4,144 results match your criteria Journal of molecular modeling[Journal]


A reactive force field molecular dynamics study of molecular nitrogen and water mixtures under high temperature and high pressure.

J Mol Model 2019 Apr 17;25(5):120. Epub 2019 Apr 17.

Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China.

Establishment of an equation of state (EOS) for detonation products is challenging through molecular modeling approaches. Molecular dynamics (MD) simulations with the reactive force fields (ReaxFF) were carried out in this work for molecular N and HO and their mixtures, which are key components of detonation products, with high density and under high temperature, and compared with the experiment-based Becker-Kistiakowsky-Wilson (BKW) and the Lennard-Jones potential-based Tsien-Zhao (TZ) equations. Phase separations were noted for the mixtures, enhanced for denser systems under low temperature, and detracted for sparse systems under high temperature. Read More

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http://link.springer.com/10.1007/s00894-019-4009-4
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http://dx.doi.org/10.1007/s00894-019-4009-4DOI Listing
April 2019
1 Read

What is semiempirical molecular orbital theory approximating?

J Mol Model 2019 Apr 16;25(5):119. Epub 2019 Apr 16.

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.

We elucidate the approaches used to incorporate electron correlation in existing semiempirical molecular orbital theory (SEMO) methods and compare them with the techniques used in other quantum chemical methods. After analyzing expressions for electron correlation in ab initio wavefunction theory, density functional theory, and density functional-based tight-binding (TB) methods, we suggest a framework for developing hybrid TB-SEMO methods. We provide a numerical proof-of-concept for such a method based on the OM2 method. Read More

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http://link.springer.com/10.1007/s00894-019-4005-8
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http://dx.doi.org/10.1007/s00894-019-4005-8DOI Listing
April 2019
1 Read

Molecular modeling and QM/MM calculation clarify the catalytic mechanism of β-lactamase N1.

J Mol Model 2019 Apr 13;25(5):118. Epub 2019 Apr 13.

Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China.

The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Staphylococcus aureus), has previously been reported in the literature, its mechanism remains elusive. Here, we show that molecular modeling and quantum-mechanical/molecular mechanics (QM/MM) calculations describing the complex of β-lactamase N1 with nitrocefin (the substrate of β-lactamase N1) can predict the catalytic mechanism of nitrocefin hydrolysis by β-lactamase N1. Read More

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http://link.springer.com/10.1007/s00894-019-4001-z
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http://dx.doi.org/10.1007/s00894-019-4001-zDOI Listing
April 2019
2 Reads

Functionalized graphene pieces to trap the insecticide imidacloprid: a theoretical analysis.

J Mol Model 2019 Apr 13;25(5):117. Epub 2019 Apr 13.

Departamento de Posgrado e Investigación, División de Mecatrónica, Instituto Tecnológico Superior de Zacapoaxtla, Carretera Acuaco-Zacapoaxtla kilómetro 8 Totoltepec, C.P. 73680, Zacapoaxtla, Puebla, México.

Eleven adducts for the interaction between imidacloprid (IMI) and some activated carbon (AC) pieces are proposed in this work. Activated carbon pieces were obtained by using a finite zig-zag graphene structure saturated with hydrogen atoms on the edges giving a pristine model with 70 carbon atoms and 22 hydrogen atoms. The zig-zag graphene structure was oxidized with -O, -COOH, -OH, and -O- groups. Read More

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http://link.springer.com/10.1007/s00894-019-4016-5
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http://dx.doi.org/10.1007/s00894-019-4016-5DOI Listing
April 2019
1 Read

Structure-activity relationship of tacrine and its analogues in relation to inhibitory activity against Alzheimer's disease.

J Mol Model 2019 Apr 11;25(5):116. Epub 2019 Apr 11.

Grupo de Química Teórica e Estrutural de Anápolis (QTEA), Câmpus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, CP 459, Anápolis, GO, 75001-970, Brazil.

Alzheimer's disease is a widespread type of neurodegenerative dementia that mainly affects the elderly. Currently, this disease can only be treated palliatively. Existing drugs can only improve patients' symptoms. Read More

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http://dx.doi.org/10.1007/s00894-019-3993-8DOI Listing

Graphical user interface for an easy and reliable construction of input files to CP2K.

J Mol Model 2019 Apr 10;25(5):115. Epub 2019 Apr 10.

Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.

Creating input files to atomistic simulations and quantum chemical calculations in the CP2K software package can be a challenge. Here, we present a new graphical user interface to reduce the complexity of the work needed to run a CP2K calculation as well as the risk for making mistakes. The program is called CP2K Editor, and it provides a user-friendly interface for both new and experienced users. Read More

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http://dx.doi.org/10.1007/s00894-019-3987-6DOI Listing

Recognition of repulsive and attractive regions of selected serotonin receptor binding site using FMO-EDA approach.

J Mol Model 2019 Apr 6;25(5):114. Epub 2019 Apr 6.

Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska, 31-155, Kraków, Poland.

The complexes of selected long-chain arylpiperazines with homology models of 5-HT, 5-HT, and 5-HT receptors were investigated using quantum mechanical methods. The molecular geometries of the ligand-receptor complexes were firstly optimized with the Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) method. Next, the fragment molecular orbitals method with an energy decomposition analysis scheme (FMO-EDA) was employed to estimate the interaction energies in binding sites. Read More

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http://dx.doi.org/10.1007/s00894-019-3995-6DOI Listing

De novo design of anticancer peptides by ensemble artificial neural networks.

J Mol Model 2019 Apr 5;25(5):112. Epub 2019 Apr 5.

Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.

Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. Read More

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http://dx.doi.org/10.1007/s00894-019-4007-6DOI Listing
April 2019
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Structure, stability, and electronic properties of niobium-germanium and tantalum-germanium clusters.

J Mol Model 2019 Apr 5;25(5):113. Epub 2019 Apr 5.

Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622, Villeurbanne, France.

The structural, electronic and magnetic properties of niobium- and tantalum-doped germanium clusters MGe (M = Nb, Ta and n = 1-19) were investigated by first principles calculations within the density functional theory (DFT) approach. Growth pattern behaviors, stabilities, and electronic properties are presented and discussed. Endohedral cage-like structures in which the metal atom is encapsulated are favored for n ≥ 10. Read More

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http://dx.doi.org/10.1007/s00894-019-3988-5DOI Listing

Microsecond molecular dynamics simulations and dynamic network analysis provide understanding of the allosteric inactivation of GSK3β induced by the L343R mutation.

J Mol Model 2019 Apr 4;25(5):111. Epub 2019 Apr 4.

Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.

Glycogen synthase kinase 3β (GSK3β), a serine/threonine protein kinase, is involved in several human diseases, including type II diabetes, mood disorders, prostate cancer, and Alzheimer's disease, representing a potential therapeutic target. GSK3β has a unique specificity, with its primed substrates binding to the primed phosphate binding site, which is critical for the catalytic activity of GSK3β. An L343R mutation located at the C-lobe of GSK3β, remote from the catalytic site, causes kinase inactivation. Read More

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http://link.springer.com/10.1007/s00894-019-4003-x
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http://dx.doi.org/10.1007/s00894-019-4003-xDOI Listing
April 2019
3 Reads

Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases.

J Mol Model 2019 Apr 3;25(5):110. Epub 2019 Apr 3.

Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, CDMX, 04510, México.

Organic photovoltaics (OPV) have been theoretically studied within the usual parameters: open circuit voltage (V), short circuit current (J), and fill factor (FF). The first two refer mostly to electronic properties, whereas the last contains all other possible contributions to cell efficiency, importantly including molecular geometrical and topological structures, both within a single molecule as amongst a system of molecules. In order to study the effects of molecular morphology of the heterostructures used in OPVs, molecular dynamic simulations (MDS) are imperative, and therefore parameterization of force fields to account for the description of planarity between aromatic rings, both intra- and inter-molecules, is of key importance. Read More

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http://dx.doi.org/10.1007/s00894-019-3984-9DOI Listing
April 2019
1 Read

Functionalization of silicene and silicane with benzaldehyde.

J Mol Model 2019 Apr 3;25(5):109. Epub 2019 Apr 3.

Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Código Postal, 22800, Ensenada, Baja California, Mexico.

Organic functionalization of nanomaterials offers exceptional flexibility in materials design, and applications in molecular sensors and molecular electronics are expected. However, more studies should be conducted to understand the interaction between nanomaterials and organic molecules. In this work, we studied the functionalization of silicene and silicane with benzaldehyde, performing nudged elastic band calculations within density functional theory. Read More

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http://link.springer.com/10.1007/s00894-019-3997-4
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http://dx.doi.org/10.1007/s00894-019-3997-4DOI Listing
April 2019
2 Reads

The polar clasps of a bank vole PrP(168-176) prion protofibril revisiting.

Authors:
Jiapu Zhang

J Mol Model 2019 Apr 2;25(5):108. Epub 2019 Apr 2.

Centre of Informatics and Applied Optimisation, The Federation University Australia, Mount Helen Campus, Mount Helen, Ballarat, Victoria, 3353, Australia.

On 2018-01-17 two electron crystallography structures (with PDB entries 6AXZ, 6BTK) on a prion protofibril of bank vole PrP(168-176) (a segment in the PrP β2-α2 loop) were released into the PDB Bank. The paper published by Gallagher-Jones et al. (Nat Struct Mol Biol 25(2):131-134, 2018) reports some polar clasps for these two crystal structures, and "an intersheet hydrogen bond between Tyr169 and the backbone carbonyl of Asn171 on an opposing strand. Read More

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http://dx.doi.org/10.1007/s00894-019-3981-zDOI Listing
April 2019
2 Reads

The unusual combination of beauty and power of furoxano-1,2,3,4-tetrazine 1,3-dioxides: a theoretical study of crystal structures.

J Mol Model 2019 Apr 1;25(4):107. Epub 2019 Apr 1.

ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, Russian Federation.

The thermodynamic stability of the furoxan ring annullated with 1,2,3,4-tetrazine 1,3-dioxide cycle was studied. Crystal structure prediction based on global energy minimization in the framework of the atom-atom potential functions method was performed for isomeric furoxano-tetrazinedioxides (FuxTDOs): [1,2,5]oxadiazolo[3,4-e][1,2,3,4]tetrazine 1,5,7-trioxide (1) and [1,2,5]oxadiazolo[3,4-e][1,2,3,4]tetrazine 1,4,6-trioxide (2). The Coulomb energy was calculated with advanced point charge models fitted with high accuracy to the molecular electrostatic potentials of these molecules. Read More

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http://dx.doi.org/10.1007/s00894-019-3986-7DOI Listing

A DFT study on catalytic oxidative desulfurization with HO over Ti-MWW zeolite.

J Mol Model 2019 Mar 30;25(4):106. Epub 2019 Mar 30.

College of Chemical Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, People's Republic of China.

The catalytic mechanism of Ti-MWW in oxidative desulfurization with HO was investigated by quantum chemical calculations. A defect model (Ti-d) and a perfect model (Ti-p) were proposed for Ti-MWW, and two possible reaction pathways starting from Ti-d and Ti-p were considered. On Ti-d, the hydroperoxy bidentate intermediate TiOOH (η) was formed by activating HO at the Ti center. Read More

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http://dx.doi.org/10.1007/s00894-019-3989-4DOI Listing
March 2019
2 Reads

Influence of polyethylene cross-linked functionalization on the interfacial properties of carbon nanotube-reinforced polymer nanocomposites: a molecular dynamics study.

J Mol Model 2019 Mar 29;25(4):105. Epub 2019 Mar 29.

Department of Mechanical Engineering, University of Maragheh, Maragheh, East Azerbaijan Province, Iran.

The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e. Read More

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http://dx.doi.org/10.1007/s00894-019-3983-xDOI Listing

Computational study on acetamiprid-molecular imprinted polymer.

J Mol Model 2019 Mar 28;25(4):104. Epub 2019 Mar 28.

Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio 74, Fábricas, São João del-Rei, Minas Gerais, 36301-160, Brazil.

In the present work we investigate, through DFT calculations, the mechanism of formation of a molecular imprinted polymer for the acetamiprid (ACT) insecticide, using four different functional monomers, four molar ratios attempts, and considering eight distinct solvents. As the main result we obtain the following theoretical protocol for the MIP synthesis: methacrylic acid (MMA) as functional monomer, 1:4 M ratio, i.e. Read More

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http://dx.doi.org/10.1007/s00894-019-3990-yDOI Listing

A computational study on the reaction between fisetin and 2,2-diphenyl-1-picrylhydrazyl (DPPH).

J Mol Model 2019 Mar 28;25(4):103. Epub 2019 Mar 28.

Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, 78060-900, Brazil.

The strategy of investigating the antioxidant potential of flavonols through the explicit modeling of chemical reactions (initiated to be employed in a previous work from our group) was taken further in this work. Therefore, a theoretical investigation on the reaction between fisetin and 2,2-diphenyl-1-picrylhydrazyl (DPPH) is presented. All the computations were performed using the density functional theory with the B3LYP functional along with the 6-31G(d,p) basis set. Read More

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http://dx.doi.org/10.1007/s00894-019-3969-8DOI Listing

Bloch Oscillations in Fibonacci lattices: polaron formation.

J Mol Model 2019 Mar 28;25(4):102. Epub 2019 Mar 28.

International Center for Condensed Matter Physics, University of Brasilia, Brasilia, 70910-900, Brazil.

We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical picture, we obtained a novel dynamical process with no counterpart in ordered lattices. Read More

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http://dx.doi.org/10.1007/s00894-019-3972-0DOI Listing

σ-Holes and Si···N intramolecular interactions.

J Mol Model 2019 Mar 27;25(4):101. Epub 2019 Mar 27.

Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA.

We report a computational study of two series of molecules, one having the Si-O-N linkage and the other with the Si-(CH)-N linkage, where n = 1-4. The silicons have various substituents-combinations of H, CH, F, Cl and CF. Many of these compounds have been prepared and characterized experimentally. Read More

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http://dx.doi.org/10.1007/s00894-019-3962-2DOI Listing
March 2019
1 Read

Benchmarking and optimization of molecular simulation models of zinc dialkyldithiophosphate and calcium sulfonate oil additives.

J Mol Model 2019 Mar 25;25(4):100. Epub 2019 Mar 25.

Lehrstuhl für Theoretische Chemie / Computer Chemie Centrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany.

We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force field (GAFF). For the latter, comparison to quantum chemical calculations shows significant errors in terms of complex structure and formation energy. Read More

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http://dx.doi.org/10.1007/s00894-019-3980-0DOI Listing

Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient.

J Mol Model 2019 Mar 23;25(4):98. Epub 2019 Mar 23.

Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, 4220, Bangladesh.

Vascular endothelial growth factor receptor-2 (VEGFR-2) is one of the regulatory elements of angiogenesis that is expressed highly in various diseases and is also essential for solid tumor growth. The present study was aimed at identifying potent inhibitors of VEGFR-2 by considering herbal secondary metabolites; as natural molecules are less toxic than synthetic derivatives. A structure-based virtual screening protocol consisting of molecular docking, MM-GBSA and ADME/T analysis was initially used to screen a library of in vivo metabolites of the herbal ingredient. Read More

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http://dx.doi.org/10.1007/s00894-019-3979-6DOI Listing

Insights into structural and inhibitory mechanisms of low pH-induced conformational change of influenza HA2 protein: a computational approach.

J Mol Model 2019 Mar 23;25(4):99. Epub 2019 Mar 23.

Department of Physics, Bharathiar University, Coimbatore, 641 046, India.

Though oseltamivir and zanamivir are the active anti-influenza drugs, the emergence of different strains of influenza A virus with mutations creates drug-resistance to these drugs. Therefore, it is essential to find a suitable approach to stop the viral infection. The present study focuses on understanding the conformational changes of the HA2 protein at different pH levels (pH 7, pH 6, pH 5) and on blocking the low pH-induced conformational changes of the HA2 protein with a suitable ligand using molecular docking and molecular dynamics (MD) simulation methods. Read More

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http://link.springer.com/10.1007/s00894-019-3982-y
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http://dx.doi.org/10.1007/s00894-019-3982-yDOI Listing
March 2019
5 Reads

Theoretical modeling of DNA electron hole transport through polypyrimidine sequences: a QM/MM study.

J Mol Model 2019 Mar 14;25(4):97. Epub 2019 Mar 14.

Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, AZ, 85721, USA.

The phenomenon of DNA hole transport (HT) has attracted of scientists for several decades, mainly due to its potential application in molecular electronics. As electron holes mostly localize on purine bases in DNA, the majority of scientific effort has been invested into chemically modifying the structures of adenine and guanine in order to increase their HT-mediating properties. In this work we examine an alternative, never yet explored, way of affecting the HT efficiency by forcing electron holes to localize on pyrimidine bases and move between them. Read More

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http://link.springer.com/10.1007/s00894-019-3976-9
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http://dx.doi.org/10.1007/s00894-019-3976-9DOI Listing
March 2019
3 Reads

A first-principles investigation of the influence of polyanionic boron doping on the stability and electrochemical behavior of NaV(PO).

J Mol Model 2019 Mar 13;25(4):96. Epub 2019 Mar 13.

Network & Education Technology Center, China University of Geosciences Wuhan, Wuhan, 430074, Hubei, People's Republic of China.

NaV(PO) (NVP) is one of the most promising candidates for use as cathodes in room-temperature sodium ion batteries owing to its high structural stability and rapid Na transportation kinetics. The cationic doping of foreign ions at Na or V sites in the NVP lattice has proven to be an effective approach for enhancing the electrochemical performance of NVP. In this work, we present a first-principles density functional theory investigation of the impact of polyanionic boron doping at P sites on the structural and electrochemical behavior of NVP. Read More

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http://dx.doi.org/10.1007/s00894-019-3971-1DOI Listing
March 2019
1 Read

Studies of hydrogen sulfide and ammonia adsorption on P- and Si-doped graphene: density functional theory calculations.

J Mol Model 2019 Mar 11;25(4):94. Epub 2019 Mar 11.

Instituto de Física Luis Rivera Terrazas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Blvd. 18 Sur, C.P. 72570, Puebla, Puebla, Mexico.

Studies of hydrogen sulfide (HS) and ammonia (NH) adsorption on phosphorus (P) and silicon (Si) doped graphene are performed by ab initio calculations using the periodic density functional theory (DFT). The P and Si incorporation in graphene distorts the unit cell altering the bond lengths and angles. Unlike the pristine, the phosphorus-doped graphene shows a metallic behavior, and the silicon-doped graphene is a semiconductor with an energy gap of 0. Read More

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http://dx.doi.org/10.1007/s00894-019-3974-yDOI Listing

Performance of DFT methods in the calculation of isotropic and dipolar contributions to N hyperfine coupling constants of nitroxide radicals.

J Mol Model 2019 Mar 11;25(4):93. Epub 2019 Mar 11.

Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow, Russia, 119991.

In the present study, we tested the widely used density functionals BP86, PBE, OLYP, TPSS, M06-L, B3LYP, PBE0, mPW1PW, B97, BHandHLYP, TPSS0, M06, M06-2X, CAM-B3LYP, ωB97x, and B2PLYP with the cc-pCVQZ basis set in calculations on a set of 23 nitroxide radicals with well-resolved N anisotropic hyperfine coupling (HFC) constants. The results were compared with those obtained using the B3LYP/N07D and PBE/N07D methods. The convergence of the HFC values to the complete basis set limit is briefly discussed. Read More

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http://dx.doi.org/10.1007/s00894-019-3966-yDOI Listing
March 2019
1 Read

Polaron formation at impurity-endowed lattices.

J Mol Model 2019 Mar 11;25(4):95. Epub 2019 Mar 11.

International Center for Condensed Matter Physics, University of Brasília, Brasília, DF, Brazil.

In semiconducting materials, lattice deformities can play the role of localizing the charge carriers. Polarons are understood as attractive interactions between charge and lattice deformations that result in a single structure composed by a charged particle surrounded by a cloud of phonons. These composite quasi-particles are vital structures when it comes to charge transport mechanism in a wide range of semiconducting materials. Read More

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http://dx.doi.org/10.1007/s00894-019-3934-6DOI Listing

DFT study of CO adsorption on nitrogen/boron doped-graphene for sensor applications.

J Mol Model 2019 Mar 9;25(4):91. Epub 2019 Mar 9.

Centro de Investigaciones Teóricas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Ave. 1° de mayo s/n Santa María las Torres, Campo 1, CP 54740, Cuautitlán Izcalli, Estado de México, Mexico.

We have performed a Density Functional study of the CO adsorption in B-doped, N-doped and BN-co-doped graphene considering a coronene based model in order to estimate the applications of this systems as CO-sensor. Different monosubstituted, disubstituted and trisubstituted alternatives of combining these two heteroatoms in a substitutional chemical doping and the influence of the relative positions of the heteroatoms are analyzed. In this study, the stability selectivity for CO adsorption and the change in the electric properties for the presence of this molecule, have been evaluated through the calculation of binding energy, CO-adsorption's energy and the gap HOMO-LUMO change due to CO adsorption. Read More

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http://dx.doi.org/10.1007/s00894-019-3973-zDOI Listing

Theoretical investigation on π-spacer effect of the D-π-A organic dyes for dye-sensitized solar cell applications: a DFT and TD-BHandH study.

J Mol Model 2019 Mar 9;25(4):92. Epub 2019 Mar 9.

Equipe d'Electrochimie et Environnement, Faculté des Sciences et Techniques, Université Moulay Ismaîl, Errachidia, Morocco.

In this paper, we present a series of sensitizers to shed light on the influence of π-spacers on the performance of dye-sensitized solar cells. We have accurately calculated key properties in energy conversion, including sunlight absorption, electron injection, electron/hole reorganization energy, ionization potential (IP) and electronic affinity (EA). We chose a series of donor-π-acceptor dyes based on methyl-indole-carbazole as the electron donor group and cyano-acrylic acid as an acceptor with various π-conjugated systems. Read More

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http://dx.doi.org/10.1007/s00894-019-3963-1DOI Listing
March 2019
1 Read

Knowledge discovery through chemical space networks: the case of organic electronics.

J Mol Model 2019 Mar 7;25(4):87. Epub 2019 Mar 7.

Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany.

Modern materials discovery and design studies often rely on the computational screening of large databases. Complementing experimental databases, virtual databases are thereby increasingly established through the first-principles calculation of computationally inexpensive, but for a given application, decisive microscopic quantities of the system. These so-called descriptors are calculated for vast numbers of candidate materials. Read More

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http://dx.doi.org/10.1007/s00894-019-3950-6DOI Listing

Retraction Note to: Computational studies on the regioselectivity of metal-catalyzed synthesis of 1,2,3 triazoles via click reaction: a review.

J Mol Model 2019 Mar 7;25(4):86. Epub 2019 Mar 7.

Department of Chemistry, Alzahra University, Vanak, Tehran, Iran.

The editor has retracted this article (1) because it contains sections that substantially overlap with a number of previously published sources without appropriate citation and acknowledgment (2, 3, 4, 5). Read More

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http://dx.doi.org/10.1007/s00894-019-3978-7DOI Listing
March 2019
2 Reads

Molecular docking and dynamic studies of crepiside E beta glucopyranoside as an inhibitor of snake venom PLA2.

J Mol Model 2019 Mar 8;25(4):88. Epub 2019 Mar 8.

Department of Computational Biology and Bioinformatics, Karyavattom, University of Kerala, Thiruvananthapuram, Kerala, 695581, India.

Alternative treatments from plant-derived small molecules for neutralizing the venom lethality in snake envenomation are prevalent now. Elephantopus scaber, a tropical plant species has been recognized for its various pharmacological activities and especially anti-snake venom property; however, the molecular basis for this property is not understood. It is reported that snake venom PLA2 is a toxic factor with pharmacological effects independent of their catalytic activity. Read More

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http://dx.doi.org/10.1007/s00894-019-3954-2DOI Listing

Evaluation of the antioxidant potential of myricetin 3-O-α-L-rhamnopyranoside and myricetin 4-O-α-L-rhamnopyranoside through a computational study.

J Mol Model 2019 Mar 8;25(4):89. Epub 2019 Mar 8.

Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, 78060-900, Brazil.

In this work, we present a computational study on the antioxidant potential of myricetin 3-O-α-L-rhamnopyranoside (Compound M3) and myricetin 4-O-α-L-rhamnopyranoside (Compound M4). Structural parameters, bond dissociation enthalpies (BDEs), ionization potentials (IPs), proton dissociation enthalpies (PDEs), proton affinities (PAs), and electron transfer enthalpies (ETEs), which are properties connected with different mechanisms related to antioxidant activity, were determined using density functional theory (DFT) with B3LYP, LC-ωPBE, M06-2X, and BMK functionals along with the 6-311G(d,p) and 6-311+G(d,p) basis sets in the gas phase, water, and pentylethanoate. The values obtained were compared with results previously available in the literature for myricetin (the parent molecule and a well-known antioxidant) and myricetin 3,4-di-O-α-L-rhamnopyranoside (Compound M3,4). Read More

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http://link.springer.com/10.1007/s00894-019-3959-x
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http://dx.doi.org/10.1007/s00894-019-3959-xDOI Listing
March 2019
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Periodic DFT modeling and vibrational analysis of silver(I) cyanide complexes of thioureas.

J Mol Model 2019 Mar 8;25(4):90. Epub 2019 Mar 8.

Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia.

The structures of non-ionic [Ag(Tu)(CN)] (1) and ionic [Ag(Dmtu)][Ag(CN)] (2) and [Ag(Imt)][Ag(CN)] (3) silver(I) complexes, where Tu = thiourea, Dmtu = N,N'-dimethylthiourea and Imt = imidazoline-2-thione), were modeled by periodic DFT/PAW-PBE calculations; results were in good agreement with experiments. The bonding ability of the thiourea ligands (Tu, Dmtu and Imt) and the rival Ag-C, Ag-S, Ag-N and Ag-Ag bonds were estimated by natural population analysis and natural bonding orbital calculations. The metal-ligand bond strengths were found to decrease in the following order Ag-C > Ag-S > Ag-N, and the main bonding contribution was covalent, donor-acceptor and electrostatic, respectively. Read More

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http://dx.doi.org/10.1007/s00894-019-3970-2DOI Listing

Motion in a crowded environment: the influence of obstacles' size and shape and model of transport.

J Mol Model 2019 Mar 2;25(3):84. Epub 2019 Mar 2.

Department of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.

Simulations of motion in a complex crowded environment were performed. We employed the dynamic lattice liquid model, which was based on the cooperative movement concept. This algorithm is capable of working at very high densities, and the motion of all objects was highly correlated. Read More

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http://dx.doi.org/10.1007/s00894-019-3968-9DOI Listing

Improving the theoretical description of charge transport in organic crystals.

J Mol Model 2019 Mar 2;25(3):83. Epub 2019 Mar 2.

Institute of Physics, University of Brasília, 70.919-970, Brasília, Brazil.

Charge hopping based on Marcus theory is often used to predict charge carrier mobilities in organic crystals, although it is known to systematically underestimate the values. Here we show that this deficiency may lie on a fundamental aspect of quantum statistical averages, rather than on the approximation itself. Under adequate Boltzmann weighing procedure used to evaluate electron and hole transfer integrals, a kinetic Monte Carlo model is employed to describe mobilities in an azacene derivative. Read More

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http://dx.doi.org/10.1007/s00894-019-3953-3DOI Listing

Retraction Note to: Theoretical study of the fragmentation of ionized benzophenone.

J Mol Model 2019 Mar 2;25(3):85. Epub 2019 Mar 2.

Laboratoire Matériaux, Molécules et Applications, Institut Préparatoire aux Etudes Scientifiques et Techniques, La Marsa, Université de Carthage, Carthage, Tunisie.

The authors have retracted this article [1] due to an error in obtaining permission to use the data generated at the Synchrotron SOLEIL. All authors agree to this retraction. Read More

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http://dx.doi.org/10.1007/s00894-019-3977-8DOI Listing

Argo: a data analysis program for quantum chemical calculations.

J Mol Model 2019 Mar 2;25(3):82. Epub 2019 Mar 2.

Laboratory of Organic Chemistry, Department of Food Science and Technology, University of West Attica, Ag. Spyridonos 28, 12210, Egaleo, Greece.

The ARGO program is designed for the analysis and display of results obtained from quantum chemical calculations. ARGO currently extracts values of geometrical parameters and energy of each conformer obtained from potential energy surface (PES) scans. It automatically arranges the data into columns and prepares input files for the Gnuplot graphing utility for two- and three-dimensional PES graphs. Read More

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http://dx.doi.org/10.1007/s00894-019-3975-xDOI Listing
March 2019
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Relationship between photo-physical and electrochemical properties of D-π-A compounds regarding solar cell applications. 1. Substituent type effect in photovoltaic performance.

J Mol Model 2019 Feb 27;25(3):81. Epub 2019 Feb 27.

Facultad de Química, Pontificia Universidad Católica de Chile, Av. V. Mackenna 4860-Macul, BP 7820436, Santiago, Chile.

Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four compounds, M8-1, M8-2, M8-O1, and M8-O2 (with a common organic structure (E)-2-cyano-3-(5-((E)-2-(9,9-diethyl-7-(phenylamino)-9H-fluoren-2-yl)vinyl)thiophen-2-yl)acrylic acid), are studied in two solvents, tetrahydrofuran (THF) and dimethylsulfoxide (DMSO). Read More

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http://dx.doi.org/10.1007/s00894-019-3955-1DOI Listing
February 2019

Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling.

J Mol Model 2019 Feb 27;25(3):79. Epub 2019 Feb 27.

Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, USA.

We discuss the relationship between the problem of protein tertiary structure prediction from the amino acid sequence and the uncertainty analysis. The algorithm presented in this paper belongs to the category of decoy-based modeling, where different known protein models are used to establish a low dimensional space via principal component analysis. The low dimensional space is utilized to perform an energy optimization via a family of very explorative particle swarm optimizers to find the global minimum. Read More

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http://dx.doi.org/10.1007/s00894-019-3956-0DOI Listing
February 2019
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Insights into DNA polymerase δ's mechanism for accurate DNA replication.

J Mol Model 2019 Feb 27;25(3):80. Epub 2019 Feb 27.

Department of Chemistry, St John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.

Our study examines the mechanisms by which DNA polymerase (pol) δ faithfully replicates DNA. To better understand this process, we have performed all-atom molecular dynamics simulations of several DNA pol δ systems to identify conformational changes occurring prior to chemistry and investigate mechanisms by which mutations in the fingers domain (R696W and A699Q) lower fidelity. Our results indicate that, without the incoming nucleotide, a distinct open conformation occurs defined by a rotation in the fingers. Read More

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http://dx.doi.org/10.1007/s00894-019-3957-zDOI Listing
February 2019

Computational insight into the contribution of para-substituents on the reduction potential, proton affinity, and electronic properties of nitrobenzene compounds.

J Mol Model 2019 Feb 26;25(3):78. Epub 2019 Feb 26.

Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa.

New insight is provided into the chemistry of 12 para-substituted nitrobenzene compounds, using the high-level computational method G3(MP2) and DFT methods. The results show that the chemical properties of the nitrobenzene molecules, such as reduction potential, ionization energy, proton affinity, pK, interaction energy of the fragments, hyperpolarizability, exaltation index, band gap, UV electron excitation, and QTAIM properties, are controlled by the strong coupling between the nitro group (NO) and the nature of the various para-substituents via the benzene ring as their conducting link. As the electron donating tendency of the para-substituent increases in the molecules, the electron cloud around the nitro group also increases, resulting in contraction of the N-C bonds and elongation of the N=O bonds, consequently leading to gradually increasing electron conductivity, polarizability, and ionization energy but lower proton affinity, thereby progressively impeding the reduction potential of the molecules. Read More

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http://link.springer.com/10.1007/s00894-019-3946-2
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http://dx.doi.org/10.1007/s00894-019-3946-2DOI Listing
February 2019
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Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations.

J Mol Model 2019 Feb 26;25(3):76. Epub 2019 Feb 26.

Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.

The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. Read More

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http://dx.doi.org/10.1007/s00894-019-3964-0DOI Listing
February 2019

Co-doped triel-pnicogen graphene as metal-free catalyst for CO oxidation: Role of multi-center covalency.

J Mol Model 2019 Feb 26;25(3):77. Epub 2019 Feb 26.

Chemical engineering department, Islamic Azad University, Robatkarim Branch, Robatkarim, Iran.

Third and fifth group atoms, named triel and pnicogen, respectively, were used for graphene doping. AlP and AlN structures were selected as co-doped graphene-based catalysts. The electronic structure and catalytic properties of binary AlN, AlP co-doped graphene were investigated through density functional theory (DFT). Read More

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http://dx.doi.org/10.1007/s00894-019-3960-4DOI Listing
February 2019
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Designing new quinoline-based organic photosensitizers for dye-sensitized solar cells (DSSC): a theoretical investigation.

J Mol Model 2019 Feb 23;25(3):75. Epub 2019 Feb 23.

School of Sciences, Department of Chemistry, São Paulo State University (UNESP), Bauru, São Paulo, 17033-360, Brazil.

In this work, 27 new quinoline-derivative dyes were proposed, and their geometries, electronic structures, and absorption spectra were investigated using density functional theory (DFT) calculations. An important feature found in most of the new compounds was that the lowest unoccupied molecular orbital (LUMO) was above the TiO conduction band, facilitating electron transfer from the excited dye to the semiconductor. The energy of the highest occupied molecular orbital (HOMO) was below the reduction potential energy of the electrolyte (I/I), improving the charge regeneration process after photooxidation. Read More

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http://dx.doi.org/10.1007/s00894-019-3958-yDOI Listing
February 2019
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Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum.

J Mol Model 2019 Feb 23;25(3):74. Epub 2019 Feb 23.

Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, 741235, India.

Our environment is densely populated with various beneficial sulfur-oxidizing prokaryotes (SOPs). These organisms are responsible for the proper maintenance of biogeochemical sulfur cycles to regulate the turnover of biological sulfur substrates in the environment. Allochromatium vinosum strain DSM 180 is a gamma-proteobacterium and is a member of SOP. Read More

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http://dx.doi.org/10.1007/s00894-019-3945-3DOI Listing
February 2019

Theoretical study of adsorption characteristics and the environmental influence for metronidazole on photocatalytic TiO anatase surfaces.

J Mol Model 2019 Feb 21;25(3):73. Epub 2019 Feb 21.

College of Chemistry and Material Science, Sichuan Normal University, Chengdu, 610068, China.

The adsorption characteristics of metronidazole on anatase TiO(101) and (001) surfaces were studied by density functional theory (DFT). The adsorption structure of metronidazole on anatase TiO(101) and (001) surfaces has been optimized under vacuum, water, acidic, and alkaline conditions, respectively. The optimum adsorption site, adsorption energy, and electronic structure of the stable adsorption model were calculated. Read More

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http://dx.doi.org/10.1007/s00894-019-3967-xDOI Listing
February 2019
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Influence of nanotube section on carboplatin confinement.

J Mol Model 2019 Feb 21;25(3):72. Epub 2019 Feb 21.

Laboratoire de Nanomédecine, Imagerie et Thérapeutiques, EA 4662, Centre Hospitalier Universitaire de Besançon, Université Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon cedex, France.

The confinement of anticancer carboplatin molecules (CBPT) in boron nitride nanotubes (BNNTs) with various sections was studied by means of density functional theory and molecular dynamic simulations. We show that the molecular insertion in BNNT is favored depending on the tube radius. The range of the energy adsorption varied from -1 eV to -2 eV depending on BNNT dimension. Read More

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http://dx.doi.org/10.1007/s00894-019-3965-zDOI Listing
February 2019
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Density functional theory study of selective aerobic oxidation of cyclohexane: the roles of acetic acid and cobalt ion.

J Mol Model 2019 Feb 20;25(3):71. Epub 2019 Feb 20.

School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China.

A computational study of cyclohexane autoxidation and catalytic oxidation to a cyclohexyl hydroperoxide intermediate (CyOOH), cyclohexanol, and cyclohexanone has been conducted using a hybrid density functional theory method. The activation of cyclohexane and O is the rate-determining step in the formation of CyOOH due to its relatively high energy barrier of 41.2 kcal/mol, and the subsequent reaction behavior of CyOOH controls whether the production of cyclohexanol or cyclohexanone is favored. Read More

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http://link.springer.com/10.1007/s00894-019-3949-z
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http://dx.doi.org/10.1007/s00894-019-3949-zDOI Listing
February 2019
2 Reads