当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > On the properties of Se⋯N interaction: the analysis of substituent effects by energy decomposition and orbital interaction.

On the properties of Se⋯N interaction: the analysis of substituent effects by energy decomposition and orbital interaction.

Abstract：

:The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive electrostatic potential of Se atoms and the accepting electron ability of X-Se σ(∗) antibonding orbital. Energy decomposition of the Se ⋯N interaction reveals that electrostatic and induction forces are comparable in the weak-bonded complexes and induction becomes more significant in the complexes with strong electron-withdrawing substituents. Natural bond orbital (NBO) analysis indicates that the primary source of the induction is the electron transfer from the N lone pair to the X-Se σ(∗) antibonding orbital. The geometry of the complex and the interaction directionality of NH3 to X-Se bond can be regarded as a consequence of the exchange-repulsion. The topological analysis on the electron density reveals the nature of closed-shell interaction in these X-Se⋯N contacts. The Se⋯N interaction in the complexes with the strong electron-withdrawing substituent has a partly covalent character.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Zhou F,Liu R,Tang J,Li P,Cui Y,Zhang H

doi

10.1007/s00894-015-2901-0

subject

Has Abstract

pub_date

2016-01-01 00:00:00

pages

29

issue

1

eissn

1610-2940

issn

0948-5023

pii

10.1007/s00894-015-2901-0

journal_volume

22

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • XRD and DFT-modelized structures of a pteridine-2,4(1H,3H)-dithione/N,N'-dimethylformamide H-bonded cluster (2:2). MO study of the coordination ability.

    abstract：:The title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molec...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1109-1

    authors： Illán-Cabeza NA,Peña-Ruiz T,Moreno-Carretero MN

    更新日期：2012-02-01 00:00:00

  • Stereodynamic study of the reaction H(²S) + ClO(²Π) → HO(²Π) + Cl(²P) via quasi-classical trajectory calculations.

    abstract：:Quasi-classical trajectory calculations were performed to investigate the stereodynamics of the reaction H(²S) + ClO(²Π) → HO(²Π) + Cl(²P) using the ground-state potential energy surface 1¹A'. The alignment and orientation of the product molecules as well as the four polarization-dependent differential cross-sections ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2151-6

    authors： Huang Y

    更新日期：2014-03-01 00:00:00

  • DFT study of structural and electronic properties of 1,4-diarylcyclopenta[d] pyridazines and oxazines for non-linear optical applications.

    abstract：:Polymer and molecular-based electronic materials incorporating heterocycles like thiophenes and pyrroles are attractive possibilities as substitutes for semimetal materials. Heterocyclic materials are heavily studied in this regard due to the large variations in possible substrates. Herein we evaluated four different ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-021-04676-6

    authors： Wild S,Tice N

    更新日期：2021-01-31 00:00:00

  • In silico characterization of residues essential for substrate binding of human cystine transporter, xCT.

    abstract：:xCT is a sodium-independent amino acid antiporter that imports L-cystine and exports L-glutamate in a 1:1 ratio. It is a component of heterodimeric amino acid transporter system Xc- working at the cross-roads of maintaining neurological processes and regulating antioxidant defense. The transporter has 12 transmembrane...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4233-y

    authors： Sharma M,Anirudh CR

    更新日期：2019-11-09 00:00:00

  • A molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface.

    abstract：:Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the sol...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0064-0

    authors： Yang H,Lu ZY,Li ZS,Sun CC

    更新日期：2006-03-01 00:00:00

  • Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations.

    abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0121-3

    authors： Meiselbach H,Horn AH,Harrer T,Sticht H

    更新日期：2007-02-01 00:00:00

  • Rational design of carbonitrile-carboxaldehyde cation receptor models: probing the nature of the heteroatom-metal interaction.

    abstract：:In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2428-9

    authors： Rosli AN,Abu Bakar MA,Lee VS,Zain SM,Ahmad MR,Abdul Manan NS,Alias Y,Woi PM

    更新日期：2014-09-01 00:00:00

  • The role of Cys179-Cys214 disulfide bond in the stability and folding of prion protein: insights from molecular dynamics simulations.

    abstract：:Prion diseases are associated with misfolding and aggregation of prion protein (PrP). Cellular prion protein contains a disulfide bond linking Cys residues at positions 179 and 214. It has been proposed that this disulfide bond plays an important role in the conversion between cellular (PrP(C)) and the scrapie form of...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2106-y

    authors： Ning L,Guo J,Jin N,Liu H,Yao X

    更新日期：2014-02-01 00:00:00

  • An investigation of folic acid-protein association sites and the effect of this association on folic acid self-assembly.

    abstract：:The contribution of folic acid (FA)-tryptophan interactions to FA-protein association was investigated in the context of using FA as a drug carrier in protein delivery systems. Bovine serum albumin (BSA) and indolicidin were used as model proteins in the study. The FA-BSA complex was characterized by using the Bradfor...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2847-2

    authors： Gupta R,Kalita P,Patil O,Mohanty S

    更新日期：2015-12-01 00:00:00

  • Simulations on the possibility of formation of complexes between fluorouracil drug and cucurbit[n]urils: ab initio van der Waals DFT study.

    abstract：:The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n = 5-8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1936-3

    authors： Sabet M,Ganji MD

    更新日期：2013-09-01 00:00:00

  • Influence of doped nitrogen and vacancy defects on the thermal conductivity of graphene nanoribbons.

    abstract：:A systematic investigation of the thermal conductivity of zigzag graphene nanoribbons (ZGNRs) doped with nitrogen and containing a vacancy defect was performed using reverse nonequilibrium molecular dynamics (RNEMD). The investigation showed that the thermal conductivity of the ZGNRs was significantly reduced by nitro...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1937-2

    authors： Yang H,Tang Y,Gong J,Liu Y,Wang X,Zhao Y,Yang P,Wang S

    更新日期：2013-11-01 00:00:00

  • Theoretical studies on the thermodynamic properties, densities, detonation properties, and pyrolysis mechanisms of trinitromethyl-substituted aminotetrazole compounds.

    abstract：:Trinitromethyl-substituted aminotetrazoles with -NH₂, -NO₂, -N₃, and -NHC(NO₂)₃ groups were investigated at the B3LYP/6-31G(d) level of density functional theory. Their sublimation enthalpies, thermodynamic properties, and heats of formation were calculated. The thermodynamic properties of these compounds increase wit...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1783-2

    authors： Lin H,Chen PY,Zhu SG,Zhang L,Peng XH,Li K,Li HZ

    更新日期：2013-06-01 00:00:00

  • Study of a ligand complexed with Cdk2/Cdk4 by computer simulation.

    abstract：:Cyclin-dependent kinases (Cdks) play important roles in the regulation of the cell cycle. Their inhibitors have entered clinical trials to treat cancer. Very recently, Davis et al. (Nat Struct Biol 9:745-749, 2002) have found a ligand NU6102, which has a high affinity with cyclin-dependent kinase 2 (K(i) = 6 nM) but a...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0263-8

    authors： Jiang Y,Zou J,Gui C

    更新日期：2005-11-01 00:00:00

  • Molecular design and screening of energetic nitramine derivatives.

    abstract：:Six nitramines (N1-6) were designed with all possible arrangements of N-NO2 groups on a cyclic skeleton and structural optimization was performed using the density functional theory (DFT). We observed that all nitramines have high positive heats of formation proportionate to the number of N-NO2 groups in their molecul...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2846-3

    authors： Devi A,Deswal S,Dharavath S,Ghule VD

    更新日期：2015-11-01 00:00:00

  • In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1).

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3761-1

    authors： Kumar A,Dhar SK,Subbarao N

    更新日期：2018-08-14 00:00:00

  • Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding.

    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

    authors： Scheib H,McLay I,Guex N,Clare JJ,Blaney FE,Dale TJ,Tate SN,Robertson GM

    更新日期：2006-09-01 00:00:00

  • Characterization of peroxo reaction intermediates in the water oxidation process on hematite surfaces.

    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

    authors： Poaty LT,Ulman K,Seriani N,M'Passi-Mabiala B,Gebauer R

    更新日期：2018-09-18 00:00:00

  • Theoretical insights into thermal cyclophanediene to dihydropyrene electrocyclic reactions; a comparative study of Woodward Hoffmann allowed and forbidden reactions.

    abstract：:The thermally allowed electrocyclic reaction syn-cyclophanediene (CPD) to dihydropyrene (DHP) was compared with the disallowed thermal electrocyclic reaction in anti CPD through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d) level. Moreover, the results were also compared with the electrocycliza...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2948-6

    authors： Saima B,Khan A,Nisa RU,Mahmood T,Ayub K

    更新日期：2016-04-01 00:00:00

  • Structural models of CFTR-AMPK and CFTR-PKA interactions: R-domain flexibility is a key factor in CFTR regulation.

    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

    authors： Siwiak M,Edelman A,Zielenkiewicz P

    更新日期：2012-01-01 00:00:00

  • Theoretical insight into the sensitive mechanism of multilayer-shaped cocrystal explosives: compression and slide.

    abstract：:Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) w...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2973-5

    authors： Gao HF,Zhang SH,Ren FD,Gou RJ,Han G,Wu JB,Ding X,Zhao WH

    更新日期：2016-05-01 00:00:00

  • Computational study on C-H...π interactions of acetylene with benzene, 1,3,5-trifluorobenzene and coronene.

    abstract：:Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C-H(…)π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1729-0

    authors： Dinadayalane TC,Paytakov G,Leszczynski J

    更新日期：2013-07-01 00:00:00

  • Benchmarking and optimization of molecular simulation models of zinc dialkyldithiophosphate and calcium sulfonate oil additives.

    abstract：:We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force f...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-3980-0

    authors： Ectors P,Zahn D

    更新日期：2019-03-25 00:00:00

  • Chalcogen-bonded complexes. Selenium-bound adducts of NH3, H2O, PH3, and H2S with OCSe, SCSe, and CSe2.

    abstract：:Recent ab initio investigations of some complexes formed between carbon dioxide and its analogues carbonyl sulfide, carbonyl selenide, carbon disulfide, and thiocarbonyl selenide and the common bases ammonia, water, phosphine, and hydrogen sulfide have revealed significant differences between the properties of those c...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2562-4

    authors： Ramasami P,Ford TA

    更新日期：2015-02-01 00:00:00

  • Open carbon frameworks - a search for optimal geometry for hydrogen storage.

    abstract：:Properties of a new class of hypothetical high-surface-area porous carbons (open carbon frameworks) have been discussed. The limits of hydrogen adsorption in these carbon porous structures have been analyzed in terms of competition between increasing surface accessible for adsorption and the lowering energy of adsorpt...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1700-0

    authors： Kuchta B,Firlej L,Mohammadhosseini A,Beckner M,Romanos J,Pfeifer P

    更新日期：2013-10-01 00:00:00

  • Ab initio DFT study of bisphosphonate derivatives as a drug for inhibition of cancer: NMR and NQR parameters.

    abstract：:DFT computations were carried out to characterize the (17)Oand (2)H electric field gradient, EFG, in various bisphosphonate derivatives. The computations were performed at the B3LYP level with 6-311++G (d,P) standard basis set. Calculated EFG tensors were used to determine the (17)O and (2)H nuclear quadrupole couplin...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1114-4

    authors： Aghabozorg H,Sohrabi B,Mashkouri S,Aghabozorg HR

    更新日期：2012-03-01 00:00:00

  • Mixtures of amino-acid based ionic liquids and water.

    abstract：:New ionic liquids (ILs) involving increasing numbers of organic and inorganic ions are continuously being reported. We recently developed a new force field; in the present work, we applied that force field to investigate the structural properties of a few novel imidazolium-based ILs in aqueous mixtures via molecular d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2783-1

    authors： Chaban VV,Fileti EE

    更新日期：2015-09-01 00:00:00

  • Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.

    abstract：:In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2992-2

    authors： Czeleń P,Czyżnikowska Ż

    更新日期：2016-06-01 00:00:00

  • Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

    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

    authors： Golebiowski J,Antonczak S,Fernandez-Carmona J,Condom R,Cabrol-Bass D

    更新日期：2004-12-01 00:00:00

  • Effect of partial atomic charges on the calculated free energy of solvation of poly(vinyl alcohol) in selected solvents.

    abstract：:It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2554-4

    authors： Noorjahan A,Choi P

    更新日期：2015-03-01 00:00:00

  • The first intermediates in the bromination of bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane, combination of experiments and theoretical results.

    abstract：:Bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane (1) and adamantylideneadamantane (Ad=Ad) are two caged olefins with closely related structures at the double bond. Both compounds react instantaneously with Br2 in chlorinated hydrocarbon solvents to give mixtures of olefin-Br2 aggregates identified as the 1:1 pi-complex an...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0038-2

    authors： Chiappe C,Pomelli CS,Lenoir D,Wattenbach C

    更新日期：2006-07-01 00:00:00