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 number of water molecules surrounding the cation. Five different complexes between an aluminum cation and different molecules containing aromatic rings were studied, and the degree of hydration of each complex was varied. Results indicated that cation-π interactions vanish when the aluminum cation is surrounded by more than three water molecules. The results also highlighted the influence of -OH ligands on the interaction strength.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Larrucea Jdoi
10.1007/s00894-012-1433-0subject
Has Abstractpub_date
2012-09-01 00:00:00pages
4349-54issue
9eissn
1610-2940issn
0948-5023journal_volume
18pub_type
杂志文章abstract：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2196-6
更新日期：2014-04-01 00:00:00
abstract：:The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3440-7
更新日期：2017-08-21 00:00:00
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
更新日期：2013-10-01 00:00:00
abstract：:Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0821-6
更新日期：2011-05-01 00:00:00
abstract：:Quantum chemical calculations are performed to study the interplay between halogen⋯nitrogen and halogen⋯carbene interactions in NCX⋯NCX⋯CH2 complexes, where X = F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that t...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1983-9
更新日期：2013-11-01 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：:Very recently, an unprecedented novel monometallic cluster of fullerenes entrapping a yttrium cyanide (YCN) cluster inside a popular C82 cage YCN@Cs(6)-C82 was synthesized and characterized. Inspired by this investigation, four non-IPR YCN@C1(17459)-C76, YCN@C2v(19138)-C76, YCN@C2(17646)-C76, and YCN@C1(17894)-C76 (1,...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3040-y
更新日期：2016-08-01 00:00:00
abstract：:Periodic DFT method has been firstly used to calculate the bulk structure, electronic structure, electrical transferring and thermodynamic properties of crystalline 5-azido-1H-tetrazole (HCN₇) and its four different salts. The anion CN₇(-) was included in all of the salts such as ammonium 5-azidotetrazolate ([NH₄](+)[...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1788-x
更新日期：2013-06-01 00:00:00
abstract：:Temperature dependences of the spontaneous polarization and the dielectric constant are calculated near the paraelectric-ferroelectric (cubic-tetragonal) transition in BaTiO3 using our mean field model. By expanding the free energy in terms of the spontaneous polarization (order parameter), expressions for the tempera...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1927-4
更新日期：2013-09-01 00:00:00
abstract：:Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4007-6
更新日期：2019-04-05 00:00:00
abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1550-9
更新日期：2013-11-01 00:00:00
abstract：:This work presents a theoretical study of gallium arsenide (GaAs) nanotubes obtained from the (100), (110) and (111) crystal planes of zincblende structure in order to evaluate the electronic properties. The DFT/B3LYP/6-31G method was used to predict structures and stabilities. It was found that nanotubes from the (11...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3371-3
更新日期：2017-07-01 00:00:00
abstract：:In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4258-2
更新日期：2019-11-28 00:00:00
abstract：:The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap regio...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1205-2
更新日期：2012-05-01 00:00:00
abstract：:Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3868-4
更新日期：2018-11-09 00:00:00
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
更新日期：2018-08-14 00:00:00
abstract：:The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reacti...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1908-7
更新日期：2013-09-01 00:00:00
abstract：:Bacillus anthracis has been employed as an agent of bioterrorism, with high mortality, despite anti-microbial treatment, which strongly indicates the need of new drugs to treat anthrax. Shikimate pathway is a seven step biosynthetic route which generates chorismic acid from phosphoenol pyruvate and erythrose-4-phospha...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0403-z
更新日期：2009-02-01 00:00:00
abstract：:The biological toxicity of uranyl ion (UO (2) (2+) ) lies in interacting with proteins and disrupting their native functions. The structural and functional consequences of UO (2) (2+) interacting with cytochrome b (5) (cyt b (5)), a small membrane heme protein, and its heme axial ligand His39Ser variant, cyt b (5) H39...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1097-1
更新日期：2012-03-01 00:00:00
abstract：:The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0787-4
更新日期：2010-11-01 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：:We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1782-3
更新日期：2013-06-01 00:00:00
abstract：:We present the synthesis and structure determination for two thiohydantoin compounds (5-benzylidene-2-sulfanylideneimidazolidin-4-one and 5-cinnamylidene-2-sulfanylideneimidazolidin-4-one), proposed as potential novel fungicides. The exact chemical structure of these molecules has not yet been determined since they ca...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4146-9
更新日期：2019-08-24 00:00:00
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
更新日期：2005-11-01 00:00:00
abstract：:The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Stap...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4001-z
更新日期：2019-04-13 00:00:00
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
更新日期：2018-07-07 00:00:00
abstract：:Understanding how temperature affects the electronic transitions of BFO is important for design of BiFeO3 (BFO)-based temperature-sensitive device. Hitherto, however, there have been only very limited reports of the quantitative simulation. Here, we used density functional theory (DFT) and two-dimensional correlation ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2583-7
更新日期：2015-04-01 00:00:00
abstract：:Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm withi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3116-8
更新日期：2016-10-01 00:00:00
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
更新日期：2018-10-20 00:00:00
abstract：:An azo bridge (-N=N-) can not only desensitize explosives but also dramatically increase their heats of formation and explosive properties. Amino and nitro are two important high energy density functional groups. Here, we present calculations on 1-nitro-1-triazene (NH2-N=N-NO2). Thermal stability and detonation parame...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2362-x
更新日期：2014-08-01 00:00:00
