Elucidating the origin of selectivity of [3 + 2]-cycloaddition reactions between thioketone and carbohydrate-derived nitrones by the DFT.

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 calculated results revealed that the 32CA reactions proceed through the asynchronous one-step manner. For the chemoselectivity in thioketone, the C=S bond as a dipolarophile attacking three-atom-component (TAC) nitrone in reactivity was more preferential than the C=O bond. The theoretical results also confirmed the stereoselectivity of two 32CA reactions of thioketone with carbohydrate-derived nitrones with the anti-form product being more favored than the syn-form product, and the predicted anti/syn product ratios are in agreement with the experimental ones in literature. Furthermore, the analysis of the conceptual density functional theory reactivity indices showed that the 32CA reactions have polar character. Weak noncovalent interaction and Parr function analyses are used to reveal the origin of the stereoselectivity. Graphical abstract [3 + 2]-cycloaddition reactions between thioketone and carbohydrate-derived nitrones.

journal_name

J Mol Model

authors

Yang J,Zhang Y,Yang Y,Xue Y

doi

10.1007/s00894-019-4104-6

subject

Has Abstract

pub_date

2019-07-02 00:00:00

pages

209

issue

7

eissn

1610-2940

issn

0948-5023

pii

10.1007/s00894-019-4104-6

journal_volume

25

pub_type

杂志文章
  • Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies.

    abstract::White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7-VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1672-0

    authors: Verma AK,Gupta S,Verma S,Mishra A,Nagpure NS,Singh SP,Pathak AK,Sarkar UK,Singh SP,Singh M,Seth PK

    更新日期:2013-03-01 00:00:00

  • A probable means to an end: exploring P131 pharmacophoric scaffold to identify potential inhibitors of Cryptosporidium parvum inosine monophosphate dehydrogenase.

    abstract::Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were ide...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04663-3

    authors: Omolabi KF,Iwuchukwu EA,Agoni C,Olotu FA,Soliman MES

    更新日期:2021-01-09 00:00:00

  • dockYard--a repository to assist modeling of protein-protein docking.

    abstract::In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-010-0758-9

    authors: Mitra P,Pal D

    更新日期:2011-03-01 00:00:00

  • A density functional theory study of the decomposition mechanism of nitroglycerin.

    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

    authors: Pei L,Dong K,Tang Y,Zhang B,Yu C,Li W

    更新日期:2017-08-21 00:00:00

  • A theoretical study of substituent effects on tautomerism of 2-hydroxybenzimidazoles.

    abstract::The geometries, relative stabilities of some 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives were calculated with full geometry optimization using AM1 and PM3 in aqueous phase. With the exception of molecules 4, 6 and 7 for all the 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives the 3H and ke...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-003-0150-0

    authors: Oğretir C,Yarligan S,Berber H,Arslan T,Topal S

    更新日期:2003-12-01 00:00:00

  • Can Fe3+ and Al3+ ions serve as cationic bridges to facilitate the adsorption of anionic As(V) species on humic acids? A density functional theory study.

    abstract::A computational chemistry investigation was undertaken to shed light on the facilitatory role played by Fe3+ and Al3+ cations in the adsorption of anionic As(V) species by humic acids through the formation of so-called cationic bridges. Geometric and energetic parameters were obtained using density functional theory a...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3219-x

    authors: Gorb L,Shukla MK

    更新日期:2017-03-01 00:00:00

  • A theoretical investigation of the energetics and spectroscopic properties of the gas-phase linear proton-bound cation-molecule complexes, XCH(+)-N2 (X = O, S).

    abstract::The structural features, spectroscopic properties, and interaction energies of the linear proton-bound complexes of OCH(+) and its sulfur analog SCH(+) with N2 were investigated using the high-level ab initio methods MP2 and CCSD(T) as well as density functional theory with the aug-cc-pVXZ (X = D, T) basis sets. The r...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-015-2866-z

    authors: Begum S,Subramanian R

    更新日期:2016-01-01 00:00:00

  • Theoretical insights into the stabilities, detonation performance, and electrostatic potentials of cocrystals containing α- or β-HMX and TATB, FOX-7, NTO, or DMF in various molar ratios.

    abstract::A molecular dynamics method was employed to study the binding energies associated with the cocrystallization (at selected crystal planes) of either 1,3,5-triamino-2,4,6-trinitro-benzene (TATB), 1,1-diamino-2,2-dinitroethylene, 3-nitro-1,2,4-triazol-5-one (TATB, FOX-7, and NTO, respectively, all of which are explosives...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-3111-0

    authors: Song KP,Ren FD,Zhang SH,Shi WJ

    更新日期:2016-10-01 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

  • Synthesis, spectroscopy, and theoretical calculations of some 2-thiohydantoin derivatives as possible new fungicides.

    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

    authors: Kobyłka K,Żuchowski G,Tejchman W,Zborowski KK

    更新日期:2019-08-24 00:00:00

  • Assessment of ten density functionals through the use of local hyper-softness to get insights about the catalytic activity : Iron-based organometallic compounds for ethylene polymerization as testing molecules.

    abstract::Ten functionals were used to assess their capability to compute a local reactivity descriptor coming from the Conceptual Density Functional Theory on a group of iron-based organometallic compounds that have been synthesized by Zohuri, G.H. et al. in 2010; these compounds bear the following substituent groups: H-, O2N-...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3576-5

    authors: Martínez-Araya JI,Glossman-Mitnik D

    更新日期:2018-01-18 00:00:00

  • A density functional theory study of simplest nanocomposites formed by graphene oxide and polyvinyl alcohol: geometry, interaction energy and vibrational spectrum.

    abstract::A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of elec...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04447-9

    authors: Gorb L,Ilchenko M,Leszczynski J

    更新日期:2020-06-25 00:00:00

  • Molecular modeling and QM/MM calculation clarify the catalytic mechanism of β-lactamase N1.

    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

    authors: Yu Y,Wang X,Gao Y,Yang Y,Sun L,Wang G,Deng X,Niu X

    更新日期:2019-04-13 00:00:00

  • Free energy calculation provides insight into the action mechanism of selective PARP-1 inhibitor.

    abstract::Selective poly (ADP-ribose) polymerase (PARP)-1 inhibitor represents promising therapy against cancers with a good balance between efficacy and safety. Owing to the conserved structure between PARP-1 and PARP-2, most of the clinical and experimental drugs show equivalent inhibition against both targets. Most recently,...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-2952-x

    authors: Cao R

    更新日期:2016-04-01 00:00:00

  • Erratum to: First hyperpolarizability of cyclooctatetraene modulated by alkali and alkaline earth metals.

    abstract::The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below. ...

    journal_title:Journal of molecular modeling

    pub_type: 已发布勘误

    doi:10.1007/s00894-017-3466-x

    authors: Roy RS,Mondal A,Nandi PK

    更新日期:2017-11-01 00:00:00

  • Charge localization and charge transfer in the Bebq2 monomer and dimer.

    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

    authors: Safonov AA,Bagaturyants AA

    更新日期:2014-08-01 00:00:00

  • Periodic density functional theory study of the high-pressure behavior of energetic crystalline 1,4-dinitrofurazano[3, 4-b]piperazine.

    abstract::A detailed study of the structural, electronic, and optical absorption properties of crystalline 1,4-dinitrofurazano[3,4-b]piperazine (DNFP) under hydrostatic pressures of 0-100 GPa was performed using periodic density functional theory. As the pressure increases, the lattice constants and cell volumes calculated by L...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1547-4

    authors: Wang W,Zhu W,Li J,Cheng B,Xiao H

    更新日期:2013-01-01 00:00:00

  • Acidity of the chlorinated phenols: DFT study and experiential affirmation.

    abstract::A quantum mechanical density functional theory (DFT) was successfully developed for the estimation of pKa values of chlorinated phenols in aqueous solution with a precision of 0.9 pKa units. The MP2/6-311++G(d,p)//B3LYP/6-31+G(d) level of theory was used for the gas phase calculation. For computation in the solution p...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4096-2

    authors: Kheirjou S,Imanzadeh G,Rezaei H,Safari N

    更新日期:2019-06-26 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

  • 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

  • Protein subunit interfaces: A statistical analysis of hot spots in Sm proteins.

    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

    authors: Stojanović SD,Zarić BL,Zarić SD

    更新日期:2010-11-01 00:00:00

  • Hydrogen bonding interactions in noradrenaline-DMSO complexes: DFT and QTAIM studies of structure, properties and topology.

    abstract::The hydrogen bonding interactions between noradrenaline (NA) and DMSO were studied with density functional theory (DFT) regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) an...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-0956-0

    authors: Huang Z,Dai Y,Yu L,Wang H

    更新日期:2011-10-01 00:00:00

  • Mechanisms on inhibition of polyethylene electrical tree aging: a theoretical study.

    abstract::A theoretical investigation is completed on inhibition mechanism of polyethylene electrical tree aging. Foremost it elucidates that it is one of the important factors for inhibiting initiation and propagation of polyethylene electrical tree through keto-enol tautomerism of acetophenone and its analogues. Geometries of...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1814-z

    authors: Zhang H,Shang Y,Zhao H,Han B,Li Z

    更新日期:2013-08-01 00:00:00

  • Rational design of the survivin/CDK4 complex by combining protein-protein docking and molecular dynamics simulations.

    abstract::Survivin, the smallest inhibitor of apoptosis protein (IAP), is a valid target for cancer research. It mediates both the apoptosis pathway and the cell cycle and has been proposed to form a complex with the cyclin-dependent kinase protein CDK4. The resulting complex transports CDK4 from the cytosol to the nucleus, whe...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1705-8

    authors: Selent J,Kaczor AA,Guixà-González R,Carrió P,Pastor M,Obiol-Pardo C

    更新日期:2013-04-01 00:00:00

  • Material identification for improving the strength of silica/SBR interface using MD simulations.

    abstract::Comprehensive molecular dynamics simulations are conducted to identify material modifications which can improve strength and reduce hysteresis losses at the nanointerfaces formed between silica, silane coupling agent (SCA) and styrene-butadiene rubber (SBR), all of which are important ingredients of green tyres. Impro...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04489-z

    authors: Joseph E,Swaminathan N,Kannan K

    更新日期:2020-08-17 00:00:00

  • A comparative interplay between small heterorings and hypofluorous acids.

    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

    authors: Oliveira BG

    更新日期:2015-11-01 00:00:00

  • CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics.

    abstract::The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or inte...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3546-y

    authors: Basu S

    更新日期:2017-12-07 00:00:00

  • Ab initio molecular dynamics of free radical-induced oxidation of ergothioneine.

    abstract::Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4220-3

    authors: Lespade L

    更新日期:2019-10-26 00:00:00

  • In-silico studies on DegP protein of Plasmodium falciparum in search of anti-malarials.

    abstract::Despite encouraging progress over the past decade, malaria caused by the Plasmodium parasite continues to pose an enormous disease burden and is one of the major global health problems. The extreme challenge in malaria management is the resistance of parasites to traditional monochemotherapies like chloroquine and sul...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-3064-3

    authors: Sharma D,Soni R,Patel S,Joshi D,Bhatt TK

    更新日期:2016-09-01 00:00:00

  • Druggability and drug-likeness concepts in drug design: are biomodelling and predictive tools having their say?

    abstract::The drug discovery process typically involves target identification and design of suitable drug molecules against these targets. Despite decades of experimental investigations in the drug discovery domain, about 96% overall failure rate has been recorded in drug development due to the "undruggability" of various ident...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章,评审

    doi:10.1007/s00894-020-04385-6

    authors: Agoni C,Olotu FA,Ramharack P,Soliman ME

    更新日期:2020-05-08 00:00:00