A theoretical thermodynamic investigation of cascade reactions in dinuclear octa-azacryptates involving carbon dioxide.

abstract：:Using molecular dynamics simulations, we investigated the thermal stability and real-time denaturation of a model mini-protein in four solvents: (1) water, (2) 1-ethyl-3-methylimidazolium alaninate [EMIM][ALA] (5 mol% in water), (3) methioninate [EMIM][MET] (5 mol% in water), and (4) tryptophanate [EMIM][TRP] (5 mol% ...

journal_title：Journal of molecular modeling

authors： Chevrot G,Fileti EE,Chaban VV

更新日期：2016-11-01 00:00:00

abstract：:Solar-assisted water splitting using photoelectrochemical cells (PECs) is one of the promising ways for the production of hydrogen to store renewable energy. Semiconducting materials are used as a key factor which controls the overall energy conversion efficiency in PECs. However, finding new semiconductors with appro...

journal_title：Journal of molecular modeling

authors： Uğur Ş,Akbudak S,Kushwaha AK,Bayrak G

更新日期：2020-05-15 00:00:00

abstract：:The binding behavior of coinage metal anions with some electron-deficient arenes has been investigated by MP2 calculations, and the character of interactions in these complexes has been examined by NBO analysis. The results indicate that coinage metal anions can interact with electron-deficient arenes to form anion-π,...

journal_title：Journal of molecular modeling

authors： Chen Y,Wang F

更新日期：2015-03-01 00:00:00

abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...

journal_title：Journal of molecular modeling

authors： Méndez-Hernández DD,Tarakeshwar P,Gust D,Moore TA,Moore AL,Mujica V

更新日期：2013-07-01 00:00:00

abstract：:Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these...

journal_title：Journal of molecular modeling

authors： Sun S,Lu M

更新日期：2018-06-23 00:00:00

abstract：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...

journal_title：Journal of molecular modeling

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00

abstract：:We present a critical discussion related to the recent definition of the intrinsic reactivity index, IRI, (Tetrahedron Lett. 2013, 54, 339-342; Tetrahedron 2013, 69, 4247-4258) formulated to describe both, electrophilicity (charge acceptance) and nucleophilicity (charge donation) reactivities. We here stress that such...

journal_title：Journal of molecular modeling

authors： Chamorro E,Melin J

更新日期：2015-03-01 00:00:00

abstract：:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...

journal_title：Journal of molecular modeling

authors： Mu X,Xu D

更新日期：2020-03-07 00:00:00

abstract：:This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed co...

journal_title：Journal of molecular modeling

authors： Donnamaria MC,de Xammar Oro JR

更新日期：2011-10-01 00:00:00

abstract：:In the present investigation, the first hyperpolarizability of alkali and alkaline earth metal derivatives of cyclooctatetraene (COT) has been calculated using BHHLYP and CAM-B3LYP functional for 6-311++G(d,p), 6-311++G(3df,3pd), and aug-pc 2 basis sets. Introduction of Na/K atoms at the axial position of COT and Li, ...

journal_title：Journal of molecular modeling

authors： Roy RS,Mondal A,Nandi PK

更新日期：2017-03-01 00:00:00

abstract：:Hydrogen dissociative chemisorption and desorption on small lowest energy Ni(n) clusters up to n=13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy pat...

journal_title：Journal of molecular modeling

authors： Zhou C,Yao S,Zhang Q,Wu J,Yang M,Forrey RC,Cheng H

更新日期：2011-09-01 00:00:00

abstract：:We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

journal_title：Journal of molecular modeling

authors： Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

更新日期：2014-03-01 00:00:00

abstract：:The equilibrium structures, spectroscopic and thermodynamic parameters [entropy (S), internal energy (E), heat capacity (C p)] of U₂, U₂O, U₂O₂ and U₂O₄ uranium oxide molecules were investigated systematically using density functional theory (DFT). Our computations indicated that the ground electronic state of U₂ is t...

journal_title：Journal of molecular modeling

authors： Li P,Niu WX,Gao T,Wang F,Jia TT,Meng DQ,Li G

更新日期：2013-12-01 00:00:00

abstract：:The geometrical structure and electronic properties of bis(10-hydroxybenzo[h]quinolinato)beryllium (Bebq2) molecule and its dimer both in the neutral and in the positively and negatively charged states were studied using quantum-chemical calculations. It is found that the excess charge in the charged systems is locali...

journal_title：Journal of molecular modeling

authors： Safonov AA,Bagaturyants AA

更新日期：2014-08-01 00:00:00

abstract：:Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A e...

journal_title：Journal of molecular modeling

authors： Lobayan RM,Schmit MC,Jubert AH,Vitale A

更新日期：2011-06-01 00:00:00

abstract：:A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p),...

journal_title：Journal of molecular modeling

authors： Shukla MK,Boddu V,Hill F

更新日期：2014-09-01 00:00:00

abstract：:Defects in the nanoscale are common in the 2D materials irrespective of the fabricated method. Material performance gets significantly affected due to the presence of defects in 2D materials. In the present study, electronic and mechanical properties of 2D-hexagonal boron nitride (hBN) are investigated. At the electro...

journal_title：Journal of molecular modeling

authors： Sagar TC,Chinthapenta V

更新日期：2020-07-03 00:00:00

abstract：:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...

journal_title：Journal of molecular modeling

authors： Purohit R,Rajendran V,Sethumadhavan R

更新日期：2011-04-01 00:00:00

abstract：:We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of wa...

journal_title：Journal of molecular modeling

authors： Mikulskis P,Genheden S,Ryde U

更新日期：2014-06-01 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：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...

journal_title：Journal of molecular modeling

authors： Victor Paul Raj FR,Exner TE

更新日期：2014-04-01 00:00:00

abstract：:Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molec...

journal_title：Journal of molecular modeling

authors： Wojdeł JC

更新日期：2009-06-01 00:00:00

abstract：:Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2 = ...

journal_title：Journal of molecular modeling

authors： Chen ES,Keith H,Lim T,Pham D,Rosenthal R,Herder C,Pai S,Flores RA,Chen EC

更新日期：2015-04-01 00:00:00

abstract：:In an attempt to analyze structure, function and evolution of HIV-1 GP120 V3, interactions among the Hartree-Fock energy, the conformational entropy and the Shannon entropy were determined for the 1NJ0 set of antibody-bound V3 loop conformers. The Hartree-Fock energy of each conformer was determined at the MINI level ...

journal_title：Journal of molecular modeling

authors： Weltman JK,Skowron G,Loriot GB

更新日期：2006-02-01 00:00:00

abstract：:Quantum chemical calculations are performed to study the interplay between halogen⋯nitrogen and halogen⋯carbene interactions in NCX⋯NCX⋯CH2 complexes, where X = F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that t...

journal_title：Journal of molecular modeling

authors： Esrafili MD,Mohammdain-Sabet F,Esmailpour P

更新日期：2013-11-01 00:00:00

abstract：:Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching, SADMET screening, and docking and toxicity studies) was performed to ...

journal_title：Journal of molecular modeling

authors： Ajay D,Sobhia ME

更新日期：2012-01-01 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：:High-level quantum chemical techniques have been utilized to accurately describe the geometrical parameters, vibrational frequencies and dissociation pathways of the X (2)A″, 1 (2)A', 2 (2)A', 2 (2)A″ states of S(2)Cl; X (1)A', 1 (3)A″, 1 (1)A″, 1 (3)A' states of S(2)Cl(+); X (1)A', 1 (3)A', (1)A″ states of S(2)Cl(-),...

journal_title：Journal of molecular modeling

authors： Czernek J,Zivný O

更新日期：2012-09-01 00:00:00

abstract：:The thermally allowed electrocyclic reaction syn-cyclophanediene (CPD) to dihydropyrene (DHP) was compared with the disallowed thermal electrocyclic reaction in anti CPD through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d) level. Moreover, the results were also compared with the electrocycliza...

journal_title：Journal of molecular modeling

authors： Saima B,Khan A,Nisa RU,Mahmood T,Ayub K

更新日期：2016-04-01 00:00:00

abstract：:Present theoretical study involves the delta shape complexes of beryllium, magnesium, and calcium where the metal atom interacts perpendicularly with disubstituted acetylene. Most of the complexes are found to be fairly stable. The dependence of second-hyperpolarizability on the basis set with increasing polarization ...

journal_title：Journal of molecular modeling

authors： Hatua K,Nandi PK

更新日期：2015-10-01 00:00:00