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Journal of Computational Chemistry

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https://www.readbyqxmd.com/read/29761520/predicting-lysine-malonylation-sites-of-proteins-using-sequence-and-predicted-structural-features
#1
Ghazaleh Taherzadeh, Yuedong Yang, Haodong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
Malonylation is a recently discovered post-translational modification (PTM) in which a malonyl group attaches to a lysine (K) amino acid residue of a protein. In this work, a novel machine learning model, SPRINT-Mal, is developed to predict malonylation sites by employing sequence and predicted structural features. Evolutionary information and physicochemical properties are found to be the two most discriminative features whereas a structural feature called half-sphere exposure provides additional improvement to the prediction performance...
May 14, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29756365/revised-mechanism-of-carboxylation-of-ribulose-1-5-biphosphate-by-rubisco-from-large-scale-quantum-chemical-calculations
#2
Peter L Cummins, Babu Kannappan, Jill E Gready
Here, we describe a computational approach for studying enzymes that catalyze complex multi-step reactions and apply it to Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5-step carboxylase reaction, the substrate Ribulose-1,5-bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2 . Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation...
May 14, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29756357/a-refined-cavity-construction-algorithm-for-the-conductor-like-screening-model
#3
Andreas Klamt, Michael Diedenhofen
A cavity construction algorithm based on the triangulation of an iso-surface is introduced as a new standard for dielectric continuum solvation calculations with the Conductor-like Screening Model COSMO. It overcomes deficiencies which have become apparent for the original COSMO standard cavity, especially in concave regions of the molecular shaped cavity. The new standard, called FINE Cavity, is described in this article with several application examples. The earlier COSMO cavity construction algorithms are described for comparison...
May 14, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29756317/free-energy-landscapes-of-prototropic-tautomerism-in-pyridoxal-5-phosphate-schiff-bases-at-the-active-site-of-an-enzyme-in-aqueous-medium
#4
Kumari Soniya, Amalendu Chandra
We have performed hybrid quantum-classical metadynamics simulations and quantum chemical calculations to investigate the free energy landscapes of intramolecular proton transfer and associated tautomeric equilibrium in pyridoxal 5 '-phosphate (PLP) Schiff Bases, namely the internal and external aldimines, at the active site of serine hydroxymethyltransferase (SHMT) enzyme in aqueous medium. It is important to determine the relative stability of the two tautomers (ketoenamine and enolimine) of the PLP aldimines to study the catalytic activity of the concerned enzyme...
May 14, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29756218/tyrosine-absorption-spectroscopy-backbone-protonation-effects-on-the-side-chain-electronic-properties
#5
Sara Del Galdo, Giordano Mancini, Isabella Daidone, Laura Zanetti Polzi, Andrea Amadei, Vincenzo Barone
The UV-vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV-vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua-p-Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations...
May 14, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29752737/fluoride-anion-sensing-mechanism-of-a-bodipy-linked-hydrogen-bonding-probe
#6
Yang Li, Junsheng Chen, Tian-Shu Chu
The sensing mechanism of a fluoride-anion probe BODIPY-amidothiourea (1c) has been elucidated through the density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. The theoretical study indicates that in the DMSO/water mixtures the fluorescent sensing has been regulated by the fluoride complex that formed between the probe 1c/two water molecules and the fluoride anion, and the excited-state intermolecular hydrogen bond (H-B) plays an important role in the fluoride sensing mechanism...
May 11, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29752734/partition-coefficients-of-methylated-dna-bases-obtained-from-free-energy-calculations-with-molecular-electron-density-derived-atomic-charges
#7
A Lara, M Riquelme, E Vöhringer-Martinez
Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account...
May 11, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29737546/combining-the-polarizable-drude-force-field-with-a-continuum-electrostatic-poisson-boltzmann-implicit-solvation-model
#8
Alexey Aleksandrov, Fang-Yu Lin, Benoît Roux, Alexander D MacKerell
In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self-consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well-experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0...
May 8, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29737541/size-guided-multi-seed-heuristic-method-for-geometry-optimization-of-clusters-application-to-benzene-clusters
#9
Hiroshi Takeuchi
Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size-guided multi-seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest-energy configurations of the cluster with n - 1 molecules (seeds)...
May 8, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29727037/molecular-dynamics-simulations-using-the-drude-polarizable-force-field-on-gpus-with-openmm-implementation-validation-and-benchmarks
#10
Jing Huang, Justin A Lemkul, Peter K Eastman, Alexander D MacKerell
Presented is the implementation of the Drude force field in the open-source OpenMM simulation package allowing for access to graphical processing unit (GPU) hardware. In the Drude model, electronic degrees of freedom are represented by negatively charged particles attached to their parent atoms via harmonic springs, such that extra computational overhead comes from these additional particles and virtual sites representing lone pairs on electronegative atoms, as well as the associated thermostat and integration algorithms...
May 4, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29727036/initial-excited-state-relaxation-of-locked-retinal-protonated-schiff-base-chromophore-an-insight-from-coupled-cluster-and-multireference-perturbation-theory-calculations
#11
Dawid Grabarek, Tadeusz Andruniów
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers...
May 4, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29727031/performance-evaluation-of-the-zero-multipole-summation-method-in-modern-molecular-dynamics-software
#12
Shun Sakuraba, Ikuo Fukuda
The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS...
May 4, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29722444/systematic-evaluation-and-refinement-of-existing-all-atom-force-fields-for-the-simulation-of-liquid-acetonitrile
#13
Mohammad H Kowsari, Leila Tohidifar
The reliability of a molecular dynamics (MD) simulation study mainly depends on the accuracy of the applied force field. Unlike the ability of some potential models for reasonably predicting the thermodynamic properties of acetonitrile (ACN), simulated dynamical properties such as self-diffusion are generally underestimated compared to experimental values. The present work focuses on the evaluation and refinement of several available all-atom force fields for ACN and proposes a refined flexible six-site potential model...
May 3, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29722442/electronic-and-structural-properties-of-li-n-be-2-b-8-n-1-14-and-li-n-be-2-b-36-n-1-21-nanoflakes-shed-light-on-possible-anode-materials-for-li-based-batteries
#14
Moein Goodarzi, Fariba Nazari, Francesc Illas
Systematic addition of Li atoms to the Be2 B8 and Be2 B36 backbones has been studied by density functional theory-based calculations with the aim to investigate properties of interest on possible anode materials for Li-based batteries. For the Be2 B8 Lin (n = 1-8) and the Be2 B36 Lin (n = 1-20) systems, lithium salts are dominant whereas a clear electride feature shows up for Be2 B8 Lin (n = 9-14) and Be2 B36 Li21 . Addition of hydrogen radicals to these systems shows that the Be2 B8 Li14 electride becomes a Be2 B8 Li14 H2 hydride electride whereas Be2 B36 Li21 leads to a Be2 B36 Li21 H salt...
May 3, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29707800/an-open-library-of-relativistic-core-electron-density-function-for-the-qtaim-analysis-with-pseudopotentials
#15
Wenli Zou, Ziyu Cai, Jiankang Wang, Kunyu Xin
Based on two-component relativistic atomic calculations, a free electron density function (EDF) library has been developed for nearly all the known ECPs of the elements Li (Z = 3) up to Ubn (Z = 120), which can be interfaced into modern quantum chemistry programs to save the .wfx wavefunction file. The applicability of this EDF library is demonstrated by the analyses of the quantum theory of atoms in molecules (QTAIM) and other real space functions on HeCuF, PtO42+, OgF4 , and TlCl3 (DMSO)2 . When a large-core ECP is used, it shows that the corrections by EDF may significantly improve the properties of some density-derived real space functions, but they are invalid for the wavefunction-depending real space functions...
April 29, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29707796/calculating-particle-pair-potentials-from-fluid-state-pair-correlations-iterative-ornstein-zernike-inversion
#16
Marco Heinen
An iterative Monte Carlo inversion method for the calculation of particle pair potentials from given particle pair correlations is proposed in this article. The new method, which is best referred to as Iterative Ornstein-Zernike Inversion, represents a generalization and an improvement of the established Iterative Boltzmann Inversion technique (Reith, Pütz and Müller-Plathe, J. Comput. Chem. 2003, 24, 1624). Our modification of Iterative Boltzmann Inversion consists of replacing the potential of mean force as an approximant for the pair potential with another, generally more accurate approximant that is based on a trial bridge function in the Ornstein-Zernike integral equation formalism...
April 29, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29707791/theoretical-insights-on-the-inhibition-mechanism-of-a-class-a-serine-hydrolase-by-avibactam
#17
Ignacio Lizana, Eduardo J Delgado
The inhibition mechanism of CTX-M-15 class A serine hydrolase by the inhibitor avibactam is addressed by a combined molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach postulating that the residue Ser70 is the sole reacting residue, that is, itself may play the role of the acid-base species required for the enzyme inhibition. Other residues located in the active site have key participation in the positioning of the inhibitor in the right conformation to favor the attack of Ser70, in addition to the stabilization of the transition state by electrostatic interactions with avibactam...
April 29, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29707787/force-constant-decomposition-for-penta-coordinated-xh-3-cl-2-x-c-si-ge-structures
#18
Ken Sakata
Based on the energy decomposition analysis of an interacting system, we propose a method for force constant decomposition analysis with respect to the specific normal coordinate. Using the presented method, we examined the penta-coordinated XH3Cl2- system (X = C, Si, Ge), which possesses a three-center four-electron bond. The origin of the difference in the stability of the penta-coordinated D3h structures was clearly shown to be the effect of electron delocalization-polarization term. © 2018 Wiley Periodicals, Inc...
April 29, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29707784/fragment-based-quantum-mechanical-calculation-of-protein-protein-binding-affinities
#19
Yaqian Wang, Jinfeng Liu, Jinjin Li, Xiao He
The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0...
April 29, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29701316/calculation-of-the-excited-states-properties-of-lh1-complex-of-thermochromatium-tepidum
#20
Maxim I Kozlov, Vladimir V Poddubnyy, Ilya O Glebov
Calculation of the excited states properties of pigment complexes is one of the key problems in the photosynthesis research. The excited states of LH1 complex of Thermochromatium tepidum were studied by means of the high-precision quantum chemistry methods. The influence of different parameters of the calculation procedure was examined. The optimal scheme of calculation was chosen by comparison of calculated results with the experimental data on absorption, electronic and magnetic circular dichroism spectra...
April 27, 2018: Journal of Computational Chemistry
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