Showing papers in "Journal of Computational Chemistry in 2019"

Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of Symmetry-Adapted Perturbation Theory.

Abstract: This work studies the underlying nature of H-bonds (HBs) of different types and strengths and tries to predict binding energies (BEs) based on the properties derived from wave function analysis. A total of 42 HB complexes constructed from 28 neutral and 14 charged monomers were considered. This set was designed to sample a wide range of HB strengths to obtain a complete view about HBs. BEs were derived with the accurate coupled cluster singles and doubles with perturbative triples correction (CCSD(T))(T) method and the physical components of the BE were investigated by symmetry-adapted perturbation theory (SAPT). Quantum theory of atoms-in-molecules (QTAIM) descriptors and other HB indices were calculated based on high-quality density functional theory wave functions. We propose a new and rigorous classification of H-bonds (HBs) based on the SAPT decomposition. Neutral complexes are either classified as "very weak" HBs with a BE ≥ -2.5 kcal/mol that are mainly dominated by both dispersion and electrostatic interactions or as "weak-to-medium" HBs with a BE varying between -2.5 and -14.0 kcal/mol that are only dominated by electrostatic interactions. On the other hand, charged complexes are divided into "medium" HBs with a BE in the range of -11.0 to -15.0 kcal/mol, which are mainly dominated by electrostatic interactions, or into "strong" HBs whose BE is more negative than -15.0 kcal/mol, which are mainly dominated by electrostatic together with induction interactions. Among various explored correlations between BEs and wave function-based HB descriptors, a fairly satisfactory correlation was found for the electron density at the bond critical point (BCP; ρBCP ) of HBs. The fitted equation for neutral complexes is BE/kcal/mol = - 223.08 × ρBCP /a. u. + 0.7423 with a mean absolute percentage error (MAPE) of 14.7%, while that for charged complexes is BE/kcal/mol = - 332.34 × ρBCP /a. u. - 1.0661 with a MAPE of 10.0%. In practice, these equations may be used for a quick estimation of HB BEs, for example, for intramolecular HBs or large HB networks in biomolecules. © 2019 Wiley Periodicals, Inc.

Image Quality Assessment through FSIM, SSIM, MSE and PSNR—A Comparative Study

Abstract: Quality is a very important parameter for all objects and their functionalities. In image-based object recognition, image quality is a prime criterion. For authentic image quality evaluation, ground truth is required. But in practice, it is very difficult to find the ground truth. Usually, image quality is being assessed by full reference metrics, like MSE (Mean Square Error) and PSNR (Peak Signal to Noise Ratio). In contrast to MSE and PSNR, recently, two more full reference metrics SSIM (Structured Similarity Indexing Method) and FSIM (Feature Similarity Indexing Method) are developed with a view to compare the structural and feature similarity measures between restored and original objects on the basis of perception. This paper is mainly stressed on comparing different image quality metrics to give a comprehensive view. Experimentation with these metrics using benchmark images is performed through denoising for different noise concentrations. All metrics have given consistent results. However, from representation perspective, SSIM and FSIM are normalized, but MSE and PSNR are not; and from semantic perspective, MSE and PSNR are giving only absolute error; on the other hand, SSIM and PSNR are giving perception and saliency-based error. So, SSIM and FSIM can be treated more understandable than the MSE and PSNR.

More bang for your buck: Improved use of GPU nodes for GROMACS 2018

Abstract: We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performa ...

BSSE-correction scheme for consistent gaussian basis sets of double- and triple-zeta valence with polarization quality for solid-state calculations.

Abstract: Revised versions of our published pob-TZVP [Peintinger, M. F.; Oliveira, D. V. and Bredow, T., J. Comput. Chem., 2013, 34 (6), 451-459.] and unpublished pob-DZVP basis sets, denoted as pob-TZVP-rev2 and pob-DZVP-rev2, have been derived for the elements HBr. It was observed that the pob basis sets suffer from the basis set superposition error (BSSE). In order to reduce this effect, we took into account the counterpoise energy of hydride dimers as an additional parameter in the basis set optimization. The overall performance, portability, and SCF stability of the resulting rev2 basis sets are significantly improved compared to the original pob basis sets. © 2019 Wiley Periodicals, Inc.

NBO 7.0: New vistas in localized and delocalized chemical bonding theory.

Abstract: We briefly outline some leading features of the newest version, NBO 7.0, of the natural bond orbital (NBO) wavefunction analysis program. Major extensions include: (1) a new NPEPA module implementing Karafiloglou's "polyelectron population analysis" in the NBO framework; (2) new RDM2 program infrastructure for describing electron correlation effects based on full evaluation of the second-order reduced density matrix; (3) improved convex-solver implementation of natural resonance theory (NRT), allowing a greatly expanded range of applications and associated "resonance NBO" (RNBO) visualization of chemical reactivity; (4) a variety of other improvements in well-established NBO algorithms. We also provide brief introduction to the new NBOPro@Jmol utility program, a plugin to the Jmol chemical structure viewer that serves as a convenient tool to provide on-demand NBO descriptors or orbital visualizations for a broad variety of chemical inquiries in research or classroom applications. © 2019 Wiley Periodicals, Inc.

Nine questions on energy decomposition analysis.

Abstract: The paper collects the answers of the authors to the following questions : Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the “natural selection” process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross‐validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the “standard model” of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another?

DFT calculations on molecular structures, HOMO–LUMO study, reactivity descriptors and spectral analyses of newly synthesized diorganotin(IV) 2‐chloridophenylacetohydroxamate complexes

Abstract: The gas-phase-optimized geometry of newly synthesized and characterized diorganotin(IV) 2-chloridophenylacetohydroxamate complexes of composition [Me2 Sn(HL)2 ] (I) and [n-Bu2 Sn(HL)2 ] (II) (where KHL = potassium 2-chloridophenylacetohydroxamate (2-ClPhAHK); [Me2 Sn(2-ClC6 H4 CH2 CONHO)2 ] (I) and [n-Bu2 Sn(2-ClC6 H4 CH2 CONHO)2 ] (II) computed by B3LYP/6-311++G(d,p) method has shown these to be distorted octahedral. Bonding through carbonyl and hydroxamic oxygen atoms (O, O coordination) has been inferred from a comparison of computed important bond lengths (CO, CN, and NO) of complexes with that of free ligand. The SnO bond lengths in complexes are suggestive of weak coordinate (through carbonyl CO) and strong covalent (through hydroxamic NO) bonding of the ligand. The magnitude of CSnC bond angles involving two methyl/n-butyl groups is suggestive of cis-conformation at tin metal. The thermodynamic parameters (G, H, S, E, Cv, and U) of complexes have been computed. From the energies of frontier molecular orbitals (HOMO-LUMO), the reactivity descriptors, namely, ionization potential, electron affinity, chemical potential (μ), hardness (η), softness (S), electronegativity (χ), and electrophilicity index (ω) have been calculated. The computed vibrational frequencies and 1 H NMR chemical shifts have substantiated the molecular structure of complexes. © 2019 Wiley Periodicals, Inc.

Identifying promising metal-organic frameworks for heterogeneous catalysis via high-throughput periodic density functional theory.

Abstract: Metal-organic frameworks (MOFs) are a class of nanoporous materials with highly tunable structures in terms of both chemical composition and topology. Due to their tunable nature, high-throughput computational screening is a particularly appealing method to reduce the time-to-discovery of MOFs with desirable physical and chemical properties. In this work, a fully automated, high-throughput periodic density functional theory (DFT) workflow for screening promising MOF candidates was developed and benchmarked, with a specific focus on applications in catalysis. As a proof-of-concept, we use the high-throughput workflow to screen MOFs containing open metal sites (OMSs) from the Computation-Ready, Experimental MOF database for the oxidative C-H bond activation of methane. The results from the screening process suggest that, despite the strong C-H bond strength of methane, the main challenge from a screening standpoint is the identification of MOFs with OMSs that can be readily oxidized at moderate reaction conditions. © 2019 Wiley Periodicals, Inc.

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.

Abstract: The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long-range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. A novel algorithm was implemented for nonbonded interactions to increase single instruction multiple data (SIMD) performance, reducing memory usage for ultra large systems. Memory usage for neighbor searches in real-space nonbonded interactions was reduced by approximately 80%, leading to significant speedup. Using experimental data describing physical 3D chromatin interactions, we constructed the first atomistic model of an entire gene locus (GATA4). Taken together, these developments enabled the first billion-atom simulation of an intact biomolecular complex, achieving scaling to 65,000 processes (130,000 processor cores) with 1 ns/day performance. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.

Efficient optimization of natural resonance theory weightings and bond orders by gram-based convex programming.

Abstract: We describe the formal algorithm and numerical applications of a novel convex quadratic programming (QP) strategy for performing the variational minimization that underlies natural resonance theory (NRT). The QP algorithm vastly improves the numerical efficiency, thoroughness, and accuracy of variational NRT description, which now allows uniform treatment of all reference structures at the high level of detail previously reserved only for leading "reference" structures, with little or no user guidance. We illustrate overall QPNRT search strategy, program I/O, and numerical results for a specific application to adenine, and we summarize more extended results for a data set of 338 species from throughout the organic, bioorganic, and inorganic domain. The improved QP-based implementation of NRT is a principal feature of the newly released NBO 7.0 program version. © 2019 Wiley Periodicals, Inc.

Achieving band convergence by tuning the bonding ionicity in n‐type Mg 3 Sb 2

Abstract: Identifying strategies for beneficial band engineering is crucial for the optimization of thermoelectric (TE) materials. In this study, we demonstrate the beneficial effects of ionic dopants on n-type Mg3 Sb2 . Using the band-resolved projected crystal orbital Hamilton population, the covalent characters of the bonding between Mg atoms at different sites are observed. By partially substituting the Mg at the octahedral sites with more ionic dopants, such as Ca and Yb, the conduction band minimum (CBM) of Mg3 Sb2 is altered to be more anisotropic with an enhanced band degeneracy of 7. The CBM density of states of doped Mg3 Sb2 with these dopants is significantly enlarged by band engineering. The improved Seebeck coefficients and power factors, together with the reduced lattice thermal conductivities, imply that the partial introduction of more ionic dopants in Mg3 Sb2 is a general solution for its n-type TE performance. © 2019 Wiley Periodicals, Inc.

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami

Abstract: Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.

Dative and electron-sharing bonding in transition metal compounds.

Abstract: Quantum chemical calculations using density functional theory at the BP86-D3(BJ)/def2-TZVPP level of theory are reported for transition metal compounds [TM]-L in high and low oxidation states involving carbene, carbyne, alkene, and alkyne ligands L. The nature of the [TM]-L bond is analyzed with the energy decomposition analysis - natural orbitals for chemical valence (EDA-NOCV) method. The calculations reveal that transition metal compounds with ligands, that are typically classified as donor-acceptor complexes possessing dative bonds (Fischer-type carbenes and carbynes, alkene, and alkyne complexes) or as TM compounds with electron-sharing bonds (Schrock-type carbenes and carbynes, metallacyclopropanes, and metallacyclopropenes), exhibit significant differences between the orbital interactions when closed-shell or open shell fragments are used. Fischer-type carbene complexes have much lower orbital interaction (ΔEorb ) values when singlet fragments are employed compared to triplet fragments. In contrast, singlet and triplet fragments of Schrock-type carbene complexes give similar ΔEorb values. The best description for Fischer-type carbyne complexes is found for neutral fragments in their electronic doublet state, which engage in a mixture of dative bonding (σ donation and π backdonation) and one electron-sharing π bond. The EDA-NOCV calculations of Schrock-type carbynes using open-shell species in their quartet electronic state give similar ΔEorb values as neutral fragments in their electronic doublet state. Alkene and alkyne complexes, but also metallacyclic species, are best described with singlet fragments, but the difference between the ΔEorb values for dative bonding and electron-sharing bonding using triplet fragments becomes much smaller for molecules that are considered as metallacycles. © 2018 Wiley Periodicals, Inc.

PPI-Detect: A support vector machine model for sequence-based prediction of protein-protein interactions.

Abstract: The prediction of peptide-protein or protein-protein interactions (PPI) is a challenging task, especially if amino acid sequences are the only information available. Machine learning methods allow us to exploit the information content in PPI datasets. However, the numerical codification of these datasets often influences the performance of data mining approaches. Here, we introduce a procedure for the general-purpose numerical codification of polypeptides. This procedure transforms pairs of amino acid sequences into a machine learning-friendly vector, whose elements represent numerical descriptors of residues in proteins. We used this numerical encoding procedure for the development of a support vector machine model (PPI-Detect), which allows predicting whether two proteins will interact or not. PPI-Detect (https://ppi-detect.zmb.uni-due.de/) outperforms state of the art sequence-based predictors of PPI. We employed PPI-Detect for the analysis of derivatives of EPI-X4, an endogenous peptide inhibitor of CXCR4, a G-protein-coupled receptor. There, we identified with high accuracy those peptides which bind better than EPI-X4 to the receptor. Also using PPI-Detect, we designed a novel peptide and then experimentally established its anti-CXCR4 activity. © 2019 Wiley Periodicals, Inc.

PyFrag 2019-Automating the exploration and analysis of reaction mechanisms.

Abstract: We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

autoCAS: A Program for Fully Automated Multiconfigurational Calculations

Abstract: We present our implementation autoCAS for fully automated multiconfigurational calculations, which we also make available free of charge on our webpages. The graphical user interface of autoCAS connects a general electronic structure program with a density-matrix renormalization group program to carry out our recently introduced automated active space selection protocol for multiconfigurational calculations (Stein and Reiher, J. Chem. Theory Comput., 2016, 12, 1760). Next to this active space selection, autoCAS carries out several steps of multiconfigurational calculations so that only a minimal input is required to start them, comparable to that of a standard Kohn-Sham density-functional theory calculation, so that black-box multiconfigurational calculations become feasible. Furthermore, we introduce a new extension to the selection algorithm that facilitates automated selections for molecules with large valence orbital spaces consisting of several hundred orbitals. © 2019 Wiley Periodicals, Inc.

A Review of Carbon Nanotube/TiO2 Composite Prepared via Sol-Gel Method

Abstract: A substantial review is performed in this work about the development and design of Carbon Nanotubes/Titanium Oxide nanocompisites. The fundamental method of sol-gel synthesis of Carbon Nanotubes is also reported here. Single-Walled and Multi-Walled Carbon Nanotubes are reviewed here. Finally, different applications for this nanocomposite are discussed.

Construction of direct Z‐Scheme photocatalysts for overall water splitting using two‐dimensional van der waals heterojunctions of metal dichalcogenides

Abstract: The direct Z-scheme system constructed by two-dimensional (2D) materials is an efficient route for hydrogen production from photocatalytic water splitting. In the present work, the 2D van der Waals (vdW) heterojunctions of MoSe2 /SnS2 , MoSe2 /SnSe2 , MoSe2 /CrS2 , MoTe2 /SnS2 , MoTe2 /SnSe2 , and MoTe2 /CrS2 are proposed to be promising candidates for direct Z-scheme photocatalysts and verified by first principles calculations. Perpendicular electric field is induced in these 2D vdW heterojunctions, which enhances the efficiency of solar energy utilization. Replacing MoSe2 with MoTe2 not only facilitates the interlayer carrier migration, but also improves the optical absorption properties for these heterojunctions. Excitingly, the 2D vdW MoTe2 /CrS2 heterojunction is demonstrated, for the first time, to be 2D near-infrared-light driven photocatalyst for direct Z-scheme water splitting. © 2018 Wiley Periodicals, Inc.

Dcdftbmd: Divide-and-Conquer Density Functional Tight-Binding Program for Huge-System Quantum Mechanical Molecular Dynamics Simulations.

Abstract: Dcdftbmd is a Fortran 90/95 program that enables efficient quantum mechanical molecular dynamics (MD) simulations using divide-and-conquer density functional tight-binding (DC-DFTB) method. Based on the remarkable performance of previous massively parallel DC-DFTB energy and gradient calculations for huge systems, the code has been specialized to MD simulations. Recent implementations and modifications including DFTB extensions, improved computational speed in the DC-DFTB computational steps, algorithms for efficient initial guess charge prediction, and free energy calculations via metadynamics technique have enhanced the capability to obtain atomistic insights in novel applications to nanomaterials and biomolecules. The energy, structure, and other molecular properties are also accessible through the single-point calculation, geometry optimization, and vibrational frequency analysis. The available functionalities are outlined together with efficiency tests and simulation examples. © 2019 Wiley Periodicals, Inc.

MLatom: A program package for quantum chemical research assisted by machine learning

Abstract: MLatom is a program package designed for computationally efficient simulations of atomistic systems with machine-learning (ML) algorithms. It can be used out-of-the-box as a stand-alone program with a user-friendly online manual. The use of MLatom does not require extensive knowledge of machine learning, programming, or scripting. The user need only prepare input files and choose appropriate options. The program implements kernel ridge regression and supports Gaussian, Laplacian, and Matern kernels. It can use arbitrary, user-provided input vectors and can convert molecular geometries into input vectors corresponding to several types of built-in molecular descriptors. MLatom saves and re-uses trained ML models as needed, in addition to estimating the generalization error of ML setups. Various sampling procedures are supported and the gradients of output properties can be calculated. The core part of MLatom is written in Fortran, uses standard libraries for linear algebra, and is optimized for shared-memory parallel computations. © 2019 Wiley Periodicals, Inc.

ACCDB: A collection of chemistry databases for broad computational purposes.

Abstract: The importance of databases of reliable and accurate data in chemistry has substantially increased in the past two decades. Their main usage is to parametrize electronic structure theory methods, and to assess their capabilities and accuracy for a broad set of chemical problems. The collection we present here-ACCDB-includes data from 16 different research groups, for a total of 44,931 unique reference data points, all at a level of theory significantly higher than density functional theory, and covering most of the periodic table. It is composed of five databases taken from literature (GMTKN, MGCDB84, Minnesota2015, DP284, and W4-17), two newly developed reaction energy databases (W4-17-RE and MN-RE), and a new collection of databases containing transition metals. A set of expandable software tools for its manipulation is also presented here for the first time, as well as a case study where ACCDB is used for benchmarking commercial CPUs for chemistry calculations. © 2018 Wiley Periodicals, Inc.

Molecular understanding of the adhesive interactions between silica surface and epoxy resin: Effects of interfacial water

Abstract: The molecular mechanism of the adhesion between silica surface and epoxy resin under atmospheric conditions is investigated by periodic density-functional-theory (DFT) calculations. Slab models of the adhesion interface were built by integrating a fragment of epoxy resin and hydroxylated (0 0 1) surface of α-cristobalite in the presence of adsorbed water molecules. Effects of adsorbed water on the adhesion interaction are evaluated on the basis of geometry-optimized structures, adhesion energies, and forces. Calculated results demonstrate that adsorbed water molecules significantly reduce both the adhesion energies and forces of the silica surface-epoxy resin interface. The reduction of adhesion properties can be associated with structural deformation of water molecules confined in the tight space between the adhesive and adherend as well as structural flexibility of the hydrogen-bonding network in the interfacial region during detachment of the epoxy resin from the hydrophilic silica surface. © 2018 Wiley Periodicals, Inc.

Thiophenols, Promising Scavengers of Peroxyl Radicals: Mechanisms and kinetics.

Abstract: The activity of 12 thiophenols as primary antioxidants in aqueous solution has been studied using density functional theory. Twelve different substituted thiophenols were tested as peroxyl radicals scavengers. Single electron transfer (SET) and formal hydrogen transfer (FHT) were investigated. The SET mechanism was found to be the main mechanism, with rate constants that are close to the diffusion limit, which means that these thiophenolic compounds have the capacity to scavenge peroxyl radicals before they can damage biomolecules. All 12 thiophenolic compounds react faster with methylperoxyl than with hydroperoxyl radicals. In addition, it was found that pH plays an important role in the reactivity of these compounds. © 2019 Wiley Periodicals, Inc.

GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters.

Abstract: Protein-protein docking methods are spotlighted for their roles in providing insights into protein-protein interactions in the absence of full structural information by experiment. GalaxyTongDock is an ab initio protein-protein docking web server that performs rigid-body docking just like ZDOCK but with improved energy parameters. The energy parameters were trained by iterative docking and parameter search so that more native-like structures are selected as top rankers. GalaxyTongDock performs asymmetric docking of two different proteins (GalaxyTongDock_A) and symmetric docking of homo-oligomeric proteins with Cn and Dn symmetries (GalaxyTongDock_C and GalaxyTongDock_D). Performance tests on an unbound docking benchmark set for asymmetric docking and a model docking benchmark set for symmetric docking showed that GalaxyTongDock is better or comparable to other state-of-the-art methods. Experimental and/or evolutionary information on binding interfaces can be easily incorporated by using block and interface options. GalaxyTongDock web server is freely available at http://galaxy.seoklab.org/tongdock. © 2019 Wiley Periodicals, Inc.

CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems.

Abstract: Nanodiscs are discoidal protein-lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many membrane scaffold proteins (MSPs) that wrap around the membrane bilayer. We have developed CHARMM-GUI Nanodisc Builder (http://www.charmm-gui.org/input/nanodisc) to facilitate the setup of nanodisc simulation systems by modeling the MSPs with defined size and known structural features. A total of 11 different nanodiscs with a diameter from 80 to 180 A are made available in both the all-atom CHARMM and two coarse-grained (PACE and Martini) force fields. The usage of the Nanodisc Builder is demonstrated with various simulation systems. The structures and dynamics of proteins and lipids in these systems were analyzed, showing similar behaviors to those from previous all-atom and coarse-grained nanodisc simulations. We expect the Nanodisc Builder to be a convenient and reliable tool for modeling and simulation of nanodisc systems. © 2019 Wiley Periodicals, Inc.

Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions

Abstract: Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies. © 2019 Wiley Periodicals, Inc.

DelPhi Suite: New Developments and Review of Functionalities

Abstract: Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large-scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

RMSD and Symmetry.

Abstract: A common approach for comparing the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the pointwise root-mean-square deviation (RMSD). We present a new, robust numerical algorithm that computes the RMSD between two molecules or all the mutual RMSDs of a list of molecules and, if desired, the corresponding rotation matrix in a minimal number of operations as compared to previous algorithms. The RMSD gradient can also be computed. We address the problem of symmetry, both in alignment (possible alternative alignments due to indistinguishable atoms) as well as geometry. In the latter case, it is possible to have degenerate superposition. A necessary condition is optimal superimposability to one's mirror image. Double (respectively, triple) degeneracy results in a one- (respectively, two)-parameter family of rotations leaving the superposition invariant. The software, frmsd, is freely available at http://www.ams.stonybrook.edu/~coutsias/codes/frmsd.tgz. © 2019 Wiley Periodicals, Inc.

Investigation of two-dimensional hf-based MXenes as the anode materials for li/na-ion batteries: A DFT study.

Abstract: Density functional theory calculations are performed to investigate electronic properties and Li/Na storage capability of Hf3 C2 and its derivatives (uniform passivated: Hf3 C2 T2 [T = F, O, OH] and hybrid passivated: Hf3 C2 Fx O2-x and Hf3 C2 Ox (OH)2-x [x = 1.0, 1.5]). For Hf3 C2 monolayer, it has excellent performance, such as good conductivity, low diffusion energy barrier, low open circuit voltage, and high storage capacities (Li(1034.70 mAh g-1 ), Na(444.90 mAh g-1 )), providing the most prospective as anode material. However, due to the unsaturated dangling bonds of surface Hf, so it is easily passivated. For the uniform passivated ones, Hf3 C2 T2 , show higher diffusion barriers and lower storage capacities than bare monolayer Hf3 C2 . Nevertheless, compared with uniform passivated ones, the hybrid passivated derivative, Hf3 C2 F1.5 O0.5 and Hf3 C2 OOH possess a lower energy barrier and a better storage capacity. Therefore, Hf3 C2 F1.5 O0.5 and Hf3 C2 OOH are deemed to be a suitable candidate as anode electrode material for Li-ion batteries. © 2019 Wiley Periodicals, Inc.

BAR-based optimum adaptive steered MD for configurational sampling.

Abstract: The equilibrium and nonequilibrium adaptive alchemical free energy simulation methods optimum Bennett's acceptance ratio and optimum crooks' equation (OCE), based on the statistically optimal bidirectional reweighting estimator named Bennett's Acceptance Ratio or Crooks' equation, perform initial sampling in the staging alchemical transformation and then determine the importance rank of different states via the time-derivative of the variance. The method is proven to give speedups compared with the equal time rule. In the current work, we extend the time derivative of variance guided adaptive sampling method to the configurational space, falling in the term of steered MD (SMD). The SMD approach biasing physically meaningful collective variable (CV) such as one dihedral or one distance to pulling the system from one conformational state to another. By minimizing the variance of the free energy differences along the pathway in an optimized way, a new type of adaptive SMD (ASMD) is introduced. As exhibits in the alchemical case, this adaptive sampling method outperforms the traditional equal-time SMD in nonequilibrium stratification. Also, the method gives much more efficient calculation of potential of mean force than the selection criterion-based ASMD scheme, which is proven to be more efficient than traditional SMD. The OCE workflow is periodicity-of-CV dependent while ASMD is not. The performance is demonstrated in a dihedral flipping case and two distance pulling cases, accounting for periodic and nonperiodic CVs, respectively. © 2019 Wiley Periodicals, Inc.