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。     

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.     

硝酸羟胺-(H_2O)_n复合物氢键相互作用的密度泛函研究

为研究硝酸羟胺-(H_2O)_n复合物的氢键作用,采用密度泛函B3LYP方法在6-311++G(d, p)基组水平上对硝酸羟胺-(H_2O)_n复合物的结构进行优化,采用MP2/6-311++G(d, p)方法,经基组叠加误差和零点能校正计算得到复合物的相互作用能.利用自然键轨道分析方法研究复合物氢键作用的本质,并对复合物中水分子的振动光谱进行分析.计算结果表明,硝酸羟胺-(H_2O)_n复合物存在着6个硝酸羟胺-H_2O稳定构型和8个硝酸羟胺-(H_2O)_2稳定构型,且最稳定构型的相互作用能分别为52.821 kJ·mol~(-1)和73.349 kJ·mol~(-1).在硝酸羟胺-(H_2O)_n复合物中,水中H-O伸缩振动频率明显红移,且红移增大的程度与复合物稳定化能的变化趋势基本一致.     

AIM Study on the Reaction of CH2SH Radical with Fluorine Atom

采用MP2(Full)/6-311G(d,p)、QCISD(T)/6-311++G(2df,p)和B3LYP/6-311G(d,p)方法研究了CH2SH自由基与F原子的反应．F原子通过进攻自由基上的C原子或S原子形成三种不同的反应通道．计算结果表明F原子进攻自由基上的C原子生成CH2S和HF为主要的反应通道．对反应进程中若干关键点进行了电子密度拓扑分析，找到了该反应的结构过渡区(结构过渡态)和能量过渡态．计算结果表明，对于比较显著的吸热或放热反应，其结构过渡区范围很小，对于吸热或放热不太显著的反应，结构过渡区范围较大.     

CH3⊕ … Br-Y(Y=H, CCH, CN, NC)缺电子体系中Br原子参与的反向卤键相互作用

采用B3LYP/6-311++G(d,p)和MP2/6-311++G(d,p)理论方法研究了CH₃^⊕…Br-Y(Y=H, CCH, CN, NC) 缺电子体系中Br参与的反向卤键(IXB)结构. 四个IXB复合物中,MP2/6-311++G(d,p)水平上考虑了基组叠加误差的分子间相互作用能分别为218.87, 219.48, 159.18和143.05 kJ/mol,相对稳定性的递增顺序CH₃^⊕…BrCN相似文献   

HeNO分子光谱常数和非谐振力场的从头算研究

本文利用Gaussian 03软件,采用密度泛函理论(B3LYP)以及二阶微扰理论(MP2)的方法结合Dunning相关一致基组cc-pVNZ (N=T,D,Q)以及6-311G、6-311G**、6-311G(2df,2pd)、6-311G(3df,3pd)基组优化了HeNO分子的几何结构,然后在此基础上计算了它们的光谱常数和非谐振力场.通过计算得到了分子的平衡几何结构、基频、转动常数、四次和六次离心畸变常数等,并与相关的实验值和理论值进行了比较;预测了部分光谱常数,其中包括谐振频率、非谐性常数、振转相互作用常数、三次力常数、四次力常数和科里奥利耦合常数.结果表明,在MP2方法下计算的结果要优于B3LYP计算的结果;基组6-311G、6-311G**、6-311G(2df,2pd)、6-311G(3df,3pd)下的结果普遍优于cc-PVNZ (N=T,D,Q)得到的结果.结果还表明,MP2理论方法结合基组6-311G、6-311G**、6-311G(2df,2pd)、6-311G(3df,3pd)基组计算的结果非常接近实验值,对实验测量某些光谱数据有较好的预测作用.     

SiF_2自由基与异硫氰酸反应机理的理论研究北大核心CSCD

采用密度泛函理论B3LYP方法研究了SiF2自由基与异硫氰酸(HNCS)的反应机理,并在B3LYP/6-311++G**水平上对反应物、中间体、过渡态进行了全几何参数优化,通过频率分析和内禀反应坐标(IRC)确定中间体和过渡态的真实性.为了得到更精确的能量值,又用CCSD(T)/6-311++G**方法计算了在B3LYP/6-311++G**水平优化后的各个驻点的相对能量.根据统计热力学及用Winger校正的Eyring过渡态理论,利用自编程序,计算不同温度下低势垒反应的平衡常数和速率常数,并且通过电子密度拓扑分析讨论了化学反应过程中主要化学键的生成和断裂.计算结果表明,单重态的SiF2自由基与HNCS反应有6条可能的反应通道,其中反应通道SiF2+HNCS→IM1→TS1→IM2HSiF2NCS(P1)为主反应通道.     

乙二醇分子间氢键结构与溶剂效应

采用密度泛函理论在B3LYP/6-311++G** (范德华校正)水平上研究乙二醇在气相中分别与乙腈、丙酮、四氢呋喃、水、乙二醇形成氢键二聚体的结构性质，根据PCM 极化统一场模型讨论氢键溶剂效应。结果表明，五种氢键二聚体分子中的氢键属于红移氢键，溶剂使氢键二聚体分子的偶极矩变大，并对OH振动频率的影响不大。     

1,3,5-三氮杂苯－水簇氢键结构性质

在B3LYP/6-31 G**和MP2/6-31 G**水平上对1,3,5-三氮杂苯-(H2O)n(n=2,3)复合物的基态氢键结构进行几何优化和性质计算,结果表明复合物之间存在较强的氢键相互作用,所有稳定复合物结构中形成一个N…H-O氢键并终止于弱O…H-C氢键的氢键水链构型最稳定.氢键的形成是水分子中H-O键振动频率减小(红移).NBO分析表明,最稳定的1:2和1:3复合物发生分子问电荷转移总量分另q为0.02501 e和0.02777 e.     

HeNO分子光谱常数和非谐振力场的从头算研究

在本论文中,我们在Gaussian 03软件下,采用密度泛函理论（B3LYP）以及二阶微扰理论（MP2）的方法结合Dunning相关一致基组cc-pVNZ (N=T,D,Q)以及6-311G、6-311G**、6-311G（2df,2pd）、6-311G（3df,3pd）基组优化了HeNO分子的几何结构,然后在此基础上计算了它们的光谱常数和非谐振力场。通过计算得到了分子的平衡几何结构、基频、转动常数、四次和六次离心畸变常数等,并与相关的实验值和理论值进行了比较;预测了部分光谱常数,其中包括谐振频率、非谐性常数、振转相互作用常数、三次力常数、四次力常数和科里奥利耦合常数。结果表明,在MP2方法下计算的结果要优于B3LYP计算的结果;基组6-311G、6-311G**、6-311G（2df,2pd）、6-311G（3df,3pd）下的结果普遍优于cc-PVNZ (N=T,D,Q)得到的结果。结果还表明,MP2理论方法结合基组6-311G、6-311G**、6-311G（2df,2pd）、6-311G（3df,3pd）基组计算的结果非常接近实验值,对实验测量某些光谱数据有较好的预测作用     

HNO二聚体蓝移氢键的理论研究

利用分子轨道从头算理论和密度泛函理论结合不同理论基组对于N-H…O蓝移氢键进行了详细的研究.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.拓扑学和自然键轨道理论对于蓝移氢键的本质进行分析.自然键轨道(NBO)分析表明,σ*(N-H)轨道上电子密度降低是电子密度重排效应的结果.分子内电子重排、轨道再杂化和电子受体内部结构重组共同作用结果导致了N-H的振动频率大幅蓝移现象的出现.     

On difference of properties between organic fluorine hydrogen bond C–H···F–C and conventional hydrogen bond

The existence of C–H···F–C hydrogen bonds in the complexes of trifluoromethane and cyclic molecule (oxirane, cyclobutanone, dioxane, and pyridine) has been experimentally proven by Caminati and co-workers. This study presents a theoretical investigation on these C–H···F–C hydrogen bonds at B97D/6-311++G^** and MP2/6-311++G^** levels, in terms of C–H vibrational frequency shifts, atoms in molecules characteristics, and the bonding feature of C–H···F–C hydrogen bonds. It is found that in three important aspects, there are significant differences in properties between C–H···F–C and conventional hydrogen bonds. The C–H···F–C hydrogen bonds show a blueshift in the C–H vibrational frequencies, instead of the X–H normal redshift in X–H···Y conventional hydrogen bonds. The natural bond orbital (NBO) analyses show that σ and p types of lone pair orbitals of the F atom to an antibonding σ^*_H–C orbital form a dual C–H···F–C hydrogen bond. Such a dual hydrogen bonding leads to the proton acceptor directionality of the C–H···F–C hydrogen bond softer. Our studies also show that the Laplacian of the electron density (▽²ρ_BCP) is not always a good criterion for hydrogen bonds. Therefore, we should not recommend the use of the Laplacian of the electron density as a criterion for C–H···F–C hydrogen bonds.     

Structural and spectroscopic investigation of the N-methylformamide–water (NMF···3H2O) complex

In this work, theoretical studies on the structure, molecular properties, hydrogen bonding, and vibrational spectra of the N-methylformamide–water (NMF···3H₂O) complex will be presented. The molecular geometry was optimised by using Hartree–Fock (HF), second Møller–Plesset (MP2), and density functional theory methods with different basis sets. The harmonic vibrational frequencies are computed by using the B3LYP method with 6-311++G(d,p) as a basis set and then scaled with a suitable scale factor to yield good coherence with the observed values. The temperature dependence of various thermodynamic functions (heat capacity, entropy, and enthalpy changes) was also studied. A detailed analysis of the nature of the hydrogen bonding, using natural bond orbital (NBO) and topological atoms in molecules theory, has been reported.     

Comparison between standard and counterpoise-corrected optimization using some hydrogen and halogen bonded systems

The effect of the counterpoise correction on the geometries, stabilization energies, and vibrational harmonic frequencies of some hydrogen- and halogen-bonded systems (B?=?CH₃CN,?HCN,?NH₃,?N₂,?CO,?H₂O,?H₂S,?PH₃;?HX?=?HF,?HCl,?HBr,?HCN,?HCF₃; XY?=?Br₂,?BrCl,?BrF,?Cl₂,?ClF,?F₂) has been analysed at the MP2 level of theory using the popular 6-311++G(d,p) basis set. The optimized B?···?H and B?···?X bond lengths increase with counterpoise (CP) correction. In some cases standard values and in other cases CP-corrected values are close to experimental data. The absolute values of complexation energies of CP-corrected structures are higher than standard by inclusion of BSSE correction. The effect of CP correction on intermolecular bond lengths and complexation energies of B?···?XY series are usually higher than B?···?HX. Also, this effect is higher for H₂S and PH₃ groups. The CP correction changes the vibrational harmonic frequencies by 0–100%. The changes are frequently lower than 20% for frequencies higher than 300?cm^?1.     

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.     

Structures and Vibrational Spectra of the Hydrogen-Bonded Complexes Between Nitrous Acid and Acetone: Ab Initio and DFT Studies

ABSTRACT

The structures, stability, and vibrational spectra of the binary complexes formed between acetone and nitrous (trans and cis) acid have been investigated using ab initio calculations at the SCF and MP2 levels and B3LYP calculations with 6-311++G(d,p) basis set. Full geometry optimization was made for the complexes studied. It was established that the complex (CH₃)₂CO···HONO-trans is more stable than the complex (CH₃)₂CO···HONO-cis by 0.5–0.8 kcal·mol^?1. The accuracy of the calculations has been estimated by comparison between the predicted values of the vibrational characteristics (vibrational frequencies and infrared intensities) and the available experimental data. It was established, that the methods, used in this study are well adapted to the problem under examination. The predicted values with the B3LYP/6-311++G(d,p) calculations are very near to the results, obtained with MP2/6-311++G(d,p). The calculated frequency shift Δν(O[sbnd]H) for the complex (CH₃)₂CO···HONO-trans (1A) is larger than for the complex (CH₃)₂CO···HONO-cis (1B). In the same time the intensity of this vibration increases dramatically upon hydrogen bonding. The calculated increase for the complex 1A is up to 15 times and for the complex 1B is up to 30 times. The changes in the vibrational characteristics (vibrational frequencies and infrared intensities) of (CH₃)₂CO upon the complexation are more insignificant than the changes in the vibrational characteristics of HONO-trans and HONO-cis.     

Mass spectrometric and ab initio study of the interaction between 9-methylguanine and amino acid amide group

The temperature dependent field ionization mass spectrometry method combined with ab initio calculations was used to determine the interaction energies and the structures of 9-methylguanine-acrylamide dimers. Acrylamide mimics the side chain amide group of the natural amino acids asparagine and glutamine. The experimental enthalpy of the dimer formation derived from the van't Hoff plot is ?59.5 ± 3.8 kJ mol^?1. The value is higher than interaction energies between acrylamide and other nucleic acid bases which were determined to be ?57.0 for 1-methylcytosine, ?52.0 for 9-methyladenine, and ?40.6 kJ mol^?1 for 1-methyl-uracil. In total, eight hydrogen bonded dimers formed by the three lowest energy 9-methylguanine tautomers and acrylamide were found in the quantum chemical calculations performed at the DFT/B3LYP/6-31++G?? and MP2/6-31++G?? levels of theory. The relative stability and the interaction energies of the dimers were calculated accounting for the basis set superposition error and the zero-point vibrational energy correction. The lowest energy dimer found in the calculations is formed by acrylamide (Ac) with the keto tautomer of 9-methylguanine (Gk). It is stabilized by two intermolecular H bonds, C6=O(Gk) · · · H—N(Ac) and Nl—H(Gk) · · ·O(Ac), and it is more stable than the second lowest energy dimer by ≈ 25 kJ mol^?1. The calculated interaction energies of the lowest energy 9-methylguanine-acrylamide dimer are ?65.0 kJ mol^?1 and ?67.7 kJ mol^?1 at the MP2 and DFT levels of theory, respectively. The experimental enthalpy of the dimer formation is in good agreement with both the calculated interaction energies of the GkAc dimer and much higher than the interaction energies calculated for all other 9-methylguanine-acrylamide dimers. This proved that only one dimer was present in the experimental samples. To verify whether acrylamide is a good model of the amino acid-amide group, we performed direct calculations of the 9-methylguanine-glutamine dimers at the same levels of theory as used for the complexes involving acrylamide. The interaction energies found for the lowest energy 9-methylguanine-glutamine dimer are ?65.1 kJ mon^?1 (MP2/6-31++G??) and ?66.2 kJ mol^?1 (DFT/B3LYP/6-31++G??) and these values are very close (within 0.5 kJ mol^?1) to the interaction energies obtained for the 9-methylguanine-acrylamide dimers.     

DFT study on abstraction reaction mechanism of oh radical with 2‐methoxyphenol

Reaction mechanism of 2‐methoxyphenol (2MP) (guaiacol) with OH radical has been performed using density functional theory methods BH&HLYP and MPW1K method with 6‐311++G(d,p) basis set. Single‐point energy calculations were done using CCSD(T)/6‐311++G(d,p). The theoretical results reveal that the hydrogen abstraction from methoxy group is found to be the dominant reaction channel with an energy barrier of 9.31 kcal/mol. Also, time‐dependent density functional theory calculations have been performed using BH&HLYP/6‐311++G(d,p) level of theory, and the results reveal that the reactions occur in ground state than the excited state. The results of reaction force profile indicate that structural rearrangements are most influential with high percentage than the relaxation process. The calculated theoretical rate constants (12.19 × 10^?11 cm³ molecule^?1 s^?1) are in good agreement with the experimental rate constant. The atmospheric lifetime of 2‐methoxyphenol with respect to OH radicals is 2.27 hours, which implies that OH radical plays an important role in the degradation of 2MP. The Wiberg bond index of the abstraction reaction reveals that the bond order is concerted, partially synchronic. The reactant‐like transition state satisfies Hammond postulate, which eventually results in an exothermic reaction, and the product‐like transition state reveals in endothermic nature.     

Kinetics and mechanism of intramolecular aldol condensation of 2,5-hexadione, a DFT and MP2 study

A theoretical study of kinetics and mechanism of intramolecular aldol condensation of 2,5-hexadione was performed using DFT methods at B3LYP and MP2 levels of theory using 6-311g, 6-311g*, 6-311G**, 6-311++G and 6-311++G** basis sets. Equilibrium molecular geometries and harmonic vibrational frequencies of the reactant, transition states, and products were calculated. Two reaction paths were studied. The considered rate constants and activation thermodynamic parameters were calculated. The results indicated a fairly good agreement with experimental data. It was demonstrated that the five member ring is the most stable one for all calculations. These calculations showed that the reaction proceeds through an asynchronous concerted mechanism.