Abstract：
:Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molecules on the structural and electronic properties of Prussian Blue were studied using state-of-the-art first principles calculations. Water-filled cavities were found to have a profound influence on the band gap and density of states of this material while simultaneously leaving many of its properties largely unchanged. The resulting model of an almost independent superimposition of dehydrated material and hydrated sites is briefly discussed.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Wojdeł JCdoi
10.1007/s00894-008-0425-6subject
Has Abstractpub_date
2009-06-01 00:00:00pages
567-72issue
6eissn
1610-2940issn
0948-5023journal_volume
15pub_type
杂志文章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：:Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cati...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1404-5
更新日期：2012-09-01 00:00:00
abstract：:Monoamine oxidase (MAO) is an enzyme of major importance in neurochemistry, because it catalyzes the inactivation pathway for the catecholamine neurotransmitters, noradrenaline, adrenaline and dopamine. In the last decade it was demonstrated that imidazoline derivatives were able to inhibit MAO activity. Furthermore, ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1390-7
更新日期：2012-08-01 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：:Since the three-dimensional structure of the NMDA receptor has not been determined experimentally, indirect computer-assisted molecular modeling techniques appear to be of great usefulness in the characterization of the common pharmacophore of all NMDA receptor noncompetitive antagonists, despite their structural diff...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-001-0067-4
更新日期：2002-02-01 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：:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3101-2
更新日期：2016-10-01 00:00:00
abstract：:The shuttling motion of a macrocycle in rotaxane-based molecular switching devices has been studied by computational density functional methods. In the test case, energy profiles corresponding to the dethreading process of different types of guest molecules in a cyclobis(paraquat-p-phenylene) host verified the experim...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0331-y
更新日期：2008-10-01 00:00:00
abstract：:With the help of quantum mechanical calculations, we have examined the series of central system X(ML)(3) (+)(X = O, S, Se; M = Au, Ag, Cu). Using a scalar-relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimen...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0156-5
更新日期：2007-01-01 00:00:00
abstract：:The geometrical structure and electronic properties of bis(10-hydroxybenzo[h]quinolinato)beryllium (Bebq2) molecule and its dimer both in the neutral and in the positively and negatively charged states were studied using quantum-chemical calculations. It is found that the excess charge in the charged systems is locali...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2397-z
更新日期：2014-08-01 00:00:00
abstract：:Abnormal expression of cyclin-dependent kinase 2 (CDK2)/cyclin-E is detected in colorectal, ovarian, breast and prostate cancers. The study of CDK2 with a bound inhibitor revealed CDK2 as a potential therapeutic target for several proliferative diseases. Several highly selective inhibitors of CDK2 are currently underg...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1620-z
更新日期：2013-02-01 00:00:00
abstract：:Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreemen...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1055-y
更新日期：2012-01-01 00:00:00
abstract：:In this study, eight oxytocin (OT) antagonists were subjected to conformational analysis. By means of simulated annealing, 2,000 structures were generated to sample the conformational space. The preferred main-chain and side-chain dihedral angles, intramolecular H-bond interactions (types 1<--4 and 1<--3), and seconda...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0104-4
更新日期：2006-09-01 00:00:00
abstract：:The Schiff base compound, 2-[(4-Fluorophenylimino)methyl]-3,5-dimethoxyphenol, has been synthesized and characterized by IR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree-Fock (HF)...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0574-2
更新日期：2010-03-01 00:00:00
abstract：:The interpretation of mass spectra (ms) of molecules containing poly-isotopic elements (e.g. Ge, Se, W, Os, Sn, Te, Zn, Yb) can be difficult due to the occurrence of fragments resulting from isotopomeric composition. MS-clusters located in the range lower than or equal to M/2 are very difficult to interpret. In this a...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0486-1
更新日期：2009-06-01 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：:The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT fu...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1286-y
更新日期：2012-06-01 00:00:00
abstract：:We report a study of the structure of (+)-catechin, which belongs to the family of the flavan-3-ols-one of the five most widely distributed phenolic groups. The biological activities and pharmaceutical utility of these compounds are related to antioxidant activity due to their ability to scavenge free radicals. A brea...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2105-z
更新日期：2014-02-01 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：: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：:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1015-6
更新日期：2011-12-01 00:00:00
abstract：:The incidence of tuberculosis infections that are resistant to conventional drug therapy has risen steadily in the last decade. Several of the quinolone antibacterials have been examined as inhibitors of M. tuberculosis infection as well as other mycobacterial infections. However, not much has been done to examine spe...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0133-z
更新日期：2007-01-01 00:00:00
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
更新日期：2014-02-01 00:00:00
abstract：:Based on the unique advantages of terahertz (THz) spectrum on the detection of energetic cocrystals, the low-temperature dependent THz spectra of CL-20/TNT cocrystal were investigated by using molecular dynamics (MD) simulations from 5 to 296 K, as well as three different crystal faces, (001), (120), and (010). When t...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4270-6
更新日期：2020-01-11 00:00:00
abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4104-6
更新日期：2019-07-02 00:00:00
abstract：:We investigate the chemical reactivities, aromatic properties, and UV-Vis absorption spectra of four constitutional isomers of 1-butoxy-4-methoxybenzenepillar[5]arene with the DFT and TDDFT methods. These characteristics in the gas and solvent phases are discussed on the basis of electronic energy, the highest occupie...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3076-z
更新日期：2016-09-01 00:00:00
abstract：:The conformational analysis of polynorbornene (PNB) chains was investigated with the AM1, MM2, AMBER and OPLS methods taking into consideration the possibility of binding of norbornene monomers to each other at various positions, i.e. exo-exo, exo-endo, endo-endo. The chain that is formed by connecting exo-endo positi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-003-0139-8
更新日期：2003-08-01 00:00:00
abstract：:Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employe...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-2020-8
更新日期：2013-12-01 00:00:00
abstract：:A coarse-grained Brownian dynamics model was used to simulate two proteins of similar sizes inside model membrane pores of varying size and hydrophobicity. The two proteins, which have radii of gyration of approximately 9.5 Å in their native states, are a 36-residue hydrophilic villin head piece (HP-36) and a 40-resid...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3985-8
更新日期：2019-04-25 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
