, 2 , was performed on the assumption of the potential anticancer activity of the compounds. Three polymorphic structures for 1 and two polymorphic structures for 2 have been studied thoroughly. The strongest intermolecular interaction is stacking of the `head‐to‐head' type in all the studied crystals. The polymorphic structures of 1 differ with respect to the intermolecular interactions between stacked columns. Two of the polymorphs have a columnar or double columnar type of crystal organization, while the third polymorphic structure can be classified as columnar‐layered. The difference between the two structures of 2 is less pronounced. Both crystals can be considered as having very similar arrangements of neighbouring columns. The formation of polymorphic modifications is caused by a subtle balance of very weak intermolecular interactions and packing differences can be identified only using an analysis based on a study of the pairwise interaction energies.     

Study on the nature of interaction of thiophene with various hydrides

The nature of interactions of thiophene with various hydrides (Y) (Y = HF, HCl, H₂O, H₂S, NH₃, PH₃) is investigated using ab initio calculations. In contrast with the previous results on similar furan complexes, only the π-type is observed for the thiophene complexes. Variations in complexes geometry can be accounted for by the differences in the electrostatic potential on the aromatic ring. To further study the nature of the intermolecular interactions, an SAPT (the symmetry-adapted perturbation theory) energy decomposition analysis was carried out and the results indicate that the dispersion and electrostatic interactions dominate the thiophene complexes.     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011