Theoretical Study of the Complexation of Lidocaine by α- and β-Cyclodextrins

2021 ◽  
Vol 43 (4) ◽  
pp. 429-429
Author(s):  
Nourredine Meddah Araibi Nourredine Meddah Araibi ◽  
Teffaha Fergoug Teffaha Fergoug ◽  
Mansour Azayez Mansour Azayez ◽  
Cherifa Zelmat Cherifa Zelmat ◽  
Jendara Ali Cherif and Youcef Bouhadda Jendara Ali Cherif and Youcef Bouhadda
Keyword(s):  
Inclusion Complex ◽  
Quantum Chemical ◽  
Driving Forces ◽  
Minimum Energy ◽  
Geometry Optimization ◽  
Empirical Method ◽  
Van Der Waals Interactions ◽  
Basis Set ◽  
The Stability ◽  
Complexation Reactions

Structure and stability of an eventual inclusion complex formed by Lidocaine and two cyclodextrins (α- and β-CD) were investigated using molecular mechanics and quantum-chemical methods in the gas phase and in water. The molecular docking and quantum chemical calculations results show that no inclusion complex is formed between α-CD and Lidocaine molecule, while the conformational research allowed observing two minimum-energy structures between this molecule and β-CD. From a potential energy scan, a partial inclusion of the two ends of Lidocaine by the secondary face of the cavity of β-CD is observed with a better stability for the complex including the ((-N(C2H5)2) group in it. The minimum energy conformers, obtained by semi empirical method (PM3), have been exposed to fully geometry optimization employing ONIOM2 calculations by combining PM3 method with B3LYP, M06-HF and WB97XD functionals at 6-311G (d,p) basis set. The results show that complexation reactions are thermodynamically favored (Gand#176; ˂ 0) and the inclusion complexes are energetically stables and well structured (Sand#176; ˂ 0). According to the analysis of natural bond orbitals, the Van der Waals interactions are the sole driving forces that ensure the stability of the formed complexes.

scholarly journals Geometric and energetic data from quantum chemical calculations of halobenzenes and xylenes

2020 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Software Package ◽  
Geometry Optimization ◽  
Theoretical Data ◽  
Basis Set ◽  
Chemical Calculation ◽  
Custom Made

<p>This article presents theoretical data on geometric and energetic features of halobenzenes and xylenes. Data were obtained from <i>ab initio</i> geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.</p>

scholarly journals Geometric and Energetic Data from Quantum Chemical Calculations of Halobenzenes and Xylenes

2020 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Software Package ◽  
Geometry Optimization ◽  
Theoretical Data ◽  
Basis Set ◽  
Chemical Calculation ◽  
Custom Made

<div>This article presents theoretical data on geometric and energetic features of halobenzenes and xylenes. Data were obtained from ab initio geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.</div>

scholarly journals Geometric and energetic data from quantum chemical calculations of halobenzenes and xylenes

2020 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Software Package ◽  
Geometry Optimization ◽  
Theoretical Data ◽  
Basis Set ◽  
Chemical Calculation ◽  
Custom Made

<p>This article presents theoretical data on geometric and energetic features of halobenzenes and xylenes. Data were obtained from <i>ab initio</i> geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.</p>

scholarly journals Molecular Modelling, Docking and Pharmacokinetic Studies of N-Arylidenequinoline-3-Carbohydrazides Analogs as Novel β-Glucuronidase Inhibitors

2019 ◽  
Vol 64 (1) ◽  
Author(s):  
Muhammad Tukur Ibrahim ◽  
Adamu Uzairu ◽  
Abdullahi Bello Umar ◽  
Abubakar Sadiq Bello ◽  
Yusuf Isyaku
Keyword(s):  
Geometry Optimization ◽  
Docking Study ◽  
Empirical Method ◽  
Basis Set ◽  
Pharmacokinetic Studies ◽  
Amino Acid Residues ◽  
Molecular Docking Study ◽  
Data Set ◽  
New Compounds ◽  
Semi Empirical

Quantitative structure-activity relationships (QSAR) modelling on 30 N-Arylidenequinoline-3-carbohydrazides analogs was performed using Multi-Linear Regression (MLR) analysis adopting Genetic Function Algorithm (GFA) method. Semi empirical method using PM6 basis set was used for complete geometry optimization of the data set. The best model was chosen based on its statistical fit due to it good internal and external validations. From the Williams plot, it can be inferred that the reported model can make prediction of new compounds that are not within the data set. The molecular docking study showed that, the most active chemical in the data set was better than the standard β-glucuronidase inhibitor both in terms of binding scores and the amino acid residues that interacted with the drug and β-glucuronidase enzyme. The Pharmacokinetic studies indicated that none of the chemicals violated any of the condition set by the Lipinski′s Rule of five which confirm the bioavailability of these chemicals. The results these findings give room for designing novel β-glucuronidase inhibitors that are highly effective.                                                Resumen. Se llevó a cabo la técnica de QSAR en 30 analogos de N-arilidenequinolina-3-carbohidrazidas mediante el analisis de regresesión lineal múltiple (MLS) adopatando el método del algoritmo de función genética (GFA). Para la optimización completa de la geometría del conjunto de datos se utilizó un método semiémpirico del conjunto de bases PM6. El mejor modelo fue elegido basado en función de su ajuste estadístico debido a su validación interna y externa. A partir de la gráfica de Williams, se puede inferir que el modelo reportado puede predecir nuevos compuestos que no se encuentran en el conjunto de datos. Este estudio de acomplamiento molecular mostró que, el químico más activo del conjunto de datos fue mejor que el inhibidor estándar β-glucuronidasa, tanto en términos de unión y en términos de  interacción de los residuos con el fármaco y la enzima β-glucuronidasa. Los estudios farmacocinéticos que indicaron que ninguno de los fármacos incumple ninguna de las condiciones establecidas por la regla de cinco de Lipinski, en donde se confirma la biodisponibilidad de estos químicos. Los resultados de los hallazgos computacionales permiten diseñar nuevos inhibidores de la β-glucuronidasa que son altamente efectivos.

scholarly journals Geometric and Energetic Data from Quantum Chemical Calculations of Halobenzenes and Xylenes

2019 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Software Package ◽  
Geometry Optimization ◽  
Theoretical Data ◽  
Basis Set ◽  
Chemical Calculation ◽  
Custom Made

<div>This article presents theoretical data on geometric and</div><div>energetic features of halobenzenes and xylenes. Data were obtained from ab initio geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure</div><div>of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.</div>

scholarly journals Formation and characterization of furfuryl mercaptan-β-cyclodextrin inclusion complex and its thermal release characteristics

2021 ◽  
Vol 23 (4) ◽  
pp. 35-40
Author(s):  
Guangyong Zhu ◽  
Zuobing Xiao ◽  
Gengfa Yu ◽  
Guangxu Zhu ◽  
Yunwei Niu ◽  
...  
Keyword(s):  
Inclusion Complex ◽  
Minimum Energy ◽  
Precipitation Method ◽  
Supporting Evidence ◽  
X Ray Diffraction ◽  
Thermal Release ◽  
Cyclodextrin Inclusion ◽  
Aroma Characteristics ◽  
Cyclodextrin Inclusion Complex ◽  
The Stability

Abstract Furfuryl mercaptan has the aroma characteristics of coffee. However, it is unstable during storage of coffee brew and roasted coffee. In order to enhance the stability of furfuryl mercaptan, furfuryl mercaptan-β-cyclodextrin inclusion complex was synthesized using the precipitation method in this work. Fourier transform infrared spectroscopy, x-ray diffraction, and thermogravimetric analysis (TG) were used to characterize the resulting products. The interaction of furfuryl mercaptan with β-cyclodextrin was investigated by the molecular mechanics (MM) method. These changes in FTIR and XRD gave supporting evidence for the successful formation of furfuryl mercaptan-β-cyclodextrin inclusion complex. The TG results showed that the formation of furfuryl mercaptan-β-cyclodextrin inclusion complex could improve the thermal stability of furfuryl mercaptan and provide a long-lasting effect. The structure of furfuryl mercaptan-β-cyclodextrin inclusion complex with the minimum energy was obtained by MM2 calculation, and the minimum binding energy was –77.0 kJ mol−1 at –1.96 × 10–10 m.

scholarly journals Molecular docking study of copaíba oil interacting with the spike protein of Sars-CoV-2

2021 ◽  
Author(s):  
Willian Oliveira Santos ◽  
José Robson da Costa Venâncio ◽  
Fernanda Carla Lima Ferreira ◽  
Glaura Caroena Azevedo de Oliveira ◽  
Aldimar Machado Rodrigues ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Inorganic Compounds ◽  
Minimum Energy ◽  
Docking Study ◽  
Binding Energies ◽  
Van Der Waals Interactions ◽  
Molecular Docking Study ◽  
Copaiba Oil ◽  
The Stability ◽  
Potential Inhibitors

Abstract COVID-19 triggered by Sars-CoV-2 has caused hundreds of thousands of deaths worldwide. Organic and inorganic compounds have been tested as potential inhibitors of this lethal virus. For these tests, several techniques are use to design molecules of biological interest for drug composition, in which molecular coupling plays an important role. In the present work, the compounds acids kaurenoic, copalic, and beta-caryophyllene that form the copaiba oil were studied as anti-inflammatories and opens the possibility to inhibit Sars-CoV-2. Molecular docking showed alkyl, pi-alkyl, conventional H-bond, unfavorable bump, and Van der Waals interactions. The calculated electrostatic potential maps showed the nucleophilic and electrophilic regions. The negative binding energies obtained for the three acids suggest the stability of the complexes. The minimum energy states for β-caryophyllene are lower than the other compounds analyzed, and it can be predicted that this is the most stable.

scholarly journals Geometric and energetic data from quantum chemical calculations of halobenzenes and xylenes

2020 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Software Package ◽  
Geometry Optimization ◽  
Theoretical Data ◽  
Basis Set ◽  
Chemical Calculation ◽  
Custom Made

<p>This article presents theoretical data on geometric and energetic features of halobenzenes and xylenes. Data were obtained from <i>ab initio</i> geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes, three structures of xylenes and one structure of benzene were generated and processed by custom-made codes in Mathematica. The quantum chemical calculation was completed in Q-Chem software package. Geometric and energetic data of the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts associated with production and extraction of data are also provided.</p>

scholarly journals THEORETICAL STUDY OF THE EFFECT OF WATER MOLECULE ADDITION ON THE CONFORMATION OF SUBSTITUTED DIBENZO-18-CROWN-6 ETHER IN ITS COMPLEXATION WITH Na+ CATION USING SEMI EMPIRICAL METHOD MNDO/d

2010 ◽  
Vol 3 (2) ◽  
pp. 111-117
Author(s):  
Harno Dwi Pranowo ◽  
Tuti Hartati Siregar ◽  
Mudasir Mudasir
Keyword(s):  
Binding Energy ◽  
Water Molecule ◽  
Metal Ion ◽  
Geometry Optimization ◽  
Semiempirical Method ◽  
Empirical Method ◽  
Trial And Error ◽  
Effect Of Water ◽  
The Stability ◽  
Semi Empirical

The effect of water molecule addition into modeling structure of complex of substituted dibenzo-18-crown-6 ether with metal ion Na+ was studied. The aim of this research is to find information about geometrical conformation of substituted DB18C6 and its selectivity to complex/coordinate metal ion Na+ in the presence of water molecule. In this research semi empirical method was used for calculation. To find the best conformation, trial and error experiments were conducted using semi empirical method available in HyperChem 6.0, finally MNDO/d method was selected. The result of geometry optimization showed that addition of water molecule improve the stability of the conformation of substituted DB18C6 and increase the selectivity of this compound to complex metal ion Na+. The presence of electron-withdrawing substituents decreased the binding energy while that of electron-donating one increase the binding energy (value of DE more negative). Cavity radii of DB18C6 in the presence of water molecule extended from 2.3 Å to 2.6 Å. This figure is almost similar to that of experimental data.   Keywords: Crown ether, molecular modelling, semiempirical method

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