Cartesian formulation of the mobile block Hessian approach to vibrational analysis in partially optimized systems

Partial optimization is a useful technique to reduce the computational load in simulations of extended systems. In such nonequilibrium structures, the accurate calculation of localized vibrational modes can be troublesome, since the standard normal mode analysis becomes inappropriate. In a previous paper [A. Ghysels et al., J. Chem. Phys. 126, 224102 (2007)], the mobile block Hessian (MBH) approach was presented to deal with the vibrational analysis in partially optimized systems. In the MBH model, the nonoptimized regions of the system are represented by one or several blocks, which can move as rigid bodies with respect to the atoms of the optimized region. In this way unphysical imaginary frequencies are avoided and the translational/rotational invariance of the potential energy surface is fully respected. In this paper we focus on issues concerning the practical numerical implementation of the MBH model. The MBH normal mode equations are worked out for several coordinate choices. The introduction of a consistent group-theoretical notation facilitates the treatment of both the case of a single block and the case of multiple blocks. Special attention is paid to the formulation in terms of Cartesian variables, in order to provide a link with the standard output of common molecular modeling programs.     

丙氨酸二肽分子二级结构与振动光谱特性

利用从头算方法探索蛋白质模型分子——丙氨酸二肽的二级结构布居特性以及体系势能变化. 引入对分子结构敏感的振动探针(酰胺振动吸收带), 借助其光谱表象, 寻求振动光谱参数与分子结构之间的联系. 研究结果表明: 丙氨酸二肽分子处于C_7eq构型(Φ/Ψ=-80°/80°)时具有最低能量值, 且分子易形成β折叠、PP_II、C₅及C₇等能量较低的稳定构型. 通过简正模式分析, 得到分子3N-6 个振动模式的吸收光谱, 并通过势能分布分析方法对分子骨架上酰胺振动吸收带的特征振动模式进行了指认. 重点考察分子骨架上酰胺-I带振动光谱参数与分子构型变化之间的相关性, 建立振动光谱参数与蛋白质二级结构之间的联系, 为在化学键水平上研究蛋白质的结构及其发挥作用的机制提供科学依据.     

Overtone spectra of 1,2-dichloro- and dibromo-ethanes in the near infrared region

The vibrational overtone spectra of the liquid phase 1,2-dichloroethane and 1,2-dibromoethane in the spectral regions of the CH stretching local mode overtones corresponding to Δυ_CH = 2 to Δυ_CH = 5 are reported. The observed spectral features are assigned using the local mode model. Local mode frequencies ω_CH and diagonal local model anharmonicities X_CH are obtained from an analysis of the spectra. The local-local combinations observed are interpreted on the basis of a coupled CH oscillator model hamiltonian. Local-normal combinations show complex structures and their possible assignments are given.     

Relaxation mode analysis of a peptide system: comparison with principal component analysis

This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.     

Dynamics of large proteins through hierarchical levels of coarse-grained structures

Elastic network models have been successful in elucidating the largest scale collective motions of proteins. These models are based on a set of highly coupled springs, where only the close neighboring amino acids interact, without any residue specificity. Our objective here is to determine whether the equivalent cooperative motions can be obtained upon further coarse-graining of the protein structure along the backbone. The influenza virus hemagglutinin A (HA), composed of N = 1509 residues, is utilized for this analysis. Elastic network model calculations are performed for coarse-grained HA structures containing only N/2, N/10, N/20, and N/40 residues along the backbone. High correlations (>0.95) between residue fluctuations are obtained for the first dominant (slowest) mode of motion between the original model and the coarse-grained models. In the case of coarse-graining by a factor of 1/40, the slowest mode shape for HA is reconstructed for all residues by successively selecting different subsets of residues, shifting one residue at a time. The correlation for this reconstructed first mode shape with the original all-residue case is 0.73, while the computational time is reduced by about three orders of magnitude. The reduction in computational time will be much more significant for larger targeted structures. Thus, the dominant motions of protein structures are robust enough to be captured at extremely high levels of coarse-graining. And more importantly, the dynamics of extremely large complexes are now accessible with this new methodology.     

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function

The docking of flexible small molecule ligands to large flexible protein targets is addressed in this article using a two-stage simulation-based method. The methodology presented is a hybrid approach where the first component is a dock of the ligand to the protein binding site, based on deriving sets of simultaneously satisfied intermolecular hydrogen bonds using graph theory and a recursive distance geometry algorithm. The output structures are reduced in number by cluster analysis based on distance similarities. These structures are submitted to a modified Monte Carlo algorithm using the AMBER-AA molecular mechanics force field with the Generalized Born/Surface Area (GB/SA) continuum model. This solvent model is not only less expensive than an explicit representation, but also yields increased sampling. Sampling is also increased using a rotamer library to direct some of the protein side-chain movements along with large dihedral moves. Finally, a softening function for the nonbonded force field terms is used, enabling the potential energy function to be slowly turned on throughout the course of the simulation. The docking procedure is optimized, and the results are presented for a single complex of the arabinose binding protein. It was found that for a rigid receptor model, the X-ray binding geometry was reproduced and uniquely identified based on the associated potential energy. However, when side-chain flexibility was included, although the X-ray structure was identified, it was one of three possible binding geometries that were energetically indistinguishable. These results suggest that on relaxing the constraint on receptor flexibility, the docking energy hypersurface changes from being funnel-like to rugged. A further 14 complexes were then examined using the optimized protocol. For each complex the docking methodology was tested for a fully flexible ligand, both with and without protein side-chain flexibility. For the rigid protein docking, 13 out of the 15 test cases were able to find the experimental binding mode; this number was reduced to 11 for the flexible protein docking. However, of these 11, in the majority of cases the experimental binding mode was not uniquely identified, but was present in a cluster of low energy structures that were energetically indistinguishable. These results not only support the presence of a rugged docking energy hypersurface, but also suggest that it may be necessary to consider the possibility of more than one binding conformation during ligand optimization.     

Coarse-graining of protein structures for the normal mode studies

The coarse-grained structural model such as Gaussian network has played a vital role in the normal mode studies for understanding protein dynamics related to biological functions. However, for the large proteins, the Gaussian network model is computationally unfavorable for diagonalization of Hessian (stiffness) matrix for the normal mode studies. In this article, we provide the coarse-graining method, referred to as "dynamic model condensation," which enables the further coarse-graining of protein structures consisting of small number of residues. It is shown that the coarser-grained structures reconstructed by dynamic model condensation exhibit the dynamic characteristics, such as low-frequency normal modes, qualitatively comparable to original structures. This sheds light on that dynamic model condensation and may enable one to study the large protein dynamics for gaining insight into biological functions of proteins.     

A critical assessment of finite element modeling approach for protein dynamics

Finite element (FE) modeling approach has emerged as an efficient way of calculating the dynamic properties of supramolecular protein structures and their complexes. Its efficiency mainly stems from the fact that the complexity of three-dimensional shape of a molecular surface dominates the computational cost rather than the molecular size or the number of atoms. However, no critical evaluation of the method has been made yet particularly for its sensitivity to the parameters used in model construction. Here, we make a close investigation on the effect of FE model parameters by analyzing 135 representative protein structures whose normal modes calculated using all-atom normal mode analysis are publicly accessible online. Results demonstrate that it is more beneficial to use a contour surface of electron densities as the molecular surface, in general, rather than to employ a solvent excluded surface, and that the solution accuracy is almost insensitive to the model parameters unless we avoid extreme values leading to an inaccurate depiction of the characteristic shapes.     

一种基于遗传算法的肽/蛋白质结合模式虚拟筛选建模技术

“合理”QSAR模型是指在了解配体与受体相互作用模式的前提下建立定量构效关系, 这样避开了传统做法仅仅依靠样本集分子自身信息来构建预测模型的诸多弊端. 本文将此思想应用于肽/蛋白质亲和活性的研究当中, 借助于遗传算法作为虚拟受体结合靶点及相互作用模式的筛选手段得到了一种新的建模技术: 肽/蛋白质结合模式遗传虚拟筛选(genetic virtual screening of combinative mode for peptide/protein, GVSC). 该法成功解决了“合理”QSAR研究中的难题, 即大多数情况下受体结构未知而难以了解配基与之发生的结合方式. 分别使用58个血管紧张素转化酶, 18个Camel抗体蛋白cAb-lys3双位点突变残基对GVSC加以检验, 其结果表明GVSC能够较好地阐明配基与受体之间的作用机理, 并能得到优于传统方法的QSAR模型.     

丙型肝炎病毒抑制剂的三维药效团和构效关系

通过ＣＡＴＡＬＹＳＴ软件包得到了两类ＨＣＶ ＮＳ３丝氨酸蛋白酶抑制剂的三维药效团模型。尽管这两类抑制剂具有完全不同的骨架结构,但得到的药效团却具有共同的特性。这当这两类抑制剂和受体发生相互作用时,可能采用了相似的结合模式。根据药效团模型,进行了三维构效关系的研究。结果表明,得到的药效团模型具有良好的预测能力（线性回归系数Ｒ＝０．８９）。     

Differentiating structural isomers of sialylated glycans by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry

Using model acidic glycans, we demonstrate the benefits of permethylation for matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI/TOF-TOF) tandem mass spectrometry. With both the linear and branched structures, extensive cross-ring fragmentation product ions were generated, yielding valuable information on sugar linkages. Elimination of the negative charges commonly associated with sialylated structures through permethylation allowed their structural analysis in the positive ion mode. Extensive A- and X-type ions were observed for the linear structures, and slightly weaker signals for the branched sialylated structures. The diagnostic cross-ring fragments, permitting a distinction between alpha2-3 and alpha2-6 linkages of the sialic acid residues, were seen in abundance. Importantly, the cross-ring fragmentation with the branched structures provides adequate information to assign sialic acid residues, with a specific linkage, to a particular antenna.     

项目式翻转学习在表界面现象教学中的尝试

According to the current status of physical chemistry teaching and problems in teaching activities, a comprehensive analysis was carried out, and a teaching mode of project-driven flipped learning was proposed. The project curriculum was optimized and designed to effectively carry out innovative teaching activities. Combined with the teaching content in the chapter of surface interface phenomenon, the specific implementation strategy of this new teaching mode is explained with specific teaching cases. This model helps to cultivate the independence of students thinking and learning autonomy, stimulates students' enthusiasm for learning, and significantly improves the quality and effect of classroom teaching.     

Sliding Mode Control in a Bioreactor Model

This article deals with an example of nonlinear control systems and the interlacing between a biochemical system, the mathematical model and the constrains derived from the discrete implementation of a continuous control policy. The theory is developed on a simplified model of a bioreactor to be regulated, and the sliding mode control is presented as a robust control technique. The biological interpretation of the results derived from the mathematical model is pointed out, especially of those more closely involved with the implementation, as is the case of sample period, which seems to be very enough with respect to the minimum time needed for sample analysis.     

The reaction between diethyl succinylsuccinate (1,4-diethoxycarbonyl-2,5-dihydroxy-1,4-cyclohexadiene) and amines and its application to polymer synthesis

Polymers having polyamine structures were obtained by the condensation reaction between diethyl succinylsuccinate (1,4-diethoxycarbonyl-2,5-dihydroxy-1,4-cyclohexadiene) and aliphatic diamines. The reactions were carried out in high polar solvents such as N-methylpyrrolidone (NMP) and N,N-dimethylformamide (DMF). The mode of the polymerization reaction and the structure of the polymers were verified by studies of model compounds. The polymers thus obtained were conveniently utilized as coating and adhesive materials and were able to be cast into films.     

结合直观推导式演进特征投影法分析原油中非烃结构和含量

提出一种分析原油非烃结构和含量的方法。用直观推导式演进特征投影法分辨有关二维数据以获得非烃的纯色谱和纯质谱,再将所获质谱在标准质谱库中检索,并结合色谱保留指数分析等来进行单个非烃化合物结构鉴定;利用实验数据,根据分辨获得的纯色谱峰面积所建立的规一化模型,进行非烃化合物定量分析。用本法确定了一原油样品中168个含氮化合物和该油样一个馏分中60个其它非烃化合物的结构和含量。本方法具有系统分析原油非烃结构和含量的通用性;标准化合物加标回收实验表明,其准确度很好。     

The semi-phenomenological model of antiferroelectricity in chiral smectic liquid crystals I. The structure of short pitch modes and a thermodynamical approach

The development of the model of short pitch modes for ferro-, antiferro- and ferri-electric chiral smectic liquid crystals is presented. Prediction of the structures of the subphases is made. The pure short pitch mode having an n-ray star structure of the n-layers of the unit cell appears to possess antiferroelectric properties. Ferrielectricity is assumed to arise as a result of the coexistence and interaction of the short pitch mode with a long pitch helix. Corresponding polarizational properties and fine structure of the peaks of the resonant X-ray scattering from such structures are calculated.     

The semi-phenomenological model of antiferroelectricity in chiral smectic liquid crystals I. The structure of short pitch modes and a thermodynamical approach

The development of the model of short pitch modes for ferro-, antiferro- and ferri-electric chiral smectic liquid crystals is presented. Prediction of the structures of the subphases is made. The pure short pitch mode having an n-ray star structure of the n-layers of the unit cell appears to possess antiferroelectric properties. Ferrielectricity is assumed to arise as a result of the coexistence and interaction of the short pitch mode with a long pitch helix. Corresponding polarizational properties and fine structure of the peaks of the resonant X-ray scattering from such structures are calculated.     

Comparative molecular field analysis (CoMFA) for phosphodiesterase (PDE) IV inhibitors

A comparative molecular field analysis (CoMFA) for phosphodiesterase (PDE) IV inhibitors has been performed to correlate their chemical structures with their observed biological activity. In this study, CoMFA model based on docking mode for active site of PDE IV can describe the relative change in magnitude of the steric and electrostatic fields as a function of the compounds. Pyridine N-oxide and pyridine group of each compound are aligned toward the metal ion in S2-sub pocket of PDE IV. The study provided a statistically valid model with good correlation and predictive power, and consequently we identified some key features that may be used to design new derivatives.     

Novel superalkali superhalogen compounds (Li3)+(SH)- (SH=LiF2, BeF3, and BF4) with aromaticity: new electrides and alkalides.

Optimized structures, with all real frequencies, of superalkali superhalides (Li(3))(+)(SH)(-) (SH=LiF(2), BeF(3), and BF(4)), are obtained, for the first time, at the B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ computational levels. These superalkali superhalides possess three characteristics that are significantly different from normal alkali halides. 1) They have a variety of structures, which come from five bonding mode types: edge-face, edge-edge, face-face, face-edge, and staggered face-edge. We find that the bonding mode type closely correlates with the Li(3)-SH bond energy. 2) The valence electrons on the Li(3) ring are pushed out by the (SH)(-) anion, and become excess electrons, conferring alkalide or electride characteristics on these Li(3)-SH species, depending on the bonding mode type. 3) The highest occupied molecular orbital of each Li(3)-SH species is a doubly occupied delocalized sigma bonding orbital on the Li(3) ring, which indicates its aromaticity. It is noticeable that the maximum negative nucleus-independent chemical shift value (about -10 ppm) moves out from the center of the Li(3) ring, owing to repulsion by the SH(-) anion. We find that these superalkali superhalides are not only complicated "supermolecules", but are also a new type of alkalide or electride, with aromaticity.     

Density functional theory studies on the structures and vibrational spectra of 3,6-dichlorocarbazole and 3,6-dibromocarbazole

Becke 3-Lee-Yang-Parr density functional theory (DFT) calculations using 6-311G** and 6-311G(2df,p) basis sets were carried out to study molecular structures and vibrational spectra of 3,6-dichlorocarbazole and 3,6-dibromocarbazole. The optimized geometries, vibrational frequencies, IR intensities, and Raman activities have been obtained. On the basis of B3LYP calculations, a normal mode analysis was performed to assign the vibrational fundamental frequencies according to the potential energy distributions. The computational frequencies are in good agreement with the observed results.