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 the rate-determining step, and the β-carbon elimination was the chirality-limiting step. The dominant product was a (S,S)- cis ketone. The phosphine ligand P(n-Bu)3 changed the rate-determining step, and greatly decreased the free energies of the rate-determining step and chirality-limiting step. The use of P(n-Bu)3 generally decreased the free energies of the intermediates and transition states. The possible role of P(n-Bu)3 was the transformation of the electron and geometry structures of those intermediates and transition states. Graphical Abstract DFT 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 phosphine ligand P(n-Bu)3 changed the rate-determining step, and greatly decreased the free energies of the rate-determining step and chirality-limiting step.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Wang F,Zhu S,Meng Q,Yin Hdoi
10.1007/s00894-015-2754-6subject
Has Abstractpub_date
2015-08-01 00:00:00pages
203issue
8eissn
1610-2940issn
0948-5023journal_volume
21pub_type
杂志文章abstract：:A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and m...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1579-9
更新日期：2013-05-01 00:00:00
abstract：:The mechanisms of LMnO3 (L = O-, Cl, NPH3, CH3, and Cp)-catalyzed oxidation of ethyne has been studied on the singlet and triplet hypersurfaces at the M06/6-311G(d) level of theory. For the first step, the [3 + 2] pathways to the formation of the metalla-2,5-dioxol-3-ene intermediate are kinetically and thermodynamica...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04569-0
更新日期：2020-10-17 00:00:00
abstract：:Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The inte...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1252-8
更新日期：2012-06-01 00:00:00
abstract：:Periplasmic binding proteins are the initial receptors for the transport of various substrates over the inner membrane of gram-negative bacteria. The binding proteins are composed of two domains, and the substrate is entrapped between these domains. For several of the binding proteins it has been established that a cl...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1991-9
更新日期：2013-11-01 00:00:00
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
doi：10.1007/s00894-002-0088-7
更新日期：2002-08-01 00:00:00
abstract：:The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range additio...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0851-0
更新日期：2011-06-01 00:00:00
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
doi：10.1007/s00894-014-2568-y
更新日期：2015-01-01 00:00:00
abstract：:The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In this work, two typical s...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2377-3
更新日期：2014-08-01 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 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：:We use density functional theory-based calculations to study structural, electronic, and magnetic properties of two key reaction intermediates on a hematite, [Formula: see text]-Fe2O3, photoanode during the solar-driven water splitting reaction. Both intermediates contain an oxygen atom bonded to a surface iron atom. ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3815-4
更新日期：2018-09-18 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
pub_type： 杂志文章
doi：10.1007/s00894-020-04479-1
更新日期：2020-07-20 00:00:00
abstract：:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0239-y
更新日期：2007-12-01 00:00:00
abstract：:Ten functionals were used to assess their capability to compute a local reactivity descriptor coming from the Conceptual Density Functional Theory on a group of iron-based organometallic compounds that have been synthesized by Zohuri, G.H. et al. in 2010; these compounds bear the following substituent groups: H-, O2N-...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3576-5
更新日期：2018-01-18 00:00:00
abstract：:The substituted effect on excited-state intramolecular proton transfer (ESIPT) of o-LHBDI derivatives (4R-o-LHBDI) was investigated by DFT and TD-DFT methods. The structures of 4R-o-LHBDI (R: OH, NH2, CN, NO2, CF3) were fully optimized, and the H-bond distances, bond angles, and infrared spectra of the atoms involved ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04378-5
更新日期：2020-04-23 00:00:00
abstract：:The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-003-0160-y
更新日期：2004-02-01 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
pub_type： 杂志文章
doi：10.1007/s00894-011-1029-0
更新日期：2012-01-01 00:00:00
abstract：:The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6 · · · NH3, B2H2X4 · · · nNH3 (n = 1, 2) and 2HF · · · B2H2X4 · · · 2NH3 (X = Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb · ·...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2776-0
更新日期：2015-09-01 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
pub_type： 杂志文章
doi：10.1007/s00894-015-2778-y
更新日期：2015-09-01 00:00:00
abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3535-1
更新日期：2017-12-05 00:00:00
abstract：:In this work, the low-lying states of several isomers of ScSi n-/0 (n = 4-6) were investigated with the B3LYP functional and CASPT2 method. The ground states of the anionic clusters were predicted to be the singlet states of the trigonal bipyramid ScSi4- (A-ScSi4-), the face-capped trigonal bipyramid ScSi5- (A-ScSi5-)...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3461-2
更新日期：2017-09-20 00:00:00
abstract：:In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3279-y
更新日期：2017-04-01 00:00:00
abstract：:CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3029-6
更新日期：2016-07-01 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
pub_type： 杂志文章
doi：10.1007/s00894-012-1694-7
更新日期：2013-07-01 00:00:00
abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0248-x
更新日期：2008-01-01 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：:Recently inulinase has regained interest due to its usage in the production of fructooligosaccharides, biofuels, and in pharmaceutical industries. Inulinases properties are experimentally reported by nomerous studies but their characteristics are just partially explained by only a few computational investigations. In ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2935-y
更新日期：2016-04-01 00:00:00
abstract：:Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2724-z
更新日期：2015-08-01 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
pub_type： 杂志文章
doi：10.1007/s00894-014-2163-2
更新日期：2014-04-01 00:00:00
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
doi：10.1007/s00894-015-2621-5
更新日期：2015-04-01 00:00:00
