Reexamination of structures, stabilities, and electronic properties of holmium-doped silicon clusters HoSi n (n = 12-20).

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 effective core potentials (ECP28MWB) for the Ho atoms. The results show that when n = 12-15, the most stable structures are predicted to be exohedral frameworks with a quartet ground state, but when n = 16-20, they are predicted to be endohedral frameworks with a sextuplet ground state. These trend in stability across the clusters (gauged from their dissociation energies) was found to be approximately the same regardless of the DFT scheme used in the calculations, with HoSi13, HoSi16, HoSi18, and HoSi20 calculated to be more stable than the other clusters. The results obtained for cluster hardness indicated that doping the Ho atom into Si13 and Si16 leads to the most stable HoSi n clusters, while doping Ho into the other Si n clusters increases the photochemical sensitivity of the cluster. Analyses of intracluster charge transfer and magnetic moments revealed that charge always shifts from the Ho atom to the Si n cluster during the creation of exohedral HoSi n (n = 12-15) structures. However, the direction of charge transfer is reversed during the creation of endohedral HoSi n (n = 16-20) structures, which implies that Ho acts as an electron acceptor when it is encapsulated in the Si n cage. Furthermore, when the most stable exohedral HoSi n (n = 12-15) structures are generated, the 4f electrons of Ho are virtually unchanged and barely participate in intracluster bonding. However, in the most stable endohedral HoSi n (n = 16-20) frameworks, a 4f electron does participate in bonding. It does this by transferring to the 5d orbital, which hybridizes with the 6s and 6p orbitals and then interacts with Si valence sp orbitals. Meanwhile, the total magnetic moments of the HoSi n (n = 16-20) clusters are considerably higher than those of HoSi n (n = 12-15). Interestingly, the endohedral HoSi16 and HoSi20 clusters can be viewed as the most suitable building blocks for novel high-density magnetic storage nanomaterials and for novel optical and optoelectronic photosensitive nanomaterials, respectively.

journal_name

J Mol Model

authors

Hou L,Yang J,Liu Y

doi

10.1007/s00894-016-3058-1

subject

Has Abstract

pub_date

2016-08-01 00:00:00

pages

193

issue

8

eissn

1610-2940

issn

0948-5023

pii

10.1007/s00894-016-3058-1

journal_volume

22

pub_type

杂志文章
  • Molecular basis of the beta-lactamase protein using comparative modelling, drug screening and molecular dynamics studies to understand the resistance of β-lactam antibiotics.

    abstract::Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04459-5

    authors: Alazmi M

    更新日期:2020-07-07 00:00:00

  • A DFT study of the unimolecular decomposition of 1,2,4-butanetriol trinitrate.

    abstract::To improve understanding of the unimolecular decomposition mechanism of 1,2,4-butanetriol trinitrate (BTTN) in the gas phase, density functional theory calculations were performed to determine various decomposition pathways at the B3LYP/6-311G** level. Two main mechanisms for the unimolecular decomposition of BTTN wer...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2081-3

    authors: Zhu W,Yan Q,Pang A,Chi X,Du X,Xiao H

    更新日期:2014-02-01 00:00:00

  • Pharmacophore and molecular dynamics based activity profiling of natural products for kinases involved in lung cancer.

    abstract::To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC-a natural product database-was employed. The work presented here is based on ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-018-3849-7

    authors: Singh PK,Silakari O

    更新日期:2018-10-20 00:00:00

  • Structure-based discovery of small molecule APC-Asef interaction inhibitors: In silico approaches and molecular dynamics simulations.

    abstract::Colorectal cancer, which is considered one of the leading causes of mortality worldwide, develops through the formation of benign polyps on the inner colon or rectum wall. Truncations in adenomatous polyposis coli (APC) gene lead to the spread of the disease in the entire colon region when combined with the guanine nu...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04467-5

    authors: Jadav SS,Macalino SJY,Alluri R

    更新日期:2020-07-16 00:00:00

  • Theoretical studies of structure, energetics and properties of Ca²⁺ complexes with alizarin glucoside.

    abstract::The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Densi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1841-9

    authors: Toczek D,Kubas K,Turek M,Roszak S,Gancarz R

    更新日期:2013-10-01 00:00:00

  • Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study.

    abstract::D222G mutation of the hemagglutinin (HA) is of special interest because of its close association with the enhanced virulence of 2009 pandemic influenza A (H1N1) virus through the increased binding affinity to α2,3-linked sialylated glycan receptors. However, there is still a lack of detailed understanding about the mo...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1423-2

    authors: Pan D,Xue W,Wang X,Guo J,Liu H,Yao X

    更新日期:2012-09-01 00:00:00

  • A genetic algorithm survey on closed-shell atomic nitrogen clusters employing a quantum chemical approach.

    abstract::The DFT potential energy hypersurfaces of closed-shell nitrogen clusters up to ten atoms are explored via a genetic algorithm (GA). An atom-atom distance threshold parameter, controlled by the user, and an "operator manager" were added to the standard evolutionary procedure. Both B3LYP and PBE exchange-correlation fun...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-018-3724-6

    authors: Silva MX,Silva FT,Galvão BRL,Braga JP,Belchior JC

    更新日期:2018-07-07 00:00:00

  • Theoretical investigation of Co(0)-catalyzed intramolecular hydroacylation of 4-pentenal.

    abstract::Density functional theory (DFT) was used to investigate cobalt(0)-catalyzed intramolecular hydroacylation of 4-pentenal. The calculated results indicated the involvement of five possible reaction pathways: the formation of cyclopentanone, cyclobutanone, butylenes, cyclobutane, and cyclopropane, respectively. The forme...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1772-5

    authors: Meng Q,Wang F,Li M

    更新日期:2013-06-01 00:00:00

  • Studies on filarial GST as a target for antifilarial drug development-in silico and in vitro inhibition of filarial GST by substituted 1,4-naphthoquinones.

    abstract::Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-010-0952-9

    authors: Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

    更新日期:2011-10-01 00:00:00

  • Characterization of molecular structures and properties of polyurethanes using molecular dynamics simulations.

    abstract::Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the d...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-004-0187-8

    authors: Repáková J,Capková P,Studenovský M,Ilavský M

    更新日期:2004-08-01 00:00:00

  • Acylthiocarbamates as non-nucleoside HIV-1 reverse transcriptase inhibitors: docking studies and ligand-based CoMFA and CoMSIA analyses.

    abstract::Acylthiocarbamates (ATCs) have been identified as a class of potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. A computational strategy based on molecular docking studies followed by comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was used t...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0441-6

    authors: Cichero E,Cesarini S,Spallarossa A,Mosti L,Fossa P

    更新日期:2009-07-01 00:00:00

  • Cyano or o-nitrophenyl? Which is the optimal electron-withdrawing group for the acrylic acid acceptor of D-π-A sensitizers in DSSCs? A density functional evaluation.

    abstract::We report a DFT, TDDFT and DFTB investigation of the performance of two donor-π-acceptor (D-π-A)-type organic dyes bearing different electron-withdrawing groups (EWG) for dye-sensitized solar cells (DSSCs) to evaluate which EWG is better for an acrylic acid acceptor, i.e., Cyano (-CN) or o-nitrophenyl (o-NO2-Ph). A se...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1719-2

    authors: Zhang J,Kan YH,Li HB,Geng Y,Wu Y,Duan YA,Su ZM

    更新日期:2013-04-01 00:00:00

  • The effect of HNS on the reinforcement of TNT crystal: a molecular simulation study.

    abstract::The effect of crystal modifier 2,2',4,4',6,6'-hexanitrostillbene(HNS) on the reinforcement of crystalline 1,3,5-trinitrotoluene (TNT) was investigated by molecular simulation. The intermolecular interactions between HNS and TNT were revealed by quantum chemistry calculations in detail, strong attractive forces were fo...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2461-8

    authors: Qian W,Shu Y,Li H,Ma Q

    更新日期:2014-10-01 00:00:00

  • Homology modeling, molecular dynamics and QM/MM study of the regulatory protein PhoP from Corynebacterium pseudotuberculosis.

    abstract::Corynebacterium pseudotuberculosis is a facultatively intracellular Gram-positive bacterium that causes caseous lymphadenitis, principally in sheep and goats, though sometimes in other species of animals, leading to considerable economic losses. This pathogen has a TCS known as PhoPR, which consists of a sensory histi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1145-x

    authors: Moraes G,Azevedo V,Costa M,Miyoshi A,Silva A,da Silva V,de Oliveira D,Teixeira MF,Lameira J,Alves CN

    更新日期:2012-03-01 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

    doi:10.1007/s00894-017-3208-0

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

    更新日期:2017-01-01 00:00:00

  • DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials.

    abstract::Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as I...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1257-3

    authors: Georgieva I,Danchova N,Gutzov S,Trendafilova N

    更新日期:2012-06-01 00:00:00

  • Molecular dynamics analysis on axial buckling of functionalized carbon nanotubes in thermal environment.

    abstract::Molecular dynamics simulations are conducted to investigate the buckling characteristics of functionalized carbon nanotubes (f-CNTs) under axial compression at various temperatures. The influences of functionalization, content of functional groups, chirality and diameter, as well as temperature on buckling response of...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3505-7

    authors: Mehralian F,Tadi Beni Y

    更新日期:2017-11-04 00:00:00

  • Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations.

    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

    authors: Wang Y,Zhu GF,Ren SY,Han YG,Luo Y,Du LF

    更新日期:2013-11-01 00:00:00

  • The molecular properties of heterocyclic and homocyclic hydrogen-bonded complexes evaluated by DFT calculations and AIM densities.

    abstract::This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O...HF and C2H5...HF) and homocyclic (C3H6...HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6-311++G(d,p) level of theory. Subsequently, ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0380-2

    authors: Oliveira BG,Araújo RC,Carvalho AB,Ramos MN

    更新日期:2009-02-01 00:00:00

  • Studies of the interaction of tetramethylcucurbit[6]uril and 5,5'-dimethyl-2,2'-bipyridyl hydrochloride.

    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

    authors: Cong H,Zhao YJ,Xue SF,Tao Z,Zhu QJ

    更新日期:2007-12-01 00:00:00

  • Assessing the quantum mechanical level of theory for prediction of linear and nonlinear optical properties of push-pull organic molecules.

    abstract::In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (βt) were calculated f...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1644-4

    authors: Paschoal D,Santos HF

    更新日期:2013-05-01 00:00:00

  • Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues.

    abstract::The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4137-x

    authors: Alves NA,Dias LG,Frigori RB

    更新日期:2019-08-19 00:00:00

  • Bonding analysis of telluroketones H₂A = Te (A = C, Si, Ge).

    abstract::Quantum chemical calculations using density functional theory BP86/def2-TZVPP and ab initio methods at CCSD(T)/def2-TZVPP have been carried for the telluroketones H2A=Te (A = C, Si, Ge). DFT calculations have also been carried out for the ketones H2C=E (E = O, S, Se, Te) and for the complexes NHC → [H2A=Te] → B(C6F5)3...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2433-z

    authors: Jaufeerally NB,Ramasami P,Jerabek P,Frenking G

    更新日期:2014-10-01 00:00:00

  • Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation.

    abstract::The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1807-y

    authors: Tian X,Jiang L,Yuan Y,Wang M,Guo Y,Zeng X,Li M,Pu X

    更新日期:2013-06-01 00:00:00

  • 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 el...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-015-2901-0

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

    更新日期:2016-01-01 00:00:00

  • Effects of L-serine amino acid functionalization on electronic properties of a graphene plane in comparison with oxygen functionalization.

    abstract::The effects of L-serine amino acid functionalization on a graphene plane were investigated through density functional theory calculations compared with those of oxygen functionalization. Three systems of 4 × 4 graphene supercells were created and functionalized by an epoxy group, a hydroxyl group, and an L-serine mole...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04466-6

    authors: Prasert K,Sutthibutpong T

    更新日期:2020-07-13 00:00:00

  • AM1 parameters for palladium and silver.

    abstract::We report the parameterization of AM1 for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1 parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-010-0940-0

    authors: Kayi H,Clark T

    更新日期:2011-10-01 00:00:00

  • G2, G3, and complete basis set calculations of the thermodynamic properties of cis- and trans-triazene.

    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

    authors: Richard RM,Ball DW

    更新日期:2008-01-01 00:00:00

  • DFT analysis of the interaction between Hg2+ and monodentate neutral ligands using NBO, EDA, and QTAIM.

    abstract::We report thermodynamic, geometric, and electronic parameters for the interaction between neutral ligands and the [Hg(H2O)]2+ dication, using the B3LYP/6-311 + G(d,p) approach. Gibbs free energies for the interaction were employed to rank the affinity order of the several neutral ligands. To identify the parameters th...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04413-5

    authors: da Silva VHM,de Mesquita Carneiro JW,da Costa LM,Ferreira GB

    更新日期:2020-05-20 00:00:00

  • New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening.

    abstract::Using ligand and receptor based virtual screening approaches we have identified potential virtual screening hits targeting type II dehydroquinase from Mycobacterium tuberculosis, an effective and validated anti-mycobacterial target. Initially, we applied a virtual screening workflow based on a combination of 2D struct...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0595-x

    authors: Kumar A,Siddiqi MI,Miertus S

    更新日期:2010-04-01 00:00:00