联苯负离子自由基与萘分子间长程电子转移的从头算研究

分离处理π σ π体系中的给体 ,受体和σ桥体 ,在HF/4 31G和HF/DZP水平上优化了联苯 ,联苯负离子自由基 ,萘和萘负离子自由基的几何构型 ,计算了分子间电子转移的内重组能 .取线性反应坐标R =0 .5 ,在STO 3G水平上用变分原理和分子轨道跃迁能方法 ,计算了π σ π体系自交换反应的电子转移矩阵元 .对交叉反应体系 ,沿线性反应坐标搜寻最小轨道能级分裂Δmin,确定了电子转移矩阵元和过渡态构型 .用Marcus双球模型计算液相电子转移的溶剂重组能 ,结合半经典模型计算了几种以联苯负离子自由基为给体 ,联苯和萘为受体的π σ π体系分子内电子转移速率常数 .     

肽链体系中的长程电子转移: 酪氨酸与色氨酸间电子转移的理论研究

用电子转移的半经典模型和量子化学半经验方法对色氨酸-酪氨酸二肽体系进行电子转移动力学参数计算.用AM1方法分别优化给体、受体和桥体几何构型,用线性反应坐标的构造了给体和受体分子间电子转移的双势阱,得到两透热势能面交叉处的反应坐标为R=(约等于)0.10,并确定了反应的内重组能及反应热.对色氨酰酪氨酸和酪氨酰色氨酸体系进行闭壳层HF自洽场计算,按Koopmans定理计算体系分子轨道分裂能值A(三角形),在R约为0处发现了A(三角形)的极小值,从而获得色氨酰酪氨酸及酪氨酰色氨酸体系分子内电子转移的电子转移矩阵元V~D~A分别为0.96kJ.mol^-^1和0.87kJ.mol^-^1.采用Marcus双球模型估算反应的溶剂重组能为64.60kJ.mol^-^1。     

二氯二氰基苯醌及其阴离子自交换电子转移反应的理论研究

基于非平衡溶剂化能的约束平衡方法和溶剂重组能的新表达式, 实现了电子转移反应溶剂重组能的数值解, 研究了二氯二氰基苯醌(DDQ)及其阴离子体系DDQ-之间的自交换电子转移反应. 考虑了DDQ与DDQ-分子以平行方式形成受体-给体络合物时的两种构型. 引入线性反应坐标, 计算了该反应在不同溶剂中的溶剂重组能. 基于两态变分模型得到了反应的电子耦合矩阵元. 根据电子转移动力学模型, 计算了该自交换电子转移反应的速率常数.     

生物体系中电子转移机理的理论研究--Ⅲ.含金属螺环化合物的分子内电子转移

用MOPAC-ET程序中AM1方法,计算了金属螺环化合物分子内电子转移的性质及它们与外加电场的相关性,结果表明随着外加电场F的不断增加,反应的势垒则不断降低,当F达到一定值时,反应的活化能为零,此时反应速率最大,计算还表明电子转移矩阵元VAB和重组能λ受外加电场的影响很小,而反应热则与之成正比.     

电子转移反应O2+O2·-→O2·-+O2的从头算研究

利用abinitio方法,在UHF,UMP2及不同基组3-21G,6-31G^*,6-311+G^*和UMP2(full)/6-311+G^*水平上,研究了O~2/O~2^.^-自交换电子转移反应。优化了电子转移前后反应物和产物的结构,研究了体系能量的变化,计算了自交换电子转移反应的内重组能。对UHF方法和UMP2方法的计算结果进行了比较,并与实验结果进行了对照。结果表明UHF方法由于没有考虑组态相互作用,计算结果存在较大偏差,UMP2(full)/6-311+G^*水平上的计算结果与实验值吻合较好。在UMP2(full)/6-311+G^*水平上计算了气相自交换电子转移反应速率常数。在优化了电子转移复合物结构的基础上考虑了溶剂效应的影响,计算了水溶液中的溶剂重组能。研究结果表明O~2/O~2^.^-体系电子转移反应的活化能主要来源于溶剂重组能的贡献。最后计算了该反应在水溶液中的反应速率常数。理论计算结果与实验值吻合得很好。     

电子转移反应O~2+O~2^.^-→O~2^.^-+O~2的从头算研究

利用abinitio方法,在UHF,UMP2及不同基组3-21G,6-31G^*,6-311+G^*和UMP2(full)/6-311+G^*水平上,研究了O~2/O~2^.^-自交换电子转移反应。优化了电子转移前后反应物和产物的结构,研究了体系能量的变化,计算了自交换电子转移反应的内重组能。对UHF方法和UMP2方法的计算结果进行了比较,并与实验结果进行了对照。结果表明UHF方法由于没有考虑组态相互作用,计算结果存在较大偏差,UMP2(full)/6-311+G^*水平上的计算结果与实验值吻合较好。在UMP2(full)/6-311+G^*水平上计算了气相自交换电子转移反应速率常数。在优化了电子转移复合物结构的基础上考虑了溶剂效应的影响,计算了水溶液中的溶剂重组能。研究结果表明O~2/O~2^.^-体系电子转移反应的活化能主要来源于溶剂重组能的贡献。最后计算了该反应在水溶液中的反应速率常数。理论计算结果与实验值吻合得很好。     

四氯化苯醌-二苯撑体系的光诱导电子转移研究

用从头算方法对四氯化苯醌-二苯撑体系分子间相互作用进行了理论计算研究.用MP2/6-31G^**方法,分别优化电子给体二苯撑,受体四氯化苯醌的稳定构型,用同样的方法优化配合物的层间距得到其最稳定构型,并计算了BSSE校正后的电子给受体配合物的稳定化能.用CIS/6-31++G^**方法,计算了给体、受体及配合物的电子激发态.理论计算验证了给体和受体间能形成稳定的电子给受体配合物,该配合物受光激发能直接产生电荷转移态.在球孔穴近似和点偶极近似下,对电荷转移吸收的理论计算结果进行了非平衡溶剂化能校正.经非平衡溶剂化能校正的电荷转移跃迁能与实验值符合较好.     

酪氨酸与色氨酸间电子转移——氧化还原活性及电子跃迁能的从头算研究

在HF/6-31G和GASSCF/6-31G水平上对色氨酸和酪氨酸间的电子转移进行了理论 研究。用类导体屏蔽模型考察体系的溶剂效应。通过对给、受体几何构型的优化, 计算了孤立的给、受体之间电子转移反应的内重组能和反应能差。分别用 Koopmans定理和CASSCF/6-31G方法计算了色氨酸和酪氨酸的电离能。计算了此两种 氨基酸从基态到最低激发态的跃迁能。理论计算结果很好地解释了N_3~·高选择性 地氧化色氨酸残基,并诱发电子从酪氨酸残基向色氨酸残基转移的实验现象。     

酪氨酸与色氨酸间电子转移——氧化还原活性及电子跃迁能的从头算研究

在HF/6-31G和GASSCF/6-31G水平上对色氨酸和酪氨酸间的电子转移进行了理论 研究。用类导体屏蔽模型考察体系的溶剂效应。通过对给、受体几何构型的优化， 计算了孤立的给、受体之间电子转移反应的内重组能和反应能差。分别用 Koopmans定理和CASSCF/6-31G方法计算了色氨酸和酪氨酸的电离能。计算了此两种 氨基酸从基态到最低激发态的跃迁能。理论计算结果很好地解释了N_3~·高选择性 地氧化色氨酸残基，并诱发电子从酪氨酸残基向色氨酸残基转移的实验现象。     

含酪氨酸和色氨酸的肽内电子转移的溶剂重组能计算

基于连续介质模型，本文考察了多肽体系Trp-(Pro)n-Tyr (n=1,2) 从酪氨酸到色氨酸的分子内电子转移，并根据电荷定域的反应物和产物构型和线性反应坐标近似构造了电子转移的双势阱，通过势能曲线的交叉点确定了电子转移过渡态。本文重点讨论了电子转移溶剂重组能。根据作者的非平衡溶剂化理论和可极化连续介质模型编写了溶剂重组能计算程序并用于本文体系的计算。计算得到Trp-Pro-Tyr 和Trp-(Pro)2-Tyr.体系的溶剂重组能分别为20.89 kcal/mol和25.30 kcal/mol.     

Water coordination structures and the excess free energy of the liquid

We assess the contribution of each coordination state to the hydration free energy of a distinguished water molecule, the solute water. We define a coordination sphere, the inner-shell, and separate the hydration free energy into packing, outer-shell, and local, solute-specific (chemical) contributions. The coordination state is defined by the number of solvent water molecules within the coordination sphere. The packing term accounts for the free energy of creating a solute-free coordination sphere in the liquid. The outer-shell contribution accounts for the interaction of the solute with the fluid outside the coordination sphere and it is accurately described by a Gaussian model of hydration for coordination radii greater than the minimum of the oxygen-oxygen pair-correlation function: theory helps identify the length scale to parse chemical contributions from bulk, nonspecific contributions. The chemical contribution is recast as a sum over coordination states. The nth term in this sum is given by the probability p(n) of observing n water molecules inside the coordination sphere in the absence of the solute water times a factor accounting for the free energy, W(n), of forming an n-water cluster around the solute. The p(n) factors thus reflect the intrinsic properties of the solvent while W(n) accounts for the interaction between the solute and inner-shell solvent ligands. We monitor the chemical contribution to the hydration free energy by progressively adding solvent ligands to the inner-shell and find that four-water molecules are needed to fully account for the chemical term. For a chemically meaningful coordination radius, we find that W(4) ≈ W(1) and thus the interaction contribution is principally accounted for by the free energy for forming a one-water cluster, and intrinsic occupancy factors alone account for over half of the chemical contribution. Our study emphasizes the need to acknowledge the intrinsic solvent properties in interpreting the hydration structure of any solute, with particular care in cases where the solute-solvent interaction strength is similar to that between the solvent molecules.     

Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study

The solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical∕molecular mechanical (QM∕MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM∕MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorption spectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorption spectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorption spectrum. In the solvent effect, the variation in C-C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.     

A simple analysis of the influence of the solvent-induced electronic polarization on the <Superscript>15</Superscript>N magnetic shielding of pyridine in water

Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/6-311++G (d,p) are used to analyze different aspects of the solvent effects on the ¹⁵N magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as −58.7 ppm, in good agreement with the experimental value of −56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of −61.8 ppm.     

Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model

In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson–Boltzmann/solvent‐accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self‐consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well‐experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0.8 kcal/mol versus 2.5 kcal/mol for the CHARMM36 additive force field. The polarization work associated with the solute transfer from the gas‐phase to the polar solvent, a term neglected in the framework of additive force fields, was found to make a large contribution to the total solvation free energy, comparable to the polar solute–solvent solvation contribution. The Drude PB/SASA also reproduces well the electronic polarization from the explicit solvent simulations of a small protein, BPTI. Model validation was based on comparisons with the experimental relative binding free energies of 371 single alanine mutations. With the Drude PB/SASA model the root mean square deviation between the predicted and experimental relative binding free energies is 3.35 kcal/mol, lower than 5.11 kcal/mol computed with the CHARMM36 additive force field. Overall, the results indicate that the main limitation of the Drude PB/SASA model is the inability of the SASA term to accurately capture non‐polar solvation effects. © 2018 Wiley Periodicals, Inc.     

在脂肪酸-水流动相中小分子在反相高效液相色谱中的保留表征

在反相液相色谱(RPLC)中用Snyder经验议程和计量置换保留模型(SDM-R)中的参数对深质为脂肪醇同系物,流动相为脂肪酸同系物时深质的保留行为进行了研究,结果表明用SDM-R参数具有明显的优越性,另外,由于用Snyder经验公式中二参数之间的作园无法准确求得斜率,且其不具有明确的物理意义,而由SDM-R二参数作图,不但能准确求得斜率j(与1mol溶剂和固相结合能有关的常数),而且j具有明确的物理意义并符合碳数规律,所以,参数j有可能用于RPLC中表征深剂强度,由此得出,在RPLC中,对同一置换剂面言,随同系物溶质的Z(1mol深剂化深质被深剂化固定相吸附时,从二接解面释放出的置换剂分子数)和logI(与1mol深质和固定相亲和势有关的常数)值增大,它们的保留时间也增大,对同一深质而言,随着在同系物置换剂中碳链的增长,Z和logI值的减小,它的保留时间也缩短,同时还可得出,随着同系物置换剂j值的减小,它们的洗脱能力也增强.     

Modeling absorption spectra of molecules in solution

The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute–solvent interactions are key to understanding solution-phase reactivity and spectroscopy, simulating accurate inhomogeneous broadening, and predicting absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practical guidelines for sampling solute–solvent configurations, choosing a solvent model, performing the excited state electronic structure calculations, and computing spectral lineshapes. We also present our recent results combining the vertical excitation energies computed from an ensemble of solute–solvent configurations with the vibronic spectra obtained from a small number of frozen solvent configurations, resulting in improved simulation of absorption spectra for molecules in solution.     

Hybrid supermolecule-polarizable continuum approach to solvation: Application to the mechanism of the Stevens rearrangement

Semiempirical molecular orbital theory has been used to study the effects of solvation by acetonitrile on the Stevens rearrangement of methylammonium formylmethylide to 2-aminopropanal. Three methods of solvation have been used to investigate both the electrostatic and specific solvent–solute effects of solvation: a supermolecule calculation involving the complete geometry optimization of up to six solvent molecules about the solute, the conductor-like screening model (COSMO) polarizable continuum method which allows for geometry optimization of the solute in a solvent defined by its dielectric constant, and a hybrid method in which up to five solvent molecules are incorporated inside the solute cavity and complete geometry optimization of the complex is carried out within the polarizable continuum. A comparison of the calculated geometries, rearrangement activation energies, and enthalpies of solvation from these approaches is presented, and the explicit versus bulk solvation effects are discussed. The overall effect of all methods for incorporating solvation effects is that the radical pair pathway is perferred over the concerted mechanism. © 1996 by John Wiley & Sons, Inc.     

Evaluation of partial interference functions of solutes in dilute metallic liquid alloys

This paper concerns the evaluation of the partial interference function of solutes in a liquid metallic solvent. The free electron model and its assumption for the solvent enables the calculation of the value of the partial interference function of the solute for zero wave vector.Comparison of the result with those deducted from thermodynamic data is made and the agreement is found to be satisfactory.On the other hand the partial interference function calculated for the whole range of wave vectors is compared for one system to the hard sphere Percus—Yevick model and to a recent model which uses a quasi chemical treatment.     

Ab initio QM/MM study of excited state electron transfer between pyrene and 4,4′‐bis(dimethylamino)‐diphenylmethane with different solvent systems: Role of hydrogen bonding within solvent molecules

The exciplex is a charge transfer species formed in the process of electron transfer between an electron donor and an electron acceptor and hence is very sensitive to solvent polarity. In order to understand the role of solvent in exciplex formation between pyrene (PY) and 4,4′‐bis(dimethylamino)diphenylmethane (DMDPM), we used two types of solvent approximations: an implicit solvent model and an explicit solvent model. The difference in energies between the excited and the meta‐stable Frank–Condon state (ΔE) of the structures were assumed to correspond to the emission maximum of the exciplex in different solvents. The ΔE values show the trend of stabilization of the exciplex with an increase in solvent polarity. This trend in stabilization is substantially more prominent in the explicit solvent model than that with the implicit solvent model. The ΔE value obtained in methanol reflects equal stabilization compared to that in a more polar solvent, N,N‐dimethylformamide. This extra stabilization of the exciplex may be explained on the basis of the H‐bonding capability of the protic solvent, methanol. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005