Critical test of some computational methods for prediction of NMR ¹H and ¹³C chemical shifts.

abstract：:In this work, the effect of the external electric field (EF) on the drug delivery performance of peptide-based metal-organic framework (MPF) for 6-mercaptopurine (6-MP) drug is investigated by means of the molecular dynamics (MD) simulations. It is found that the strength interaction of drug molecule with MPF is decre...

journal_title：Journal of molecular modeling

authors： Shahabi M,Raissi H

更新日期：2019-09-06 00:00:00

abstract：:The present study analyzed binding of Cu(2+) to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches in...

journal_title：Journal of molecular modeling

authors： Czyżnikowska Z,Brasuń J

更新日期：2012-04-01 00:00:00

abstract：:Selective poly (ADP-ribose) polymerase (PARP)-1 inhibitor represents promising therapy against cancers with a good balance between efficacy and safety. Owing to the conserved structure between PARP-1 and PARP-2, most of the clinical and experimental drugs show equivalent inhibition against both targets. Most recently,...

journal_title：Journal of molecular modeling

authors： Cao R

更新日期：2016-04-01 00:00:00

abstract：:The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a varie...

journal_title：Journal of molecular modeling

authors： Petelski AN,Peruchena NM,Pamies SC,Sosa GL

更新日期：2017-08-14 00:00:00

abstract：:Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...

journal_title：Journal of molecular modeling

authors： Ciftci YO,Evecen M,Alp İO

更新日期：2021-01-03 00:00:00

abstract：: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 dissoci...

journal_title：Journal of molecular modeling

authors： Kosar N,Ayub K,Gilani MA,Mahmood T

更新日期：2019-01-28 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：:In recent years, several new chelating reagents have been synthesized and tested for their collecting power in sulfide and non-sulfide minerals flotation. Many researchers have indicated that chelating reagents have the advantage of offering better selectivity and specificity as flotation collectors. Therefore, densit...

journal_title：Journal of molecular modeling

authors： Yekeler H,Yekeler M

更新日期：2006-09-01 00:00:00

abstract：:Quercetin is the most abundant flavonoid with potent antioxidant activities. In the current research, the antioxidant properties of quercetin and quercetin-DNA complex were investigated theoretically and experimentally. Free radical scavenging experiments with thiobarbituric acid-reactive substances (TBARS) and 1,1-di...

journal_title：Journal of molecular modeling

authors： Song X,Wang Y,Gao L

更新日期：2020-05-12 00:00:00

abstract：:To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP...

journal_title：Journal of molecular modeling

authors： Singh KhD,Kirubakaran P,Nagarajan S,Sakkiah S,Muthusamy K,Velmurgan D,Jeyakanthan J

更新日期：2012-01-01 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：:In erythrocytes, actively multiplying Plasmodium falciparum parasites exhibit a unique signature of virulence associated histone modifications, thereby epigenetically regulating the expression of the majority of genes. Histone acetylation is one such modification, effectuated and maintained by the dynamic interplay of...

journal_title：Journal of molecular modeling

authors： Kumar A,Dhar SK,Subbarao N

更新日期：2018-08-14 00:00:00

abstract：:Zeolites are a group of microporous aluminosilicate frameworks with numerous applications in, for example, catalysis and ion-exchange and sorption processes. One of the most important tools for analyzing the properties of zeolite structures is vibrational spectroscopy. However, the complexity of these structures often...

journal_title：Journal of molecular modeling

authors： Mikuła A,Król M,Koleżyński A

更新日期：2015-10-01 00:00:00

abstract：:The preferential selectivity of dicyclohexano-18-crown-6 (DCH18C6) for bivalent Sr(+2) ion over tetravalent Th(+4) ion was investigated using generalized gradient approximated (GGA) BP86 and the hybrid B3LYP density functional, employing split valence plus polarization (SV(P)) and triple-zeta valence plus polarization...

journal_title：Journal of molecular modeling

authors： Boda A,Joshi JM,Ali SM,Shenoy KT,Ghosh SK

更新日期：2013-12-01 00:00:00

abstract：:The Solanum lycopersicum aspartic protease inhibitor (SLAPI), which belongs to the STI-Kunitz family, is an effective inhibitor of the aspartic proteases human cathepsin D and Saccharomyces proteinase A. However, in contrast with the large number of studies on the inhibition mechanism of the serine proteases by the ST...

journal_title：Journal of molecular modeling

authors： Guerra Y,Valiente PA,Berry C,Pons T

更新日期：2012-06-01 00:00:00

abstract：:To improve understanding of the unimolecular decomposition mechanism of 1,2,4-butanetriol trinitrate (BTTN) in the gas phase, density functional theory calculations were performed to determine various decomposition pathways at the B3LYP/6-311G** level. Two main mechanisms for the unimolecular decomposition of BTTN wer...

journal_title：Journal of molecular modeling

authors： Zhu W,Yan Q,Pang A,Chi X,Du X,Xiao H

更新日期：2014-02-01 00:00:00

abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...

journal_title：Journal of molecular modeling

authors： Mitra P,Pal D

更新日期：2011-03-01 00:00:00

abstract：:The capture of N3-chains and N5-rings on the outer surface of C60 was studied using density functional calculations. For the neutral N5-ring, it was found that a N5-ring trapped by a C60 cage becomes more stable than an isolated N5-ring radical, and a C60-N5 compound with a C-N bond at an exohedral position of C60 is ...

journal_title：Journal of molecular modeling

authors： Liang Y,Gao X,Li N,Zhang X

更新日期：2015-10-01 00:00:00

abstract：:Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and t...

journal_title：Journal of molecular modeling

authors： Zhang J,Wang Z,Zhu Z

更新日期：2013-12-01 00:00:00

abstract：:The geometrical parameters and static electric properties of several metal porphyrin halides, including Fe(III) porphine chloride (FePCl), Fe(III) porphine bromide (FePBr), Fe(III) tetraphenylporphine chloride (FeTPPCl), aluminum phthalocyanine chloride (AlPcCl), gallium(III) phthalocyanine chloride (GaPcCl), and mang...

journal_title：Journal of molecular modeling

authors： Asghari-Khiavi M,Safinejad F

更新日期：2010-03-01 00:00:00

abstract：:Adsorption of three heavy metals (Ni, Pd, Cd) onto (10,0) single-walled carbon nanotube (SWCNT) was investigated using density functional theory (DFT). Metals were adsorbed to both inside and outside of SWCNT and their structures and electronic properties [e.g., band structures and density of states (DOS)] were calcul...

journal_title：Journal of molecular modeling

authors： Aghashiri A,Fotooh FK,Hashemian S

更新日期：2019-06-10 00:00:00

abstract：:Adsorption of paracresol and water into the silicalite-1 (MFI) zeolite has been investigated using canonical and grand-canonical Monte Carlo simulations. The most stable sites of adsorption of paracresol are found to be located at the channel intersections. Grand-canonical simulations have shown that at low loading, w...

journal_title：Journal of molecular modeling

authors： Boulet P,Narasimhan L,Berg'e-Lefranc D,Kuchta B,Schäf O,Denoyel R

更新日期：2009-06-01 00:00:00

abstract：:Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) fo...

journal_title：Journal of molecular modeling

authors： Gao Z,Lv S,Yang W,Yang P,Ji S,Meng X

更新日期：2015-06-01 00:00:00

abstract：:Cystic fibrosis (CF), the most common lethal genetic disease among Caucasians, is caused by mutations in cystic fibrosis transmembrane conductance regulator (CFTR). CFTR's main role is to transport chloride ions across epithelial cell membranes. It also regulates many cell functions. However, the exact role of CFTR in...

journal_title：Journal of molecular modeling

authors： Siwiak M,Edelman A,Zielenkiewicz P

更新日期：2012-01-01 00:00:00

abstract：:We report the parameterization of AM1 for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1 parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, ...

journal_title：Journal of molecular modeling

authors： Kayi H,Clark T

更新日期：2011-10-01 00:00:00

abstract：:The aim of the present work entitled electronic structure of PVA-PEG-Y2O3 (54 atom) is to present a theoretical study based on the hybrid function of three parameters Lee-Yang-Parr B3LYP of the density functional theory "DFT" quantum mechanical approach together with LanL2DZ basis sets for optoelectronics applications...

journal_title：Journal of molecular modeling

authors： Ahmed H,Hashim A

更新日期：2020-07-20 00:00:00

abstract：:We have systematically explored and investigated the geometrical structures, stability, growth pattern, bonding character, and potential energy surface (PES) of the possible isomers of each cluster for planar B(n)P (n = 1 ∼ 7) at the CCSD(T)/6-311+;G(d)//B3LYP/6-311+G(d) level. A large number of planar structures for ...

journal_title：Journal of molecular modeling

authors： Shi R,Shao J,Wang C,Zhu X,Lu X

更新日期：2011-05-01 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：:A novel mechanism for switching a molecular junction based on a proton transfer reaction triggered by an external electrostatic field is proposed. As a specific example to demonstrate the feasibility of the mechanism, the tautomers [2,5-(4-hydroxypyridine)] and {2,5-[4(1H)-pyridone]} are considered. Employing a combin...

journal_title：Journal of molecular modeling

authors： Hofmeister C,Härtle R,Rubio-Pons O,Coto PB,Sobolewski AL,Thoss M

更新日期：2014-04-01 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