Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.     

Software package SIMPRE—Revisited

This article elucidates the pitfalls identified in the software package SIMPRE recently developed by Baldoví et al. (J. Comput. Chem. 2013, 34, 1961) for modeling the spectroscopic and magnetic properties of single ion magnets as well as single‐molecule magnets. Analysis of the methodology used therein reveals that the crystal field parameters (CFPs), expressed nominally in the Stevens formalism, exhibit features characteristic for the CFPs expressed in the Wybourne notation. The resemblance of the two types of CFPs introduces a serious confusion that may lead to wrong comparisons of the CFPs taken from various sources. To clarify this confusion, the properties of the CFPs ( , ) associated with the Stevens operators ( X = S , J , or L ), which belong to the class of the tesseral‐tensor operators, are contrasted with those of the CFPs B_kq associated with the Wybourne operators , which belong to the class of the spherical‐tensor operators. Importantly, the confused properties of Stevens and Wybourne operators may bear on reliability of SIMPRE calculations. To consider this question independent calculations are carried out using the complete approach and compared with those of the restricted approach utilized earlier. It appears that the numerical results of the package SIMPRE are formally acceptable, however, the meaning of the CFPs must be properly reformulated. Several other conceptual problems arising from misinterpretations of the crucial notions and the CFP notations identified therein are also discussed and clarified. © 2014 Wiley Periodicals, Inc.     

Conductor‐like screening model for relaxed excited states: Implementation in the semiempirical method MSINDO

Two approaches to treat solvent polarization and reorientation effects for excited states of molecules and surfaces have been implemented in the recently developed MSINDO‐sCIS method (Gadaczek, Krause, Hintze, Bredow, J. Chem. Theory Comput. 2011, 7, 3675). They allow for an efficient calculation of analytical energy gradients and hence open the opportunity to investigate fluorescence effects or photochemical reactions in solution for large molecules that are difficult to treat with high‐level methods. Both approaches are based on the conductor‐like screening model (COSMO) (Klamt and Schüürmann, J. Chem. Soc., Perkin Trans. 1993, 2, 799) in combination with the configuration interaction singles (CIS) method (Foresman, Head‐Gordon, Pople, and Frisch, J. Phys. Chem. 1992, 96, 135). The paper gives a brief outline of the theoretical background. As a first application, solvent shifts of three well‐studied, environment‐sensitive fluorescent dyes (Kucherak, Didier, Mély, and Klymchenko, J. Phys. Chem. Lett. 2010, 1, 616) have been calculated and compared with experimental results and standard time‐dependent density functional theory. A statistical evaluation of MSINDO‐COSMO‐sCIS is provided for a set of 39 molecules suggested recently by Jacquemin et al. (Jacquemin, Planchat, Adamo, and Mennucci, J. Chem. Theory Comput. 2012, 8, 2359). Calculated vertical and adiabatic excitation energies and fluorescence energies are compared to experimental data. © 2014 Wiley Periodicals, Inc.     

The cyclic cluster model at hartree–fock level

We present the implementation of the cyclic cluster model (CCM) formalism at the Hartree–Fock (HF) level. In contrast to other periodic models, the CCM is a Γ‐point approach. Integration is carried out in real space within a finite interaction area determined by the size and the shape of the cluster that corresponds to a supercell of the solid, surface, or polymer. Particular care has to be taken for the proper treatment of three‐ and four‐center integrals that involve basis functions located at the boundaries of the Wigner–Seitz supercell, which defines the interaction region. The similarity between the CCM formalism and molecular approaches allows in principle the application of sophisticated post HF methods to solid‐state problems with only moderate modification of the molecular code. We show for selected model systems, that with our approach, the electronic structure and energetics obtained by the conventional supercell model is fully reproduced. © 2014 Wiley Periodicals, Inc.     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

Study of Bimodal Drop Size Distributions of Emulsion

In order to increase the present understanding of bimodal emulsion drop size distributions, systematic series of experiments have been carried out to investigate the effects of formulation variables on bimodal drop size distributions, and probability distribution functions were proposed to analyze the distribution. The results show that, the span of the drop size and Sauter mean diameter become larger when the dispersed phase volume fraction becomes higher and rotor speed becomes lower; the Frechet function represents the experimental data satisfactorily. The prediction model of Sauter mean diameter established by combining the prediction theory of the maximum stable drop diameter and experimental analysis results can fit the experimental data well.     

煤液化沥青分析表征及结构模型

对从煤液化残渣中萃取出的沥青类物质进行了固体13C-CP/MAS NMR分析、元素分析、红外光谱分析(FT-IR)和光电子能谱(XPS)分析,得到煤液化沥青的芳香结构单元信息及相关结构参数信息。结果表明,煤液化沥青芳香桥碳与周碳之比为0.115,芳香碳原子的存在形式以苯结构为主;脂肪结构多以甲基和环状亚甲基形式存在;氧主要以羰基、酯基的形式存在;氮主要以吡咯的形式存在。利用结构参数和分析表征结果构建了煤液化沥青的大分子结构模型,并运用13C-NMR预测软件ACD/CNMR Predictor计算了煤精制沥青大分子结构模型的13C化学位移。根据计算结果对大分子结构模型进行了修正,获得了与实验谱图吻合较好的大分子结构模型。     

TG-MS与Py-GC相结合法研究惰性气氛下含硫模型化合物热解过程中硫的脱除及释放行为研究

采用热重-质谱法(TG-MS)和热解-气相色谱法(Py-MS)相结合的方法对模型化合物(十四硫醇、二丁基硫醚、苯硫醚、二甲基噻吩、苯并噻吩和二苯并噻吩等)在惰性气氛下硫的脱除及释放行为进行研究。惰性气氛下硫的脱除顺序为:十四硫醇>二丁基硫醚>二甲基噻吩>苯并噻吩>苯硫醚>二苯并噻吩,苯硫醚除外,该顺序与含硫官能团的热分解顺序一致。在热解过程中,所有模型化合物在质谱和气相色谱仪上均被检测到SO₂;除苯硫醚和二苯并噻吩外,其他模型化合物中均检测到了COS;而只在十四硫醇、二丁基硫醚和二甲基噻吩中检测到了H₂S。且热解气中SO₂含量要显著高于H₂S和COS。这是由于活性炭作载体时,惰性气氛下内部氢的含量显著小于内部氧的含量,所以大多数的含硫自由基易与内部氧结合以SO₂的形式逸出。对于苯硫醚、苯并噻吩和二苯并噻吩中没有检测到H₂S,是由于内部氢的不足,使得含硫自由基不能与内部氢结合,所以没有检测到H₂S逸出。     

Determination of the n‐octanol/water partition coefficients of weakly ionizable basic compounds by reversed‐phase high‐performance liquid chromatography with neutral model compounds

A strategy to utilize neutral model compounds for lipophilicity measurement of ionizable basic compounds by reversed‐phase high‐performance liquid chromatography is proposed in this paper. The applicability of the novel protocol was justified by theoretical derivation. Meanwhile, the linear relationships between logarithm of apparent n‐octanol/water partition coefficients (logK_ow′′) and logarithm of retention factors corresponding to the 100% aqueous fraction of mobile phase (logk_w) were established for a basic training set, a neutral training set and a mixed training set of these two. As proved in theory, the good linearity and external validation results indicated that the logK_ow′′–logk_w relationships obtained from a neutral model training set were always reliable regardless of mobile phase pH. Afterwards, the above relationships were adopted to determine the logK_ow of harmaline, a weakly dissociable alkaloid. As far as we know, this is the first report on experimental logK_ow data for harmaline (logK_ow = 2.28 ± 0.08). Introducing neutral compounds into a basic model training set or using neutral model compounds alone is recommended to measure the lipophilicity of weakly ionizable basic compounds especially those with high hydrophobicity for the advantages of more suitable model compound choices and convenient mobile phase pH control.