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Journal of Molecular Modeling

Sivakumar Prasanth Kumar
Ensemble methods are gaining more importance in structure-based approaches as single protein-ligand complexes strongly influence the outcomes of virtual screening. Structure-based pharmacophore modeling based on a single protein-ligand complex with complex feature combinations is often limited to certain chemical classes. The REPHARMBLE (receptor pharmacophore ensemble) approach presented here examines the ability of an ensemble of selected protein-ligand complexes to populate pharmacophore space in the ligand binding site, rigorously assesses the importance of pharmacophore features using Poisson statistic and information theory-based entropy calculations, and generates pharmacophore models with high probabilities...
September 15, 2018: Journal of Molecular Modeling
Guillaume Hoffmann, Vincent Tognetti, Laurent Joubert
In this paper, we assess the ability of various intrinsic molecular and atomic descriptors, grounded in the conceptual density functional theory and the quantum theory of atoms-in-molecules frameworks, to predict the electrophilicity of Michael acceptors, which are fundamental organic reagents involved in the formation of carbon-carbon bonds. To this aim, linear and multilinear regressions between these theoretical properties and the experimental values gathered in Mayr-Patz' scale were performed. The relevance of quantum chemical descriptors are then discussed...
September 14, 2018: Journal of Molecular Modeling
Shyantani Maiti, Pralay Mitra
Flagellar rotation regulates the phenomenon of chemotaxis in bacteria. The interaction between the stator unit and the rotor unit of the flagellar motors is responsible for switching the direction of bacterial flagellar rotation. However, the molecular interaction mechanism between the stator (MotA/MotB) and the rotor (FliG/FliM/FliN) proteins for the flagellar rotational direction switching was not very clear. To address this, the asymmetry in the copies of FliG, FliM, and FliN molecules was resolved by reconstructing the switch complex using a modeled rotor unit that fulfills the experimentally available geometric constraints...
September 13, 2018: Journal of Molecular Modeling
K Harrath, S Hussain Talib, S Boughdiri
The present work carried out a theoretical study of the electronic structures, absorption spectra, and photovoltaic performance of two series of transition metal-phthalocyanine derived from nonperipheral electron-donating substituents, either (2-phenyl) phenoxy(M-PC1) or quinoleinoxy(M-PC2). The DFT and TD-DFT were employed for this study. The effect of modifying the central metal atoms and the substitution on cell performance were investigated in terms of polarizability (α), hyper-polarizability (β), chemical potential (μ), chemical hardness (η), electrophilicity power (ω), FMOs, energy gaps, UV/vis absorption spectra and injected driving force (ΔGinject ), light harvesting efficiencies (LHE), total reorganization energy (λtot ), open circuit photovoltage (Voc ), and life time of the excited state (τ)...
September 13, 2018: Journal of Molecular Modeling
Barnali Bhattacharya, Rajkumar Mondal, Utpal Sarkar
Density functional theory (DFT) combined with nonequilibrium Green's function (NEGF) formalism are used to investigate the effects of substitutional doping by nitrogen and sulfur on transport properties of AGNR-pentalene-AGNR nanojunction. A considerable spin filtering capability in a wide bias range is observed for all systems, which may have potential application in spintronics devices. Moreover, all model devices exhibit a negative differential effect with considerable peak-to-valley ratio. Thus, our findings provide a way to produce multifunctional spintronic devices based on nitrogen and sulfur doped pentalene-AGNR nanojunctions...
September 12, 2018: Journal of Molecular Modeling
K Vijay Reddy, Snehanshu Pal
In this paper, constant load bending tests were performed on a nanocrystalline Ni nanowire specimen at different deformation temperatures using molecular dynamics simulation to investigate deformation behavior and mechanisms responsible for fracture. The nature of the fracture occurred in this nanowire specimen is found to transit from brittle to ductile as the temperature rises from 500 to 800 K. Also, with an increase in temperature, the fracture strain is increased indicating more plastic deformation prior to fracture...
September 8, 2018: Journal of Molecular Modeling
Julio César González-Torres, Luis A Cipriano, Enrique Poulain, Víctor Domínguez-Soria, Raúl García-Cruz, Oscar Olvera-Neria
Charge carriers (electrons and holes) are generated on the TiO2 using UV radiation; this excitation energy can be reduced by modifying the material electronic structure, for example, by doping or creating oxygen vacancies. Here, the electronic structure of a transition metal-doped anatase, bulk and surface, and their interaction with oxygen vacancies are studied using density functional theory. The visible light response of metal-doped TiO2 (101) is also determined. Transition metals generate intra-band gap states, which reduce the excitation energy but may also act as charge recombination sites...
September 7, 2018: Journal of Molecular Modeling
Hourieh Kalhor, Mansour Poorebrahim, Hamzeh Rahimi, Ali Akbar Shabani, Morteza Karimipoor, Mohammad Reza Akbari Eidgahi, Ladan Teimoori-Toolabi
Wnt and Frizzled (Fzd) family members play crucial roles in the self-renewal of tumor-initiating cells. Until now, only a few studies have addressed the distinct mechanism of Wnt-Fzd interactions. In this study, we suggest a possible interaction mode of Wnt2 with the Fzd7 cysteine-rich domain (CRD)-both of which are up-regulated in some types of cancer. A combination of homology modeling, molecular docking and molecular dynamics (MD) simulations was carried out to study this ligand-receptor complex in great detail...
September 6, 2018: Journal of Molecular Modeling
Guillaume Acke, Patrick Bultinck
When going beyond the Hartree-Fock level to correlated methods, one observes a significant reduction in the delocalization index. This is commonly interpreted as a weakening of electron sharing due to electron correlation, although this is rather counter-intuitive to the concomitant energy lowering. In this study, we use an analytical valence bond model and full CI calculations to show that this reduction in the delocalization index actually goes hand in hand with increased covalent contributions at the expense of ionic contributions...
September 6, 2018: Journal of Molecular Modeling
Noura Khemiri, Manef Abderrabba, Sabri Messaoudi
A detailed theoretical study of the various possible fragmentation reactions of the benzophenone radical cation was carried out for the first time. In the first step, we optimized the geometries of all the structures resulting from the fragmentation of this cation using density functional theory (DFT). Our calculations were performed in the gas phase using the aug-cc-pVTZ basis set and the PBE1PBE functional. We determined the optimized structural parameters and the harmonic and anharmonic frequencies. The energies corresponding to all the optimized molecules were recalculated using the coupled cluster method CCSD(T)...
September 5, 2018: Journal of Molecular Modeling
Tadsanee Awang, Prapasiri Pongprayoon
Human α-defensin 5 (HD5) is one of the important antimicrobial peptides (AMPs) used against a broad-spectrum of pathogens, especially Gram-negative bacteria. HD5 kills by disrupting and making a pore in the bacterial membrane. The presence of lipopolysaccharide (LPS), located on a membrane surface, is found to have an impact on HD5's activity, where such binding mechanism in microscopic detail remains unclear. In this work, we therefore employed molecular dynamics (MD) simulations to investigate the binding mechanisms of HD5 on LPS in comparison to a bare DMPC lipid membrane...
September 5, 2018: Journal of Molecular Modeling
Oliver Weingart, Artur Nenov, Piero Altoè, Ivan Rivalta, Javier Segarra-Martí, Irina Dokukina, Marco Garavelli
We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments...
September 3, 2018: Journal of Molecular Modeling
Nabil Omri, Noura Khemiri, Manef Abderrabba, Fathi Moussa, Sabri Messaoudi
In this paper, we perform the synthesization of carbon nanoparticles for active principle vectorization, with the suggestion of a reaction mechanism of tryptophan methyl ester addition on [60]fullerene. Firstly, we studied the effect of tryptophan form on its addition reaction on [60]fullerene. So, in order to determine the preferred environment that makes this reaction the most favorable, we considered all tryptophan possible forms in our investigation: the molecular, the zwitterionic, and the dibasic forms...
September 3, 2018: Journal of Molecular Modeling
Peter Holland
Using the trajectory conception of state, we give a simple demonstration that the quantum state of a many-body system may be expressed as a set of states in three-dimensional space, each associated with a different particle. It follows that the many-body wavefunction may be derived from a set of waves in 3-space. Entanglement is represented in the trajectory picture by the mutual dependence of the 3-states on the trajectory labels.
September 3, 2018: Journal of Molecular Modeling
Jorge Gutiérrez-Flores, Alfredo Moreno, Francisco J Vázquez, Citlalli Rios, Betzabeth Minutti, Guadalupe Morales, Aura Suarez, Estrella Ramos, Roberto Salcedo
Epoxide of oestradiol is one of the main risk factors for the genesis and evolution of breast cancer; hence, in recent years there has been considerable interest in the investigation of new inhibitors capable of reducing its carcinogenic activity. The aim of this article is to study the [2 + 2] cycloaddition reaction of epoxide of oestradiol in different pristine (C76 and D5h -C80 ) and endohedral metallofullerene (C72 @Sc2 C2 , C76 @Sc2 and C80 @Sc2 ) by means of molecular electrostatic potential (MEP) topological analysis...
September 1, 2018: Journal of Molecular Modeling
Peter Politzer, Jane S Murray
The Hellmann-Feynman theorem has, with a few exceptions, not been exploited to the degree that it merits. This is due, at least in part, to a widespread failure to recognize that its greatest value may be conceptual rather than numerical, i.e., in achieving insight into molecular properties and behavior. In this brief overview, we shall discuss three examples of significant concepts that have come out of the Hellmann-Feynman theorem: (1) The forces exerted upon the nuclei in molecules are entirely Coulombic in nature...
August 31, 2018: Journal of Molecular Modeling
Zhengyang Gao, Yao Sun, Minghui Li, Wentao Han
Density functional theory calculations were performed to gain insight into the mechanism and kinetic studies of homogeneous gas-phase formation of polychlorinated dibenzodioxins and polychlorinated dibenzofurans (PCDD/Fs) via aliphatic hydrocarbons (C2 H2 , C2 H4 , C3 H6 and C4 H8 ). The calculated results demonstrated that the intra-annular elimination of H is the rate-determining step throughout the reaction chain; the presence of ortho-Cl increases the abstraction barrier of arene H and decreases the reactivity of the molecule...
August 31, 2018: Journal of Molecular Modeling
Sukanta Mondal, Pallavi Sarkar, Alvaro Muñoz-Castro
Being monocyclic planar, benzene retains 6π Hückel aromatic backbone. However, for larger analogues, the repulsion between vicinal C-H bonds makes them nonplanar, as for [10]-annulene. Thus, on this basis, a planar 10-π-aromatic C10 H10 is unreachable. A detailed structural comparison among the C3 H3 + , C4 H4 2+ , C5 H5 - , C6 H6 , C7 H7 + , C8 H8 2+ , C9 H9 - , and C10 H10 systems supports that the repulsion between vicinal C-H bonds is the primary reason for the loss of planarity, despite the favorable aromatic electron count...
August 31, 2018: Journal of Molecular Modeling
Anastasios Haskopoulos, George Maroulis, T Bancewicz
We investigated the interaction (hyper)polarizability of neon-dihydrogen pairs by performing high-level ab initio calculations with atom/molecule-specific, purpose-oriented Gaussian basis sets. We obtained interaction-induced electric properties at the SCF, MP2, and CCSD levels of theory. At the CCSD level, for the T-shaped configuration, around the respective potential minimum of 6.437 a0 , the interaction-induced mean first hyperpolarizability varies for 5 <  R/a0  < 10 as[Formula: see text]Again, at the CCSD level, but for the L-shaped configuration around the respective potential minimum of 6...
August 31, 2018: Journal of Molecular Modeling
S Ajori, R Ansari, R Hassani, S Haghighi
Based on molecular dynamics (MD) simulations, the buckling analysis of a perfect carbon nanotorus is presented herein. First of all, the minimum length of single-walled carbon nanotubes (SWCNTs) with different radii is determined at which perfect toroidal CNTs can be formed without any ripple at the inner side of the rings. According to the results, by increasing the radius of SWCNT (r), the radius of its corresponding perfect nanotorus (R) increases. Also, for SWCNTs with various lengths, it is found that the buckling force and strain of related carbon nanotoruses increase by increasing R/r...
August 30, 2018: Journal of Molecular Modeling
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