A general,recursive, and open‐ended response code

We present a new implementation of a recent open‐ended response theory formulation for time‐ and perturbation‐dependent basis sets (Thorvaldsen et al., J. Chem. Phys. 2008, 129, 214108) at the Hartree–Fock and density functional levels of theory. A novel feature of the new implementation is the use of recursive programming techniques, making it possible to write highly compact code for the analytic calculation of any response property at any valid choice of rule for the order of perturbation at which to include perturbed density matrices. The formalism is expressed in terms of the density matrix in the atomic orbital basis, allowing the recursive scheme presented here to be used in linear‐scaling formulations of response theory as well as with two‐ and four‐component relativistic wave functions. To demonstrate the new code, we present calculations of the third geometrical derivatives of the frequency‐dependent second hyperpolarizability for HSOH at the Hartree–Fock level of theory, a seventh‐order energy derivative involving basis sets that are both time and perturbation dependent. © 2014 Wiley Periodicals, Inc.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion

READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. © 2014 Wiley Periodicals, Inc.     

Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of isotropic chromophore orientation, detailed insight into the lengthscale of molecular phenomena. This study illustrates the application of a FRET efficiency restraint during classical atomistic molecular dynamics simulations of a mutant mastoparan X peptide in either water or 7 M aqueous urea. The restraint forces acting on the donor and acceptor chromophores ensure that the sampled peptide configurational ensemble satisfies the experimental primary data by modifying interchromophore separation and chromophore transition dipole moment orientations. By means of a conformational cluster analysis, it is seen that indeed different configurational ensembles may be sampled without and with application of the restraint. In particular, while the FRET efficiency and interchromophore distances monitored in an unrestrained simulation may differ from the experimentally‐determined values, they can be brought in agreement with experimental data through usage of the FRET efficiency restraining potential. Furthermore, the present results suggest that the assumption of isotropic chromophore orientation is not always justified. The FRET efficiency restraint allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom. Thus, it offers an additional tool to connect the realms of computer and wet‐lab experimentation. © 2014 Wiley Periodicals, Inc.     

TiS2 and ZrS2 single‐ and double‐wall nanotubes: First‐principles study

Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL‐2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single‐walled TiS₂ and ZrS₂ nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS₂ and ZrS₂ nanotubes is small, does not depend on the tube chirality, and approximately obeys to D^–2 law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO₂ and ZrO₂ nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single‐wall components of the double‐wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross‐section of the external walls in the armchair‐like double‐wall nanotubes. © 2013 Wiley Periodicals, Inc.     

Developing Thermodynamic Micellization Approach to Model Asphaltene Precipitation Behavior

An little known yet significant issue in petroleum production processes in petroleum reservoirs is asphaltene precipitation/deposition. Asphaltene has not only a fuzzy and vague nature but it also can cause detrimental problems like reservoir blockage and, as a result, low oil recovery. To tackle this issue, many researchers have attempted to monitor asphaltene behavior versus thermodynamic conditions. A thermodynamic micellization approach is implemented in this work to describe asphaltene precipitation behavior for two sample fluids from Iranian reservoirs. First, the basic structures of the addressed approach and different contributions to Gibbs free energy of micellization proposed by Victorov and Firoozabadi (VF) are demonstrated. Second, a detailed sensitivity analysis with respect to the model parameters is performed by utilizing a new calculation strategy. Finally, a comparison between the predicted precipitation curve and the experimental one is illustrated; moreover, comparing our results with those reported by Victorov proves the superiority of the new strategy over the conventional one. The significance of this study shows the effect of each micellization parameter on the asphaltene precipitation behavior curve and illustrates the ability of the micellization approach evolved by VF in monitoring the effect of pressure on asphaltene precipitation using the new calculation procedure. Outcomes from this study could couple with commercial reservoir simulation software to improve precision and integrity for designing robust and effective production units.     

Pairwise decomposition of an MMGBSA energy function for computational protein design

Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an enormous sequence and conformation space. The difficulty can be reduced by considering a fixed backbone and a discrete set of sidechain conformations. Another common strategy consists in precalculating a pairwise energy matrix, from which the energy of any sequence/conformation can be quickly obtained. In this work, we examine the pairwise decomposition of protein MMGBSA energy functions from a general theoretical perspective, and an implementation proposed earlier for CPD. It includes a Generalized Born term, whose many‐body character is overcome using an effective dielectric environment, and a Surface Area term, for which we present an improved pairwise decomposition. A detailed evaluation of the error introduced by the decomposition on the different energy components is performed. We show that the error remains reasonable, compared to other uncertainties. © 2014 Wiley Periodicals, Inc.     

花状硫化铟纳米多级结构的液相合成及形貌调控机理

以C2H5NS和In(NO3)3为前驱物,采用简单的液相法成功制备了In2S3纳米多级结构,C2H5NS作为硫源的同时也起到了模板剂的作用.研究结果表明,前驱物浓度对In2S3形貌控制起着重要作用.随着In(NO3)3/C2H5NS摩尔比从1∶1.5增加到1∶6,In2S3纳米花呈现了不同的形貌和尺寸.XRD谱图显示,In2S3纳米花晶体具有立方结构.SEM和TEM照片显示,制备的In2S3纳米结构呈多级花状结构,这种结构由纳米片堆积组装而成.通过第一性原理计算并结合实验结果对C2H5NS影响纳米片生长的机理进行了分析,结果表明C2H5NS在In2S3(001)晶面上的吸附可以有效降低晶面的表面能,起到稳定晶面的作用;纳米花的形成是在C2H5NS影响In2S3的晶面稳定性及其成核速率之间的一个协同效应.In2S3纳米晶的形貌可以通过调整反应溶液中的C2H5NS浓度来调节.     

铱(Ir~Ⅲ)-稀土(Ln~Ⅲ)异核配合物发光性能研究

稀土离子(LnⅢ)丰富的4f电子跃迁能级,使稀土发光材料获得重要而广泛的应用.稀土配合物中天线基团的引入,弥补了稀土离子f-f跃迁禁阻而导致吸收较低的不足.而具有三重态吸收的过渡金属配合物作为天线基团,更使稀土离子的激发窗口红移.相关研究具有重要的理论意义和实际应用价值.本文主要综述近年来有关铱(IrⅢ)-稀土(LnⅢ)异核发光配合物方面的研究进展.