Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank,which uses dihedral angles as independent variables

We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein–DNA complex, a protein–tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.     

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.     

How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? The case of the divide-and-conquer method

The authors have developed a fragmentation-based linear-scaling electronic structure calculation strategy named the divide-and-conquer (DC) method, which has been implemented into the Gamess program package. Although there are many sorts of fragmentation-based linear-scaling schemes, most of them require the charge and spin multiplicity of each fragment a priori. Therefore, their applications to delocalized and/or open-shell systems have been limited. However, the DC method is a notable exception because the distribution of electrons in the entire system is automatically determined by the universal Fermi level. In this perspective, the authors have summarized the performance of the linear-scaling self-consistent field (SCF) and post-SCF calculations of delocalized and/or open-shell systems based on the DC method. Furthermore, some future prospects of the method have been discussed.     

Multiple isomers in the photoelectron spectra of small mono-niobium carbide clusters

We calculate the photoelectron spectrum of small mono-niobium carbide clusters (NbC(n)) using density functional theory for clusters with n = 2-7 and the symmetry adapted cluster configuration interaction method for the smallest clusters (n = 2-4). Theoretical spectra of a single structure cannot explain all peaks present in the spectrum measured by Zhai et al. [J. Chem. Phys. 115, 5170 (2001)]. However, we can match all peaks in the experimental spectra if we assume that the beam contains a combination of cyclic and linear structures. This finding is even more surprising given the fact that some of the excited metastable geometries have energies as large as 0.5 eV above the ground state. Our result is confirmed by both theoretical approaches. We suggest further experiments, using additional beam cooling, to corroborate this observation.     

High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection

We describe a novel approach to the rapid collection and processing of multidimensional NMR data: "high-resolution iterative frequency identification for NMR" (HIFI-NMR). As with other reduced dimensionality approaches, HIFI-NMR collects n-dimensional data as a set of two-dimensional (2D) planes. The HIFI-NMR algorithm incorporates several innovative features. (1) Following the initial collection of two orthogonal 2D planes, tilted planes are selected adaptively, one-by-one. (2) Spectral space is analyzed in a rigorous statistical manner. (3) An online algorithm maintains a model that provides a probabilistic representation of the three-dimensional (3D) peak positions, derives the optimal angle for the next plane to be collected, and stops data collection when the addition of another plane would not improve the data model. (4) A robust statistical algorithm extracts information from the plane projections and is used to drive data collection. (5) Peak lists with associated probabilities are generated directly, without total reconstruction of the 3D spectrum; these are ready for use in subsequent assignment or structure determination steps. As a proof of principle, we have tested the approach with 3D triple-resonance experiments of the kind used to assign protein backbone and side-chain resonances. Peaks extracted automatically by HIFI-NMR, for both small and larger proteins, included approximately 98% of real peaks obtained from control experiments in which data were collected by conventional 3D methods. HIFI-NMR required about one-tenth the time for data collection and avoided subsequent data processing and peak-picking. The approach can be implemented on commercial NMR spectrometers and is extensible to higher-dimensional NMR.     

多参考态二级微扰方法的改进

本文提出一个新的扩大模型空间的方案用于改进多参考态二级微扰理论(MRPT2)计算. 新方案保持了原方案中扩大模型空间之前的简单程序结构, 理论上完全可以避免势能面计算中入侵态的出现, 并在一系列比较计算中得到证实. 新MRPT2程序是研究分子激发态和电子光谱的有用工具.     

Does the proton-transfer reaction take place in the ground state of phenol?(H2O)4 clusters?

In recent experimental studies of infrared (IR) spectra of hydrated phenol clusters, the Mikami and Ebata group at Tohoku University attributed apparently two very different spectra to PhOH(H₂O)₄. The first spectrum has a wide transparent region between 3500 and 3700 cm^-1, which they named a window region. The second spectrum has several absorption bands in this window region. Our previous study revealed that the first spectrum was assigned to the isomers which have a single-ring structure of a hydrogen-bonding network of OH's of phenol and waters. The experimentalists suggested that the second spectrum might be identified to a proton-transferred phenol(SINGLEBOND)water cluster. In the present article, the geometrical structures of proton-transferred hydrated phenol clusters were determined with the ab initio molecular orbital method and their IR spectra were calculated. The proton-transferred phenol(SINGLEBOND)water cluster is at a stable local minimum, but the energy is much higher than that of the most stable nontransferred cluster. The calculated IR spectrum has a still wider window region and is far different from the experimental spectrum of the second type. © 1996 John Wiley & Sons, Inc.     

Surface‐directed morphology evolution in ternary blends of polyethylene,polypropylene, and ethylene–propylene copolymer: A study by laser scanning confocal fluorescence microscopy

With laser scanning confocal fluorescence microscopy, we demonstrate a novel type of morphology evolution in moderately thick films (70–100 μm) of ternary blends of polypropylene (PP), polyethylene (PE), and ethylene–propylene rubber (EPR), in which EPR is labeled with a benzothioxanthene dye (HY‐EPR). The blends are prepared by solution blending, and the phase morphology evolves during the annealing of the blend films in a stainless steel mold. Our results indicate that wetting of the mold surface is a driving force in morphology evolution for the two blend compositions investigated. For 81/14/5 PP/PE/HY‐EPR, phase evolution within the mold results in a laminar structure and hydrodynamic channels, features which have previously been found in thin films of polymer blends as a result of surface‐directed spinodal decomposition. In a blend with a lower weight fraction of the dispersed phase (92/7/1 PP/PE/HY‐EPR), we find that the PE/HY‐EPR domains are larger and more polydisperse closer to the surface because of wetting of the mold wall. We also show that the phase morphology in these films can be controlled by the nature of one or both of the surfaces being varied. When one of the mold surfaces is replaced with a thin film of PP homopolymer, we observe draining of PE/HY‐EPR from the PP to the mold surface, which results in a bilayer structure. A trilayer morphology is likewise obtained by the replacement of both mold surfaces with PP. We also carry out three‐dimensional image reconstruction on a single PE/HY‐EPR particle within the 81/14/5 PP/PE/HY‐EPR blend to obtain detailed information on the interphase structure. We find that HY‐EPR of this composition (30/70 ethylene/propylene) fully coats the PE dispersed phase and partially penetrates the PE droplets. This result falls between the interphase structures found for previously investigated EPR compositions (40/60 and 80/20 ethylene/propylene). © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 637–654, 2003     

Simple DFT model of clusters embedded in rare gas matrix: trapping sites and spectroscopic properties of Na embedded in Ar

We present a theoretical model to study the dynamics of metallic clusters embedded in a rare gas matrix. We describe the active electrons of the embedded cluster using time dependent density functional theory, while the surrounding matrix is described in terms of classical molecular dynamics of polarizable atoms. The coupling between the cluster and the rare gas atoms is deduced from the work of Gross and Spiegelmann [J. Chem. Phys. 108, 4148 (1998)] and reformulated explicitly in a simple and efficient density functional form. The electron rare gas interaction takes the form of an averaged dipole fluctuation term, which retains the van der Waals long range interaction, and a short range repulsive pseudopotential, which accounts for the Pauli repulsion of the electron by the rare gas atom. We applied our model to Na clusters embedded in Ar matrix. For the latter we developed an efficient local pseudopotential, which allows studying systems containing more than 10(3) Ar atoms. We show that large systems are indeed necessary to account properly for long range polarization of the matrix, that competes with the matrix confinement effect. We focus our study on Na(2), Na(4), and Na(8). For each system, we have determined the geometry of the most favorable trapping site by means of damped molecular dynamics. We present the effect of matrix embedding on the optical absorption spectrum. For Na(2), the trapping site can be unambiguously identified by comparison of the absorption spectrum with experiment. For Na(4) the spectrum of the embedded cluster is significantly different from the free cluster spectrum, while for Na(8) differences are less pronounced.     

Generating water clusters and other directed graphs

In this paper we will describe an efficient method to generate directed graphs with bounded in- and out-degree. Though developed for the special case of water clusters, which can be modelled as directed graphs with indegree and outdegree at most 2 that have no two directed edges with the same endpoints, the algorithm is also applicable and implemented in the more general context.     

Alternative search strategy for minimal energy nanocluster structures: the case of rhodium, palladium, and silver

An alternative strategy to find the minimal energy structure of nanoclusters is presented and implemented. We use it to determine the structure of metallic clusters. It consists in an unbiased search, with a global minimum algorithm: conformational space annealing. First, we find the minima of a many-body phenomenological potential to create a data bank of putative minima. This procedure assures us the generation of a set of cluster configurations of large diversity. Next, the clusters in this data bank are relaxed by ab initio techniques to obtain their energies and geometrical structures. The scheme is successfully applied to magic number 13 atom clusters of rhodium, palladium, and silver. We obtained minimal energy cluster structures not previously reported, which are different from the phenomenological minima. Moreover, they are not always highly symmetric, thus casting some doubt on the customary biased search scheme, which consists in relaxing with density functional theory global minima chosen among high symmetry structures obtained by means of phenomenological potentials.     

Photoabsorption in sodium clusters on the basis of time-dependent density-functional theory

The photoabsorption spectra of a continuous series of Na(n) clusters (n相似文献   

Build-up algorithm for atomic correspondence between chemical structures

Determining a one-to-one atom correspondence between two chemical compounds is important to measure molecular similarities and to find compounds with similar biological activities. This calculation can be formalized as the maximum common substructure (MCS) problem, which is well-studied and has been shown to be NP-complete. Although many rigorous and heuristic algorithms have been developed, none of these algorithms is sufficiently fast and accurate. We developed a new program, called "kcombu" using a build-up algorithm, which is a type of the greedy heuristic algorithms. The program can search connected and disconnected MCSs as well as topologically constrained disconnected MCS (TD-MCS), which is introduced in this study. To evaluate the performance of our program, we prepared two correct standards: the exact correspondences generated by the maximum clique algorithms and the 3D correspondences obtained from superimposed 3D structure of the molecules in a complex 3D structure with the same protein. For the five sets of molecules taken from the protein structure database, the agreement value between the build-up and the exact correspondences for the connected MCS is sufficiently high, but the computation time of the build-up algorithm is much smaller than that of the exact algorithm. The comparison between the build-up and the 3D correspondences shows that the TD-MCS has the best agreement value among the other types of MCS. Additionally, we observed a strong correlation between the molecular similarity and the agreement with the correct and 3D correspondences; more similar molecule pairs are more correctly matched. Molecular pairs with more than 40% Tanimoto similarities can be correctly matched for more than half of the atoms with the 3D correspondences.     

Kick: constraining a stochastic search procedure with molecular fragments

An extension of the Kick program developed by Bera et al. (J Phys Chem A 2006, 110, 4287) is described in which chemically sensible molecular fragments are used in an automated stochastic search algorithm. This results in a vastly reduced region of the potential energy surface which can be explored very quickly. We present use of this modified algorithm to the search for low-lying isomers, and we present candidates for the global energy minimum, for a range of chemical systems. We highlight the usefulness of this procedure for exploring reactions of molecules with transition metal clusters and to the microsolvation of a small dipeptide.     

Monte Carlo temperature basin paving with effective fragment potential: an efficient and fast method for finding low-energy structures of water clusters (H2O)20 and (H2O)25

Determining low-energy structures of large water clusters is a challenge for any optimization algorithm. In this work, we have developed a new Monte Carlo (MC)-based method, temperature basin paving (TBP), which is related to the well-known basin hopping method. In the TBP method, the Boltzmann weight factor used in MC methods is dynamically modified based on the history of the simulation. The states that are visited more are given a lower probability by increasing their temperatures and vice versa. This allows faster escapes from the states frequently visited in the simulation. We have used the TBP method to find a large number of low-energy minima of water clusters of size 20 and 25. We have found structures energetically same to the global minimum structures known for these two clusters. We have compared the efficiency of this method to the basin-hopping method and found that it can locate the minima faster. Statistical efficiency of the new method has been investigated by running a large number of trajectories. The new method can locate low-energy structures of both the clusters faster than some of the reported algorithms for water clusters and can switch between high energy and low-energy structures multiple times in a simulation illustrating its efficiency. The large number of minima obtained from the simulations is used to get both general and specific features of the minima. The distribution of minima for these two clusters based on the similarity of their oxygen frames shows that the (H(2)O)(20) can have different variety of structures, but for (H(2)O)(25), low-energy structures are mostly cagelike. Several (H(2)O)(25) structures are found with similar energy but with different cage architectures. Noncage structures of (H(2)O)(25) are also found but they are 6-7 kcal/mol higher in energy from the global minimum. The TBP method is likely to play an important role for exploring the complex energy landscape of large molecules.     

Analyzing the Vibrational Signatures of Thiophenol Adsorbed on Small Gold Clusters by DFT Calculations

Using density functional theory, we calculate the IR and Raman signatures of the thiophenol (TP) molecule adsorbed on gold clusters by mimicking the different types of adsorption sites, and we analyze these signatures by using advanced tools implemented into the pyvib2 program. First, we follow the evolution of the vibrational normal modes from the isolated TP molecule to those of TP adsorbed on different clusters to highlight the influence of the site of adsorption on the vibrational motions. The use of the overlap matrix between the modes enables mode permutations, mode mixings, and mode splittings to be highlighted, all of which depend not only on the adsorption but also on the type of cluster and its symmetry. Second, the IR and Raman signatures were analyzed by using group coupling matrices and atomic contribution patterns based on the Hug decomposition scheme. Key results include 1) the fact that Raman spectroscopy is more sensitive than IR spectroscopy with respect to the nature of the coordination site, 2) an IR criterion that distinguishes between on‐top coordination (onefold coordinated) with respect to the bridge (twofold coordinated) and hexagonal close‐packed hollow site coordination (threefold coordinated), and 3) the best agreement to the experimental Raman spectrum with regard to signatures in the 500 to 1200 cm^?1 region is obtained for bridged, twofold coordination.     

Particle-swarm structure prediction on clusters

We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Li(n) (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction.     

A hybrid elastic band string algorithm for studies of enzymatic reactions

A common challenge in theoretical biophysics is the identification of a minimum energy path (MEP) for the rearrangement of a group of atoms from one stable configuration to another. The structure with maximum energy along the MEP approximates the transition state for the process and the energy profile itself permits estimation of the transition rates. In this work we describe a computationally efficient algorithm for the identification of minimum energy paths in complicated biosystems. The algorithm is a hybrid of the nudged elastic band (NEB) and string methods. It has been implemented in the pDynamo simulation program and tested by examining elementary steps in the reaction mechanisms of three enzymes: citrate synthase, RasGAP, and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated using the new algorithm and previous versions of the NEB and string techniques, and also those obtained by the common method of adiabatic exploration of the potential energy surface as a function of predefined reaction coordinates. Precisely refined structures of the saddle points along the paths may be subsequently obtained with the climbing image variant of the NEB algorithm. Directions in which the utility of the methods that we have implemented can be further improved are discussed.     

杂合型全局优化法优化水分子团簇结构

基于遗传算法、快速模拟退火及共轭梯度方法提出了一种快速的杂合型全局优化方法(fast hybrid global optimization algorithm, FHGOA),并将这一方法应用于TIP3P和TIPS2模型水分子团簇(H2O)n结构的优化.在进行TIP3P模型水分子团簇结构的优化过程中,发现了能量比文献值更低的团簇结构,且执行效率有较大提高.把该方法应用到优化TIPS2模型的水分子团簇,发现最优结构和采用TTM2-F模型优化的水分子团簇结构在n < 17时完全相同,为全表面结构;而在n=17、19、22时为单中心水分子笼状结构;在n=25、27时为双中心水分子笼状结构.说明随着团簇中水分子个数的增加,采用TIPS2和TTM2-F势能函数优化的团簇最优结构有相同的变化趋势.     

A modified multi-reference second order perturbation theory

A new scheme with extended model space is proposed to improve the calculation of multi-reference second order perturbation theory (MRPT2). The new scheme preserves the concise code structure of the original program, and avoids intruder states in constructions of the potential energy surface, which is confirmed by a series of comparable calculations. The new MRPT2 program is an available tool for the research of molecular excited states and electronic spectrum.