Density functional theory based molecular-dynamics study of aqueous fluoride solvation

We use density functional theory based molecular-dynamics simulations to study the aqueous solvation of the fluoride anion. Our studies are focused on the first solvation shell and have resulted in detailed information on its structural and dynamical properties. The fluoride ion leads to the formation of a rigid solvation shell, qualitatively consistent with simulation and experimental studies, classifying fluoride as a "structure making" particle. However, quantitatively we find the solvation shell to be less structured and more mobile than predicted from empirical force-field simulation. The influence on the intramolecular electronical and structural properties of water is minimal, as observed for other halogens. We propose two distinct mechanisms for the exchange of bulk and first solvation shell water molecules.     

Density functional theory based molecular-dynamics study of aqueous iodide solvation

We study the solvation of iodide in water using density functional theory based molecular-dynamics simulations. Detailed analysis of the structural and dynamical properties of the first solvation shell is presented, showing a disruptive influence of the ion on the local water structure. Iodide-water hydrogen bonding is weak, compared to water-water hydrogen bonds. This effective repulsive ion-water interaction leads to the formation of a quite unstructured solvation shell. The dynamics of water molecules surrounding the iodide is relatively fast. The intramolecular structural and electronical properties of water molecules around the ion are not affected.     

Density functional theory study of high-pressure behavior of crystalline hexanitrostilbene

A detailed study of the structural, electronic, and absorption properties of crystalline hexanitrostilbene (HNS) under hydrostatic pressure of 0–80 GPa was performed with density functional theory. The results show that the structure is much stiffer in the b and c direction than along the a axis, showing that the compressibility of HNS crystal is anisotropic. As the pressure increases, the band gap gradually decreases. An analysis of density of states shows that the electronic delocalization in HNS gradually increases under the influence of pressure. An understanding of the stabilities of HNS under compression based on the electronic structure shows that an applied pressure increases the impact sensitivity of HNS to detonation initiation. As the pressure increases, HNS has relatively high optical activity. The absorption spectra of HNS at high-pressure display a few, strong bands in the fundamental absorption region.     

Density functional theory analysis of dimethylphosphate hydrolysis: effect of solvation and nucleophile variation

We model the hydrolytic cleavage of dimethylphosphate by hydroxide ion and water in the gas phase and in implicit water using density functional theory. In all cases the rate-determining step is the nucleophilic attack. The barrier for this nucleophilic attack in vacuum is much larger for the hydroxide than for the neutral nucleophile. However, in water the barriers are similar. The rate-determining step in the attack by the neutral nucleophile involves the concerted transfer of a proton from the water molecule to the phosphate ion and the formation of the P–O bond.     

Density functional theory of solvation and its relation to implicit solvent models

We describe a density functional theory approach to solvation in molecular solvents. The solvation free energy of a complex solute can be obtained by direct minimization of a density functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the knowledge of the direct correlation function of the pure solvent. After discussing general molecular solvents, we present a generic density functional describing a dipolar solvent and we show how it can be reduced to the conventional implicit solvent models when the solvent microscopic structure is neglected. With respect to those models, the functional includes additional effects such as the microscopic structure of the solvent, the dipolar saturation effect, and the nonlocal character of the dielectric constant. We also show how this functional can be minimized numerically on a three-dimensional grid around a solute of complex shape to provide, in a single shot, both the average solvent structure and the absolute solvation free energy.     

Density functional theory study on carbon dioxide absorption into aqueous solutions of 2-amino-2-methyl-1-propanol using a continuum solvation model

We used density functional theory (DFT) calculations with the latest continuum solvation model (SMD/IEF-PCM) to determine the mechanism of CO(2) absorption into aqueous solutions of 2-amino-2-methyl-1-propanol (AMP). Possible absorption process reactions were investigated by transition-state optimization and intrinsic reaction coordinate (IRC) calculations in the aqueous solution at the SMD/IEF-PCM/B3LYP/6-31G(d) and SMD/IEF-PCM/B3LYP/6-311++G(d,p) levels of theory to determine the absorption pathways. We show that the carbamate anion forms by a two-step reaction via a zwitterion intermediate, and this occurs faster than the formation of the bicarbonate anion. However, we also predict that the carbamate readily decomposes by a reverse reaction rather than by hydrolysis. As a result, the final product is dominated by the thermodynamically stable bicarbonate anion that forms from AMP, H(2)O, and CO(2) in a single-step termolecular reaction.     

Density functional theory study on the interaction of catechin and cytosine

The interacting patterns and mechanism of the catechin and cytosine have been investigated using the density functional theory B3LYP method with 6-31+G* basis set.Eleven stable structures of the catechin-cytosine complexes have been found respectively.The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions.Theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been utilized to investigate the hydrogen bonds involved in all the systems.The interactio...     

Density functional theory study of the 5-pyrrolidin-2-yltetrazole-catalyzed aldol reaction

The replacement of the carboxylic acid functionality with a tetrazolic acid in the proline-catalyzed asymmetric aldol reaction between acetone and trimethylacetaldehyde has been studied using DFT methods at the B3LYP/6-31G** computational level. For the C–C bond-formation step, four reactive channels corresponding to the syn and anti arrangement of the enamine and the re and si attack modes have been analyzed. The B3LYP/6-31G** results allowed us to explain the stereoselectivity and the increase in reactivity relative to the proline-catalyzed process in DMSO.     

吲哚分子振动光谱的密度泛函理论研究

用多种密度泛函理论(DFT)方法(BLYP/6-31G^*^*,B3LYP/6-31G^*^*,B3PW91/6-31G^*^*和SVWN/6-31G^*^*)对吲哚分子的平衡几何构型进行了优化。在优化构型的基础上计算了吲哚分子的谐力场、振动基频和红外光谱强度。计算得到的振动频率与实验值比较平均偏差对四种计算方法(BLYP/6-31G^*^*,P3LYP/6-31G^*^*,B3PW91/6-31G^*^*和SVWN/6-31G^*^*)分别为16.3,40.5,45.1和26.4cm^-^1。BLYP/6-31G^*^*理论力场被用于吲哚分子的简正坐标分析计算中。根据振动率的势能分布(PEDs)对此分子的振动基频进行了理论归属。     

苯酚分子拉曼光谱的密度泛函理论研究

采用B3LYP杂化泛函,6-31++G(d,p)基组,对苯酚分子的结构进行了优化.通过频率计算,获得了苯酚分子的拉曼光谱,并利用势能函数分布(PED)对拉曼光谱进行了指认.绘制了苯酚分子的静电势分布图,讨论了苯酚分子发生化学反应的位置,同时计算了HOMO-LUMO的能级差.通过TD-DFT计算获得了苯酚分子的吸收光谱和激发态.     

儿茶素-胞嘧啶分子间相互作用的密度泛函研究

采用密度泛函理论的B3LYP方法,在6-31+G*基组水平上研究了儿茶素-胞嘧啶分子间相互作用机制,得到稳定的儿茶素-胞嘧啶复合物11个.计算结果表明氢键对于复合物的稳定性起着重要的作用,并且当复合物形成2个或更多的氢键时,氢键的类型及强度共同决定着复合物的稳定性.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11种复合物中氢键的性质和特征进行了分析.通过研究发现,所有的氢键复合物进行基组重叠误差(BSSE)校正后的相互作用能为-17.35～-43.27kJ/mol,相互作用能主要由氢键所贡献.振动分析显示,氢键的形成使相对应键的对称伸缩振动频率减小,说明这些复合物中形成的氢键都是正常的红移型氢键,与实验结果相一致.     

Density functional theory study on the structure and vibrational frequencies of glycylglycine

Eleven possible conformers of glycylglycine have been studied by using the BLYP, B3LYP methods of density functional theory and the HF method at the basis set of 6-311++G**. BLYP (using Becke's and Lee-Yang-Parr's correlation functionals), ab initio Hartree-Fock (HF) and hybrid DFT/HF B3LYP calculations have been carried out to study the structure and vibrational spectra of glycylglycine. Glycylglycine crystal structure has been determined by X-ray diffraction analysis. The title compound has been crystallizes in the orthorhombic space group C1, with Z=4. And the unit cell parameters are: a=8.1184(12)A, b=9.5542(14)A, c=7.8192(11)A and V=577.95(15)A(3). Molecular conformation calculations have got 11 possible conformers. In these possible conformers, the most stable one has been selected. The BLYP/6-311++G** and scaled HF/6-311++G** frequencies correspond well with available experimental assignments of the normal vibrational modes. Comparison of the observed fundamental vibrational frequencies of glycylglycine and calculated results by density functional B3LYP and Hartree-Fock (HF) methods indicates that B3LYP is superior to the scaled Hartree-Fock (HF) for molecular vibrational issues.     

白藜芦醇清除自由基活性的密度泛函理论研究

采用密度泛函理论(DFT)方法,从静态与动态两大方面分析了白藜芦醇分子酚羟基在不同溶剂中清除自由基活性的能力大小.通过白藜芦醇的结构参数、前线轨道理论、3种抽氢反应机制等方面分析了分子活性位与其性质的关系.探讨了白藜芦醇分子不同位置酚羟基清除·OH和·OOH的抗氧化机理,得到了该分子与·OOH发生抽氢反应时的过渡态结构.计算结果表明,在任何溶剂中白藜芦醇分子C(4')位上酚羟基活性最高,发生抽氢反应时反应热最小,是高活性位点.     

Density functional theory study on the hydrolysis process of COS and CS2 on a graphene surface

Research on Chemical Intermediates - The adsorption behavior and hydrolysis mechanism of COS and CS2 on a graphene surface were studied by using density functional theory. It could be concluded...     

Density functional study of lithium hexamethyldisilazide (LiHMDS) complexes: effects of solvation and aggregation

The title compound, lithium hexamethyldisilazide (LiHMDS), has been studied using modern quantum-chemical methods in the form of the B3LYP approach. Monomers, dimers, trimers, and tetramers, microsolvated with up to four THF molecules have been considered. The choice of model complex is seen to be important-for instance, the simpler water molecule is shown to be an inappropriate substitute for the THF solvent. Calculated lithium NMR shieldings are reported, but by themselves, they seem to be insufficient for unequivocal assignments of the different species. The energetics of aggregation and solvation have been studied. Temperature effects are seen to be important, and the degrees of solvation and aggregation are higher at 0 K than at 298 K. The highest degree of THF solvation for the monomer and dimer is found to be three (0 K) and two (298 K), respectively. The highest possible degree of aggregation for unsolvated LiHMDS is four. However, in nonpolar solvents, formation of the LiHDMS dimer from the trimer is thermodynamically preferred. The pathway is likely to involve an intermediate tetramer. In THF solution, di-solvated monomers and dimers are the most likely species.     

儿茶素结构和振动光谱的密度泛函理论研究

本文利用密度泛函理论方法B3LYP在6-311 G(d,p)水平上研究了儿茶素及其异构体表儿茶素分子的几何构型,计算结果与实验所得结构参数一致.计算了儿茶素分子平衡构型下的力常数,使用Wilson的GF矩阵方法计算了振动基频以及相应的势能分布,据此结合理论计算的光谱强度,对儿茶素分子的振动基频进行了完善合理的理论归属.     

三聚氰胺结构和热力学性质的密度泛函理论研究

采用Materials Studio 软件中的DMol~3模块对三聚氰胺的结构和性质进行了理论研究.得到了分子的几何构型、振动频率、各原子上的电荷分布、热力学、以及Fukui指数和前线分子轨道.计算结果表明:三聚氰胺分子中的C原子易得电子,是亲核试剂进攻点,而胺基上的N原子因含孤对电子是亲电反应中心.     

Density functional theory study on the interaction between metalloporphyrins and NH3

The binding behaviors of eight bivalent metalloporphyrins (MPs) (M?Zn, Mg, Cu, Mn, Fe, Co, Ni, and Cd) with NH₃ were investigated by density functional theory. For both MPs and corresponding complexes MPs‐NH₃, good linear correlations are found between the partial charge on metal M and that on atom N (nitrogen of porphyrin) as well as the M? N bond length. Natural population and frontier orbital analysis demonstrate that charge transfer in CoP‐NH₃ is much easier and greater. As a consequence of the charge transfer and the hybridization of molecular energy levels, striking disparities of electronic properties of MPs‐NH₃ are observed. Particularly, a modest linear relationship is obtained between the magnitude of charge transfer and the binding energy. The much greater Fukui functions of CoP, together with its larger binding strength, suggest that CoP is more favorable to the interaction with NH₃, which might be a promising sensing material to response NH₃. © 2013 Wiley Periodicals, Inc.