4-硝基-1,3-丁二烯基胺分子的氢键效应

在从头计算的水平上, 利用杂化密度泛函理论研究了溶剂对4-硝基-1,3-丁二烯基胺分子的几何结构、分子内的电荷分布和电荷转移态的能量漂移的影响. 在四种极性溶剂中, 我们构造了包括氢键作用的超分子结构. 分别研究了由极化连续模型模拟的溶剂和溶质分子的长程相互作用, 溶剂和溶质分子的氢键作用, 以及溶剂和溶质分子的整体作用对分子结构和性质的影响. 研究结果表明氢键作用引起了溶质分子结构和性质的较大变化, 从而将明显地影响该类分子的非线性光学性质. 因此, 在模拟溶剂效应时需要考虑氢键作用.     

利用浮动电荷力场对N-甲基乙酰胺水溶液的分子动力学模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对N-甲基乙酰胺(NMA)分子的水溶液体系进行了分子动力学模拟. 与经典的力场模型相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理体现了分子中的电荷分布. 相对其它极化力场模型, 该模型具有计算量较小的特点. 在该模型下对NMA纯溶液和其水溶液体系进行了分子动力学模拟, 得到的径向分布函数、汽化热和偶极矩等物理量与实验值和其它极化力场方法符合很好, 合理描述了溶质与溶剂之间的静电极化和分子内的电荷转移.     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,氢键键长r(H…O)伸长,氢键强度减弱.自然键轨道(NBO)分析表明,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子n(O)对N-H的反键轨道σ~*(N-H)的二阶相互作用稳定化能增加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

方酸与2, 6-二苯并咪唑的超分子自组装及氢键实验与理论研究

在氘代的二甲基亚砜的溶剂中合成了方酸与2, 6-二苯并咪唑的超分子的化合物,并用X射线单晶衍射对其结构进行了表征。晶体结构分析表明:超分子是通过π-π堆积和分子之间氢键所形成的一维链状的聚合物。探讨了不同温度和不同浓度CCl₄溶剂对聚合物中氢键的影响。此外,用密度泛函理论和分子中原子理论对其进行了理论分析,计算结果表明分子间的键能分别是135.65和49.40 J·mol^-1。     

醌型D-π-A类化合物AMTOE在不同溶剂中吸收和发射光谱的蓝移现象

采用连续介质模型(PCM)以及明确/连续的混合溶剂模型,运用密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)方法,研究了溶剂极性对D-π-A类两性离子化合物1-(4-aza-4-methylphenyl)-2-trans-(4-oxyphenyl)ethane(AMTOE)分子几何、电子结构以及光谱性质的影响.计算结果表明,随着溶剂极性和超分子簇大小的增加,AMTOE基态(S0)分子几何从醌式结构向芳式结构转化.从基态(S0)到激发态(S1),化合物AMTOE醌式结构增强.从弱极性的氯仿溶液到强极性的水溶液,AMTOE分子的吸收光谱和发射光谱均发生蓝移,并且吸收光谱的蓝移程度大于发射光谱的蓝移程度,与实验现象定性一致.吸收光谱和发射光谱发生蓝移的原因是随着溶剂极性增强,HOMO轨道能级与LUMO轨道能级之间的能隙增大.对于具有明显电荷转移的AMTOE分子的溶剂化显色效应,长程矫正的含时密度泛函TD-CAM-B3LYP方法比传统的含时密度泛函TD-B3LYP方法更为合理.另外,明确/连续的混合溶剂模型能更好的描述该类体系在强极性溶剂中的溶剂化显色效应.     

7-吡啶吲哚同分异体结构与电子光谱性质的理论研究

运用密度泛函理论对7-吡啶吲哚可能存在的构型进行优化,计算异构体的几何构型、电子结构、前线分子轨道;应用含时密度泛函理论计算了异构体b,c和e的电子光谱性质以及溶剂效应对光谱性质的影响.结果表明,溶剂极性的增加使b的电子光谱蓝移,而c和e的电子光谱红移,且溶剂极性对最大吸收波长影响幅度较小.前线分子轨道分析,表明该类化合物的主要吸收光谱主要对应于分子中的HOMO→LUMO电子跃迁,且为π→π*跃迁.     

DFT方法研究基于脲及硫脲衍生物的阴离子受体

采用密度泛函理论(DFT)模拟了两个基于脲和硫脲衍生物的受体分子对卤素阴离子的识别过程.结构优化表明基于脲衍生物的受体分子1最稳定构象为"反反"构象,分子内部形成稳定的C~α-H…O=C分子内氢键;而基于硫脲衍生物的受体分子2,不能形成分子内氢键,最稳定构象为"反顺"构象.受体1、2与卤素阴离子F~-、Cl~-可形成稳定的双氢键复合物,在此过程中,受体2经历了由"反顺"构象到"反反"构象的异构化过程.结构和能量分析表明,1、2受体分子与F~-离子间的氢键强度远大于其与Cl~-离子间的氢键;另一方面,受体2与阴离子间的氢键明显强于受体1,这是由于硫脲基N-H键具有更强的酸性.此外,对受体分子、氢键复合物及去质子化产物的吸收光谱计算结果表明,受体与F~-离子作用可产生明显的吸收光谱红移,而与Cl~-离子的作用对光谱影响较小.     

吡啶类离子液体在气-液界面吸附的量子化学研究

采用量子化学密度泛函理论,在B3LYP/6-311+G水平上,对吡啶离子液体阳离子[BuPy]+及其水合物(水分子数为1～6)的分子模型进行结构优化和频率分析,得到各种水合物的热力学性质,由此计算水合过程的标准反应焓变和吉布斯自由能变,从分子水平上研究吡啶类离子液体与水分子的相互作用.结果表明,离子液体阳离子极性头与水分子以氢键形式构成水合层,该类氢键属于中强氢键;其水合过程是一个自发的放热过程,并且随着水分子数的增加水合物的稳定性也逐渐增强.     

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。     

碱/脲水溶液体系中纤维素包合物构型及纤维素与溶剂分子间相互作用力的分子动力学模拟

采用分子动力学模拟方法研究了纤维素分子在碱/脲水溶液体系中形成的包合物结构,研究了纤维素包合物的空间构型、氢键网格结构、纤维素分子与溶剂分子的相互作用以及碱金属阳离子对包合物稳定性的影响.在纤维素包合物结构中,碱金属阳离子和OH-主要吸附在纤维素分子链羟基的附近,与纤维素上的羟基氧直接接触形成稳定的吸附构型;尿素分子更倾向于在纤维素糖环面结构上聚集,可以与纤维素上的羟基氧和醚键氧相互作用形成氢键.通过对纤维素与溶剂分子间非键相互作用的研究发现,在纤维素羟基附近,羟基与金属阳离子之间的相互作用能最大,其次为与尿素分子、氢氧根离子的相互作用,最小的为与水分子的相互作用;在纤维素糖环面结构上,Na~+、OH~-、尿素、水与纤维素醚键氧的相互作用远小于与纤维素羟基的相互作用,纤维素上的醚键氧与尿素分子相互作用能最大.比较KOH/尿素和NaOH/尿素2种溶剂体系中碱金属阳离子与纤维素羟基形成的吸附构型的结合能,发现Na~+对纤维素分子内和分子间的氢键具有更强的破坏作用,NaOH/尿素溶剂体系中的分子与纤维素分子形成的包合物构型更稳定.     

Solvent effects on electronic structures and chain conformations of alpha-oligothiophenes in polar and apolar solutions

Solvent effects on electronic structures and chain conformations of alpha-oligothiophenes nTs (n = 1 to 10) are investigated in solvents of n-hexane, 1,4-dioxane, carbon tetrachloride, chloroform, and water by using density functional theory (DFT) and molecular dynamics (MD) simulations. Both implicit and explicit solvent models are employed. The polarized continuum model (PCM) calculations and MD simulations demonstrate the weak solvent effects on the electronic structures of alpha-oligothiophenes. The lowest dipole-allowed vertical excitation energies of nTs, obtained from time-dependent DFT/PCM calculations at the B3LYP/6-31G(d) level, exhibit a red shift as the solvent polarity increases, in agreement with experiments. The studied solvents have little impact on the state order of the low-lying excited states provided that the nTs are kept in C2h or C2v symmetry. The MD simulations demonstrate that the chain conformations are distorted to some extent in polar and nonpolar solvents. A qualitative picture of the distribution of solvent molecules around the solvated nTs is drawn by means of radial and spatial distribution functions. The S...H-O and pi...H-O solute-solvent interactions are insignificant in aqueous solution.     

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations

In this work, we present a hybrid explicit/implicit solvation model, well suited for first-principles molecular dynamics simulations of solute-solvent systems. An effective procedure is presented that allows to reliably model a solute with a few explicit solvation shells, ensuring solvent bulk behavior at the boundary with the continuum. Such an approach is integrated with high-level ab initio methods using localized basis functions to perform first-principles or mixed quantum mechanics/molecular mechanics simulations within the extended-Lagrangian formalism. A careful validation of the model along with illustrative applications to solutions of acetone and glycine radical are presented, considering two solvents of different polarity, namely, water and chloroform. Results show that the present model describes dynamical and solvent effects with an accuracy at least comparable to that of conventional approaches based on periodic boundary conditions.     

Solvation dynamics in acetonitrile: a study incorporating solute electronic response and nuclear relaxation

The solvent reorganization process after electronic excitation of a polar solute in a polar solvent such as acetonitrile is related mainly to the time evolution of the solute-solvent electrostatic interaction. Modern laser-based techniques have sufficient time resolution to follow this decay in real time, providing information to be confirmed and interpreted by theories and models. We present here a study aimed at the investigation of the different steps involved in the process taking place after a vertical S(0) --> S(1) excitation of a large size chromophore, coumarin 153 (C153), in acetonitrile, from both the solute and the solvent points of view. To do this, we use accurate quantum mechanical calculations for the solute properties within the polarizable continuum model (PCM) and classical molecular dynamics (MD) simulations, both equilibrium and nonequilibrium, for C153 in the presence of the solvent. The geometry of the solute is allowed to change in order to study the role of internal motions in the time-dependent solvation process. The solvent response function has been obtained from the simulation data and compared to experiment, while the comparison between equilibrium and nonequilibrium MD results for the solvation response confirms the validity of the linear response approximation in the C153-acetonitrile system. The MD trajectories have also been used to monitor the structure of the solvation shell and to determine its change in response to the change in the solute partial charges.     

Solute-solvent friction kernels and solution properties of methyl oxazoline-phenyl oxazoline (MeOx-PhOx) copolymers in binary ethanol-water mixtures

Solvent mixtures often alter the solubility of polymeric substances. Statistical copolymers made from 2-methyl-2-oxazoline (MeOx) and 2-phenyl-2-oxazoline (PhOx) are known for their varying solubilities in pure ethanol, pure water and in binary mixtures of ethanol-water. Constrained Molecular Dynamics (MD) simulations have been carried out with an aim to explain the varying solubilities of the statistical MeOx-PhOx copolymers. The solute-solvent dynamic friction kernels calculated through constrained MD simulations corroborate the solubility pattern in these copolymers. The solvation characteristics have been analyzed in terms of the solute-solvent radial distribution functions (RDFs). The ethanol-soluble MeOx-PhOx copolymers exhibit characteristic solute-composition dependence in the dynamic solute-solvent friction kernels, indicating the strength of the solute-solvent correlations. The aggressive solvation by the ethanol molecules in the binary solvent mixtures has been brought out by the O(solute)-H(ethanol) RDFs which exhibit a characteristic dependence on the ethanol content in the solvent composition. The corresponding O(solute)-H(water) RDFs are devoid of any such composition dependence. For all the MeOx-PhOx copolymers, the O-site solvation is strongly dominated by the water molecules and the N-sites are solvated equally by both ethanol and water molecules.     

Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.     

Probing supercritical water with the n-pi* transition of acetone: a Monte Carlo/quantum mechanics study

The n-pi(*) electronic transition of acetone is a convenient and important probe to study supercritical water. The solvatochromic shift of this transition in supercritical water (adopting the experimental condition of P=340.2 atm and T=673 K) has been studied theoretically using Metropolis NPT Monte Carlo (MC) simulation and quantum mechanics (QM) calculations based on INDO/CIS and TDDFT-B3LYP6-31+G(d) methods. MC simulations are used to analyze hydration shells, solute-solvent interaction, and for generating statistically relevant configurations for subsequent QM calculations of the n-pi(*) transition of acetone. The results show that the average number of hydrogen bonds between acetone and water is essentially 13 of that in normal water condition of temperature and pressure. But these hydrogen bonds have an important contribution in the solute stabilization and in the solute-solvent interaction. In addition, they respond for nearly half of the solvatochromic shift. The INDO/CIS calculations explicitly considering all valence electrons of the water molecules, using different solvation shells, up to the third shell (170 water molecules), give a solvatochromic shift of 670+/-36 cm(-1) in very good agreement with the experimentally inferred result of 500-700 cm(-1). It is found that the solvatochromic effect on n-pi(*) transition of acetone in the supercritical condition is essentially given by the first solvation shell. The time-dependent density-functional theory (TDDFT) calculations are also performed including all solvent molecules up to the third shell, now represented by point charges. This TDDFT-B3LYP6-31+G(d) also gives a good but slightly overestimated result of 825+/-65 cm(-1). For comparison the same study is also made for acetone in water at normal condition. Finally, all average results reported here are statistically converged.     

Solvent effects on NMR isotropic shielding constants. a comparison between explicit polarizable discrete and continuum approaches

The gas-to-aqueous solution shifts of the 17O and 13C NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.