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Quantum Chemistry Prediction of Molecular Lipophilicity Using Semi-Empirical AM1 and Ab InitioHF/6-311++G Levels

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Computational Chemistry 2017年第1期5卷 38-50页

作者： Ouanlo Ouattara nahossé ziao Laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR-SFA Université Nangui Abrogoua Abidjan C&ocirc te d’Ivoire

Reliable prediction of lipophilicity in organic compounds involves molecular descriptors determination. In this work, the lipophilicity of a set of twenty-three molecules has been determined using up to eleven quantum various descriptors calculated by means of quantum chemistry methods. According to Quantitative Structure Property Relationship (QSPR) methods, a first set of fourteen molecules was used as training set whereas a second set of nine molecules was used as test set. Calculations made at AM1 and HF/6-311++G theories levels have led to establish a QSPR relation able to predict molecular lipophilicity with over 95% confidence.

关键词： Molecular Lipophilicity Molecular Descriptors Quantum Chemistry Statistical Analysis

DFT Study of Dimerization Sites in Imidazo[1,2-a]pyridinyl-chalcone Series

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Computational Chemistry 2021年第1期9卷 1-17页

作者： Bibata Konate Sopi Thomas Affi nahossé ziao Laboratoire de Thermodynamique et de Physico-Chimie du Milieu Université Nangui Abrogoua Abidjan C&#244te d’Ivoire

Quantum chemistry methods were performed in order to characterize the chemical reactivity on series of imidazo[1,2-a]pyridinyl-chalcone (IPC). In particular, the B3LYP/6-311G(d) theory level has been used to determine parameters which characterize the global and local reactivity on five molecules of the series. These compounds differ from one to another with the aryl groups. There are: 1-(2-methylimidazo[1,2-a]pyridin-3-yl)-3-phenylprop-2-en-1-one, 3-(4-fluorophenyl)-1-(2-methylimidazo [1,2-a]pyridin-3-yl)prop-2-en-1-one, 3-[4-(dimethylamino)phenyl]-1-(2-methylimidazo [1,2-a]pyridin- 3-yl)prop-2-en-1-one, 3-(2,4-dichlorophenyl)-1-(2-methylimidazo [1,2-a]pyridin-3-yl)prop-2-en-1-one, 3-(2,4-dichlorophenyl)-1-(2-methylimidazo [1,2-a]pyridin-3-yl)prop-2-en-1-one. All results lead to finding out that local nucleophilicity and electrophilicity of compounds are not substituent-dependant contrarily to their global nucleophilicity which prove to be more sensitive to the electron-donating character of the substituents. 3-[4-(Dimethylamino) phenyl]-1-(2-methylimidazo[1,2-a]pyridin-3-yl)prop-2-en-1-one was identified as the unique nucleophile compound by global reactivity. Respectively, the carbon atoms C5 and C14 are the prediction sites of electrophilic and nucleophilic attacks in the molecular skeleton of both molecules. Identification of interactions centres on IPC series is of great importance for organic synthesis and medicinal chemistry where the molecular hybridization strategy is very often used to improve biological activities of interesting therapeutic systems.

关键词： Chemical Reactivity Conceptual DFT Imidazopyridinyl-Chalcone Nematicidal Activity Quantum Chemistry

SARs Investigation of α-, β-, γ-, δ-, ε-RuCl₂(Azpy)₂ Complexes as Antitumor Drugs

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Computational Chemistry 2016年第1期4卷 1-10页

作者： Kafoumba Bamba Ouattara Wawohinlin Patrice N’Guessan Kouakou Nobel nahossé ziao Laboratoire de Thermodynamique et de Pysico-Chimie du Milieu UFR-SFA Université Nangui Abrogoua Abidjan C&ocirc te d’Ivoire

Structure Activity-Relationships (SARs) of the five possible isomers of RuCl2(Azpy)2 were predicted thanks to DFT method. Azpy stands for 2-phenylazopyridine and the structure of the isomers α-RuCl2(Azpy)2, β-RuCl2(Azpy)2, γ-RuCl2(Azpy)2, δ-RuCl2(Azpy)2 and ε-RuCl2(Azpy)2 call respectively α-Cl, β-Cl, γ-Cl, δ-Cl and ε-Cl are defined according to chlorine atoms orientations. Hence, they are divided into two groups. In the first group comprising α-Cl, β-Cl and ε-Cl, both chlorine atoms are in cis position and Azpy ligands are intervertical. Whereas the two others isomers (γ-Cl and δ-Cl), they form the second group. Here, both chlorine are in trans position and Azpy are planar. The five synthesized isomers were investigated as potential antitumor agents. Then, regarding the DNA, its bases are stacked by pair. Therefore, complexes are assumed to insert and to stack on them through intercalative mode. So the electronic and geometric structures become more important to describe their SARs. Consequently, group 2 regarding γ-Cl and δ-Cl presents the best structure to allow intercalation between DNA base-pairs. Besides, the energy order of the lower unoccupied molecular orbital (LUMO) of the isomers is ELUMO(β-Cl) > ELUMO(α-Cl) > ELUMO(ε-Cl) > ELUMO(γ-Cl) > ELUMO(δ-Cl). The energy gap between LUMO and HOMO was also sorted as Δ(L-H)(β-Cl) > Δ(L-H)(α-Cl) > Δ(L-H)(ε-Cl) > Δ(L-H)(γ-Cl) > Δ(L-H)(δ-Cl). In addition, the total dipole moment was classified as μ(ε-Cl) > μ(β-Cl) > μ(α-Cl) > μ(γ-Cl) > μ(δ-Cl). Finally, net charge of the ligand Azpy was also classified as QL(δ-Cl) > QL(γ-Cl) > QL(ε-Cl) > QL(α-Cl) > QL(β-Cl). All those parameters show that δ-Cl isomer displays the highest activity as antitumor drug when intercalating between the DNA basepairs Cytosine-Guanine/Cytosine-Guanine (CG/CG).

关键词： Structure Activity-Relationship (SARs) Ru (II) Complexes Azpy DFT Lanl2dz DNA-Binding

NBO Population Analysis and Electronic Calculation of Four Azopyridine Ruthenium Complexes by DFT Method

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Computational Chemistry 2017年第1期5卷 51-64页

作者： N’Guessan Kouakou Nobel Kafoumba Bamba Ouattara Wawohinlin Patrice nahossé ziao Laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR-SFA Université Nangui Abrogoua Abidjan C&ocirc te d’Ivoire

The molecular structure, the Natural Bond orbital (NBO) and the Time Dependent-DFT of both isomers cis or γ-Cl and trans or δ-Cl of RuCl2(L)2, where L stands respectively for 2-phenylazopyridine (Azpy), 2,4-dimethyl-6-[phenylazo]pyridine (Dazpy), 2-[(3,5-dimethylphenyl)azopyridine] (Mazpy) and 2-pyridylazonaphtol (Nazpy) were calculated with DFT method at B3LYP/LANL2DZ level. The prediction of the frontier orbitals (Highest Occupied Molecular Orbital or HOMO and Lowest Unoccupied Molecular Orbital or LUMO) shows that the most active complexes suitable for electronic reactions are admitted to be the trans isomers. Moreover, δ-RuCl2 (Azpy)2 is discovered to react more actively as photo-sensitizer since its energy gap is the minimum. Besides, electronic structures of all complexes through NBO calculation indicate that Ru-N bonds are made of delocalization of occupancies from lone pair orbital of N atoms to the ruthenium. Moreover, Ru was assumed to have almost the same charge regardless the structure of the azopyridine ligands in the complex indicating that the ligands provide only a steric effect that is responsible for the ruthenium’s selectivity. Concerning the transition state, NBO analysis also highlights that the transition LP(Ru) π*(N1-N2) does correspond to t2g?π*(L). This transition is assumed to correspond to Metal to Ligand Charge Transfer (MLCT) that is responsible for the photo-sensitiveness of the metallic complex. Besides, TDDFT calculation of complexes showed that δ-RuCl2(Nazpy)2 displays the largest band during the absorption. For that reason, it is admitted to be the best photosensitizer due to a large system of conjugation provided by Nazpy ligand.

关键词： Natural Bond Orbital (NBO) HOMO LUMO Azopyridine Ligand MLCT LLCT

Molecular Structure, Electronic Structure, Properties and Analyses of Five Azopyridine Ruthenium Complexes α-Cl, β-Cl, γ-Cl, δ-Cl and ε-Cl of RuCl2(4,6-Dimethyl-Phenylazopyridine)2as Potential Cancer Drugs: DFT and TD-DFT Investigations

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Computational Chemistry 2018年第3期6卷 27-46页

作者： Nobel Kouakou N’Guessan Kafoumba Bamba Ouattara Wawohinlin Patrice nahosséziao Laboratoire de Thermodynamique et Physico-Chimie du Milieu UniversitéNangui AbrogouaAbidjanC&ocirc te d’Ivoire

Ground state geometries, natural bond orbital (NBO), analysis of frontier molecular orbitals (FMOs), analysis and spectral (RMN and UV-Visible) properties of five azopyridine ruthenium (II) complexes α-Cl, β-Cl, γ-Cl, δ-Cl and ε-Cl of RuCl2(Dazpy)2 have been theoretically studied by the Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) methods using two basis sets: Lanl2DZ and a generic basis set in gas or in chloroform solvent. Dazpy stands for 4,6-dimethyl-phenylazopyridine. Optimized geometry shows that, except β-Cl, all the other four isomers α-Cl, γ-Cl, δ-Cl and ε-Cl are C2 symmetrical. Otherwise, a good agreement was found between experimental and the calculated geometry and NMR data. Moreover, Lanl2DZ effective core potential basis set provides good chemical shifts and geometric properties. Furthermore, the prediction of the frontier orbitals (Highest Occupied Molecular Orbital or HOMO and Lowest Unoc-cupied Molecular Orbital or LUMO) shows that the most active isomer suita-ble for electronic reactions is admitted to be δ-Cl. Besides, the NBO analysis indicates that the Ru-N is formed by the electron delocalization of lone pair atomic orbital of N2 and Npy to Ru. Also, the strongest interactions between LP(N) with LP*(Ru) and LP(Cl) with LP*(Ru) stabilize the molecular struc-ture. In addition, NBO shows that the five d orbitals of Ru in the complex are organized so that there is no order of priority from one complex to another. Therefore, the transition LP(Ru) → π*(N1 = N2) corresponding to Metal to Li-gand Charge Transfer (MLCT) is in reality no more than d → π*. Besides, TDDFT prediction in chloroform solvent reveals that all the five isomerics complexes absorb in the visible region as well as efficient photosensitizers. What’s more, δ-RuCl2(dazpy)2 can potentially act as the excellent sensitizer with a large band of absorption in visible region and a small excited energy. This study can help design and find out the abili

关键词： Azopyridine DFT NBO Pseudo-Potential Ru(II) Complexes

Theoretical and Electrochemical Characterization of δ-RuCl₂(Nazpy)₂: Application to Oxidation of D-Glucose

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American Journal of Analytical Chemistry 2016年第1期7卷 57-66页

作者： Wawohinlin Patrice Ouattara Kafoumba Bamba nahossé ziao Kouakou Nobel N’guessan Laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR-SFA Université Nangui-Abrogoua Abidjan Cote d’Ivoire

The heterogenized δ-RuCl2(Nazpy)2 deposited on carbon toray (CT) was studied for the first time as electrochemical catalyst. Before, it was characterized by visible-ultraviolet spectra and theoretically by TDDFT method at B3LYP/Lanl2DZ level. It displayed an MLCT t2geg → π* transition where t2geg due to the structure of Nazpy that considerably reduces energy between d AOs of Ru represents the HOMO of the complex and π* is identified as the LUMO. Electrochemistry study shows two redox ranges in both negative and positive sides of the potential. The positive side that corresponds to the couple RuIV/RuIII of catalyst appears to be active for oxidation of D-glucose in carbonate buffer with a high turnover. Therefore, Keto-2-gluconic and gluconic acids were the two main products obtained with respectively 80% and 17.6% of selectivity. Moreover, a small amount of tartaric and glycol acids coming from the c-c bond cleavage due to non-protection of the anomeric carbon of D-glucose were also observed.

关键词： DFT Calculation HOMO-LUMO Analysis NBO Electrochemistry Ruthenium Complex D-Glucose

Prediction of Anti-Inflammatory Activity of a Series of Pyrimidine Derivatives, by Multiple Linear Regression and Artificial Neural Networks

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Computational Chemistry 2022年第4期10卷 186-202页

作者： Yafigui Traoré Jean Missa Ehouman Mamadou Guy-Richard Koné Donourou Diabaté nahossé ziao Laboratory of Thermodynamics and Environmental Physico-Chemistry Nangui Abrogoua University Abidjan Ivory Coast Training and Research Unit Biological Sciences University Peleforo Gon Coulibaly Korhogo Ivory Coast Ivorian Research Group in Disease Modeling (GIR2M) Abidjan Ivory Coast

Anti-inflammatory activity of a series of tri-substituted pyrimidine derivatives was predicted using two Quantitative Structure-Activity Relationship models. These relationships were developed from molecular descriptors calculated using the DFT quantum chemistry method using the B3LYP/6-31G(d,p) level of theory and molecular lipophilicity. Thus, the four descriptors which are the dipole moment μD, the energy of the highest occupied molecular orbital EHOMO, the isotropic polarizability α and the ACD/logP lipophilicity were selected for this purpose. The Multiple Linear Regression (MLR) and Artificial Neural Network (ANN) models are respectively accredited with the following statistical indicators: R2=91.28%, R2aj=89.11%, RMCE = 0.2831, R2ext=86.50% and R2=98.22%, R2aj=97.75%, RMCE = 0.1131, R2ext=98.54%. The results obtained with the artificial neural network are better than those of the multiple linear regression. However, these results show that the two models developed have very good predictive performance of anti-inflammatory activity. These two models can therefore be used to predict anti-inflammatory activity of new similar pyrimidine derivatives.

关键词： Anti-Inflammatory Activity Multiple Linear Regression Artificial Neural Network QSAR

In Silico Docking of Rhodanine Derivatives and 3D-QSAR Study to Identify Potent Prostate Cancer Inhibitors

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Computational Chemistry 2022年第2期10卷 19-52页

作者： Koffi Alexis Respect Kouassi Adenidji Ganiyou Diomande Gbe Gondo Didier Anoubilé Benié ziao nahossé Laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR SFA Université Nangui Abrogoua Abidjan C&#244 te d’Ivoire Laboratoire de Constitution et de Réaction de la matière UFR-SSMT Université Félix Houphou&#235 t-Boigny Abidjan C&#244 te d’Ivoire Laboratoire de Chimie Bio-Organique et de Substances Naturelles UFR-SFA Université Nangui Abrogoua Abidjan C&#244 te d’Ivoire

The 3VHE protein is considered as a potential target for the treatment of prostate cancer. In order to find new 3VHE inhibitors, pharmacophore models based on the molecular structure of rhodanine derivatives and a three-dimensional quantitative structure-activity relationship model (3D-QSAR) have been developed and validated by different methods. The 3D-QSAR model was evaluated for its predictive performance on a diverse test set containing 18 prostate cancer inhibitors. It presents very interesting internal and external statistical validation parameters (SD = 0.081;R2 = 0.903;Q2 = 0.869;;F = 247.2). This result suggests that the 3D-QSAR combinatorial model can be used to search for new 3VHE inhibitors and predict their potential activity. Based on the combinatorial pharmacophore model, a virtual screening of the Enamine database was performed. Compounds selected after virtual screening were subjected to molecular docking protocols (HTVS, SP, XP and IFD). Twenty new active compounds have been identified and their absorption, distribution, metabolism and excretion (ADME) property calculated using Schr?dinger’s Qikprop module. These results suggest that these new compounds could constitute new chemical starting points for further structural optimization of 3VHE inhibitors.

关键词： Rhodanine Pharmacophores 3D-QSAR Molecular Docking

Protonation Sites in Benzimidazolyl-Chalcones Molecules: An ab Initio and DFT Investigation

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Computational Chemistry 2016年第3期4卷 65-72页

作者： Mamadou Guy-Richard Kone Sopi Thomas Affi nahossé ziao Kafoumba Bamba Edja Florentin Assanvo Laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR SFA Université Nangui Abrogoua Abidjan République de C&Ocirc te-d’Ivoire

In this work, we have focused our investigations on the protonation sites predilection in the benzimidazolyl- chalcones (BZC) derivatives. Particularly, we are interested in the study of geometrical and energetical parameters. BZC are well known for their particularly nematicidal activity. Ten (10) BZC derivatives coded BZC-1 to BZC-10, with various larvicidal concentrations, have been selected for this work. They all are different one from another by the phenyl ring which is substituted by electron modulators such as alkyl, hydroxyl, alkoxy, aminoalkyl, halogen and nitro or replaced by the furan. Quantum chemical methods, namely HF/6-311 + G(d,p) and MPW1PW91/6- 311 + G(d,p) theory levels have been used to determine the geometrical and energetical parameters by the protonation on each heteroatom of the BZC derivative. An accuracy results with relatively less time consuming has been obtained using Hartree-Fock (HF) and Density Functional Theory methods (DFT/MPW1PW91). The calculations results allow identifying the sp2 nitrogen as the preferential site of protonation in BZC derivative compounds.

关键词： Benzimidazolyl-Chalcone Quantum Chemistry Protonation Proton Affinity Gas Phase Basicity