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 other surfaces were rarely studied. In this work, we employed the density functional theory calculations to fully investigate the adsorption of all intermediates and products of CO2 hydrogenation on three low-index surfaces as Cu(111), Cu(100), and Cu(110), which have been reported as the main facets of Cu nanoparticles under reaction conditions. Besides, the reaction pathways were also discussed. Our results indicated CO2 hydrogenation is preferred to adopt formate pathways on the Cu surfaces, while the COOH pathway is least favorable. Moreover, Cu(100) and Cu(110) surfaces have the comparable (even better) catalytic activities compared with Cu(111) surface. This study provides the fundamental data for the adsorption and reaction of CO2 hydrogenation, which will be helpful for the design of Cu-based nanocatalysts.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Wang R,Zhu B,Zhang G,Gao Ydoi
10.1007/s00894-020-04448-8subject
Has Abstractpub_date
2020-07-09 00:00:00pages
202issue
8eissn
1610-2940issn
0948-5023pii
10.1007/s00894-020-04448-8journal_volume
26pub_type
杂志文章abstract::Although there are a multitude of aromaticity indexes, only a few have a widespread usage. All famous aromaticity indexes are limited: HOMA and FLU are reference-dependent; ELF is π-bond-dependent; PDI is structurally dependent and NICS is ring size dependent. These limitations stimulate the continuous search for bett...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3433-6
更新日期:2017-09-01 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
pub_type: 杂志文章
doi:10.1007/s00894-017-3557-8
更新日期:2017-12-20 00:00:00
abstract::The interaction between tetramethylcucurbit[6]uril (host) and 5,5'-dimethyl-2,2'-bipyridyl hydrochloride (guest) was studied by 1H NMR, X-ray crystallography, electronic absorption spectroscopy, fluorescence emission spectra and quantum chemistry calculations. This experimental-computational study that indicated the h...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-007-0243-2
更新日期:2007-12-01 00:00:00
abstract::A computational study was carried out to characterize the hydrogen-bonded dimers of Zoledronate (ZOL), which is used widely in treating skeletal diseases. The stable conformations, hydrogen bonding interactions, IR spectra, thermodynamic properties, and electronic characteristics of nine possible ZOL dimers were studi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3826-1
更新日期:2018-10-09 00:00:00
abstract::The electron transport of the 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate (S-FNPPB-o) molecule assembled in two Au (111) electrodes, was studied using two approaches: in the first approximate approach an electric field was applied to the pure molecule attached to two thiolate ends fi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1106-4
更新日期:2012-02-01 00:00:00
abstract::The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surf...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0454-9
更新日期:2009-09-01 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
pub_type: 杂志文章
doi:10.1007/s00894-010-0732-6
更新日期:2011-04-01 00:00:00
abstract::We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2472-5
更新日期:2014-11-01 00:00:00
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
doi:10.1007/s00894-015-2656-7
更新日期:2015-05-01 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
pub_type: 杂志文章
doi:10.1007/s00894-014-2165-0
更新日期:2014-03-01 00:00:00
abstract::The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi n (n = 12-20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effe...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3058-1
更新日期:2016-08-01 00:00:00
abstract::In this work, a computational framework is proposed by utilizing molecular dynamics simulation to explore the existing relation between molecular structure and ionic conductivity of the electrolyte system [LiPF6+(EC+DMC 1:1)] consisting of a mixture of cyclic ethylene carbonate (EC) and acyclic dimethyl carbonate (DMC...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04464-8
更新日期:2020-08-01 00:00:00
abstract::Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammatory and autoimmune diseases. The structure based antagonists design for many GPCRs, including CCR2, is restricted by the lack of an experimental three dimensional structure. Homology modeling is widely used for...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0943-x
更新日期:2011-10-01 00:00:00
abstract::The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2272-y
更新日期:2014-06-01 00:00:00
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
doi:10.1007/s00894-019-4274-2
更新日期:2020-01-06 00:00:00
abstract::Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowe...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3139-1
更新日期:2016-11-01 00:00:00
abstract::In this work molecular modeling was applied to generate homology models of the pore region of the Na(v)1.2 and Na(v)1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-005-0066-y
更新日期:2006-09-01 00:00:00
abstract::Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-004-0216-7
更新日期:2004-12-01 00:00:00
abstract::The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0443-4
更新日期:2009-08-01 00:00:00
abstract::In this work, the structural, electronic, and optical features of quinoline derivatives were carried out by experiment and density functional theory (DFT). Our results show that a change in the substitution position of methyl group (CH3) gives rise to a decrease in the bandgap of quinoline derivatives from 2.75 to 2.5...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04405-5
更新日期:2020-05-11 00:00:00
abstract::The pathway and ab initio direct kinetics of the decomposition 5-aminotetrazole (5-ATZ) to HN(3) and NH(2)CN was investigated. Reactant, products and transition state were optimized with MP2 and B3LYP methods using 6-311G** and aug-cc-pVDZ basis sets. The intrinsic reaction coordinate curve of the reaction was calcula...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0290-3
更新日期:2008-05-01 00:00:00
abstract::Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3665-0
更新日期:2018-05-07 00:00:00
abstract::Checkpoint kinase 1 (Chk1), a member of the serine/threonine kinase family, is an attractive therapeutic target for anticancer combination therapy. A structure-based modeling approach complemented with shape components was pursued to develop a reliable pharmacophore model for ATP-competitive Chk1 inhibitors. Common ch...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0630-y
更新日期:2010-07-01 00:00:00
abstract::Cation-π interactions are known to be one of the strongest noncovalent forces in the gas phase, but they rarely occur in a fully solvated environment. The present work used two different ab initio molecular dynamics-based approaches to describe the correlation between the strength of the cation-π interactions and the ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1433-0
更新日期:2012-09-01 00:00:00
abstract::Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titani...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3086-x
更新日期:2016-09-01 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
pub_type: 杂志文章
doi:10.1007/s00894-013-1930-9
更新日期:2013-11-01 00:00:00
abstract::In this work, the poly(ethylene oxide) bulk as one example has been iteratively heated and cooled back using MD simulations to examine the effects of thermal history on the resulting Tg. It is demonstrated that, after the system is equilibrated once at the high temperatures, the simulated Tg does not exhibit a systema...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3439-0
更新日期:2017-08-22 00:00:00
abstract::The nitrogen doping and phenyl substitution effects on the geometries, molecular stacking character, electronic, and charge transport properties of tetrabenzoheptacene (TTBH) have been investigated by means of density functional theory (DFT) calculation and incoherent charge hopping model. Our results indicate that th...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2677-2
更新日期:2015-05-01 00:00:00
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
doi:10.1007/s00894-016-2929-9
更新日期:2016-03-01 00:00:00
abstract::Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2825-8
更新日期:2015-11-01 00:00:00