Three‐dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model

The three‐dimensional solution conformation of teicoplanin aglycone was determined using NMR spectroscopy. A combination of NOE and dihedral angle restraints in a DMSO solvation model was used to calculate an ensemble of structures having a root mean square deviation of 0.17 Å. The structures were generated using systematic searches of conformational space for optimal satisfaction of distance and dihedral angle restraints. Comparison of the NMR‐derived structure of teicoplanin aglycone with the X‐ray structure of a teicoplanin aglycone analog revealed a common backbone conformation with deviation of two aromatic side chain substituents. Experimentally determined backbone ¹³C chemical shifts showed good agreement with those computed at the density functional level of theory, providing a cross validation of the backbone conformation. The flexible portion of the molecule was consistent with the region that changes conformation to accommodate protein binding. The results showed that a hydrogen‐bonded DMSO molecule in combination with NMR‐derived restraints together enabled calculation of structures that satisfied experimental data. Copyright © 2015 John Wiley & Sons, Ltd.     

La(Ⅲ)-乙醇溶液微团簇理论和光谱研究

利用分子光谱和基于密度泛函理论的第一性原理,采用改进的TPSSTPSS泛函方法对C、H、O原子用6-31G基组并添加极化和弥散函数,对La原子选用Def2-SV(P)赝势基组,研究La3+/乙醇溶液微团簇构型。优化计算La3+在水溶液中的溶剂化结构,得出气相中的优化结果可以近似代替液相结果的结论;理论优化计算La3+/乙醇溶液可能存在的结构构型的结果表明,溶剂化数n=6时结构最稳定。采用荧光光谱和核磁共振实验对结果进行了验证,表明La3+的加入使荧光强度显著增强,在高浓度时生成的团簇构型比较稳定,且随着溶剂化数目的增加,O—H键长增大,La3+使其附近的质子产生强大的屏蔽效应,化学位移向高场移动,溶剂化数n=6时绝对误差最小,最稳定,与理论计算结论相吻合。     

Accuracy assessment of the linear Poisson–Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid–protein complexes

The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson–Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev–Bashford–Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson–Boltzmann model. © 2015 Wiley Periodicals, Inc.     

Solvation Rule for Solid‐Electrolyte Interphase Enabler in Lithium‐Metal Batteries

Despite the exceptionally high energy density of lithium metal anodes, the practical application of lithium‐metal batteries (LMBs) is still impeded by the instability of the interphase between the lithium metal and the electrolyte. To formulate a functional electrolyte system that can stabilize the lithium‐metal anode, the solvation behavior of the solvent molecules must be understood because the electrochemical properties of a solvent can be heavily influenced by its solvation status. We unambiguously demonstrated the solvation rule for the solid‐electrolyte interphase (SEI) enabler in an electrolyte system. In this study, fluoroethylene carbonate was used as the SEI enabler due to its ability to form a robust SEI on the lithium metal surface, allowing relatively stable LMB cycling. The results revealed that the solvation number of fluoroethylene carbonate must be ≥1 to ensure the formation of a stable SEI in which the sacrificial reduction of the SEI enabler subsequently leads to the stable cycling of LMBs.     

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.     

DFT modeling of reactivity in an ionic liquid: How many ion pairs?

The modeling of reactivity in an ionic liquid is examined with DFT and DFT/MM calculations on the S(N)2 intramolecular rearrangement of the Z-phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole into 4-benzoylamino-2,5-diphenyl-1,2,3-triazole induced by amines. Experimental research has shown that the reaction occurs in 1-butyl-3-methylimidazolium tetrafluoroborate, and in conventional organic solvents such as acetonitrile with comparable rates. The structure for the reactants, transition states and products for the rate-determining step are optimized, and the energy barrier is computed in three different environments: gas phase, water solvent, and ionic liquid. The results are encouraging in describing the energy barrier in the ionic liquid. A simple model is formulated to explain the effect of the solvent in this particular process, and a procedure to study theoretically the reactivity in an ionic liquid is proposed.     

A size-modified poisson–boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel

We present a new size-modified Poisson–Boltzmann ion channel (SMPBIC) model and use it to calculate the electrostatic potential, ionic concentrations, and electrostatic solvation free energy for a voltage-dependent anion channel (VDAC) on a biological membrane in a solution mixture of multiple ionic species. In particular, the new SMPBIC model adopts a membrane surface charge density and a natural Neumann boundary condition to reflect the charge effect of the membrane on the electrostatics of VDAC. To avoid the singularity difficulties caused by the atomic charges of VDAC, the new SMPBIC model is split into three submodels such that the solution of one of the submodels is obtained analytically and contains all the singularity points of the SMPBIC model. The other two submodels are then solved numerically much more efficiently than the original SMPBIC model. As an application of this SMPBIC submodel partitioning scheme, we derive a new formula for computing the electrostatic solvation free energy. Numerical results for a human VDAC isoform 1 (hVDAC1) in three different salt solutions, each with up to five different ionic species, confirm the significant effects of membrane surface charges on both the electrostatics and ionic concentrations. The results also show that the new SMPBIC model can describe well the anion selectivity property of hVDAC1, and that the new electrostatic solvation free energy formula can significantly improve the accuracy of the currently used formula. © 2019 Wiley Periodicals, Inc.     

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.     

Generating Excess Protons in Microsolvated Acid Clusters under Ambient Conditions: An Issue of Configurational Entropy versus Internal Energy

Acid dissociation, and thus liberation of excess protons in small water droplets, impacts on diverse fields such as interstellar, atmospheric or environmental chemistry. At cryogenic temperatures below 1 K, it is now well established that as few as four water molecules suffice to dissociate the generic strong acid HCl, yet temperature-driven recombination sets in simply upon heating that cluster. Here, the fundamental question is posed of how many more water molecules are required to stabilize a hydrated excess proton at room temperature. Ab initio path integral simulations disclose that not five, but six water molecules are needed at 300 K to allow for HCl dissociation independently from nuclear quantum effects. In order to provide the molecular underpinnings of these observations, the classical and quantum free energy profiles were decomposed along the dissociation coordinate in terms of the corresponding internal energy and entropy profiles. What decides in the end about acid dissociation, and thus ion pair formation, in a specific microsolvated water cluster at room temperature is found to be a fierce competition between classical configurational entropy and internal energy, where the former stabilizes the undissociated state whereas the latter favors dissociation. It is expected that these are generic findings with broad implications on acid–base chemistry depending on temperature in small water assemblies.