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Journal of Computational Chemistry

Adam K Sieradzan, Rafał Jakubowski
In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible...
January 11, 2017: Journal of Computational Chemistry
Francesc Viñes, Francesc Illas
The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects, calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ∼0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ∼0...
January 11, 2017: Journal of Computational Chemistry
Noèlia Pueyo Bellafont, Francesc Viñes, Wolfgang Hieringer, Francesc Illas
Here, we assess the accuracy of various approaches implemented in Vienna ab initio simulation package code to estimate core-level binding energy shifts (ΔBEs) using a projector augmented wave method to treat core electrons. The performance of the Perdew-Burke-Ernzerhof (PBE) and the Tao-Perdew-Staroverov-Scuseria (TPSS) exchange-correlation density functionals is examined on a dataset of 68 molecules containing B→F atoms in diverse chemical environments, accounting for 185 different 1s core level binding energy shifts, for which both experimental gas-phase X-ray photoemission (XPS) data and accurate all electron ΔBEs are available...
January 4, 2017: Journal of Computational Chemistry
Yang Xie, Jinyong Ying, Dexuan Xie
SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol...
January 4, 2017: Journal of Computational Chemistry
Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong, Guo-Wei Wei
Solvent excluded surface (SES) is one of the most popular surface definitions in biophysics and molecular biology. In addition to its usage in biomolecular visualization, it has been widely used in implicit solvent models, in which SES is usually immersed in a Cartesian mesh. Therefore, it is important to construct SESs in the Eulerian representation for biophysical modeling and computation. This work describes a software package called Eulerian solvent excluded surface (ESES) for the generation of accurate SESs in Cartesian grids...
January 4, 2017: Journal of Computational Chemistry
Robert C Harris, Nanjie Deng, Ronald M Levy, Ryosuke Ishizuka, Nobuyuki Matubayasi
Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations...
December 23, 2016: Journal of Computational Chemistry
Elena I Davydova, Anna S Lisovenko, Alexey Y Timoshkin
Complex beryllium amidoboranes Mx [Be(NH2 BH3 )x+2 ] (M = Li-Cs, x = 1,2) have been computationally studied at M06-2X/def2-TZVPPD//B3LYP/def2-TZVPPD level of theory. Compounds are predicted to be stable at room temperature but release H2 on heating. Agostic Be…HB bonds play an important role in stabilization of oligomeric beryllium imidoboranes. Polymeric imidoborane, hydrogen, and ammonia are expected as major thermal decomposition products of complex beryllium amidoboranes. Ammonia evolution is predicted to proceed at slightly higher temperatures than hydrogen evolution...
December 19, 2016: Journal of Computational Chemistry
Fouad S Husseini, David Robinson, Neil T Hunt, Anthony W Parker, Jonathan D Hirst
The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types...
November 21, 2016: Journal of Computational Chemistry
Sam Tonddast-Navaei, Bharath Srinivasan, Jeffrey Skolnick
Conventional small molecule drug-discovery approaches target protein pockets. However, the limited number of geometrically distinct pockets leads to widespread promiscuity and deleterious side-effects. Here, the idea of COmposite protein LIGands (COLIG) that interact with each other as well as the protein within a single ligand binding pocket is examined. As a practical illustration, experimental evidence that E. coli Dihydrofolate reductase inhibitors are COLIGs is presented. Then, analysis of a non-redundant set of all holo PDB structures indicates that almost 47-76% of proteins (based on different sequence identity thresholds) can simultaneously bind multiple, interacting ligands in the same pocket...
November 16, 2016: Journal of Computational Chemistry
Sunhwan Jo, Xi Cheng, Jumin Lee, Seonghoon Kim, Sang-Jun Park, Dhilon S Patel, Andrew H Beaven, Kyu Il Lee, Huan Rui, Soohyung Park, Hui Sun Lee, Benoît Roux, Alexander D MacKerell, Jeffrey B Klauda, Yifei Qi, Wonpil Im
CHARMM-GUI,, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field...
November 14, 2016: Journal of Computational Chemistry
Catherine A Hurd, Nicholas A Besley, David Robinson
Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory-based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12...
November 14, 2016: Journal of Computational Chemistry
Peter L Walters, Thomas C Allen, Nancy Makri
We present a direct procedure for determining the parameters of a discrete harmonic bath modeling the influence of a complex condensed phase environment on the system of interest. The procedure employs an efficient discretization of the spectral density into modes that correspond to equal fractions of the reorganization energy. The new procedure uses directly the classical correlation function (available from molecular dynamics calculations) as input, avoiding numerical computation of the spectral density by means of a discrete Fourier transform...
November 14, 2016: Journal of Computational Chemistry
Ester Sesmero, Jodian A Brown, Ian F Thorpe
Hepatitis C virus (HCV) is a global health concern for which there is no vaccine available. The HCV polymerase is responsible for the critical function of replicating the RNA genome of the virus. Transitions between at least two conformations (open and closed) are necessary to allow the enzyme to replicate RNA. In this study, molecular dynamic simulations were initiated from multiple crystal structures to understand the free energy landscape (FEL) explored by the enzyme as it interconverts between these conformations...
November 12, 2016: Journal of Computational Chemistry
James S M Anderson, Juan I Rodríguez, Paul W Ayers, Andreas W Götz
The Quantum Theory of Atoms in Molecules (QTAIM) is used to elucidate the effects of relativity on chemical systems. To do this, molecules are studied using density-functional theory at both the nonrelativistic level and using the scalar relativistic zeroth-order regular approximation. Relativistic effects on the QTAIM properties and topology of the electron density can be significant for chemical systems with heavy atoms. It is important, therefore, to use the appropriate relativistic treatment of QTAIM (Anderson and Ayers, J...
November 10, 2016: Journal of Computational Chemistry
Christopher Ehlert, Tillmann Klamroth
Near edge X-ray absorption fine structure (NEXAFS) simulations based on the conventional configuration interaction singles (CIS) lead to excitation energies, which are systematically blue shifted. Using a (restricted) open shell core hole reference instead of the Hartree Fock (HF) ground state orbitals improves (Decleva et al., Chem. Phys., 1992, 168, 51) excitation energies and the shape of the spectra significantly. In this work, we systematically vary the underlying SCF approaches, that is, based on HF or density functional theory, to identify best suited reference orbitals using a series of small test molecules...
November 9, 2016: Journal of Computational Chemistry
Lisa E Felberg, David H Brookes, Eng-Hui Yap, Elizabeth Jurrus, Nathan A Baker, Teresa Head-Gordon
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants...
November 2, 2016: Journal of Computational Chemistry
Yosuke Sumiya, Tetsuya Taketsugu, Satoshi Maeda
The branching ratio of unimolecular decomposition can be evaluated by solving the rate equations. Recent advances in automated reaction path search methods have enabled efficient construction of the rate equations based on quantum chemical calculations. However, it is still difficult to solve the rate equations composed of hundreds or more elementary steps. This problem is especially serious when elementary steps that occur in highly different timescales coexist. In this article, we introduce an efficient approach to obtain the branching ratio from a given set of rate equations...
October 31, 2016: Journal of Computational Chemistry
Enrico Benassi
A number of programs and tools that simulate (1) H and (13) C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory...
October 31, 2016: Journal of Computational Chemistry
Charles C Kirkpatrick, John N Truong, Bruce A Kowert
Electronic structure calculations for late transition metals coordinated by two dithiolene ligands are found to be consistent with existing structures and also predict the geometries of Ni(I) species for which no solid state structures have been reported. Of particular interest are the compounds [M(mnt)2 ](n)(-) (M = Ni, Pd, and Pt with n = 1, 2, 3; M = Cu with n = 2). Calculations have been performed with and without ion-paring with M(diglyme)(+) (M = Li, Na, K) and R4 N(+) (R = Me, Bu)...
October 27, 2016: Journal of Computational Chemistry
E Prabhu Raman, Sirish Kaushik Lakkaraju, Rajiah Aldrin Denny, Alexander D MacKerell
Accurate and rapid estimation of relative binding affinities of ligand-protein complexes is a requirement of computational methods for their effective use in rational ligand design. Of the approaches commonly used, free energy perturbation (FEP) methods are considered one of the most accurate, although they require significant computational resources. Accordingly, it is desirable to have alternative methods of similar accuracy but greater computational efficiency to facilitate ligand design. In the present study relative free energies of binding are estimated for one or two non-hydrogen atom changes in compounds targeting the proteins ACK1 and p38 MAP kinase using three methods...
October 26, 2016: Journal of Computational Chemistry
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