Intermolecular complexes of nido-C<Subscript>2</Subscript>B<Subscript>3</Subscript>H<Subscript>7</Subscript> with HF and LiH molecules: the theoretical studies,bonding properties and natural bond orbital (NBO) analysis

The changes in stabilization energy upon the formation of intermolecular hydrogen, dihydrogen and lithium bond complexes between C₂B₃H₇, LiH and HF have been investigated using MP2 method with aug-cc-pVDZ basis set. The interaction of HF with nido-C₂B₃H₇ could occur through the formation of B–H^?δ···^+δH–F, C–H^+δ···F^?δ–H and B–C···H–F classical and non-classical hydrogen bonds. The B–C bonds in backbone of the C₂B₃H₇ as electron donor interact with σ* orbital of HF as electron acceptor. Also interaction of LiH with nido-C₂B₃H₇ resulted in B–C···Li–H and B–H···LiH lithium bonds as well as C–H···H–Li dihydrogen bond complexes. In some of these complexes, LiH interacts with B–C bonds. Results are indicating that more stable complexes belong to interaction of HF and LiH with backbone of the nido-C₂B₃H₇. The AIM and NBO methods were used to analyze the intermolecular interactions; also the electron density at the bond critical point and the charge transfer of obtained complexes were studied.     

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.     

Density Functional Theory Study of Hydrogen Bonding Dimers with 4-Pyridinecarboxylic Acid Hydrazine

The H‐bonding dimers of 4‐pyridinecarboxylic acid hydrazine were studied using density functional theory (DFT) at B3LYP/6‐311++G** level. The results showed that the most stable dimer D1 had two same linear N H···O hydrogen bonds, and the interaction energy between them was 51.038 kJ·mol⁻¹ which was corrected by the basis set superposition error and zero‐point. The stretching vibration frequency of N H bond had a red shift because of the hydrogen bonds. The natural bond orbital analysis showed that each N H···O hydrogen bond in D1 had the biggest interaction stabilization energy of 69.078 kJ·mol⁻¹. Thermodynamic analysis indicated that the formation process of D1 was exothermic and spontaneous at low and room temperatures.     

Synthesis and crystal structure of 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate

The compound 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate has been prepared and characterized by IR, ¹H NMR, ¹³C NMR and mass spectra. The crystal and molecular structure were further confirmed using single crystal X-ray diffraction. The crystal structure has been found to be stabilized by intermolecular C–H···O interaction generating bifurcated hydrogen bonds whereas the C–H···N interactions generate chain of molecules. The intramolecular N–H···N hydrogen bond forms a ring with S(7) graph-set motif.     

4-羟甲基吡啶－水红移氢键的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-311++G**基函数对4-羟甲基吡啶与水形成的1:1和1:2（摩尔比）氢键复合物进行了理论计算研究,分别得到稳定的4-羟甲基吡啶－H₂O和4-羟甲基吡啶－(H₂O)₂氢键复合物3个和8个。经基组重叠误差和零点振动能校正后,最稳定的1:1和1:2氢键复合物的相互作用能分别为-20.536和-44.246 kJ/mol。振动分析显示O-H···N(O)氢键的形成使复合物中O-H键对称伸缩振动频率红移(减小)。自然键轨道分析表明,4-羟甲基吡啶与水形成最稳定的1:1和1:2氢键复合物时,分子间电荷转移分别为0.02642 e 和0.03813 e 。含时密度泛函理论TD-B3LYP/ 6-311++G**计算显示,相对于4-羟甲基吡啶单体分子,氢键H-OH···N和H-OH···OH的形成分别使最大吸收光谱波长兰移8~16纳米和红移4~11纳米。     

GIAO,DFT, AIM and NBO analysis of the N?H···O intramolecular hydrogen‐bond influence on the 1J(N,H) coupling constant in push–pull diaminoenones

In the series of diaminoenones, large high‐frequency shifts of the ¹H NMR of the N? H group in the cis‐position relative to the carbonyl group suggests strong N? H···O intramolecular hydrogen bonding comprising a six‐membered chelate ring. The N? H···O hydrogen bond causes an increase of the ¹J(N,H) coupling constant by 2–4 Hz and high‐frequency shift of the ¹⁵N signal by 9–10 ppm despite of the lengthening of the relevant N? H bond. These experimental trends are substantiated by gauge‐independent atomic orbital and density functional theory calculations of the shielding and coupling constants in the 3,3‐bis(isopropylamino)‐1‐(aryl)prop‐2‐en‐1‐one (12) for conformations with the Z‐ and E‐orientations of the carbonyl group relative to the N? H group. The effects of the N? H···O hydrogen‐bond on the NMR parameters are analyzed with the atoms‐in‐molecules (AIM) and natural bond orbital (NBO) methods. The AIM method indicates a weakening of the N? H···O hydrogen bond as compared with that of 1,1‐di(pyrrol‐2‐yl)‐2‐formylethene (13) where N? H···O hydrogen bridge establishes a seven‐membered chelate ring, and the corresponding ¹J(N,H) coupling constant decreases. The NBO method reveals that the LP(O) →σ*_{N? H} hyperconjugative interaction is weakened on going from the six‐membered chelate ring to the seven‐membered one due to a more bent hydrogen bond in the former case. A dominating effect of the N? H bond rehybridization, owing to an electrostatic term in the hydrogen bonding, seems to provide an increase of the ¹J(N,H) value as a consequence of the N? H···O hydrogen bonding in the studied diaminoenones. Copyright © 2010 John Wiley & Sons, Ltd.     

Hydrogen‐bonded complexes of nicotine with simple alcohols

Ab initio and density functional theory studies have been performed on the hydrogen‐bonded complexes of neutral and protonated nicotine with ethanol, methanol, and trifluromethanol to explore their relative stability in a systematic way. Among all the hydrogen‐bonded nicotine complexes considered here, protonated forms in nicotine–ethanol and nicotine–methanol, and neutral form in nicotine–trifluromethanol complexes have been found to be the most stable. In the former two complexes, the proton attached to the pyrrolidine nitrogen acts as a strong hydrogen bond donor, whereas the pyrrolidine nitrogen atom acts as a hydrogen bond acceptor in the latter case. Neutral complex of nicotine with trifluromethanol has been found to possess a very short hydrogen bond (1.57 Å) and basis set superposition error corrected hydrogen bond energy value of 19 kcal/mol. The nature of the various hydrogen bonds formed has been investigated through topological aspects using Bader's atoms in molecules theory. From the calculated topological results, excellent linear correlation is shown to exist among the hydrogen bond length, electron density, and its Laplacian at the bond critical points for all the complexes considered. The natural bond orbital analysis has been carried out to investigate the charge transfer in the nicotine alcohol complexes. In contrast to the blue shifting behavior that is generally exhibited by other C? H···O hydrogen bonds involving sp³ carbon atom, the C? H···O hydrogen bond in the protonated nicotine–ethanol and methanol complexes has been found to be proper with red shifting in nature. © 2011 Wiley Periodicals, Inc.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Intermolecular interactions in uracil–nitrous acid complexes: structures,binding energy,topological properties,and nuclear magnetic resonance study

Molecular interactions between uracil and nitrous acid (U–NA) [C₄N₂O₂H₄? NO₂H] have been studied using B3LYP, B3PW91, and MP2 methods with different basis sets. The optimized geometries, harmonic vibrational frequencies, charge transfer, topological properties of electron density, nucleus‐independent chemical shift (NICS), and nuclear magnetic resonance one‐ and two‐bonds spin–spin coupling constants were calculated for U–NA complexes. In interaction between U and NA, eight cyclic complexes were obtained with two intermolecular hydrogen bonds N(C)HU…N(O) and OH_NA…O_U. In these complexes, uracil (U) simultaneously acts as proton acceptor and proton donor. The most stable complexes labeled, UNA1 and UNA2, are formed via NH bond of U with highest acidity and CO group of U with lowest proton affinity. There is a relationship between hydrogen bond distances and the corresponding frequency shifts. The solvent effect on complexes stability was examined using B3LYP method with the aug‐cc‐pVDZ basis set by applying the polarizable continuum model (PCM). The binding energies in the gas phase have also been compared with solvation energies computed using the PCM. Natural bond orbital analysis shows that in all complexes, the charge transfer takes place from U to NA. The results predict that the Lone Pair (LP)(O)_U → σ*(O? H) and LP(N(O)_NA → σ*(N(C)? H)_U donor–acceptor interactions are most important interactions in these complexes. Atom in molecule analysis confirms that hydrogen bond contacts are electrostatic in nature and covalent nature of proton donor groups decreases upon complexation. The relationship between spin–spin coupling constant (^1hJ_H…_Y and ^2hJ_H…_Y) with interaction energy and electronic density at corresponding hydrogen bond critical points and H‐bonds distances are investigated. NICS used for indicating of aromaticity of U ring upon complexation. © 2013 Wiley Periodicals, Inc.     

Time‐dependent density functional theory study on the electronic excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in aqueous solution: 4AP and 4AP–(H2O)1,2 clusters

The time‐dependent density functional theory (TDDFT) method has been carried out to investigate the excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in hydrogen‐donating water solvent. The infrared spectra of the hydrogen‐bonded solute?solvent complexes in electronically excited state have been calculated using the TDDFT method. We have demonstrated that the intermolecular hydrogen bond C? O···H? O and N? H···O? H in the hydrogen‐bonded 4AP?(H₂O)₂ trimer are significantly strengthened in the electronically excited state by theoretically monitoring the changes of the bond lengths of hydrogen bonds and hydrogen‐bonding groups in different electronic states. The hydrogen bonds strengthening in the electronically excited state are confirmed because the calculated stretching vibrational modes of the hydrogen bonding C?O, amino N? H, and H? O groups are markedly red‐shifted upon photoexcitation. The calculated results are consistent with the mechanism of the hydrogen bond strengthening in the electronically excited state, while contrast with mechanism of hydrogen bond cleavage. Furthermore, we believe that the transient hydrogen bond strengthening behavior in electroniclly excited state of chromophores in hydrogen‐donating solvents exists in many other systems in solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

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     

Hydrogen Bonding Interaction of Formic Acid-, Formaldehyde-, Formylfluoride-Nitrosyl Hydride： Theoretical Study on the Geometries, Interaction Energies and Blue- or Red-Shifted Hydrogen Bonds

The hydrogen bonding interaction of formic acid-, formaldehyde-, formylfluoride-nitrosyl hydride complexes was investigated by the density functional theory （DFT） and ab inito method in conjunction with 6-311＋＋G（2d,2p） basis set. The geometries, vibrational frequencies and interaction energies of the complexes were calculated by both standard and CP-corrected methods respectively. Moreover, G3B3 method was employed to estimate the interaction energies. There are C--H…O, N--H…O, N--H…F blue-shifted H-bonds and red-shifted O----H…O H-bond in the complexes. Electron density redistribution and rehybridization contribute to the N--H and C--H blue shifts. All geometric reorganizations contribute to the N--H blue shifts and partial geometric reorganizations contribute to the C--H blue shifts. The geometric reorganizations of the complex C except ZH（5）-O（4）-C（1） contribute to the O----H red shift. For the N--H blue shifts, the effect of r（N--O） variation on the N--H blue shifts is larger than that of ZH-N-O variation. Rehybridization plays a dominant role in the degree of N--H blue shifts, whereas the electron density redistribution contributes more to the degree of C--H blue shifts than the other effects do.     

TD-DFT Study on the Excited-State Hydrogen Bonding of the p-Cresol–NH3–H2O Complex

In this work, the time-dependent density functional theory (TD-DFT) method was used to study the electronic excited-state dynamics of the hydrogen-bonded p-Cresol–NH₃–H₂O complex. The intermolecular hydrogen bonds O₁–H₁···N and C–O₁···H₂ were demonstrated by the optimized geometric structure of the hydrogen-bonded p-Cresol–NH₃–H₂O complex. The infrared spectra (IR spectra) of the hydrogen-bonded p-Cresol–NH₃–H₂O complex in the ground and excited states were also calculated by using the density functional theory (DFT) and TD-DFT methods. It is demonstrated that hydrogen bond O₁–H₁···N can be strengthened while hydrogen bond C–O₁···H₂ is weakened upon photoexcitation to the S₁ state. The significant changes of the hydrogen bond from the calculated bond lengths in different electronic states can be observed. In addition, the spectral shifts of the stretching vibrational mode of the hydrogen-bonded O–H group in different electronic states are accounted for the hydrogen bond changes in the S₁ state too.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Time-Dependent Density Functional Theory Study on Hydrogen and Dihydrogen Bonding in Electronically Excited State of 2-Pyridone–Borane–Trimethylamine Cluster

In this work, the intermolecular dihydrogen and hydrogen bonding interactions in electronically excited states of a 2-pyridone (2PY)–borane–trimethylamine (BTMA) cluster have been theoretically studied using time-dependent density functional theory method. Our computational results show that the S₁ state of 2PY–BTMA cluster is a locally excited state, in which only 2PY moiety is electronically excited. The theoretical infrared (IR) spectra of the 2PY–BTMA cluster demonstrate that the N–H stretching vibrational mode is slightly blue-shifted upon the electronic excitation. Moreover, the computed IR spectrum of the 2PY–BTMA cluster exhibits no carbonyl character due to the extension of the C=O bond length in the S₁ state. However, the N–H bond is shortened slightly upon photoexcitation. At the same time, the H···H and H···O distances are obviously lengthened in the S₁ sate by comparison with those in ground state. In addition, the electron density of the carbonyl oxygen is diminished due to the electronic excitation. Consequently, the proton acceptor ability of carbonyl oxygen is decreased in the electronic excited state. As a result, it is demonstrated that the intermolecular dihydrogen and hydrogen bonds are significantly weakened in the electronically excited state.     

Revealing substituent effects on the concerted interaction of pnicogen, chalcogen, and halogen bonds in substituted s-triazine ring

Quantum chemical calculations have been performed to gauge the effect of substituents on concerted interactions of pnicogen, chalcogen, and halogen bonds in the X–TAZ···Y complexes (X = CN, F, Cl, Br, H, CH₃, OH, and NH₂, where TAZ and Y denote s-triazine ring and P, S, and Cl atoms, respectively) at the M06-2X/aug-cc-pVDZ level. The mutual interplay of these interactions is also investigated. The results indicate that diminutive effects are observed when the three kinds of noncovalent interactions pnicogen, chalcogen, and halogen bonds are coexisted in the complexes. These effects are studied in terms of energetic and geometric features of the complexes. In addition, Bader’s theory of “atoms in molecules” is used to analyze their strength of varying electron density at bond critical points. Natural bond orbital (NBO) theory is used to characterize the orbital interactions. The results indicate that the electron-withdrawing/donating substituents decrease/increase the magnitude of the binding energies compared to the unsubstituted X–TAZ···Y (X = H) complex. Good correlations among binding energies, Hammett constants, geometrical, atoms in molecular and NBO parameters are established in X–TAZ···Y complexes. By taking advantage of all the aforementioned computational methods, this study examines how these interactions mutually influence each other.     

Synthesis and Characterization of Organotin Compounds of a New Schiff Base Ligand with α‐Oxoglutaric Acid Isonicotinyl Hydrazone

Organotin compounds are a recurring motif in organometallic chemistry. The syntheses and characterization of new diorganotin compounds with α‐oxoglutaric acid isonicotinyl hydrazone are described, prepared compounds were characterized by elemental analysis, UV/Vis, ¹H, and ¹³C NMR spectroscopy, and X‐ray diffraction. They both have a distorted pentagonal bipyramidal arrangement, with a heptacoordinated central tin atom. Compound 1 presents a centrosymmetric dinuclear framework. Interestingly, intermolecular O–H ··· N and O–H ··· O hydrogen bonds contribute to the two‐dimensional network. Compound 2 is a simple mononuclear compound, which exhibits a rare one‐dimensional chain constructed by intermolecular O–H ··· Cl and N–H ··· O hydrogen bonds.     

Hydrogen bonding characterization of XH2NH2···HNO(X = B,Al, Ga) complexes: A theoretical investigation

The complexes of XH₂NH₂···HNO(X = B, Al, Ga) are characterized as head to tail with hydrogen bonding interactions. The structural characteristics can be confirmed by atoms in molecules (AIM) analysis, which also provide comparisons of hydrogen bonds strengths. The calculated interaction energies at G2MP2 level show that stability of complexes decrease as BH₂NH₂···HNO > AlH₂NH₂···HNO > GaH₂NH₂···HNO. On the basis of the vibrational frequencies calculations, there are red‐shifts for ν(X1? H) and blue‐shifts for ν(N? H) in the complexes on dihydrogen bonding formations (X1? H···H? N). On hydrogen bonding formations (N? H···O), there are red‐shifts for ν(N? H) compared to the monomers. Natural bond orbital (NBO) analysis is used to discuss the reasons for the ν(X1? H) and ν(N? H) stretching vibrational shifts by hyperconjugation, electron density redistribution, and rehybridization. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008