Tunable electronic properties of ultra-thin boron-carbon-nitrogen heteronanotubes for various compositions.

abstract：:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...

journal_title：Journal of molecular modeling

authors： Armaković S,Armaković SJ,Abramović BF

更新日期：2016-10-01 00:00:00

abstract：:In this paper, we theoretically studied the geometries, stabilities, and the electronic and thermodynamic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiopene S-oxide derivatives (BTO-X, with X = BH(2), SiH(2), S, S=O, or O) using semi-empirical methods, ab initio methods, and density functional theory. The geometries ...

journal_title：Journal of molecular modeling

authors： Banjo S,Ayobami OO,Ajibade AI

更新日期：2012-06-01 00:00:00

abstract：:DFT calculations were carried out on the homo- and hetero-bimetallic model wires [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Fe(dpe)(η(5)-C5H5)] (1'), [(η(7)-C7H7)(dpe)Mo-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (2'), and [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (3') used to tentatively mimic [(η(5)-C5Me5)(dppe)Fe-C≡C-C6H4-C...

journal_title：Journal of molecular modeling

authors： Ladjarafi A,Costuas K,Meghezzi H,Halet JF

更新日期：2015-04-01 00:00:00

abstract：:Physical and chemical adsorption of CO2 on ZnO surfaces were studied by means of two different implementations of periodic density functional theory. Adsorption energies were computed and compared to values in the literature. In particular, it was found that the calculated equilibrium structure and internuclear distan...

journal_title：Journal of molecular modeling

authors： Farias SA,Longo E,Gargano R,Martins JB

更新日期：2013-05-01 00:00:00

abstract：:Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein seque...

journal_title：Journal of molecular modeling

authors： Saraswathi S,Fernández-Martínez JL,Kolinski A,Jernigan RL,Kloczkowski A

更新日期：2012-09-01 00:00:00

abstract：:The potential energy surfaces in gas phase and in aqueous solution for the nitration of benzene, chlorobenzene, and phenol have been elucidated with density functional theory at the M06-2X/6-311G(d,p) level combined with the polarizable continuum solvent model (PCM). Three reaction intermediates have been identified a...

journal_title：Journal of molecular modeling

authors： Liljenberg M,Stenlid JH,Brinck T

更新日期：2017-12-18 00:00:00

abstract：:Intramolecular and intermolecular hydrogen bonding in electronic excited states of calixarene building blocks bis(2-hydroxyphenyl)methane (2HDPM) monomer and hydrogen-bonded 2HDPM-H₂O complex were studied theoretically using the time-dependent density functional theory (TDDFT). Twenty-four stable conformations (12 pai...

journal_title：Journal of molecular modeling

authors： Wang S,Hao C,Gao Z,Chen J,Qiu J

更新日期：2013-04-01 00:00:00

abstract：:Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out stron...

journal_title：Journal of molecular modeling

authors： Oliveira BG

更新日期：2015-11-01 00:00:00

abstract：:NBO-NJC decomposition of vicinal (3)J HH spin-spin coupling constants into Lewis, delocalization, and repolarization contributions are presented. A deep study allows to assign the main contributions to specific orbitals or electron delocalizations between two orbitals. (3)J HH torsional dependence and the substituent ...

journal_title：Journal of molecular modeling

authors： García de la Vega JM,San Fabián J

更新日期：2014-07-01 00:00:00

abstract：:G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...

journal_title：Journal of molecular modeling

authors： Cashman DJ,Buscaglia R,Freyer MW,Dettler J,Hurley LH,Lewis EA

更新日期：2008-02-01 00:00:00

abstract：:Quantum chemical calculations using density functional theory BP86/def2-TZVPP and ab initio methods at CCSD(T)/def2-TZVPP have been carried for the telluroketones H2A=Te (A = C, Si, Ge). DFT calculations have also been carried out for the ketones H2C=E (E = O, S, Se, Te) and for the complexes NHC → [H2A=Te] → B(C6F5)3...

journal_title：Journal of molecular modeling

authors： Jaufeerally NB,Ramasami P,Jerabek P,Frenking G

更新日期：2014-10-01 00:00:00

abstract：:Two uridine 2',3'-cyclic monophosphate (cUMP) derivatives, 5'-deoxy (DcUMP) and 5'-O-methyl (McUMP), were studied by means of quantum chemical methods. Aqueous solvent effects were estimated based on the isodensity-surface polarized-continuum model (IPCM). Gas phase calculations revealed only slight energy differences...

journal_title：Journal of molecular modeling

authors： Grabarkiewicz T,Hoffmann M

更新日期：2006-01-01 00:00:00

abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...

journal_title：Journal of molecular modeling

authors： de Oliveira BG,Araújo RC,Chagas FF,Carvalho AB,Ramos MN

更新日期：2008-10-01 00:00:00

abstract：:The contribution of folic acid (FA)-tryptophan interactions to FA-protein association was investigated in the context of using FA as a drug carrier in protein delivery systems. Bovine serum albumin (BSA) and indolicidin were used as model proteins in the study. The FA-BSA complex was characterized by using the Bradfor...

journal_title：Journal of molecular modeling

authors： Gupta R,Kalita P,Patil O,Mohanty S

更新日期：2015-12-01 00:00:00

abstract：:Artificial neural networks (ANNs) have been successfully trained to model and predict the acidity constants (pK(a)) of 128 various phenols with diverse chemical structures using a quantitative structure-activity relationship. An ANN with 6-14-1 architecture was generated using six molecular descriptors that appear in ...

journal_title：Journal of molecular modeling

authors： Habibi-Yangjeh A,Danandeh-Jenagharad M,Nooshyar M

更新日期：2006-02-01 00:00:00

abstract：:Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cati...

journal_title：Journal of molecular modeling

authors： Gushchin IY,Gordeliy VI,Grudinin S

更新日期：2012-09-01 00:00:00

abstract：:Geometries and energies of formation of bilirubin formed by reduction of biliverdin via three meso carbon sites, the beta, gamma and delta positions, have been calculated using semiempirical methods. It has been shown that gamma-bilirubin with a ridge-tile conformation forms six intramolecular hydrogen bonds and is th...

journal_title：Journal of molecular modeling

authors： Zahedi M,Kamalipour M,Safari N

更新日期：2002-04-01 00:00:00

abstract：:We report a study of the structure of (+)-catechin, which belongs to the family of the flavan-3-ols-one of the five most widely distributed phenolic groups. The biological activities and pharmaceutical utility of these compounds are related to antioxidant activity due to their ability to scavenge free radicals. A brea...

journal_title：Journal of molecular modeling

authors： Bentz EN,Pomilio AB,Lobayan RM

更新日期：2014-02-01 00:00:00

abstract：:A theoretical investigation of the adsorption of CO₂ onto ZrO₂ is presented. Various cluster models were used to mimic different basic and acidic sites on the surface. The method used was the density functional theory with the generalized gradient approximation and including Grimme's empirical model in order to proper...

journal_title：Journal of molecular modeling

authors： Boulet P,Knöfel C,Kuchta B,Hornebecq V,Llewellyn PL

更新日期：2012-11-01 00:00:00

abstract：:Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochem...

journal_title：Journal of molecular modeling

authors： Ahmadi S,Manickam Achari V,Nguan H,Hashim R

更新日期：2014-03-01 00:00:00

abstract：:Density functional theory investigations at the DFT-B3LYP/6-311++G** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH3, 4-R-F, 4-R-NO2) in the selected solvent (acetone, acetonitrile...

journal_title：Journal of molecular modeling

authors： Shiroudi A,Safaei Z,Kazeminejad Z,Repo E,Pourshamsian K

更新日期：2020-02-13 00:00:00

abstract：:Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynam...

journal_title：Journal of molecular modeling

authors： Kulczycka-Mierzejewska K,Sadlej J,Trylska J

更新日期：2018-07-03 00:00:00

abstract：:The computational fragility spectra of atoms on the reaction path are presented for a selection of canonical processes represented by an amino group rotation around the (X)HC-NH(Y) bond (X = O, S; Y=H, CH3). Calculated spectra are found to very accurately describe the variation of atomic valence. Significant linear co...

journal_title：Journal of molecular modeling

authors： Zaklika J,Komorowski L,Ordon P

更新日期：2019-04-26 00:00:00

abstract：:Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm withi...

journal_title：Journal of molecular modeling

authors： Gisdon FJ,Culka M,Ullmann GM

更新日期：2016-10-01 00:00:00

abstract：:The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, m...

journal_title：Journal of molecular modeling

authors： Honarparvar B,Skelton AA

更新日期：2015-04-01 00:00:00

abstract：:The efficiency and high specificity of tobacco etch virus protease (TEVp) has made it widely used for cleavage of recombinant fusion proteins. However, TEVp suffers from a few intrinsic defects such as self-cleavage, poorly expressed in E. coli and less soluble. So some mutants were designed to improve it, such as S21...

journal_title：Journal of molecular modeling

authors： Wang Y,Zhu GF,Ren SY,Han YG,Luo Y,Du LF

更新日期：2013-11-01 00:00:00

abstract：:Cathepsin S has been demonstrated to play a crucial role in the remodeling of extracellular matrix proteins such as elastin and collagen, which in turn contribute to the structural integrity of the cardiovascular wall. Atherosclerotic lesions, aneurysm formation, plaque rupture, thrombosis, and calcification are some ...

journal_title：Journal of molecular modeling

authors： Ahmad S,Siddiqi MI

更新日期：2017-03-01 00:00:00

abstract：:The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized ...

journal_title：Journal of molecular modeling

authors： Kumar M,Bhattacharyya N,Bandyopadhyay D

更新日期：2012-01-01 00:00:00

abstract：: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. In this work, we present ...

journal_title：Journal of molecular modeling

authors： Grisoni F,Neuhaus CS,Hishinuma M,Gabernet G,Hiss JA,Kotera M,Schneider G

更新日期：2019-04-05 00:00:00

abstract：:The theoretical three-dimensional structure of a novel δ-endotoxin Cry1Id (81 kDa) belonging to Cry1I class, toxic to many of the lepidopteran pests has been investigated through comparative modeling. Molecular dynamics (MD) simulations was carried out to characterize its structural and dynamical features at 10 ns in ...

journal_title：Journal of molecular modeling

authors： Dehury B,Sahu M,Sahu J,Sarma K,Sen P,Modi MK,Barooah M,Choudhury MD

更新日期：2013-12-01 00:00:00