Aluminum cluster for CO and O2 adsorption.


:Low temperature oxidation of CO to CO2 is an important process for the environment. Similarly adsorption of CO from the releasing sources is also of major concern today. Whereas the potential of gold and silver clusters is well proven for the catalysis of the above mentioned reaction, the potential of aluminum (Al) clusters remains unexplored. The present study proves that, similar to the transition metals, Al clusters can also be used for adsorption of gases. We first tested the potential of Al cluster as adsorbents for CO. The high binding energy (BE) values prove that Al clusters can be used for adsorbing both CO and O2. Since oxygen binding is more facile, we adsorbed oxygen on Al and then checked the effect of this O2 on the BE of CO. The results were obtained by DFT calculations at M062X/TZVP level of theory. Graphical abstract Activation of carbon monoxide (CO) on oxygen-adsorbed aluminum (Al) cluster.


J Mol Model


Samanta B,Sengupta T,Pal S




Has Abstract


2018-12-06 00:00:00














  • First principles calculations on the influence of water-filled cavities on the electronic structure of Prussian Blue.

    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

    pub_type: 杂志文章


    authors: Wojdeł JC

    更新日期:2009-06-01 00:00:00

  • CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics.

    abstract::The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or inte...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Basu S

    更新日期:2017-12-07 00:00:00

  • Structural analysis of secretory phospholipase A2 from Clonorchis sinensis: therapeutic implications for hepatic fibrosis.

    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

    pub_type: 杂志文章


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

    更新日期:2012-07-01 00:00:00

  • Enhancing effect of metal coordination interaction on pnicogen bonding.

    abstract::The ternary complexes ML∙∙∙PyZX2∙∙∙NH3 (ML = CuCl, CuCN, AgCN, and AuCN; Z = P, As, and Sb; X = H and F) have been investigated with quantum chemical calculations. The results showed that the existence of coordination interaction has a prominent enhancing effect on the strength of pnicogen bonding. Even in ML∙∙∙PySbH2...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Tang Q,Li Q

    更新日期:2016-03-01 00:00:00

  • Switching the conductance of a molecular junction using a proton transfer reaction.

    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

    pub_type: 杂志文章


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

    更新日期:2014-04-01 00:00:00

  • Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3).

    abstract::A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Poulsen A,William A,Blanchard S,Nagaraj H,Williams M,Wang H,Lee A,Sun E,Teo EL,Tan E,Goh KC,Dymock B

    更新日期:2013-01-01 00:00:00

  • In-silico analysis of the structure and binding site features of an α-expansin protein from mountain papaya fruit (VpEXPA2), through molecular modeling, docking, and dynamics simulation studies.

    abstract::Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MA

    更新日期:2015-05-01 00:00:00

  • Markovian chemicals "in silico" design (MARCH-INSIDE), a promising approach for computer aided molecular design II: experimental and theoretical assessment of a novel method for virtual screening of fasciolicides.

    abstract::A novel method for in silico selection of fluckicidal drugs is introduced. Two QSARs that permit us to discriminate between fasciolicide and non-fasciolicide drugs (the first) and to outline some conclusions about the possible mechanism of action of a chemical (the second) are performed. The first model correctly clas...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: González Díaz H,Olazabal E,Castañedo N,Sánchez IH,Morales A,Serrano HS,González J,de Armas RR

    更新日期:2002-08-01 00:00:00

  • A comparative study of one- and two-photon absorption properties of pyrene and perylene diimide derivatives.

    abstract::Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ(T)(max)). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Liu XT,Zhao Y,Ren AM,Feng JK

    更新日期:2011-06-01 00:00:00

  • Theoretical study of the reaction mechanism of CH₃NO₂ with NO₂, NO and CO: the bimolecular reactions that cannot be ignored.

    abstract::The intriguing decompositions of nitro-containing explosives have been attracting interest. While theoretical investigations have long been concentrated mainly on unimolecular decompositions, bimolecular reactions have received little theoretical attention. In this paper, we investigate theoretically the bimolecular r...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Zhang JD,Kang LH,Cheng XL

    更新日期:2015-01-01 00:00:00

  • A theoretical study of the inhibition effect of PAMAM molecule on silica scale.

    abstract::In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-termi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Chen C,Bai N,Zhang Y,Jiao L,Xia M,Chen G

    更新日期:2017-01-01 00:00:00

  • Characteristics of protein residue-residue contacts and their application in contact prediction.

    abstract::Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Wozniak PP,Kotulska M

    更新日期:2014-11-01 00:00:00

  • Structures and stabilities of ScBn (n = 1-12) clusters: an ab initio investigation.

    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

    pub_type: 杂志文章


    authors: Jia J,Ma L,Wang JF,Wu HS

    更新日期:2013-08-01 00:00:00

  • A computational approach to the synthesis of dirithromycin.

    abstract::Dirithromycin is a macrolide antibiotic derived from erythromycin A. Dirithromycin is synthesized by the condensation of 9(S)-erythromycylamine with 2-(2-methoxyethoxy)-acetaldehyde. To gain insight into the synthesis, the condensation mechanism has been analyzed computationally by the AM1 method in the gas phase. Fir...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Duran D,Aviyente V,Baysal C

    更新日期:2004-04-01 00:00:00

  • Computer-aided rational design of novel EBF analogues with an aromatic ring.

    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

    pub_type: 杂志文章


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

    更新日期:2016-06-01 00:00:00

  • Molecular interactions between mitochondrial membrane proteins and the C-terminal domain of PB1-F2: an in silico approach.

    abstract::PB1-F2 is a recently described influenza A viral protein that induces apoptosis by binding with two mitochondrial membrane proteins, i.e. VDAC1 (outer membrane) and ANT3 (inner membrane). Knowledge of this binding mechanism could provide insights that would aid in the design of novel inhibitors against this protein. T...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Danishuddin M,Khan SN,Khan AU

    更新日期:2010-03-01 00:00:00

  • Water dimer isomers: interaction energies and electronic structure.

    abstract::The energetic and electronic structure of various water dimer isomers has been explored through DFT methodology. Six different possible water dimers come in two broad categories, planar and non-planar. In each of the categories, three distinct topologies (i) linear, (ii) ring and (iii) bifurcated, have been obtained. ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Ghosh SR,Debnath B,Jana AD

    更新日期:2020-01-06 00:00:00

  • Theoretical studies on identity S(N)2 reactions of lithium halide and methyl halide: a microhydration model.

    abstract::Reactions of lithium halide (LiX, X = F, Cl, Br and I) and methyl halide (CH₃X, X = F, Cl, Br and I) have been investigated at the B3LYP/6-31G(d) level of theory using the microhydration model. Beginning with hydrated lithium ion, four or two water molecules have been conveniently introduced to these aqueous-phase hal...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Zheng S,Xiong Y,Wang J

    更新日期:2010-12-01 00:00:00

  • Chemical reactivity analysis of deoxyribonucleosides and deoxyribonucleoside analogues (NRTIs): a first-principles density functional approach.

    abstract::The structures, energetics, as well as several important chemical parameters, of antiretroviral drugs - nucleoside reverse transcriptase inhibitors (NRTIs) - and natural deoxyribonucleosides in both neutral, and positively and negatively charged states, are investigated. These studies are carried out within the frame ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Kumar V,Kishor S,Ramaniah LM

    更新日期:2012-08-01 00:00:00

  • Comparison of the electronic properties, and thermodynamic and kinetic parameters of the aquation of selected platinum(II) derivatives with their anticancer IC50 indexes.

    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

    pub_type: 杂志文章


    authors: Bradác O,Zimmermann T,Burda JV

    更新日期:2008-08-01 00:00:00

  • Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study.

    abstract::Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Kaur H,Sasidhar YU

    更新日期:2015-04-01 00:00:00

  • Role of hydrogen bonding interactions within of the conformational preferences of calix[n = 4,6,8]arene: DFT and QTAIM analysis.

    abstract::Understanding the interactions of the cage molecules with a variety of invited molecules is getting very important. But, the hydrogen bonds can also play a crucial role in the interaction phenomenon. In this work, natural population analysis (NPA), chemical shifts, and atom in molecules (AIM) analysis have been used t...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Gassoumi B,Chaabene M,Ghalla H,Chaabane RB

    更新日期:2019-12-13 00:00:00

  • QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism.

    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

    pub_type: 杂志文章


    authors: Mu X,Xu D

    更新日期:2020-03-07 00:00:00

  • Does molecular docking reveal alternative chemopreventive mechanism of activation of oxidoreductase by sulforaphane isothiocyanates?

    abstract::Isothiocyanates (ITC) are well-known chemopreventive agents extracted from vegetables. This activity results from the activation of human oxidoreductase. In this letter, the uncompetitive activatory mechanism of ITC was investigated using docking and molecular dynamics simulations. This indicates that NAD(P)H:quinone ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Mazur P,Magdziarz T,Bak A,Chilmonczyk Z,Kasprzycka-Guttman T,Misiewicz-Krzemińska I,Skupińska K,Polanski J

    更新日期:2010-07-01 00:00:00

  • Adsorption into the MFI zeolite of aromatic molecule of biological relevance. Investigations by Monte Carlo simulations.

    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

    pub_type: 杂志文章


    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

  • A study on antimalarial artemisinin derivatives using MEP maps and multivariate QSAR.

    abstract::Artemisinin and some derivatives with activity against D-6 strains of Plasmodium falciparum were studied. Molecular electrostatic potential (MEP) maps were used in an attempt to identify key features of the compounds that are necessary for their activities, and then use those to propose new artemisinin derivatives. Th...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Cardoso FJ,de Figueiredo AF,da Silva Lobato M,de Miranda RM,de Almeida RC,Pinheiro JC

    更新日期:2008-01-01 00:00:00

  • Computational studies on nitro derivatives of BN indole as high energetic material.

    abstract::Nitrogen-rich heterocycles and their nitro derivatives are one of the important classes of energetic materials. In the present study, the computational methods have been applied to determine the thermodynamic and detonation properties of nitro derivatives of BN indole molecule. Structure optimization and electronic en...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Gupta S,Singh HJ

    更新日期:2020-03-24 00:00:00

  • Addition theorems for Slater-type orbitals in momentum space and their application to three-center overlap integrals.

    abstract::Using addition theorems for complete orthonormal sets of exponential type orbitals in the momentum representation introduced by the author, the addition theorems are established for Slater type orbitals in momentum space. With the help of these addition theorems, the general series expansion formulae in terms of the p...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Guseinov II

    更新日期:2005-03-01 00:00:00

  • Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes.

    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

    pub_type: 杂志文章


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

    更新日期:2014-03-01 00:00:00

  • DFT study of sulfur derivatives of cumulenes and their protonated forms of interstellar interest and calculations of dissociation energies of protonated forms (SC(CH)C(n-2)S)(+) (n = 3-8).

    abstract::A theoretical study of the sulfur cumulenes SCnS (n = 3-8), CnS ( n = 1-8) and of their protonated forms (SCnS)H(+) and (CnS)H(+) that might exist in the interstellar environment, has been carried out by means of the standard B3LYP/6-311G** method. The geometries and relative energies of singlet and triplet states acc...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章


    authors: Benmensour MA,Djennane-Bousmaha S,Boucekkine A

    更新日期:2014-07-01 00:00:00