HArF和HNO二聚体相互作用氢键的理论研究

用二阶微扰理论结合6-311+G**、6-311++G**和6-311++G(2d,2p)基组对氢键相互作用二聚体HNO···HArF进行研究．在MP2/6-311+G**、MP2/6-311++G**和MP2/6-311++G(2d,2p)水平上，利用标准方法和均衡校正方法对二聚体进行了几何优化、振动频率和相互作用能的计算．对于相互作用能采用G2MP2方法计算．计算结果表明存在两种稳定的二聚体HNO···HArF结构，在这两种结构中，Dimer I(H···F)比Dimer II(H···O)更加稳定．通过振动频率的计算表明，在Dimer I(H···F)中存在N-H···F蓝移氢键，在DimerII(H···O)中存在Ar-H···O红移氢键，并对蓝移氢键加以确认．利用电子密度拓扑学分析和自然键轨道分析对于氢键红移和蓝移进行了合理解释．     

HOX(X=F,Cl)二聚体红移氢键的理论研究

用理论方法研究了二聚体HOX(X=F,Cl)分子间氢键,在B3LYP/6-31+G(d,p)、 B3LYP/6-311++G(d,p)、MP2/6-31+G(d,p)和MP2/6-311++G(d,p)水平上,利用标准方法和均衡校正方法对二聚体进行了几何优化、振动频率和相互作用能的计算。同时,利用电子密度拓扑分析和自然键轨道分析对红移氢键的本质进行了分析。研究表明：分子间O—H…O和O—H…X(X=F,Cl)氢键的形成使二聚体中O—H键伸长,伸缩振动频率减小,形成红移氢键。NBO分析表明,电荷转移效应占优势,因此形成O—H…O和O—H…X(F,Cl)红移氢键。     

胞嘧啶-水分子氢键团簇结构特性理论研究

使用密度泛函理论B3LYP方法,在6-311++G(d,p)基组水平上,研究了C_4H_5N_3O·(H_2O)_n(n=1~3)分子团簇的基态结构及红外线光谱.通过对C_4H_5N_3O·(H2_O)n(n=1~3)分子团簇结构优化,获得了团簇的六种稳定结构.三种最稳定结构的分子团簇的红外光谱表明O—H…O和N—H…O氢键的形成使得O—H和N—H之间伸缩频率减小,发生了红移;O—H…N氢键使O—H之间的伸缩振动频率变大,发生了蓝移.AIM程序分析表明:电子密度ρ的强弱反映了红移和蓝移的大小.之后使用Veda4软件对C_4H_5N_3O·(H_2O)n(n=1~3)分子团簇红外光谱的振动频率进行了分析,并对振动频率进行了比较.     

腺嘌呤-水分子团簇结构与振动频率的理论研究

利用密度泛函理论在B3LYP/6-311++G(d,p)基组水平上对C_5H_5N_5·(H_2O)m(m=1~3)进行了优化与振动频率计算,得到了团簇的六种稳定结构.应用AIM程序计算了三种最稳定结构的氢键临界点的拓扑参数,结果表明,O—H…N氢键的形成使得O—H之间电子密度减小,伸缩振动频率减小,产生了红移;N—H…O氢键的形成使得N—H之间的电子密度减小,键的强度变弱,伸缩振动频率变小,发生了红移.利用veda4软件对团簇C_5H_5N_5·(H_2O)m(m=0~3)的红外光谱的振动频率进行模式指认,并对部分振动频率进行了比较.     

苯酚-水团簇C_6H_5OH(H_2O)_n(n=1-6)结构与电子性质的密度泛函理论研究

利用密度泛函理论,在B3LYP/6-31+G(d, p)基组水平上对苯酚-水团簇C_6H_5OH(H_2O)_n(n=1-6)的可能构型进行全优化,得到了团簇的稳定结构;在B3LYP/6-311++G(d, p)基组水平上计算得到了各团簇构型的总能量和结合能,结果显示,在团簇尺寸较小(n≤5)时,团簇C_6H_5OH(H_2O)_n的最稳定结构为平面的环状结构,团簇尺寸较大(n5)时,团簇C_6H_5OH(H_2O)_n的最稳定结构为三维立体结构.通过对团簇结合能的二阶差分、最高占据轨道与最低空轨道之间的能隙、费米能级和电离能的分析发现,团簇C_6H_5OH(H_2O)_2的最低能量结构具有较高的稳定性,可能具有幻数结构.     

HX与H_2O分子间氢键理论研究

在B3LYP/6-311++G~(**)水平上对H_2O与HX(F,C1,Br,I)分子间形成的(H_2O)_2HX和H_2O(HX)_2六元环氢键复合物的构型进行了全优化,频率计算表明,所有构型中O(2)—H(1),O(6)—H(5)及X(6)—H(5)的伸缩振动频率均发生红移,而对于X(4)—H(3)的伸缩振动频率在(H_2O)_2HF、(H_2O)_2HCl、H_2O(HF)_2体系中发生红移,在(H_2O)_2HBr、(H_2O)_2HI、H_2O(HCl)_2、H_2O(HBr)_2、H_2O(HI)_2体系中发生蓝移.在MP2/6-311++G~(**)水平上计算了体系的相互作用能,得到F、Cl、Br所形成的复合物其总相互作用能均为负值,而I形成的复合物其总相互作用能为正值.采用SCRF(PCM)方法研究了体系的溶剂化效应,结果表明溶剂化效应使复合物更稳定.自然键轨道(NBO))分析表明,复合物分子中的直接超共轭作用,导致了复合物中O(2)—H(1)、O(6)—H(5)及X(6)—H(5)键有所拉长,同时增加了复合物的稳定性.综合分析得到八种复合物的稳定性顺序为:H_2O(HF)_2(H_2O)_2HF(H_2O)_2HCl(H_2O)_2HBrH_2O(HCl)_2H_2O(HBr)_2(H_2O)_2HIH_2O(HI)_2.     

胸腺嘧啶-水分子团簇结构特性研究

根据量子化学理论,应用Gaussian09W程序中密度泛函理论(DFT)B3LYP方法,在6-311++G(d,p)基组水平上,研究了胸腺嘧啶与水分子团簇C_5H_6N_2O_2·(H_2O)n(n=1~4)分子团簇的基态结构以及红外光谱.通过对C_5H_6N_2O_2·(H_2O)n(n=1~4)分子团簇的结构优化,获得了团簇最稳定的结构.AIM程序分析表明:分子团簇间形成了氢键,而且电子密度ρ的强弱也反映了红移和蓝移的大小.之后使用Veda4软件对C_5H_6N_2O_2·(H_2O)n(n=1~4)分子团簇红外光谱的振动频率进行了分析,并对振动频率进行了比较.最后,分析四种最稳定结构的分子团簇的红外光谱表明O-H…O和N-H…O氢键的形成使得O-H和N-H之间伸缩频率减小,发生了红移;O-H…N氢键使O-H之间的弯曲振动频率变大,发生了蓝移.     

1,1,3,3-四甲基脲—溶剂氢键复合物的理论研究

采用密度泛函理论在B3LYP/6-311++G(d,p)水平上对水、苯胺、氯仿与1,1,3,3-四甲基脲分子形成的1:1气相氢键复合物进行计算研究.结果表明,三种物质与1,1,3,3-四甲基脲形成的复合物存在氢键,表现为羰基氧原子的孤对电子与H—X(X=O,N,C)反键轨道的相互作用.氢键的形成使C=O和H—X的伸缩振动频率红移.在标准压力和298.15 K下,氢键复合物的形成是一个放热的非自发过程.     

C6H5COOH⋯X分子间氢键的理论研究

在B3LYP/6-311++G(3df,2p)理论水平,计算研究C6H5COOH...X分子间氢键的理论研究(X=H2O, HCOH, CH3COCH3, NH3, CH2NH和HCN)氢键体系。获得氢键复合物稳定结构、氢键相互作用能、振动频率、热力学性质等。计算结果表明,C6H5COO—H...X体系存在较强的O—H...O与O—H...N红移氢键。C6H5COO—H...X氢键复合物气态分子的自发形成过程温度不同,C6H5COOH...NH3和C6H5COOH...CH2NH 体系在室温下能自发进行,其余二聚体要在低温下才能自发进行。     

C6H5COOH⋯X分子间氢键的理论研究

在B3LYP/6-311++G(3df,2p)理论水平,计算研究C6H5COOH...X分子间氢键的理论研究(X=H2O, HCOH, CH3COCH3, NH3, CH2NH和HCN)氢键体系。获得氢键复合物稳定结构、氢键相互作用能、振动频率、热力学性质等。计算结果表明,C6H5COO—H...X体系存在较强的O—H...O与O—H...N红移氢键。C6H5COO—H...X氢键复合物气态分子的自发形成过程温度不同,C6H5COOH...NH3和C6H5COOH...CH2NH 体系在室温下能自发进行,其余二聚体要在低温下才能自发进行。     

The prominent enhancing effect and mechanism of the methyl group in the X···Y (X=O,S, H3CO,H3CS, (H3C)2O, (H3C)2S; Y=HCN,HNC) hydrogen-bonded complex

An ab initio computational study of the enhancing role of the methyl group in the M···H (M=S and O) hydrogen bond has been carried out at the QCISD/6-311++G(2df,2p) level. The bond lengths, frequency shifts, and interaction energies were analysed. The methyl group of the electron donor plays a positive role in the formation of the hydrogen bond. Its enhancing role is stronger in the O···H hydrogen bond than in the S···H hydrogen bond. The results show that the methyl group has a prominent effect on the strength of the hydrogen bond. The interaction energy is increased by 347% for the Me₂O–HCN complex relative to that for the O–HCN complex. The enhancing mechanism of the methyl group has been analysed by means of natural bond orbital (NBO) theory. The electrostatic interaction is of more importance to the O···H hydrogen bond, whereas dispersion and charge-transfer interactions play a more significant role in the S···H hydrogen bond.     

The structure and vibrational spectral parameters of a complex of HF with the planar (H<Subscript>2</Subscript>CO)<Subscript>2</Subscript> dimer

Equilibrium nuclear configurations of the planar formaldehyde homodimer (H₂CO)₂ and the (H₂CO)₂···HF complex are determined in the MP2/6-311++G(3df, 3pd) approximation taking into account the superposition error of basis sets of monomers. Harmonic values of the frequencies and intensities of fundamental transitions between vibrational states of these hydrogen-bonded complexes were calculated using the Gaussian 09 package of programs. Anharmonic values of the frequencies and intensities of the ν(H–F) stretching vibration and several intermolecular vibrations in the (H₂CO)₂···HF trimer were obtained from variational solutions of one-, two-, and three-dimensional vibrational Schrödinger equations. The anharmonic influence of the C=O and hydrogen bond O···H–F stretching vibrations, as well as of librational vibrations of monomers, on the spectral parameters of the strongest ν(H–F) absorption band of trimer was studied.     

紫草素与胞嘧啶相互作用的理论研究

采用密度泛函理论的M06方法在6-311++G**基组水平下对紫草素-胞嘧啶复合物进行了结构优化,得到了14个稳定的紫草素-胞嘧啶复合物。我们还应用了分子中的原子(AIM)理论和自然键轨道(NBO)理论对这14个复合物中的氢键的性质和特征进行了分析。通过基组重叠误差(BSSE)校正后的相互作用能、成键临界点电荷密度、二阶稳定化能的计算和分析,发现复合物1的结构是最稳定的。     

Chiral discrimination in hydrogen-bonded complexes of 2-fluorooxirane with hydrogen peroxide

The paper reports on an ab initio investigation of an extensive series of propylene oxide (PO)···hydrogen peroxide (HOOH) complexes to investigate chiral discrimination. Second-order Møller–Plesset perturbation theory (MP2) with the 6-311++G(d,p) basis set was used. Four complexes of 2–fluorooxirane (FO)···HOOH were identified and their structures as well as their calculated stability ordering were determined. Only–O–is the main interaction point and the–F is not a hydrogen bond acceptor in the four complexes. In this study, the four complexes were defined in a similar way as for PO···HOOH. The largest chirodiastaltic energy between RP-syn and RM-anti is 0.899 kcal mol^?1 and the largest diastereofacial energy between RP-syn and RP-anti is 1.116 kcal mol^?1. For the chiral 2,3-difluorooxirane (R,R), the chirodiastaltic energy is identical to the diastereomeric energy at 0.277 kcal mol^?1. The results obtained were compared with previously reported results on propylene oxide(PO)···HOOH and 2-methylol oxirane(M-olOx)···HOOH complexes. The mechanisms of chiral discrimination in FO···HOOH, PO···HOOH and M-olOx···HOOH were discussed. The harmonic frequencies, IR intensities, rotational constants and dipole moments for the complexes were also presented to assist future spectroscopic investigation.     

The mutual relationship between H-bonding and π-stacking interactions: the estimation of individual binding energies in the phenylalanine:G ··· C ternary complex

The mutual relationship between stacked interaction and the individual hydrogen bonds in the phenylalanine:guanine?···?cytosine (Ph:G-C) and phenylalanine:cytosine?···?guanine (Ph:C-G) complexes have been studied at the MPWB1K/6-311++G** and M05-2X/cc-pVDZ levels of theory. The interplay of π-stacking and H-bonding results in the weakening of both interactions. The effect of π-stacking on the geometries and individual hydrogen bond (HB) energies of guanine–cytosine (G-C) base pair have been investigated using electron densities calculated by the atoms in molecules (AIM) method at the hydrogen bond critical points (BCP). The results of AIM analysis are in good agreement with the calculated individual hydrogen bond energies. The π-stacking interactions strengths the HB1 and weakens HB2 and HB3 in the Ph:G-C complexes, while the opposite is true in the Ph:C-G complex. With the increase in the distance between phenylalanine ring and the groups involved in H-bond interactions the change in the H-bond energy increases and the changes in the individual H-bond and π-stacking energies decrease in the ternary complexes.     

5-氟尿嘧啶与一氧化碳复合物的结构与性质

采用量子化学密度泛函理论在B3LYP/6-311++G**水平上对5-氟尿嘧啶(5-FU)与CO形成的复合物体系进行了理论计算. 计算共获得了稳定的5-FU异构体12个,双酮式结构5-FU0为其最稳定的构型. 优化获得了稳定复合物44个,其结合方式是CO中的C或O原子与5-FU 的H8或H12键形成氢键;CO分子的C 与5-FU结合具有更大的优势,形成复合物的结合能大,更稳定. 研究还发现,复合物的稳定性与其单体稳定性和C13对氢键相邻单键的二阶稳定化能有关,5-FU0-A为最稳定复合物.     

5-氟尿嘧啶与一氧化碳复合物的结构与性质

采用量子化学密度泛函理论在B3LYP/6-311++G**水平上对5-氟尿嘧啶(5-FU)与CO形成的复合物体系进行了理论计算. 计算共获得了稳定的5-FU异构体12个,双酮式结构5-FU0为其最稳定的构型. 优化获得了稳定复合物44个,其结合方式是CO中的C或O原子与5-FU 的H8或H12键形成氢键;CO分子的C 与5-FU结合具有更大的优势,形成复合物的结合能大,更稳定. 研究还发现,复合物的稳定性与其单体稳定性和C13对氢键相邻单键的二阶稳定化能有关,5-FU0-A为最稳定复合物.     

Computational study on structures,thermochemical properties,and bond energies of disulfide oxygen (S–S–O)‐bridged CH3SSOH and CH3SS(=O)H and radicals

Cleavage of disulfide bonds is a common method used in linking peptides to proteins in biochemical reactions. The structures, internal rotor potentials, bond energies, and thermochemical properties (Δ_fH°, S°, and Cp(T)) of the S–S bridge molecules CH₃SSOH and CH₃SS(=O)H and the radicals CH₃SS?=O and C?H₂SSOH that correspond to H‐atom loss are determined by computational chemistry. Structure and thermochemical parameters (S° and Cp(T)) are determined using density functional Becke, three‐parameter, Lee–Yang–Parr (B3LYP)/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p). The enthalpies of formation for stable species are calculated using the total energies at B3LYP/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p), and the higher level composite CBS–QB3 levels with work reactions that are close to isodesmic in most cases. The enthalpies of formation for CH₃SSOH, CH₃SS(=O)H are ?38.3 and ?16.6 kcal mol^?1, respectively, where the difference is in enthalpy RSO–H versus RS(=O)–H bonding. The C–H bond energy of CH₃SSOH is 99.2 kcal mol^?1, and the O–H bond energy is weaker at 76.9 kcal mol^?1. Cleavage of the weak O–H bond in CH₃SSOH results in an electron rearrangement upon loss of the CH₃SSO–H hydrogen atom; the radical rearranges to form the more stable CH₃SS· = O radical structure. Cleavage of the C–H bond in CH₃SS(=O)H results in an unstable [CH₂SS(=O)H]* intermediate, which decomposes exothermically to lower energy CH₂ = S + HSO. The CH₃SS(=O)–H bond energy is quite weak at 54.8 kcal mol^?1 with the H–C bond estimated at between 91 and 98 kcal mol^?1. Disulfide bond energies for CH₃S–SOH and CH3S–S(=O)H are low: 67.1 and 39.2 kcal mol^?1. Copyright © 2011 John Wiley & Sons, Ltd.     

2-F-环氧丁烷与几种生物小分子间的赝氢键结构

采用密度泛函B3LYP(Becke,three-parameter,Lee-Yang-PaH)/6-311++G**和HF(Hartree Fock)/6-311++G**方法,从理论上探讨了2-F-环氧丁烷分别与几种常见而重要的生物小分子咪唑(Iminazole)、噻唑(Thiazole)和恶唑(Oxazo1e)等分子间的弱相互作用,发现分子间同时存在N…H常规氢键和C-F…H-C赝氢键结构.弱相互作用能计算表明3个复合物的相对稳定性相当.计算结果表明,在C-F…H-C赝氢键结构中,与电子的直接供体F密切相关的共价键C-F键长增大,伸缩振动的频率红移,而作为电子受体的H-C基团,其C-H键伸缩振动光谱蓝移;另外,电子密度拓扑性质表明C-F…H-C赝氢键的共价性及离子性均与常规氢键相当.