Theoretical study of the complementarity in halogen-bonded complexes involving nitrogen and halogen as negative sites.

abstract：:Three potential anticancer agents {trans-[PtCl(2)(NH(3))(thiazole)], cis-[PtCl(2)(NH(3))(piperidine)], and PtCl(2)(NH(3))(cyclohexylamine) (JM118)} were explored and compared with cisplatin and the inactive [PtCl(dien)](+) complex. Basic electronic properties, bonding and stabilization energies were determined, and th...

journal_title：Journal of molecular modeling

authors： Bradác O,Zimmermann T,Burda JV

更新日期：2008-08-01 00:00:00

abstract：:CO2 reduction has attracted extensive attentions for its wide applications in chemical engineering and green chemistry. As one of major commercial catalysts, Cu have been widely studied considering its low price and high catalytic efficiency. However, previous studies were mostly focused on the Cu(111) surface, while ...

journal_title：Journal of molecular modeling

authors： Wang R,Zhu B,Zhang G,Gao Y

更新日期：2020-07-09 00:00:00

abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...

journal_title：Journal of molecular modeling

authors： Yang J,Zhang Y,Yang Y,Xue Y

更新日期：2019-07-02 00:00:00

abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...

journal_title：Journal of molecular modeling

authors： Melicherčík M,Holúbeková A,Hianik T,Urban J

更新日期：2013-11-01 00:00:00

abstract：:Density functional theory (DFT) was used to investigate nickel-catalyzed ring-opening hydroacylation of methylenecyclopropanes and benzaldehydes. The results indicated that the Ni-P(n-Bu)3 complex exhibited much more excellent catalysis than the other two complexes (Ni-PMe3 and Ni-P(t-Bu)3). The hydrogen migration was...

journal_title：Journal of molecular modeling

authors： Wang F,Zhu S,Meng Q,Yin H

更新日期：2015-08-01 00:00:00

abstract：:Carbon monoxide (CO) and oxygen (O2) catalyzed by small neutral iron oxide clusters (FeO(1-3)) was investigated at the density functional level of theory using the Becke-Perdew-Wang functional (BPW91). Three reaction pathways along with singlet, triplet and quintet states were calculated for ascertaining the presence ...

journal_title：Journal of molecular modeling

authors： Wang HJ,Wang YC

更新日期：2014-06-01 00:00:00

abstract：:The structures of the 4,4',4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree-Fock (HF) and density functional theory (DFT) levels of theory using several exchange-...

journal_title：Journal of molecular modeling

authors： Safonov A,Rykova E,Bagaturyants A

更新日期：2018-11-28 00:00:00

abstract：:The adsorption behavior of sulfur-based toxic gases (H2S and SO2) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restrict...

journal_title：Journal of molecular modeling

authors： Walia GK,Randhawa DKK

更新日期：2018-03-16 00:00:00

abstract：:In the present study, DFT calculations are carried out on domestically designed 7-methyl-2-phenyl-5'H-spiro[chromene-4,2'-chromeno[3,4-e][1,3]oxazin]-5'-one spiropyran and merocyanine derivatives to recognize alkali and alkaline earth metal ions. Detection of these metal ions can be attained by exploiting the variatio...

journal_title：Journal of molecular modeling

authors： Arif AM,Yousaf A,Zhong RL,Akhtar M,Muhammad S,Xu HL,Su ZM

更新日期：2019-07-06 00:00:00

abstract：:Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode ...

journal_title：Journal of molecular modeling

authors： Wang S,Sun Y,Du S,Qin Y,Duan H,Yang X

更新日期：2016-06-01 00:00:00

abstract：:Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...

journal_title：Journal of molecular modeling

authors： Hariprasad G,Kaur P,Srinivasan A,Singh TP,Kumar M

更新日期：2012-07-01 00:00:00

abstract：:Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA...

journal_title：Journal of molecular modeling

authors： Shokuhfar A,Arab B

更新日期：2013-09-01 00:00:00

abstract：:Very recently, an unprecedented novel monometallic cluster of fullerenes entrapping a yttrium cyanide (YCN) cluster inside a popular C82 cage YCN@Cs(6)-C82 was synthesized and characterized. Inspired by this investigation, four non-IPR YCN@C1(17459)-C76, YCN@C2v(19138)-C76, YCN@C2(17646)-C76, and YCN@C1(17894)-C76 (1,...

journal_title：Journal of molecular modeling

authors： Gao FW,Xu HL,Su ZM

更新日期：2016-08-01 00:00:00

abstract：:The mechanism and regioselectivity of [3+2] cycloaddition (32CA) reactions of benzonitrile oxide with ethyl trans-cinnamate, ethyl crotonate and trans-2-penten-1-ol has been studied in gas phase and in acetonitrile, ethyl acetate and tetrahydrofuran using the B3LYP functional in connection with 6-31G(d) basis set. The...

journal_title：Journal of molecular modeling

authors： Abbiche K,Acharjee N,Salah M,Hilali M,Laknifli A,Komiha N,Marakchi K

更新日期：2020-09-22 00:00:00

abstract：:The structures and intramolecular interactions of complexes (FeCNT-CO, FeCNT-NO, NiCNT-CO, and NiCNT-NO) formed by the Fe or Ni doped single-wall carbon nanotube (FeCNT or NiCNT) and gas CO or NO were studied using density functional theory, quantum theory of atom in molecule (QTAIM), and natural bond orbital methods....

journal_title：Journal of molecular modeling

authors： Zhang X,Gong X

更新日期：2015-09-01 00:00:00

abstract：:BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DN...

journal_title：Journal of molecular modeling

authors： Štěpán J,Kabelka I,Koča J,Kulhánek P

更新日期：2017-12-20 00:00:00

abstract：:5-Nitro-3-trinitromethyl-1H-1,2,4-triazole (NTMT, A) and its substituted derivatives A-CH3, A-OCH3, A-NH2, A-OH, A-NO2, and A-ONO2 were studied using density functional theory (DFT). For all of the molecules except for A-ONO2, the C-NO2 bond in the trinitromethyl group was found to be the weakest, and no transition st...

journal_title：Journal of molecular modeling

authors： Zhang X,Gong X

更新日期：2015-02-01 00:00:00

abstract：:A molecular modeling strategy is proposed to describe the temperature (T) dependence of solubility parameter (δ) for the amorphous polymers which exhibit glass-rubber transition behavior. The commercial forcefield "COMPASS" is used to support the atomistic simulations of the polymer. The temperature dependence behavio...

journal_title：Journal of molecular modeling

authors： Chen X,Yuan C,Wong CK,Zhang G

更新日期：2012-06-01 00:00:00

abstract：:The drug discovery process typically involves target identification and design of suitable drug molecules against these targets. Despite decades of experimental investigations in the drug discovery domain, about 96% overall failure rate has been recorded in drug development due to the "undruggability" of various ident...

journal_title：Journal of molecular modeling

authors： Agoni C,Olotu FA,Ramharack P,Soliman ME

更新日期：2020-05-08 00:00:00

abstract：:PcFK1 is a member of the cysteine knot inhibitor family that displays anti-malarial properties. The naturally occurring molecule is ∼ 40 amino acids in length and forms a highly constrained 3D structure due to the presence of 3 disulfide and multiple intra-molecular H-bonds. Recent experimental studies on PcFK1 wild-t...

journal_title：Journal of molecular modeling

authors： Gleeson MP,Deechongkit S,Ruchirawat S

更新日期：2011-04-01 00:00:00

abstract：:Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with...

journal_title：Journal of molecular modeling

authors： Kroutil O,Předota M,Kabeláč M

更新日期：2017-10-28 00:00:00

abstract：:The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6-311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6-311++G**, B3LYP/6-311++G(2df,2p), MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p)...

journal_title：Journal of molecular modeling

authors： Tang HF,Zhong H,Zhang LL,Gong MX,Song SQ,Tian QP

更新日期：2018-05-31 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 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：:Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbital...

journal_title：Journal of molecular modeling

authors： Wick CR,Hennemann M,Stewart JJ,Clark T

更新日期：2014-03-01 00:00:00

abstract：:Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density...

journal_title：Journal of molecular modeling

authors： Mihaylov T,Trendafilova N,Georgieva I

更新日期：2008-05-01 00:00:00

abstract：:A survey of the fascinating history of anesthetics and the many critical findings that have improved our understanding of anesthetic activity is followed by an expanded analysis of the electrostatic potentials of 27 molecules and two noble gases with anesthetic activities ranging from high to totally inactive. We agai...

journal_title：Journal of molecular modeling

authors： Shields ZP,Seybold PG,Murray JS

更新日期：2017-12-19 00:00:00

abstract：:The geometries, stabilities, and electronic properties of ScBn (n = 1-12) clusters have been systematically investigated by using density functional theory B3LYP method and coupled-cluster theory CCSD(T) method. It is found that the ground state isomers of ScBn have planar or quasi-planar structure when n ≤ 6, which c...

journal_title：Journal of molecular modeling

authors： Jia J,Ma L,Wang JF,Wu HS

更新日期：2013-08-01 00:00:00

abstract：:Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding ene...

journal_title：Journal of molecular modeling

authors： Karhánek D,Kacer P,Kuzma M,Splíchalová J,Cervený L

更新日期：2007-09-01 00:00:00

abstract：:Comprehensive molecular dynamics simulations are conducted to identify material modifications which can improve strength and reduce hysteresis losses at the nanointerfaces formed between silica, silane coupling agent (SCA) and styrene-butadiene rubber (SBR), all of which are important ingredients of green tyres. Impro...

journal_title：Journal of molecular modeling

authors： Joseph E,Swaminathan N,Kannan K

更新日期：2020-08-17 00:00:00