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Journal of Computational Chemistry

Jason W Labonte, Jared Adolf-Bryfogle, William R Schief, Jeffrey J Gray
The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side-chain conformations, and ring forms, and it utilizes a glycan-specific term within its scoring function...
November 30, 2016: Journal of Computational Chemistry
Marek Szczepaniak, Jerzy Moc
We present a comprehensive benchmark computational study which has explored a complete path of the anomerization reaction of bare d-erythrose involving a pair of the low-energy α- and β-furanose anomers, the former of which was observed spectroscopically (Cabezas et al., Chem. Commun. 2013, 49, 10826). We find that the ring opening of the α-anomer yields the most stable open-chain tautomer which step is followed by the rotational interconversion of the open-chain rotamers and final ring closing to form the β-anomer...
November 29, 2016: Journal of Computational Chemistry
Xiaoling Zhan, Hu Shi, Hongguang Liu, Jin Yong Lee
A key parameter dictating the rate of charge transfer (CT) is reorganization energy (λ), an energy associated with geometry changes during hole/electron transfer. We show that "ironing" the inter-ring dihedral angles of oligothiophenes via proper substitutions or insertions (e.g., -OR, -F or -C≡C-), decreases the λ and thus promotes CT according to Marcus equation. Our results demonstrate, to attain a smaller λ, extending oligomer length is only significant if the flattened backbone structure is realized...
November 26, 2016: Journal of Computational Chemistry
Peter P Passler, Thomas S Hofer
Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short-coming has little impact on structural and short-time dynamic properties, it can be shown that dynamics in the long-time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved...
November 26, 2016: Journal of Computational Chemistry
Salvador Cardona-Serra, Stefano Sanvito
Molecules exhibiting a spin-crossover transition have been proposed for a number of applications such as molecular switches, spintronic tunable interfaces, and single molecule gates. Both the rational design of new spin-crossover systems and the improvement of the properties of the already existing ones require a theoretical understanding of the relative energy of the high (HS) and low spin state (LS) molecules in the solid-state. This has proved to be very challenging so far. Here, we shed some light on the importance of considering the symmetry and the geometry of the crystallographic cell to correctly evaluate the influence of the dipolar interactions on the relative energies of the molecular complex in both different spin states...
November 24, 2016: Journal of Computational Chemistry
Song Liu, Lizhe Zhu, Fu Kit Sheong, Wei Wang, Xuhui Huang
We present an efficient density-based adaptive-resolution clustering method APLoD for analyzing large-scale molecular dynamics (MD) trajectories. APLoD performs the k-nearest-neighbors search to estimate the density of MD conformations in a local fashion, which can group MD conformations in the same high-density region into a cluster. APLoD greatly improves the popular density peaks algorithm by reducing the running time and the memory usage by 2-3 orders of magnitude for systems ranging from alanine dipeptide to a 370-residue Maltose-binding protein...
November 21, 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
Amir Karton
Density functional theory (DFT) is the only quantum-chemical avenue for calculating thermochemical/kinetic properties of large polycyclic aromatic hydrocarbons (PAHs) such as graphene nanoflakes. Using CCSD(T)/CBS PAH isomerization energies, we find that all generalized gradient approximation (GGA) and meta GGA DFT functionals have severe difficulties in describing isomerization energies in PAHs. The poor performance of these functionals is demonstrated by the following root-mean-square deviations (RMSDs) obtained for a database of C14 H10 and C18 H12 isomerization energies...
November 17, 2016: Journal of Computational Chemistry
Cheng Wang, Yingkai Zhang
The development of new protein-ligand scoring functions using machine learning algorithms, such as random forest, has been of significant interest. By efficiently utilizing expanded feature sets and a large set of experimental data, random forest based scoring functions (RFbScore) can achieve better correlations to experimental protein-ligand binding data with known crystal structures; however, more extensive tests indicate that such enhancement in scoring power comes with significant under-performance in docking and screening power tests compared to traditional scoring functions...
November 17, 2016: Journal of Computational Chemistry
Julien Pilmé
This work addresses the decomposition of the Electron Localization Function (ELF) into partial density contributions using an appealing split of kinetic energy densities. Regarding the degree of the electron localization, the relationship between ELF and its usual spin-polarized formula is discussed. A new polarized ELF formula, built from any subsystems of the density, and a localization function, quantifying the measure of electron localization for only a subpart of the total system are introduced. The methodology appears tailored to describe the electron localization in bonding patterns of subsystems, such as the local nucleophilic character...
November 17, 2016: Journal of Computational Chemistry
Valter H Carvalho-Silva, Vincenzo Aquilanti, Heibbe C B de Oliveira, Kleber C Mundim
A formulation is presented for the application of tools from quantum chemistry and transition-state theory to phenomenologically cover cases where reaction rates deviate from Arrhenius law at low temperatures. A parameter d is introduced to describe the deviation for the systems from reaching the thermodynamic limit and is identified as the linearizing coefficient in the dependence of the inverse activation energy with inverse temperature. Its physical meaning is given and when deviation can be ascribed to quantum mechanical tunneling its value is calculated explicitly...
November 17, 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
Yuta Kajiwara, Satoshi Yasuda, Yuuki Takamuku, Takeshi Murata, Masahiro Kinoshita
We recently developed a physics-based method for identifying thermostabilizing mutations of a membrane protein. The method uses a free-energy function F where the importance of translational entropy of hydrocarbon groups within the lipid bilayer is emphasized. All of the possible mutations can rapidly be examined. The method was illustrated for the adenosine A2a receptor (A2a R) whose three-dimensional (3D) structure experimentally determined was utilized as the wild-type structure. Nine single mutations and a double mutation predicted to be stabilizing or destabilizing were checked by referring to the experimental results: The success rate was remarkably high...
November 14, 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
Fahimeh Ghasemi, Afshin Fassihi, Horacio Pérez-Sánchez, Alireza Mehri Dehnavi
Thousands of molecules and descriptors are available for a medicinal chemist thanks to the technological advancements in different branches of chemistry. This fact as well as the correlation between them has raised new problems in quantitative structure activity relationship studies. Proper parameter initialization in statistical modeling has merged as another challenge in recent years. Random selection of parameters leads to poor performance of deep neural network (DNN). In this research, deep belief network (DBN) was applied to initialize DNNs...
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
Bastien Belzunces, Sophie Hoyau, Magali Benoit, Nathalie Tarrat, Fabienne Bessac
Atrazine, a pesticide belonging to the s-triazine family, is one of the most employed pesticides. Due to its negative impact on the environment, it has been forbidden within the European Union since 2004 but remains abundant in soils. For these reasons, its behavior in soils and water at the atomic scale is of great interest. In this article, we have investigated, using DFT, the adsorption of atrazine onto two different clay surfaces: a pyrophyllite clay and an Mg-substituted clay named montmorillonite, with Ca(2+) compensating cations on its surface...
November 12, 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
John P Cvitkovic, George A Kaminski
We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water...
November 11, 2016: Journal of Computational Chemistry
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