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Journal of Computational Chemistry

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https://www.readbyqxmd.com/read/28643394/incorporating-deep-learning-with-convolutional-neural-networks-and-position-specific-scoring-matrices-for-identifying-electron-transport-proteins
#1
Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou
In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80...
June 22, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28643353/multistructural-microiteration-technique-for-geometry-optimization-and-reaction-path-calculation-in-large-systems
#2
Kimichi Suzuki, Keiji Morokuma, Satoshi Maeda
We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized...
June 22, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28643344/optimization-and-transferability-of-non-electrostatic-repulsion-in-the-polarizable-density-embedding-model
#3
Dalibor Hršak, Jógvan Magnus Haugaard Olsen, Jacob Kongsted
Embedding techniques in combination with response theory represent a successful approach to calculate molecular properties and excited states in large molecular systems such as solutions and proteins. Recently, the polarizable embedding model has been extended by introducing explicit electronic densities of the molecules in the nearest environment, resulting in the polarizable density embedding (PDE) model. This improvement provides a better description of the intermolecular interactions at short distances...
June 22, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28627078/gas-adsorption-in-mg-porphyrin-based-porous-organic-frameworks-a-computational-simulation-by-first-principles-derived-force-field
#4
Yujia Pang, Wenliang Li, Jingping Zhang
A novel type of porous organic frameworks, based on Mg-porphyrin, with diamond-like topology, named POF-Mgs is computationally designed, and the gas uptakes of CO2 , H2 , N2 , and H2 O in POF-Mgs are investigated by Grand canonical Monte Carlo simulations based on first-principles derived force fields (FF). The FF, which describes the interactions between POF-Mgs and gases, are fitted by dispersion corrected double-hybrid density functional theory, B2PLYP-D3. The good agreement between the obtained FF and the first-principle energies data confirms the reliability of the FF...
June 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28623871/simple-computing-of-the-viscosity-of-water-dioxane-mixtures-according-to-a-fluctuating-spc-e-ih-interstitial-model
#5
Anis Ghazouani, Jalel M'halla
In this contribution, we propose a new simple and fast computing approach to model liquid water and water-1,4 dioxane mixture, which is intermediate between molecular dynamics calculation and lattice fluid H-bonding theory in which water molecules are arranged according to a fluctuating hexagonal Ih network. It generalizes the interstitial mixture models of Samoilov and Pauling by increasing the number of spatial configurations into the space of phases due to the addition of rotations and vibrations of the molecules around their equilibrium positions...
June 17, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28618024/first-principles-modeling-of-hafnia-based-nanotubes
#6
Robert A Evarestov, Andrei V Bandura, Vitaly V Porsev, Alexey V Kovalenko
Hybrid density functional theory calculations were performed for the first time on structure, stability, phonon frequencies, and thermodynamic functions of hafnia-based single-wall nanotubes. The nanotubes were rolled up from the thin free layers of cubic and tetragonal phases of HfO2 . It was shown that the most stable HfO2 single-wall nanotubes can be obtained from hexagonal (111) layer of the cubic phase. Phonon frequencies have been calculated for different HfO2 nanolayers and nanotubes to prove the local stability and to find the thermal contributions to their thermodynamic functions...
June 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28618021/calculation-of-photoionization-differential-cross-sections-using-complex-gauss-type-orbitals
#7
Rei Matsuzaki, Satoshi Yabushita
Accurate theoretical calculation of photoelectron angular distributions for general molecules is becoming an important tool to image various chemical reactions in real time. We show in this article that not only photoionization total cross sections but also photoelectron angular distributions can be accurately calculated using complex Gauss-type orbital (cGTO) basis functions. Our method can be easily combined with existing quantum chemistry techniques including electron correlation effects, and applied to various molecules...
June 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28608507/revisiting-the-thermochemistry-of-chlorine-fluorides
#8
Hernán R Sánchez
In this work, accurate calculations of standard enthalpies of formation of chlorine fluorides (ClFn, n = 1-7; Cl2 F and Cl3 F2 ) were performed through the isodesmic reactions scheme. It is argued that, for many chlorine fluorides, the gold standard method of quantum chemistry (CCSD(T)) is not capable to predict enthalpy values nearing chemical accuracy if atomization scheme is used. This is underpinned by a thorough analysis of total atomization energy results and the inspection of multireference features of these compounds...
June 13, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28608423/a-toolchain-for-the-automatic-generation-of-computer-codes-for-correlated-wavefunction-calculations
#9
Martin Krupička, Kantharuban Sivalingam, Lee Huntington, Alexander A Auer, Frank Neese
In this work, the automated generator environment for ORCA (ORCA-AGE) is described. It is a powerful toolchain for the automatic implementation of wavefunction-based quantum chemical methods. ORCA-AGE consists of three main modules: (1) generation of "raw" equations from a second quantized Ansatz for the wavefunction, (2) factorization and optimization of equations, and (3) generation of actual computer code. We generate code for the ORCA package, making use of the powerful functionality for wavefunction-based correlation calculations that is already present in the code...
June 13, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28605037/gaudimm-a-modular-multi-objective-platform-for-molecular-modeling
#10
Jaime Rodríguez-Guerra Pedregal, Giuseppe Sciortino, Jordi Guasp, Martí Municoy, Jean-Didier Maréchal
GaudiMM (for Genetic Algorithms with Unrestricted Descriptors for Intuitive Molecular Modeling) is here presented as a modular platform for rapid 3D sketching of molecular systems. It combines a Multi-Objective Genetic Algorithm with diverse molecular descriptors to overcome the difficulty of generating candidate models for systems with scarce structural data. Its grounds consist in transforming any molecular descriptor (i.e. those generally used for analysis of data) as a guiding objective for PES explorations...
June 12, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28602026/treating-ion-distribution-with-gaussian-based-smooth-dielectric-function-in-delphi
#11
Zhe Jia, Lin Li, Arghya Chakravorty, Emil Alexov
The standard treatment of ions in the framework of the Poisson-Boltzmann equation relies on molecular surfaces, which are commonly constructed along with the Stern layer. The molecular surface determines where ions can be present. In the Gaussian-based smooth dielectric function in DelPhi, smooth boundaries between the solute and solvent take the place of molecular surface. Therefore, this invokes the question of how to model mobile ions in the water phase without a definite solute-solvent boundary. This article reports a natural extension of the Gaussian-based smooth dielectric function approach that treats mobile ions via Boltzmann distribution with an added desolvation penalty...
June 11, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28600826/tinker-openmm-absolute-and-relative-alchemical-free-energies-using-amoeba-on-gpus
#12
Matthew Harger, Daniel Li, Zhi Wang, Kevin Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay Ponder, Pengyu Ren
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core...
June 10, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28580696/on-low-lying-excited-states-of-extended-nanographenes
#13
Takao Tsuneda, Raman K Singh, Ayako Nakata
Low-lying excited states of planarly extended nanographenes are investigated using the long-range corrected (LC) density functional theory (DFT) and the spin-flip (SF) time-dependent density functional theory (TDDFT) by exploring the long-range exchange and double-excitation correlation effects on the excitation energies, band gaps, and exciton binding energies. Optimizing the geometries of the nanographenes indicates that the long-range exchange interaction significantly improves the CC bond lengths and amplify their bond length alternations with overall shortening the bond lengths...
June 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28580613/update-of-the-attract-force-field-for-the-prediction-of-protein-protein-binding-affinity
#14
Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci
Determining the protein-protein interactions is still a major challenge for molecular biology. Docking protocols has come of age in predicting the structure of macromolecular complexes. However, they still lack accuracy to estimate the binding affinities, the thermodynamic quantity that drives the formation of a complex. Here, an updated version of the protein-protein ATTRACT force field aiming at predicting experimental binding affinities is reported. It has been designed on a dataset of 218 protein-protein complexes...
June 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28573687/computational-insights-into-the-s3-transfer-reaction-a-special-case-of-double-group-transfer-reaction-featuring-bicyclically-delocalized-aromatic-transition-state-geometries
#15
Andrés G Algarra
An unusual pericyclic process that involves the intermolecular transfer of thiozone (S3 ) is computationally described. The process can be considered as a special case of double group transfer reaction whereby the two migrating groups are connected to the same substituent, taking place in a concerted manner via transition states featuring two five-membered C2 S3 rings fused together. Analysis of the aromaticity at the TS geometries by computing NICS values at the (3,+1) RCPS as well as ACID calculations confirms the aromatic character of each C2 S3 ring, thus resulting in bicyclically delocalized aromatic structures...
June 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28568844/effect-of-sampling-on-bace-1-ligands-binding-free-energy-predictions-via-mm-pbsa-calculations
#16
Nicolas Chéron, Eugene I Shakhnovich
The BACE-1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM-PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme. After showing that the most probable protonation state of the catalytic dyad is mono-protonated (on ASP32), we performed a thorough analysis of the parameters influencing the sampling of the conformational space (in total, more than 35 μs of simulations were performed). We show that ten simulations of 2 ns gives better results than one of 50 ns...
June 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28568014/interdependence-of-icd-rates-in-paired-quantum-dots-on-geometry
#17
Fabian Weber, Emad F Aziz, Annika Bande
Using state-of-the-art antisymmetrized multiconfiguration time-dependent Hartree (MCTDH) electron dynamics calculations we study the interdependence of the intermolecular Coulombic decay (ICD) process on the geometric parameters of a doubly-charged paired quantum dot (PQD) model system in the framework of the effective mass approximation (EMA). We find that ICD displays a maximum rate for a certain geometry of the electron-emitting quantum dot, which is simultaneously dependent on both the distance between the quantum dots as well as the photon-absorbing quantum dot's geometry...
June 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28558168/importance-of-explicit-smeared-lone-pairs-in-anisotropic-polarizable-molecular-mechanics-torture-track-angular-tests-for-exchange-repulsion-and-charge-transfer-contributions
#18
Léa El Khoury, Sehr Naseem-Khan, Karolina Kwapien, Zeina Hobaika, Richard G Maroun, Jean-Philip Piquemal, Nohad Gresh
A correct representation of the short-range contributions such as exchange-repulsion (Erep ) and charge-transfer (Ect ) is essential for the soundness of separable, anisotropic polarizable molecular mechanics potentials. Within the context of the SIBFA procedure, this is aimed at by explicit representations of lone pairs in their expressions. It is necessary to account for their anisotropic behaviors upon performing not only in-plane, but also out-of-plane, variations of a probe molecule or cation interacting with a target molecule or molecular fragment...
May 30, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28558151/accurate-van-der-waals-force-field-for-gas-adsorption-in-porous-materials
#19
Lei Sun, Li Yang, Ya-Dong Zhang, Qi Shi, Rui-Feng Lu, Wei-Qiao Deng
An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements...
May 30, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28558123/dlpno-ccsd-t-scaled-methods-for-the-accurate-treatment-of-large-supramolecular-complexes
#20
Joaquín Calbo, Juan C Sancho-García, Enrique Ortí, Juan Aragó
In this work, we present scaled variants of the DLPNO-CCSD(T) method, dubbed as (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T), to obtain accurate interaction energies in supramolecular complexes governed by noncovalent interactions. The novel scaled schemes are based on the linear combination of the DLPNO-CCSD(T) correlation energies calculated with the standard (LoosePNO and NormalPNO) and modified (Loose2PNO and Normal2PNO) DLPNO-CCSD(T) accuracy levels. The scaled DLPNO-CCSD(T) variants provide nearly TightPNO accuracy, which is essential for the quantification of weak noncovalent interactions, with a noticeable saving in computational cost...
May 30, 2017: Journal of Computational Chemistry
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