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Designing Artemisinins with Antimalarial potential, Combining molecular electrostatic potential, Ligand-Heme Interaction and Multivariate Models

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Computational Chemistry 2023年第1期11卷 1-23页

作者： Josué de Jesus Oliveira Araújo Ricardo Morais de Miranda Jeferson Stiver Oliveira de Castro Antonio Florêncio de Figueiredo Ana Cecília Barbosa Pinheiro Sílvia Simone dos Santos Morais Marcos Antonio Barros dos Santos Andréia de Lourdes Ribeiro Pinheiro Andréia de Lourdes Ribeiro Pinheiro Fábio dos Santos Gil Heriberto Rodrigues Bitencourt Gustavo Nery Ramos Alves José Ciríaco Pinheiro Laboratório de Química Teórica e Computacional Universidade Federal do Pará Belém PA Brasil Instituto Federal de Educaç ã o Ciência e Tecnologia do Pará Belém PA Brasil Universidade do Estado do Amapá Macapá AP Brasil Fundaç ã o Santa Casa de Misericórdia do Pará Belém PA Brasil Universidade do Estado do Pará Barcarena PA Brasil Departamento de Biologia Universidade do Estado do Maranh&atilde o S&atilde o Luís MA Brasil Laboratório de Síntese Organica Universidade Federal do Pará Belém PA Brasil

Artemisinins tested against W-2 strains of malaria falciparum are investigated with molecular electrostatic potential (MEP), in an attempt to identify key features of the compounds that are necessary for their activities, as well as to investigate likely interactions with the receptor in a biological process and to use that information to propose new molecules. In order to discover the best geometry involving the ligand-receptor complexes (heme) studied and help in the proposition of the new derivatives, molecular simulations of interactions between the most negative charged region around the peroxide and heme locates (the ones around the Fe2+ ion) were carried out. In addition, PCA (principal components analysis), HCA (hierarchical cluster analysis), SDA (stepwise discriminant analysis), and KNN (K-nearest neighbor) multivariate models were employed to investigate which descriptors are responsible for the classification between the higher and lower antimalarial activity of the compounds, and also this information was used to propose new potentially active molecules. The information accumulated in studies of MEP, molecular docking, and multivariate analysis supported the proposal of new structures with potential antimalarial activities. The multivariate models constructed were applied to the new structures and indicated numbers 19 and 20 as the most prominent for syntheses and biological assays.

关键词： Artemisinins Antimalarial potential molecular electrostatic potential Ligand-Heme Interaction Multivariate Models

Theoretical Investigation on the Stability and Reactivity of Imidazo [1,2-a] Pyridine N-Acylhydrazone Derivatives Using Density Functional Theory

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Computational Chemistry 2024年第1期12卷 1-23页

作者： Camara Tchambaga Etienne Sangare Kassoum Dosso Ouehi Ablo Evrard Sekou Diomande Souleymane Coulibaly Siomenan Coulibali Laboratoire de Constitution et de Raction de la Matire (LCRM) de lUFR SSMT Universit Flix Houphout-Boigny Abidjan Cte dIvoire Dpartement des Sciences et Technologies Agro-industrielles (STAgI) UFR Agriculture ressources halieutiques et agro-industrie (ARHAI) Universit de San Pedro San Pedro Cte dIvoire Laboratoire des Procds Industriels de Synthse de lEnvironnement et des nergies Nouvelles (LAPISEN) Institut National Polytechnique FlixHouphout-Boigny Yamoussoukro Cte dIvoire

The reactivity and stability of seventeen (17) imidazo [1,2-a]pyridine N-acylhydrazone derivatives were investigated using density functional theory at the B3LYP/6-31+ G (d, p) level. Analysis of the molecular electrostatic potential (MEP) and determination of the dual descriptor revealed that in most cases, the nitrogen atoms of the 6-πelectron conjugation, the oxygen, and the sulfur atom are nucleophilic site. Chemical reactivity of the compounds was assessed through analysis of frontier molecular orbitals (HOMO and LUMO), energy gap (Δℰ), chemical hardness (η), and the softness (S). Consequently, the compound 9e exhibited the lowest reactivity, least electron donating, and the highest stability. This comprehensive study offers valuable insights into the chemical behavior of these derivatives, crucial for further exploration and potential applications.

关键词： N-Acylhydrazones Imidazo [1 2-a] Pyridine DFT molecular electrostatic potential Reactivity Stability

Separation of Aromatic Carboxylic Acids in IC and the Study on the Relationship Between Retention Behavior and electrostatic potential

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Chinese Journal of Structural Chemistry 2010年第4期29卷 641-646页

作者：王艳花韩小江陈雪松李立朱岩 College of Biology and Environment Engineering Zhejiang Shuren University Department of Chemistry Zhejiang University

A method has been developed for separation of 20 kinds of aromatic carboxylic acid using anion-exchange chromatography. A Dionex IonPac AS9-HC guard column （250mm×2mm） was used with a 9mmol/L sodium carbonate solution containing 50% （v/v） acetonitrile as eluent. A set of retention time data has been obtained using a conductivity detector DS6. Furthermore, geometrical optimization and electrostatic potential calculation of 20 kinds of aromatic carboxylic acid have been performed at the HF/6-31G＊ level of theory. A number of statistically-based parameters derived from molecular surface electrostatic potential have been obtained. Linear relationship between retention time and structural parameters has been established by multiple regression method. The result shows that parameters derived from electrostatic potential Vs ＋, Vs -, П together with the dipole moment μ can be well used to express the quantitative structure-retention time of this kind of aromatic carboxylic acid. Good predictive capability has also been demonstrated. The result has provided a framework which further proves the general applicability of this electrostatic potential parameter set to a great extent,and with which the ion chromatographic adsorption mechanism can be investigated.

关键词： Ion chromatography Retention time QSRR molecular electrostatic potential aromatic carboxylic acid

Exploration and elaboration of photo-induced proton transfer dynamical mechanism for novel 2-[1,3]dithian-2-yl-6-(7aH-indol-2-yl)-phenol sensor

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Chinese Physics B 2020年第5期29卷 208-213页

作者： Lei Xu Tian-Jie Zhang Qiao-Li Zhang Da-Peng Yang School of Physics and Electronics North China University of Water Resources and Electronic PowerZhengzhou 450046China Collaborative Innovation Center of Light Manipulations and Applications Shandong Normal UniversityJinan 250358China

In this work, we theoretically probe into the photo-induced hydrogen bonding effects between S0 state and S1 state as well as the excited state intramolecular proton transfer(ESIPT) behavior for a novel 2-[1,3]dithian-2-yl-6-(7aH-indol-2-yl)-phenol(DIP) probe system. We first study the ground-state hydrogen bonding O–H··· N behavior for DIP. Then we analyze the primary geometrical parameters(i.e., bond length, bond angle, and infrared(IR) stretching vibrational mode)involved in hydrogen bond, and confirm that the O–H··· N of DIP should be strengthened in the first excited state. It is the significant prerequisite for ESIPT reaction. Combining the frontier molecular orbitals(MOs) with vertical excitation analyses, the intramolecular charge transfer(ICT) phenomenon can be found for the DIP system, which reveals that the charge redistribution facilitates ESIPT behavior. By constructing potential energy curves for DIP along the ESIPT reactional orientation, we obtain quite a small energy barrier(3.33 kcal/mol) and affirmed that the DIP molecule undergoes ultrafast ESIPT process once it is excited to the S1 state and quickly transfers its proton, forming DIP-keto tautomer. That is why no fluorescence of DIP can be observed in experiment, which further reveals the ultrafast ESIPT mechanism proposed in this work.

关键词： intramolecular charge transfer ESIPT molecular electrostatic potential potential energy curves

QSPR Studies on the Physicochemical Properties of Polychlorinated Diphenyl Sulfides——The Application of Theoretical Descriptors Derived from electrostatic potentials on molecular Surface

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Chinese Journal of Structural Chemistry 2015年第7期34卷 995-1003页

作者：王维许惠英周侣艳唐东跃 Zhejiang Surveying Institute of Estuary and Coast College of Biology & Environment Engineering Zhejiang Shuren University Hangzhou Environmental Monitoring Station

Based on the relationship between the quantitative structure and property（QSPR） of organic compounds, the surface electrostatic potential parameters of 29 polychlorinated diphenyl sulfides（PCDPSs） with experimental values were calculated and extracted, and Multiple Linear Regression（MLR） was used to model the linear relationship between the physicochemical properties（octanol/water partition coefficient, high performance liquid chromatography capacity factor） and molecular structure parameters of PCDPSs. The result shows that the main factors that affect the n-octanol/water partition coefficient and high performance liquid chromatography capacity factor are respectively the number of chlorin atoms substituted on the benzene ring（NCl） and the lowest unoccupied molecular orbital energy（ELUMO）. Secondly, there are also molecular surface electrostatic potentials. This indicates that the molecular surface electrostatic potentials can effectively express the quantitative relationship between the physicochemical properties of PCDPSs and their molecule descriptions. The QSPR models established have strong stability and predictive ability. This also has proved the applicability of molecular surface electrostatic potential parameters in QSPR of PCDPSs.

关键词： polychlorinated diphenyl sulfides(PCDPSs) molecular electrostatic potential physicochemical property QSPR

Surface electrostatic potentials of Polychlorinated Dibenzofurans and Their Applications in Quantitative Structure-toxicity Relationships

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Chinese Journal of Structural Chemistry 2005年第4期24卷 407-412页

作者： ZOUJian-Wei HUGui-Xiang JIANGYong-Jun ZENGMin ZHUANGShu-Lin YUQing-Sen KeyLaboratoryformolecularDesignandNutritionEngineering NingboInstituteofTechnolog3 ZhejiangUniversity Ningbo315104China

Polychlorinated dibenzofurans (PCDFs) represent an important kind of serious pollutant. They are highly toxic and persistent in environment. In this paper, geometrical optimizations and subsequent calculations of electrostatic potentials (ESPs) on molecular surface have been performed for all 135 PCDF congeners at the HF/6-31G* level. The effects of substitution value and variation of substitution position upon the surface ESPs have been discussed. A series of statistic-based structural descriptors derived from the surface ESPs have been calculated. For some PCDF congeners, linear relationships between aryl hydrocarbon receptor (AhR) biding affinity and aryl hydrocarbon hydroxylase (AHH) induction potency as well as theoretical descriptors have been established by multiple linear regression method. It appears that the quantities derived from the surface ESPs, Vs,min, Vs , VS +, σ+ and Nvmin, 2 together with the molecular surface area and the energy gap between HOMO and LUMO can be well used to express the quantitative structure-toxicity relationships of PCDFs.

关键词： QSAR molecular electrostatic potential ab initio polychlorinated dibenzofuran

(E)-1-[4-(2-hydroxy-5-methoxybenzylideneamino)-phenyl]ethanone and (E)-1-[4-(2-hydroxy-4-methoxybenzylideneamino) phenyl]ethanone:X-ray and DFT-calculated structures

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Chinese Journal of Structural Chemistry 2011年第1期30卷 111-119页

作者： SAHN Onur BYKGNGR Orhan ALBAYRAK igdem ODABASOGLU Mustafa Department of Physics Faculty of Arts and SciencesOndokuz Mayls University Department of Science Education Sinop University Chemistry Programme Pamukkale University 20159 Denizli

The isomeric structures of（E）-1-[4-（2-hydroxy-5-methoxybenzylideneamino）-phenyl] ethanone（I） and（E）-1-[4-（2-hydroxy-4-methoxybenzylideneamino） phenyl]ethanone（Ⅱ） ,both C16H15NO3,have been determined using X-ray diffraction techniques and characterized by IR,and their molecular structures have also been optimized at the B3LYP/6-31G（d,p） level using density functional theory（DFT） . The energetic behaviors of the title compounds in solvent media have been examined using B3LYP method with the 6-31G（d,p） basis set by applying the polarizable continuum model（PCM） . The total energies of the title compounds decrease with the increasing polarity of the solvent. In addition,DFT calculations of the title compounds＇ molecular electrostatic potentials（MEP） were performed at the B3LYP/6-31G（d,p） level of theory. X-ray study shows that the title compounds both have strong intramolecular O-H…N hydrogen bonds. The molecules of Ⅰ are linked into a one-dimensional framework structure by C-H…π interactions,while in Ⅱ,intermolecular π···π interactions result in the formation of infinite chains running along the [010].

关键词： crystal structure Schiff base DFT molecular electrostatic potential

Surface electrostatic potentials of Polychlorinated Dibenzo-p-dioxins and Their Applications in the Quantitative Structure-properties Relationships

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Chinese Journal of Structural Chemistry 2011年第6期30卷 793-798页

作者：许惠英王维柴水英 College of Biology & Environment Engineering Zhejiang Shuren University Center of Modern Education Technology Zhejiang Shuren University Zhenhai Environmental Monitoring Station

Polychlorinated dibenzo-p-dioxins（PCDDs） are a group of important persistent organic *** are highly toxic and persistent in *** the present study,geometrical optimization and electrostatic potential calculations have been performed for 75 PCDD congeners and dibenzo-p-dioxin（DD） at the HF/6-31G＊ level of theory.A number of statistically based parameters have been *** relationships between vapor pressures（logpL）,aqueous solubilities（logSw）,n-octanol/water partition coefficients（logKow） of PCDDs and structural descriptors have been established by stepwise linear regression *** result shows that the quantities derived from the surface electrostatic potentials Vmin,Π,and Vs,av＋,together with Vmc（the molecular volume） and ELUMO（the energy of the lowest unoccupied molecular orbital） can be well used to express the quantitative structure-property relationships of *** capabilities of the models have also been demonstrated by leave-one-out cross-validation with the cross-validated correlation coefficient（Rcv） above *** on these QSPR models,the predicted values have been presented for those PCDD congeners whose experimentally determined physicochemical properties are unavailable.

关键词： QSPR polychlorinated dibenzo-p-dioxin molecular electrostatic potential

Prediction of Infinite Dilution Activity Coefficients of Alcohol and Ether Organic Compounds in Water

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Chinese Journal of Structural Chemistry 2010年第12期29卷 1808-1813页

作者：王维许惠英 Zhenhai Environmental Monitoring Station College of Biology & Environment Engineering Zhejiang Shuren University

Based on QSPR of alcohol and ether organic compounds in water,geometrical optimization and electrostatic potential calculations were performed at the HF/6-31G＊ level for 73 alcohol and ether organic *** relationships between infinite dilution activity coef-ficient（lnγ∞） of alcohols and ethers in water and theoretical descriptors of the molecular structure were established by multiple regression *** result shows that the parameters derived from molecular electrostatic potential together with molecular surface area can be preferably used to express the quantitative structure-lnγ∞ relationship of alcohols and ethers in *** reveals that this model has good predictive capabilities（RCV=0.969）.The molecular electrostatic potential has also been proved to have the general applicability in QSPR model of alcohol and ether organic compounds about γ∞ in *** QSPR model established may provide a new powerful method for predicting γ∞ of organic compounds in aqueous systems.

关键词： alcohol and ether organic compounds infinite dilution activity coefficient(γ∞) molecular electrostatic potential QSPR