4,093 results match your criteria Journal of molecular modeling[Journal]


Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis.

J Mol Model 2019 Feb 14;25(3):68. Epub 2019 Feb 14.

Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.

Mycobacterium tuberculosis remains a persistent pathogen, partly due to its lipid rich cell wall, of which mycolic acids (MAs) are a major component. The fluidity and conformational flexibilities of different MAs in the bacterial cell wall significantly influence its properties, function, and observed pathogenicity; thus, a proper conformational description of different MAs in different environments (e.g. Read More

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http://dx.doi.org/10.1007/s00894-019-3943-5DOI Listing
February 2019

An in silico design of bioavailability for kinase inhibitors evaluating the mechanistic rationale in the CYP metabolism of erlotinib.

J Mol Model 2019 Feb 14;25(3):65. Epub 2019 Feb 14.

Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India.

Soft spot analysis helps evaluate the site of the metabolic lability that impacts the bio-availability of the drug. However, given its laborious and time consuming experimentation, we propose a reliable and cheap in silico strategy. In this context, we hypothesized a mechanistic rationale for metabolism of erlotinib by the CYP3A4 enzyme. Read More

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http://dx.doi.org/10.1007/s00894-018-3917-zDOI Listing
February 2019

A DFT-based study of the hydrogen-bonding interactions between myricetin and ethanol/water.

J Mol Model 2019 Feb 14;25(3):67. Epub 2019 Feb 14.

Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing, 100093, People's Republic of China.

Flavonoids are vital constituents of propolis that are responsible for its medicinal activity. Flavonoid extraction commonly employs ethanol and water as solvents. In the extraction reaction, hydrogen-bonding interactions play a crucial role. Read More

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http://dx.doi.org/10.1007/s00894-019-3940-8DOI Listing
February 2019

CO adsorption in nitrogen-doped single-layered graphene quantum dots: a spectroscopic investigation.

J Mol Model 2019 Feb 14;25(3):66. Epub 2019 Feb 14.

Institute of Physics, University of Brasilia, Campus Universitario Darcy Ribeiro, Brasilia, 70.910-900, Brazil.

In this work, we investigate the adsorption process of CO in graphene quantum dots from the electronic structure and spectroscopic properties point of view. We discuss how a specific doping scheme could be employed to further enhance the adsorbing properties of the quantum dots. This is evaluated by considering the depth of the potential well, the spectroscopic constants, and the lifetime of the compound. Read More

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http://dx.doi.org/10.1007/s00894-019-3951-5DOI Listing
February 2019

Donor-acceptor symmetric and antisymmetric tunneling matrix elements: a pathway model investigation of protein electron transfer.

J Mol Model 2019 Feb 13;25(3):64. Epub 2019 Feb 13.

Instituto de Física, Universidade Federal de Uberlândia, Av. João Naves de Ávila 2121, Santa Maria, Uberlândia, MG, 38408-100, Brazil.

In protein electron transfer reaction rate calculations, the electronic Hamiltonian is apportioned into donor-acceptor (D-A) and protein bridge subspaces, and a two-state system is defined for the D-A subspace. Löwdin partitioning is used to perform the two-state reductions necessary to compute the tunneling matrix element between D and A sites. Here, a method of performing donor and acceptor state analysis for a non-orthogonal basis set in both the weak and strong electronic coupling regimes is developed. Read More

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http://dx.doi.org/10.1007/s00894-019-3936-4DOI Listing
February 2019

Influences of pressure on structural and electronic properties of four types of HMX.

J Mol Model 2019 Feb 13;25(3):63. Epub 2019 Feb 13.

Key Laboratory of Advanced Technologies of Materials, Ministry of Education of China, School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 610031, People's Republic of China.

The crystal and electronic structures of four polymorphs of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) from 0 to 30 GPa were investigated by using density functional theory. The obtained structural parameters based on the GGA-PBE+TS calculations are in agreement with experimental results at ambient pressure. As the pressure increases, the volumes of the four types of HMX decrease monotonically and the band gaps gradually decrease without any significant discontinuity. Read More

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http://dx.doi.org/10.1007/s00894-019-3947-1DOI Listing
February 2019

Partial combination of composite strategy and the B3LYP functional for the calculation of enthalpies of formation.

J Mol Model 2019 Feb 12;25(3):62. Epub 2019 Feb 12.

Instituto de Química, Universidade Estadual de Campinas, Barão Geraldo, 13083-970 Campinas, PO Box 6154, São Paulo, Brazil.

The B3LYP functional was re-optimized using partially composite methods for the calculation of standard enthalpies of formation. Two initial methods (B3LYP-MCM1 and B3LYP-MCM2) differing in the type and number of optimized parameters were analyzed using B3LYP/6-31 + G(2df,p) as the reference energy. For the first method (B3LYP-MCM1), the exchange-correlation and higher-level correction parameters (HLC) were optimized and for the second method (B3LYP-MCM2), in addition to the previous parameters, scaling of the basis functions responsible for large errors in the enthalpy of formation were also optimized. Read More

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http://dx.doi.org/10.1007/s00894-019-3952-4DOI Listing
February 2019

Exploring the mechanism of alkene hydrogenation catalyzed by defined iron complex from DFT computation.

J Mol Model 2019 Feb 12;25(3):61. Epub 2019 Feb 12.

Leibniz-Institut für Katalyse e.V. an der Universität Rostock, Albert-Einstein-Strasse 29a, 18059, Rostock, Germany.

UB3LYP computation including dispersion and toluene solvation has been carried to elucidate the mechanisms of alkene hydrogenation catalyzed by bis(imino)pyridine iron dinitrogen complex (PDI)Fe(N), which has low stability towards N dissociation. The coordinatively unsaturated complexes, (PDI)Fe(N) and (PDI)Fe(1-CH), favor open-shell singlet ground states. On the basis of our computations, we propose a new mechanism of 1-butene coordination and hydrogenation after N dissociation. Read More

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http://dx.doi.org/10.1007/s00894-019-3942-6DOI Listing
February 2019

State-specific electrostatic potential descriptors for estimating solvatochromic effects.

J Mol Model 2019 Feb 12;25(3):60. Epub 2019 Feb 12.

Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, Shaanxi, China.

The Lippert-Mataga equation is used widely to describe the solvatochromic effects of fluorescent molecules through the evaluation of solute-solvent interactions on the basis of the point-dipole model. A large dipole deviation of molecules in the ground-state and the lowest excited-state is a basic requirement for the design of a polarity-sensitive fluorescent probe. Some recently synthesized probes with center-symmetry have near zero dipole deviation while undergoing notably solvatochromic behaviors. Read More

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http://dx.doi.org/10.1007/s00894-019-3948-0DOI Listing
February 2019

Atomistic analysis of the thermomechanical properties of Sn-Ag-Cu solder materials at the nanoscale with the MEAM potential.

J Mol Model 2019 Feb 11;25(3):59. Epub 2019 Feb 11.

Department of Mechanical Engineering, Auburn University, Auburn, AL, 36849, USA.

Sn-Ag-Cu, commonly known as SAC, is considered to be among the most promising of all lead-free solder alloys. Research aimed at making electronic components smaller has pointed to the possible use of nanosized solder joints in the future. In this study, for the first time, molecular dynamics simulations were used to analyze the thermomechanical properties of SAC solder materials at the nanoscale. Read More

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http://dx.doi.org/10.1007/s00894-019-3939-1DOI Listing
February 2019

Spin polarization in graphene nanoribbons functionalized with nitroxide.

J Mol Model 2019 Feb 9;25(3):58. Epub 2019 Feb 9.

Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia.

Fine-tuning of magnetic states via an understanding of spin injection on the edge of graphene nanoribbons should allow for greater flexibility of the design of graphene-based spintronics. On the basis of calculations, we predict that coupling constants of the exchange interaction in the series of nitroxide-functionalized ribbon compounds are antiferromagnetic across the ribbons with values 0.2-0. Read More

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http://dx.doi.org/10.1007/s00894-019-3944-4DOI Listing
February 2019

Effect of external electric field on C-X ··· π halogen bonds.

J Mol Model 2019 Feb 8;25(3):57. Epub 2019 Feb 8.

Department of Physics, Faculty of Arts and Sciences, Süleyman Demirel University, 32260, Isparta, Turkey.

In this study, ab initio calculations (RI-MP2(full)/aug-cc-pVDZ) are performed to investigate the effect of an external electric field (EEF) on the nature, properties, and structures of C-X ··· π halogen bonds in CFBr complexes with π systems (benzene, ethene, and ethyne), for the first time. This EEF effect is analyzed by a myriad of methods, including molecular electrostatic potential (MEP), symmetry adapted perturbation theory (SAPT), natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and noncovalent interaction (NCI) methods. A linear relationship is found between RI-MP2 interaction energy and the strength of the EEF, indicating that the stability of C-X ··· π halogen bonds is sensitive to both the strength and direction of the EEF. Read More

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http://dx.doi.org/10.1007/s00894-019-3938-2DOI Listing
February 2019

Molecular modeling and experimental study of a new peptide-based microextraction fiber for preconcentrating morphine in urine samples.

J Mol Model 2019 Feb 8;25(3):54. Epub 2019 Feb 8.

Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.

Antimicrobial peptides (AMPs) are best known for their bactericidal properties; however, due to their unique and flexible structures, they have also been proposed as potential selective sorbents for specific molecules. In the present study, we aimed to design and produce a new peptide-based microextraction fiber for preconcentrating morphine in urine samples. The binding of morphine to the peptide was first evaluated by computational simulation using the Molecular Operating Environment (MOE) 2015. Read More

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http://dx.doi.org/10.1007/s00894-019-3925-7DOI Listing
February 2019

A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis.

J Mol Model 2019 Feb 8;25(3):56. Epub 2019 Feb 8.

New Industry Creation Hatchery Center, Tohoku University, Aza-Aoba, Aoba-ku, Sendai, 980 8579, Japan.

The polyphenolic compound resveratrol, classified under stilbenes, offers a broad range of health advantages, including neuroprotection and playing a role in autophagy in the nervous system. However, resveratrol has poor water solubility and is soluble in the gel phase in liposomal membranes. The main aim of this work was to understand the nature of the interactions between resveratrol and water molecules. Read More

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http://dx.doi.org/10.1007/s00894-019-3941-7DOI Listing
February 2019

Analysis of two novel 1-4 quinolinone structures with bromine and nitrobenzyl ligands.

J Mol Model 2019 Feb 8;25(3):55. Epub 2019 Feb 8.

Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, Anápolis, GO, Brazil.

The scientific community has shown particular interest in the study of quinolinones-a class of bicyclic organic compounds. An example of these compounds are the 4-quinolinones, considered to be very useful building blocks, since they can adapt their molecular structures with different ligands for applications in various fields such as pharmacy, medicine, physics and engineering. The compounds (E)-3-(benzylidene)-2-(3-nitrophenyl)-2,3-dihydro-1-(phenylsulfonyl)-quinolin-4-(1H)-one (NFQ) and (E)-3-(benzylidene)-2-(4-bromophenyl)-2,3-dihydro-1-(phenylsulfonyl) quinolin-4-(1H)-one (BFQ) were synthesized and characterized by infrared spectroscopy, H and C NMR, and melting point. Read More

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http://dx.doi.org/10.1007/s00894-019-3937-3DOI Listing
February 2019

Correction to: Gas-phase reaction of benzo[a]anthracene with hydroxyl radical in the atmosphere: products, oxidation mechanism, and kinetics.

J Mol Model 2019 Feb 2;25(2):53. Epub 2019 Feb 2.

Environment Research Institute, Shandong University, Jinan, 250100, China.

The original version of this article unfortunately contained a mistake. The sequence of the author affiliations was incorrect. The correct information is given below. Read More

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http://dx.doi.org/10.1007/s00894-019-3933-7DOI Listing
February 2019

Foreword for the Festschrift on the occasion of the 60th birthday of Professor Pratim Kumar Chattaraj.

Authors:
Utpal Sarkar

J Mol Model 2019 Feb 2;25(2):52. Epub 2019 Feb 2.

Department of Physics, Assam University, Silchar, India.

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http://dx.doi.org/10.1007/s00894-019-3931-9DOI Listing
February 2019

Theoretical studies on the structures, material properties, and IR spectra of polymorphs of 3,4-bis(1H-5-tetrazolyl)furoxan.

J Mol Model 2019 Feb 1;25(2):51. Epub 2019 Feb 1.

Singapore Institute of Technology, 10 Dover Drive, Singapore, 138683, Singapore.

Theoretical studies on the structures, densities, and heats of formation of conformational isomers of 3,4-bis(1H-5-tetrazolyl)furoxan (HBTF) were performed based on density functional theory (DFT) calculations. Two stable planar conformational isomers, the face-to-back and the back-to-face conformers, and one stable slightly twisted conformer, the back-to-back conformer, were predicted for HBTF at the M06-2X/6-311 + G(d,p) level of theory. The face-to-back conformer was calculated to be the most stable conformational isomer on the potential energy surface. Read More

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http://dx.doi.org/10.1007/s00894-018-3896-0DOI Listing
February 2019
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Molecular designing of four high performance pyrazine-based non-fullerene acceptor materials with naphthalene diimide-based small organic solar cells.

J Mol Model 2019 Jan 31;25(2):50. Epub 2019 Jan 31.

Department of Physics, University of Agriculture, Faisalabad, 38040, Pakistan.

We design four high performance non-fullerene acceptor materials by applying strong electron withdrawing groups at the end of A-D-A-D-A type organic solar cells molecules and compute their different opto-electronic and photovoltaic properties, including absorption spectrum, electron density, solubility strength, charge mobilities for electrons and holes, stability of HOMO/LUMO energy orbitals, excitation energies required for charge transfer mechanisms, and morphology of device with the help of DFT approaches using the principles of quantum mechanics. The newly designed molecules showed strong absorption bands between 420 to 650 nm, low HOMO energy values from -7.24 to -7. Read More

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http://dx.doi.org/10.1007/s00894-019-3932-8DOI Listing
January 2019
1 Read

Correlation between molecular acidity (pK) and vibrational spectroscopy.

J Mol Model 2019 Jan 30;25(2):48. Epub 2019 Jan 30.

Computational and Theoretical group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA.

Molecular acidity is an important physicochemical property, which is often represented by the pK value as the measure of acidity strength. However, the accurate calculation and prediction of pK values is still an unsolved problem for computational chemistry. In this work, we present for the first time a direct correlation between pK values and local vibrational frequencies for 15 different groups of compounds with various substituents. Read More

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http://dx.doi.org/10.1007/s00894-019-3928-4DOI Listing
January 2019

3-Aminopropyltriethoxysilane-aided cross-linked chitosan membranes for gas separation: grand canonical Monte Carlo and molecular dynamics simulations.

J Mol Model 2019 Jan 30;25(2):49. Epub 2019 Jan 30.

Separation Processes Research Group (SPRG), Department of Engineering, University of Kashan, Kashan, Iran.

Molecular simulations were performed to consider the structural and transport properties of chitosan/3-aminopropyltriethoxysilane (APTEOS) mixed matrix membranes (MMMs). In order to consider the presence of APTEOS content on the performances of membrane, various amounts of APTEOS were added to the polymeric matrix as a cross-linker. Structural characterizations such as radial distribution function (RDF), fractional free volume (FFV) and X-ray diffraction (XRD) were carried out on the simulated cells. Read More

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http://dx.doi.org/10.1007/s00894-019-3929-3DOI Listing
January 2019

Benchmark DFT studies on C-CN homolytic cleavage and screening the substitution effect on bond dissociation energy.

J Mol Model 2019 Jan 28;25(2):47. Epub 2019 Jan 28.

Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad, 22060, Pakistan.

Nitriles are important chemical species in organic transformations, material chemistry, and environmental sciences. Nitriles are used as cyanating reagents in many organic reactions, where the C-CN bond dissociation has an important role. The reactivity of nitriles can be better understood by studying the bond dissociation energy (BDE) of the C-CN bond. Read More

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http://dx.doi.org/10.1007/s00894-019-3930-xDOI Listing
January 2019

Chemical reactivity and adsorption properties of pro-carbazine anti-cancer drug on gallium-doped nanotubes: a quantum chemical study.

J Mol Model 2019 Jan 28;25(2):46. Epub 2019 Jan 28.

Department of Chemistry, Rasht Branch, Islamic Azad University, Rasht, Iran.

In this study, we propose new armchair single-walled nanotubes (SWNTs) for stable adsorption, increasing drug delivery performance and decreasing side effects of pro-carbazine (Pro-CB) anti-cancer in the framework of B3LYP/6-31 g*/Lanl2DZ level of theory. Indeed, doping gallium (Ga) metal in SWNTs is naturally followed by changing of geometry, increasing dipole moment, and creating one site with high reactivity in order to better adsorption of the drug molecule. Chemical reactivity descriptors show that SWNTs and Pro-CB have electrophile and nucleophile roles in interaction, respectively. Read More

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http://dx.doi.org/10.1007/s00894-018-3914-2DOI Listing
January 2019
1 Read

Formation of metallacarboxylic acids through Hieber base reaction. A density functional theory study.

J Mol Model 2019 Jan 25;25(2):45. Epub 2019 Jan 25.

School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.

Using density functional theory (B97-D/ECP2/PCM//RI-BP86/ECP1 level), we have studied the effects of ligand variation on OH uptake by transition-metal carbonyls (Hieber base reaction), i.e., LM(CO) + OH → [LM(COH)], M = Fe, Ru, Os, L = CO, PMe, PF, py, bipy, Cl, H. Read More

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http://dx.doi.org/10.1007/s00894-018-3915-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347588PMC
January 2019
1 Read

Structural, energetic, and vibrational properties of the homodimers of the silyl, germyl, and stannyl halides, (MHX) (M = Si, Ge, Sn; X = F, Cl, Br, I).

J Mol Model 2019 Jan 24;25(2):44. Epub 2019 Jan 24.

School of Chemistry and Physics, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa.

A number of properties of the homodimers of the three families of molecules MHX, where M is Si, Ge, and Sn and X is F, Cl, Br, and I are computed. The results are compared with those of a similar study of the homodimers of the methyl halides containing the same four halogen atoms, and some notable differences are observed among related sets of monomer species. The interaction energies, the primary intermolecular geometrical parameters, the changes in the intramolecular bond lengths, and the vibrational data (wavenumber shifts and dimer/monomer infrared intensity ratios) of some of the modes most closely associated with the site of interaction show, for the most part, regular variations as the central atom and the halogen atom are systematically varied. Read More

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http://dx.doi.org/10.1007/s00894-019-3927-5DOI Listing
January 2019

Mechanistic investigation of the atmospheric oxidation of bis(2-chloroethyl) ether (ClCHCHOCHCHCl) by OH and NO radicals and Cl atoms: a DFT approach.

J Mol Model 2019 Jan 24;25(2):43. Epub 2019 Jan 24.

Department of Chemical Sciences, Tezpur University, Tezpur, Assam, 784028, India.

The oxidation of bis(2-chloroethyl) ether (ClCHCHOCHCHCl) in the atmosphere, as initiated by various oxidants (OH and NO radicals and Cl atoms), was examined using the functional M06-2X in conjunction with the basis set 6-31 + G(d,p). We explored the oxidation pathways and reaction energies (enthalpies and Gibb's free energies) for the abstraction of H from the -CHCl and -OCH sites of ClCHCHOCHCHCl by oxidants. The energy profile shows that H abstraction from the -OCH site of the title molecule by each atmospheric oxidant is more likely than H abstraction from the other site. Read More

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http://dx.doi.org/10.1007/s00894-019-3923-9DOI Listing
January 2019

How to design potent and selective DYRK1B inhibitors? Molecular modeling study.

J Mol Model 2019 Jan 23;25(2):41. Epub 2019 Jan 23.

Selvita S.A., Bobrzyńskiego 14, 30-348, Kraków, Poland.

DYRK1B protein kinase is an emerging anticancer target due to its overexpression in a variety of cancers and its role in cancer chemoresistance through maintaining cancer cells in the G (quiescent) state. Consequently, there is a growing interest in the development of potent and selective DYRK1B inhibitors for anticancer therapy. One of the major off-targets is another protein kinase, GSK3β, which phosphorylates an important regulator of cell cycle progression on the same residue as DYRK1B and is involved in multiple signaling pathways. Read More

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http://dx.doi.org/10.1007/s00894-018-3921-3DOI Listing
January 2019

New types of organic semiconductors based on diketopyrrolopyrroles and 2,1,3-benzochalcogenadiazoles: a computational study.

J Mol Model 2019 Jan 23;25(2):42. Epub 2019 Jan 23.

Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Guwahati, Assam, 781035, India.

A comprehensive computational study is performed on model compounds based on 2,1,3-benzochalcogenadiazoles and diketopyrrolopyrroles of A-π-A'-π-A architecture (A and A' represent 2,1,3-benzochalcogenadiazoles and diketopyrrolopyrroles, respectively, and π is the bridging unit between them including thiophene, furan, and selenophene) for their utility as organic semiconductors. The compounds were found to possess planar geometry, which is a desired property for organic semiconductors. The electronic properties, including adiabatic and vertical electron affinity (EA), adiabatic and vertical ionization potential (IP), reorganization energy (λ), hole injection barrier and electron injection barrier, transfer integral, and charge mobility, were calculated. Read More

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http://dx.doi.org/10.1007/s00894-019-3922-xDOI Listing
January 2019
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The prediction of intermolecular proton-transfer of guanine-cytosine base pair under the influence of fragments from decomposed MOFs.

Authors:
Ying Han Dejie Li

J Mol Model 2019 Jan 21;25(2):40. Epub 2019 Jan 21.

College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, People's Republic of China.

Metal-organic frameworks (MOFs) can be decomposed into various fragments, including negative/positive charges, Zn or Cu when used as drug delivery materials. To evaluate the safety of MOFs, different mechanisms of intermolecular proton-transfer in guanine-cytosine (GC) base pair under the influence of such fragments were investigated by density functional theory methods. In a vacuum, calculation results show that an excess electron assists proton transfer in the anionic GC radical, and a hole assists proton transfer in the cationic GC radical with small energy barriers. Read More

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http://dx.doi.org/10.1007/s00894-019-3926-6DOI Listing
January 2019

Improved GAFF2 parameters for fluorinated alkanes and mixed hydro- and fluorocarbons.

J Mol Model 2019 Jan 18;25(2):39. Epub 2019 Jan 18.

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

We present improved molecular mechanics models for perfluorocarbons and mixed hydro- and fluorocarbons, based on the GAFF2 force field. Benchmarking was performed for a series of single molecule geometries and for condensed phases, namely self-assembled monolayers comprising perfluoro-octadecane phosphonic acids. From this, considerable improvement of the torsion angles is demonstrated. Read More

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http://dx.doi.org/10.1007/s00894-018-3911-5DOI Listing
January 2019

Segmented all-electron basis sets of triple zeta quality for the lanthanides: application to structure calculations of lanthanide monoxides.

J Mol Model 2019 Jan 15;25(2):38. Epub 2019 Jan 15.

Departamento de Física, Universidade Federal do Espírito Santo, Vitória, ES, 29060-900, Brazil.

Nonrelativistic and relativistic (Douglas-Kroll-Hess, DKH) segmented all-electron Gaussian basis sets of valence triple zeta quality plus polarization functions (TZP) for the lanthanides were developed. As some atomic and molecular properties depend on a good description of the electrons far from the nuclei, these basis sets are augmented with diffuse functions, giving rise to the augmented TZP (ATZP) and ATZP-DKH basis sets. At the DKH level of theory, the B3LYP hybrid functional in conjunction with the TZP-DKH basis set were used to calculate the atomic charges and valence orbital populations of the lanthanide and oxygen atoms, the bond lengths, and the equilibrium dissociation energies of lanthanide monoxides. Read More

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http://dx.doi.org/10.1007/s00894-019-3924-8DOI Listing
January 2019

Alkali ion influence on structure and stability of fibrillar amyloid-β oligomers.

J Mol Model 2019 Jan 12;25(2):37. Epub 2019 Jan 12.

Bioinformatik Institut für Biochemie Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054, Erlangen, Germany.

Alzheimer's disease is characterized by the aggregation of Amyloid-β (Aβ) peptide into oligomers, fibrils and plaques. Many factors influencing this process as well as the stability of the various Aβ aggregates are known to date, and include the concentration and type of metal ions. Most experimental and theoretical studies have concentrated on heavy metal ions, like Fe, Zn, or Cu, while the smaller alkali ions Li, Na, and K have not gained much attention notwithstanding their role and ubiquity in physiological environments. Read More

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http://dx.doi.org/10.1007/s00894-018-3920-4DOI Listing
January 2019

Theoretical studies on a new series of 1,2,3,4-tetrazine 1,3-dioxide annulation with an imidazole ring or oxazole ring.

J Mol Model 2019 Jan 10;25(2):36. Epub 2019 Jan 10.

Department of Chemistry, Nanjing University of Science and Technology, Nanjing, 210094, China.

To continue our previous work, the structure and some properties of a new series of 1,2,3,4-tetrazine 1,3-dioxides annulated with an imidazole ring or oxazole ring were studied in this paper. Four imidazolo-v-tetrazine 1,3-dioxides (ITDOs) I1-I4 and eight oxazolo-v-tetrazine 1,3-dioxides (OTDOs) O1-O8 were designed. We employed the density functional theory (DFT) in B3LYP/6-311++G(d,p) to study their geometrical structures and the homodesmotic reaction method to calculate the enthalpies of formation. Read More

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http://dx.doi.org/10.1007/s00894-018-3918-yDOI Listing
January 2019

Molecular dynamics of combustion reactions in supercritical carbon dioxide. Part 4: boxed MD study of formyl radical dissociation and recombination.

J Mol Model 2019 Jan 10;25(2):35. Epub 2019 Jan 10.

Center for Advanced Turbomachinery and Energy Research (CATER), Mechanical and Aerospace Engineering, University of Central Florida, Orlando, Florida, 32816, USA.

Fossil fuel oxy-combustion is an emergent technology where habitual nitrogen diluent is replaced by high pressure (supercritical) carbon dioxide. The supercritical state of CO increases the efficiency of the energy conversion and the absence of nitrogen from the reaction mixture reduces pollution by NO. However, the effects of a supercritical environment on elementary reactions kinetics are not well understood at present. Read More

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http://dx.doi.org/10.1007/s00894-018-3912-4DOI Listing
January 2019

Methanol, ethanol, propanol, and butanol adsorption on H-ZSM-5 zeolite: an ONIOM study.

J Mol Model 2019 Jan 9;25(2):34. Epub 2019 Jan 9.

Computational Chemistry Laboratory, Institute of Chemistry, University of Brasília, CP 4478, Brasília, DF, CEP 70904970, Brazil.

The search for renewable raw materials less harmful to the environment, such as methanol, ethanol, 1-propanol, and 1-butanol has become attractive. These products are obtained more rapidly and efficiently by specific solid catalysts, mainly the zeolites. The Brønsted acid sites distributed over the sinusoidal and the straight channels are important for the alcohol dehydration reaction that produces widely used chemicals. Read More

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http://dx.doi.org/10.1007/s00894-018-3894-2DOI Listing
January 2019
2 Reads

Diels-Alder reactivities of cycloalkenediones with tetrazine.

J Mol Model 2019 Jan 9;25(2):33. Epub 2019 Jan 9.

Department of Chemistry and Biochemistry, University of California, Los Angeles, 90095, CA, USA.

Quantum chemical calculations were used to investigate the Diels-Alder reactivities for a series of cycloalkenediones with tetrazine. We find that the reactivity trend of cycloalkenediones toward tetrazine is opposite to cycloalkenes. The electrostatic interactions between the cycloalkenediones and tetrazine become more stabilizing as the ring size of the cycloalkenediones increases, resulting in lower activation energies. Read More

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http://dx.doi.org/10.1007/s00894-018-3909-zDOI Listing
January 2019

Learning the initial mechanical response of composite material: structure evolution and energy profile of a plastic bonded explosive under rapid loading.

J Mol Model 2019 Jan 7;25(2):31. Epub 2019 Jan 7.

CNOOC Safety and Technology Services Co., Ltd, Zhanjiang, Guangzhou, 524057, China.

Plastic bonded explosive (PBX) is a typical composite material used widely in the defense industry and in aerospace engineering. The mechanical behavior of PBX is an important factor to be considered in its formulation design, but the initial mechanical response is not well understood due to the complexities of atomic interactions in a multi-component system. We applied a hybrid force field to investigate the initial mechanical response of cyclotrimethylenetrinitramine(RDX)-based PBX, by molecular dynamics. Read More

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http://link.springer.com/10.1007/s00894-018-3913-3
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http://dx.doi.org/10.1007/s00894-018-3913-3DOI Listing
January 2019
4 Reads

Proton disorder and elasticity of hexagonal ice and gas hydrates.

J Mol Model 2019 Jan 8;25(2):32. Epub 2019 Jan 8.

Tyumen Scientific Center, SB RAS, 86 Malygina str., Tyumen, 625026, Russia.

This work is devoted to the study of the mechanical properties of hexagonal ice Ih and gas hydrate frameworks sI, sII and sH, taking into account the disorder in the positions of the hydrogen atoms (protons). The article emphasizes the critical role of the elastic energy for the evaluation of the relative energy of the proton configurations. The calculations are performed with the help of the TINKER package using the AMOEBA polarizable force field. Read More

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http://link.springer.com/10.1007/s00894-018-3919-x
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http://dx.doi.org/10.1007/s00894-018-3919-xDOI Listing
January 2019
5 Reads

Theoretical study of the reactions between arsenic and nitrogen oxides during coal combustion.

J Mol Model 2019 Jan 7;25(2):30. Epub 2019 Jan 7.

Department of Energy Power & Mechanical Engineering, North China Electric Power University, Baoding, 071003, China.

The reactions between arsenic and nitrogen oxides (NO, NO, and NO) were investigated using density functional theory. The geometries of the reactants, intermediates, transition states, and products in each reaction were optimized. Frequency analysis was applied to verify those geometries, and the authenticity of each transition state was checked using intrinsic reaction coordinate analysis (IRC). Read More

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http://dx.doi.org/10.1007/s00894-018-3916-0DOI Listing
January 2019
1 Read

Revisiting the halogen bonding between phosphodiesterase type 5 and its inhibitors.

J Mol Model 2019 Jan 7;25(2):29. Epub 2019 Jan 7.

Department of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.

Halogenated ligands are nowadays commonly designed in order to increase their potency against protein targets. Although novel computational methods of evaluating the affinity of such halogenated inhibitors have emerged, they still lack the sufficient accuracy, which is especially noticeable in the case of empirical scoring functions, being the method of choice in the drug design process. Here, we evaluated a series of halogenated inhibitors of phosphodiesterase type 5 with ab initio methods, revealing the physical nature of ligand binding and determining the components of interaction energy that are essential for proper inhibitor ranking. Read More

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http://dx.doi.org/10.1007/s00894-018-3897-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321839PMC
January 2019
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Theoretical calculations about nitro-substituted pyridine as high-energy-density compounds (HEDCs).

J Mol Model 2019 Jan 5;25(1):23. Epub 2019 Jan 5.

School of Chemistry and Materials Science, Guizhou Education University, Guiyang, 051008, China.

A series of derivatives of pyridine were designed through substituting hydrogen atoms by nitro groups systematically. By using the density functional theory at B3PW91/6-311++G(d,p)//MP2/311++G(d,p) level, heats of formation, bond orders, and bond dissociation energies were calculated to explore the thermodynamic stabilities of title molecules. Furthermore, the regularity of stability was explained based on the electronic population. Read More

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http://dx.doi.org/10.1007/s00894-018-3904-4DOI Listing
January 2019
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Thermochemistry and kinetic analysis for the conversion of furfural to valuable added products.

J Mol Model 2019 Jan 5;25(1):26. Epub 2019 Jan 5.

Química de Recursos Energéticos y Medio Ambiente, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.

Furfural is a valuable oxygenated compound derived from the thermal decomposition of biomass, and is one of the major problems of bio-oil upgrading. Due to its high reactivity, this compound requires further upgrading to more stable products such as furfuryl alcohol, 2-methylfuran (MF), furan, 2-methyltetrahydrofuran, and tetrahydrofuran. The thermochemical data and kinetic analysis of the reactions involved in the conversion of furfural were investigated by molecular modeling to guide experimental investigations in the process of designing efficient catalysts that allows the control of the reaction pathways in specific directions, towards the production of fuel precursors or chemicals. Read More

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http://dx.doi.org/10.1007/s00894-018-3908-0DOI Listing
January 2019

Functionalization of the transition metal oxides FeO, CoO, and NiO with alkali metal atoms decreases their ionization potentials by 3-5 eV.

J Mol Model 2019 Jan 5;25(1):24. Epub 2019 Jan 5.

Laboratory of Quantum Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.

The existence and stabilities of various neutral metal oxides of formula MON and MON (M = Fe, Co, Ni; N = Li, Na) and their corresponding cations MON and MON are predicted using density functional theory (B3LYP) with the 6-311 + G(d) basis set. Ab initio calculations carried out at the CCSD(T)/6-311 + G(3df) level of theory reveal that the ionization potentials (IPs) of the oxides MO decrease by ca. 3-5 eV upon functionalization with N to give either MON or MON. Read More

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http://dx.doi.org/10.1007/s00894-018-3901-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320745PMC
January 2019

Theoretical study on polynitro imidazo [4, 5-e] oxadiazolo [3, 4-b] pyrazine compounds.

J Mol Model 2019 Jan 5;25(1):25. Epub 2019 Jan 5.

State Key Laboratory of Fluorine & Nitrogen Chemicals, Xi'an Modern Chemistry Research Institute, Xi'an, 710065, China.

The B3PW91/6-31G** theoretical method was carried out to optimize the structure of 12 polynitro imidazo [4,5-e] oxadiazolo [3,4-b] pyrazine compounds (two structural type). The influence of nitro groups on the structure, oxygen balance, density, heat of formation, detonation performances, and charge were investigated. The results showed that the oxygen balance, density, heat of formation, detonation velocity, detonation pressure, and detonation heat increased with different relationships when the number of nitro groups increased. Read More

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http://dx.doi.org/10.1007/s00894-018-3903-5DOI Listing
January 2019

Geometries, stabilities, and magnetic properties of CoB (n = 1-10) clusters.

J Mol Model 2019 Jan 6;25(1):27. Epub 2019 Jan 6.

Key Laboratory of Magnetic Molecules & Magnetic Information Materials Ministry of Education, the School of Chemical and Material Science, Shanxi Normal University, Linfen, 041004, China.

The geometries, stabilities, and magnetic properties of CoB (n = 1-10) clusters were systematically investigated by performing spin-polarized density functional theory calculations. We found that doping B clusters with Co significantly changed their structures. CoB and CoB had planar and quasi-planar structures, while CoB and CoB had bipyramidal structures. Read More

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http://dx.doi.org/10.1007/s00894-018-3906-2DOI Listing
January 2019

Theoretical and conceptual DFT study of pnicogen- and halogen-bonded complexes of PHX---BrCl.

J Mol Model 2019 Jan 6;25(1):28. Epub 2019 Jan 6.

School of Chemical Biology and Materials Engineering, Suzhou University of Science and Technology, Suzhou, China.

The pnicogen and halogen bonding interactions in the PHX---BrCl(X = H, F, OH, OCH and CH) complexes have been studied at the MP2/aug-cc-pVTZ level. Analysis of interaction energies shows that the pnicogen-bonded structures are less stable than the corresponding halogen-bonded structures. The pnicogen and halogen bonds were also studied by conceptual DFT reactivity indices. Read More

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http://dx.doi.org/10.1007/s00894-018-3905-3DOI Listing
January 2019
2 Reads

Correction of diffusion calculations when using two types of non-rectangular simulation boxes in molecular simulations.

J Mol Model 2019 Jan 4;25(1):22. Epub 2019 Jan 4.

Department of Physics, North University of China, Taiyuan, 030051, China.

Although simulation boxes used in molecular dynamics are normally chosen to be cubic or rectangular, two other cell shapes that are very familiar to crystallographers-the truncated octahedron and the rhombic dodecahedron-could also be used because they are also space-filling cells. Due to their spherical nature, these boxes have been intentionally applied in simulations of biomolecular solutions and liquid structures. Indeed, due to the advantages of running many molecular dynamic codes in parallel, simulations based on these non-rectangular boxes have been growing in popularity in recent years. Read More

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http://dx.doi.org/10.1007/s00894-018-3910-6DOI Listing
January 2019
1 Read

Structure and function prediction of arsenate reductase from Deinococcus indicus DR1.

J Mol Model 2019 Jan 4;25(1):15. Epub 2019 Jan 4.

Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India.

Arsenic prevalence in the environment impelled many organisms to develop resistance over the course of evolution. Tolerance to arsenic, either as the pentavalent [As(V)] form or the trivalent form [As(III)], by bacteria has been well studied in prokaryotes, and the mechanism of action is well defined. However, in the rod-shaped arsenic tolerant Deinococcus indicus DR1, the key enzyme, arsenate reductase (ArsC) has not been well studied. Read More

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http://link.springer.com/10.1007/s00894-018-3885-3
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http://dx.doi.org/10.1007/s00894-018-3885-3DOI Listing
January 2019
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A QM/MM study on ethene and benzene oxidation using silica-supported chromium trioxide.

J Mol Model 2019 Jan 4;25(1):17. Epub 2019 Jan 4.

Theoretical and Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.

Oxidation of ethene and benzene by chromium oxide (CrO) supported on silica (SiO) was investigated by employing hybrid quantum mechanics/molecular mechanics (QM/MM) model calculations. Various mechanistic possibilities, such as C-H or C=C bond activation of hydrocarbons, were investigated in detail for the reaction of ethene and benzene with CrO grafted on a silica surface. While activation of the C-H bond leads to the formation of alcohol, epoxide is obtained via C=C bond activation. Read More

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http://dx.doi.org/10.1007/s00894-018-3899-xDOI Listing
January 2019

The chalcogen bond in FP(S)N⋅⋅⋅SX, FPNS⋅⋅⋅SX, FPSN⋅⋅⋅SX (X = F, Cl, Br, OH, CH, NH) complexes.

J Mol Model 2019 Jan 4;25(1):19. Epub 2019 Jan 4.

College of Chemistry and Material Science, Hebei Normal University, Road East of 2nd Ring South, Shijiazhuang, 050024, China.

As a kind of intermolecular noncovalent interaction, chalcogen bonding plays a critical role in the fields of chemistry and biology. In this paper, S⋅⋅⋅S chalcogen bonds in three groups of complexes, FP(S)N⋅⋅⋅SX, FPNS⋅⋅⋅SX, and FPSN⋅⋅⋅SX (X = F, Cl, Br, OH, CH, NH), were investigated at the MP2/aug-cc-pVTZ level of theory. The calculated results show that the formation of S⋅⋅⋅S chalcogen bond is in the manner of attraction between the positive molecular electrostatic potential (V) of chalcogen bond donator and the negative V of chalcogen bond acceptor. Read More

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http://dx.doi.org/10.1007/s00894-018-3895-1DOI Listing
January 2019