Electrical switching effect in a photochromic molecule between two graphene electrodes

We propose a single-molecule electrical switches consisting of a photochromic dimethyldihydropyrene/cyclophanediene molecule sandwiched between two graphene electrodes and investigate the electronic transport by using density-functional theory and nonequilibrium Green's function methods. The “open” and “closed” isomers of the photochromic molecule are shown to have electrical switching behavior and negative differential resistance effect. Moreover, it is also found that the switching ratio between two different conductive states depends on the ambient temperature, and the device behaves as a stable electrical switch around room temperature, which is in agreement with a recent experimental study of another photochromic molecule diarylethene reported by Jia et al. (2016) [17].     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Li＋在PC＋DMF混合溶剂中优先溶剂化的13C NMR研究

利用¹³C NMR光谱技术研究了Li^＋在碳酸丙烯酯(PC)＋N,N-二甲基甲酰胺(DMF)混合溶剂中的优先溶剂化现象. 根据溶剂分子中碳原子的化学位移随锂盐浓度的变化关系, 确定了与Li^＋发生配位的原子. 碳原子的配位位移值随混合溶剂组成的变化关系表明, 在LiClO₄＋PC＋DMF混合物中, DMF分子对Li^＋的溶剂化作用较PC分子强. 定量计算得到, 在n(PC)∶n(DMF)＝1∶1(摩尔比)的混合溶剂中, PC与DMF分子数在Li^＋第一溶剂化层中的比率为0.12, 说明Li^＋优先被DMF分子溶剂化.     

Solvent Reorganization Energy and Electronic Coupling for Intramolecular Electron Transfer in Biphenyl-Acceptor Anion Radicals

基于非平衡溶剂化理论和连续介质模型修改了GAMESS中的相关程序,实现了电子转移溶剂重组能的数值计算. 采用修改后的程序计算得到了联苯-雄甾烷-萘和联苯-雄甾烷-菲这两个体系电子转移的溶剂重组能约为60 kJ/mol. 这个结果与实验拟合值符合的很好. 利用线性反应坐标与Koopmans定理计算了电子转移耦合矩阵元,结果与实验拟合值有可比性.     

Apparent Molar Volumes of Multicharged Cations in Dimethyl Sulfoxide Solutions at 25°C

Densities for DMSO solutions of iron(III), aluminium(III), beryllium(II) and magnesium(II) perchlorates and silver nitrate are reported. Densities for DMSO solutions of tetraethylammonium perchlorate and nitrate and tetrabutylammonium perchlorate and tetraphenylborate are also presented. The partial molar volumes of the DMSO-solvated cations are derived and discussed in terms of variation with the charge number.     

Comparison of solubility of gases and vapours in wet and dry alcohols,especially octan‐1‐ol

Equations for the solubility of gases and vapours into dry alcohols from methanol to decan‐1‐ol and into water‐saturated alcohols from butan‐1‐ol to decan‐1‐ol have been compared through the use of the Abraham solvation equation. It is shown that there are noticeable differences in solvation into the dry and wet alcohols, and that these differences become larger as the alcohols become smaller and take up more water. The two main factors that lead to the differences in solvation are the solute hydrogen‐bond basicity, B, and solute size, L. Increase in solute hydrogen‐bond basicity favours the wet alcohols and increase in solute size favours the dry alcohols. Solute hydrogen‐bond acidity plays no part, because the hydrogen‐bond basicity of water, wet alcohols and dry alcohols is almost the same. Copyright © 2008 John Wiley & Sons, Ltd.     

Chelation of Na+ cations in nonaqueous solvents. Structural requirements and methodological considerations

Intrinsic formation constants for complexes of Na⁺ ions with a series of polyamines have been determined from²³Na NMR measurements in binary mixtures of tetrahydrofuran (THF) and amines. The results show in a totally unambiguous manner a regular decrease in the magnitude of the chelate effect with the number of atoms intervening between the nitrogen ligators. The key assumption, tetracoordination of the cation, is critically examined, and experimental evidence is adduced in its support.     

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

The parameterization and validation of generalized born models using the pairwise descreening approximation

Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson-Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution.