Abstract：
:The interactions between the template molecule paclitaxel (PTX) and seven functional monomers containing methacrylic acid (MA), acrolein (AC), 4-vinylbenzoic acid (4VA), acrylonitrile (AN), 2-vinylpyridine (2VP), 2,6-bisacrylamide pyridine (BAP) and methyl methacrylate (MM) were systematically investigated adopting the density functional theory (DFT) method. Moreover, the different binding sites on PTX and solvents embracing chloroform, acetone, ethanol, methanol, and acetonitrile were considered. The calculated solvent energies (ΔEsolvent) and template-monomer binding energies (ΔEb) suggest that the chloroform is the most suitable solvent for the molecular imprinting reaction of PTX among the studied five solvents. Furthermore, from the obtained ΔEb, we can find that the monomer 4VA combining with PTX in the form of the specific intermolecular hydrogen bonds would present the most stable structure among the investigated monomers. These results can provide valuable theoretical guidance for the efficient extraction of PTX by the molecular imprinting technique in experiments. Graphical abstracts.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Wang L,Yang F,Zhao X,Li Ydoi
10.1007/s00894-019-4277-zsubject
Has Abstractpub_date
2020-01-11 00:00:00pages
26issue
2eissn
1610-2940issn
0948-5023pii
10.1007/s00894-019-4277-zjournal_volume
26pub_type
杂志文章abstract：:Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2969-1
更新日期：2016-05-01 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：:Artificial neural networks (ANNs) have been successfully trained to model and predict the acidity constants (pK(a)) of 128 various phenols with diverse chemical structures using a quantitative structure-activity relationship. An ANN with 6-14-1 architecture was generated using six molecular descriptors that appear in ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-005-0050-6
更新日期：2006-02-01 00:00:00
abstract：:The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the a...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2384-4
更新日期：2014-08-01 00:00:00
abstract：:The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3729-1
更新日期：2018-07-12 00:00:00
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
更新日期：2014-09-01 00:00:00
abstract：:The increase of multidrug-resistant strains of bacteria to known classes of antibiotics present a severe challenge for modern medicine. The most promising strategy to combat pathogenic bacteria is to discover new drug targets. In this regard, aminoacyl-tRNA synthetases are particularly well suited to develop novel dru...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0421-x
更新日期：2009-06-01 00:00:00
abstract：:This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2101-3
更新日期：2014-02-01 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：:This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G and B3LYP/6-31 + G study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1107-3
更新日期：2012-02-01 00:00:00
abstract：:In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2990-4
更新日期：2016-06-01 00:00:00
abstract：:Both [5]-circulene and [7]-circulene can be selected to design the molecular tweezers theoretically using the DFT method. Leaning on the cyclic polymerization mechanism, we obtain four new tweezer compounds. Theoretical results offer that tweezer compound (I) is additionally stable than other compounds because it has ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04558-3
更新日期：2020-09-29 00:00:00
abstract：:Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices)--one based solely on topological considerations without discriminating atom or bond types, and another based on topological and elec...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2164-1
更新日期：2014-04-01 00:00:00
abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3955-1
更新日期：2019-02-27 00:00:00
abstract：:Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching, SADMET screening, and docking and toxicity studies) was performed to ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1037-0
更新日期：2012-01-01 00:00:00
abstract：:Quercetin is the most abundant flavonoid with potent antioxidant activities. In the current research, the antioxidant properties of quercetin and quercetin-DNA complex were investigated theoretically and experimentally. Free radical scavenging experiments with thiobarbituric acid-reactive substances (TBARS) and 1,1-di...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04356-x
更新日期：2020-05-12 00:00:00
abstract：:Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out stron...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2829-4
更新日期：2015-11-01 00:00:00
abstract：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3305-0
更新日期：2017-04-01 00:00:00
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
更新日期：2015-02-01 00:00:00
abstract：:In recent years, it has become clear that the neuronal nicotinic acetylcholine receptor (nAChR) is a valid target in the treatment of a variety of diseases, including Alzheimer's disease, anxiety, and nicotine addiction. As with most membrane proteins, information on the three-dimensional (3D) structure of nAChR is li...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0340-x
更新日期：2008-10-01 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：:The applicability of the newly developed PM6 method for modeling proteins is investigated. In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent field (SCF) equ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0420-y
更新日期：2009-07-01 00:00:00
abstract：:Cathepsin S has been demonstrated to play a crucial role in the remodeling of extracellular matrix proteins such as elastin and collagen, which in turn contribute to the structural integrity of the cardiovascular wall. Atherosclerotic lesions, aneurysm formation, plaque rupture, thrombosis, and calcification are some ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3255-6
更新日期：2017-03-01 00:00:00
abstract：:The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surf...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0454-9
更新日期：2009-09-01 00:00:00
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
更新日期：2019-08-19 00:00:00
abstract：:The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and l...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2588-2
更新日期：2015-03-01 00:00:00
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
更新日期：2017-01-01 00:00:00
abstract：:The effects of substituting nitrogen atoms on the stability of novel singlet (s) and triplet (t) forms of germylenes (1-20) are compared and contrasted, at B3LYP/AUG-cc-pVTZ level of theory. Every one of the 40 new divalents scrutinized appears as a minimum on its energy surface, for showing no negative force constant...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04570-7
更新日期：2020-10-31 00:00:00
abstract：:Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet-triplet energy gaps, and spin-orbit matrix elements were co...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3727-3
更新日期：2018-06-29 00:00:00
abstract：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0219-2
更新日期：2007-09-01 00:00:00
