scholarly journals Molecular geometry-dependent atomic charge calculation with modified charge equilibration method

2009 ◽  
Vol 9 ◽  
pp. 30-40 ◽  
Author(s):  
Kozo Aoki ◽  
Shigenori Tanaka ◽  
Tatsuya Nakano
Keyword(s):  
Atomic Charge ◽  
Molecular Geometry ◽  
Charge Equilibration

scholarly journals Computational Aspects of (E)-O-Carbomethoxy Methyl Oxime Ether of 1,3-Dimethyl-2,6-Diphenylpiperidin-4-One

2019 ◽  
Vol 9 (2S2) ◽  
pp. 701-706
Keyword(s):  
Molecular Orbital ◽  
Density Functional ◽  
Atomic Charge ◽  
Molecular Geometry ◽  
Biologically Active ◽  
Oxime Ether ◽  
Structure And Property ◽  
Highest Occupied Molecular Orbital ◽  
Computational Aspects ◽  
Lowest Unoccupied Molecular Orbital

Density Functional Theoretical (DFT) studies on the biologically active oxime ether derived from 1,3-dimethyl-2,6-diphenylpiperidin-4-one has been carried out. Various quantum chemical parameters of the molecule viz. molecular geometry, Highest Occupied Molecular Orbital – Lowest Unoccupied Molecular Orbital (HOMO–LUMO) energies, Non-Linear Optical (NLO) properties, Mulliken atomic charge distribution were obtained theoretically and compared with the single crystal data. An insight into the structure and property correlation revealed the probable behavior of the molecule studied

scholarly journals DFT and Molecular Docking Study of 2-[2-(4-Chlorophenylaminothiazol-5-yl]benzothiazole

2019 ◽  
Vol 31 (3) ◽  
pp. 695-698
Author(s):  
N.S. Femila Nirmal ◽  
T.F. Abbs Fen Reji
Keyword(s):  
Molecular Docking ◽  
Atomic Charge ◽  
Molecular Geometry ◽  
Docking Study ◽  
Vibrational Frequencies ◽  
Molecular Docking Study ◽  
B3lyp Method ◽  
Homo And Lumo ◽  
Charge Analysis ◽  
Vibrational Bands

The title compound was computed by means of DFT chemical quantum calculations to obtain optimized molecular geometry, harmonic vibrational frequencies and atomic charges. Vibrational bands to the various structural groups and their importance were predicted by analyzing the vibrational spectra. The data showed that B3LYP method provide satisfactory data for assigning vibrational frequencies and structural properties.The HOMO and LUMO energies calculated permit the determination of atomic and molecular parameters and they also represented the transfer of charge in the molecule. Mulliken atomic charge analysis was also done. A comprehensive molecular picture of 2-[2-(4-chlorophenylaminothiazol-5-yl]benzothiazole and its interactions were got from NBO investigations. The molecular docking study indicates that benzothiazole derivative may possess inhibitory activity against BCL2 pancreatic cancer cell lines.

scholarly journals Zinc, copper and nickel complexes of a macrocycle synthesized from pyridinedicarboxylic acid: A spectroscopic, thermal and theoretical study

2017 ◽  
Vol 82 (6) ◽  
pp. 665-680
Author(s):  
Esmaiel Soleimani ◽  
Sayed Taheri ◽  
Mohsen Sargolzaei
Keyword(s):  
Theoretical Data ◽  
Atomic Charge ◽  
Molecular Geometry ◽  
Dft Method ◽  
1H And 13C Nmr ◽  
Antibacterial And Antifungal Activities ◽  
Pyridinedicarboxylic Acid ◽  
Amine Groups ◽  
Antibacterial And Antifungal ◽  
Cl Atoms

The metal(II) ion complexes of a pentadentate macrocycle 1, namely 3,12-dioxa-6,9,18-triazabicyclo[12.3.1]octadeca-1(18),14,16-triene-2,13-dione are synthesized. This macrocycle is prepared from the reaction of dipotassium salt of 2,6-pyridinedicarboxylic acid with ethylenediamine and 1,2-dibromoethane. The reaction of 1 (L) in methanol with MCl2.xH2O gave complexes with the general formula [M(L)Cl2] (where M= Ni(II) 2, Cu(II) 3 and Zn(II) 4, respectively). The analysis of IR, 1H- and 13C-NMR spectral data of all complexes propose that 1 is bonded to metal(II) ions through a nitrogen atom of pyridine ring, two nitrogen atoms of amine groups and two oxygen atoms of ester moieties. The thermal analysis indicated that there are no water molecules of hydration or coordinated in the structure of the complexes. Among these complexes, the Cu(II) 3 complex demonstrated good antibacterial and antifungal activities. The molecular geometry, AIM atomic charge and frontier molecular orbitals of the compounds are investigated theoretically using DFT method. Based on the theoretical data of these complexes represented, a bipyramidal pentagonal arrangement can be envisaged in such a way that the N3O2 pentadentate donor sites form the planar pentagonal base of the bipyramid and the two Cl atoms occupy the vertexes.

scholarly journals Optimized SQE atomic charges for peptides accessible via a web application

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Ondřej Schindler ◽  
Tomáš Raček ◽  
Aleksandra Maršavelski ◽  
Jaroslav Koča ◽  
Karel Berka ◽  
...  
Keyword(s):  
Web Application ◽  
Atomic Charge ◽  
Atomic Charges ◽  
Calculation Methods ◽  
Minimization Method ◽  
Large Molecules ◽  
Charge Equilibration ◽  
Electronegativity Equalization Method ◽  
Macromolecular Systems ◽  
Partial Atomic Charges

Abstract Background Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations—e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible. Results In this article, we present for the first time an optimized guided minimization method (optGM) for the fast parameterization of empirical charge calculation methods and compare it with the currently available guided minimization (GDMIN) method. Then, we introduce a further extension to SQE, SQE+qp, adapted for peptide datasets, and compare it with the common approaches EEM, QEq EQeq, SQE, and SQE+q0. Finally, we integrate SQE and SQE+qp into the web application Atomic Charge Calculator II (ACC II), including several parameter sets. Conclusion The main contribution of the article is that it makes SQE methods with their parameters accessible to the users via the ACC II web application (https://acc2.ncbr.muni.cz) and also via a command-line application. Furthermore, our improvement, SQE+qp, provides an excellent solution for peptide datasets. Additionally, optGM provides comparable parameters to GDMIN in a markedly shorter time. Therefore, optGM allows us to perform parameterizations for charge calculation methods with more parameters (e.g., SQE and its extensions) using large datasets. Graphic Abstract

Theoretical study of intramolecular hydrogen bonding and molecular geometry of 2-trifluoromethylphenol

10.1002/jcc.2 ◽  
1996 ◽  
Vol 17 (16) ◽  
pp. 1804-1819 ◽  
Author(s):  
Attila Kov�cs ◽  
Istv�n Kolossv�ry ◽  
G�bor I. Csonka ◽  
Istv�n Hargittai
Keyword(s):  
Hydrogen Bonding ◽  
Theoretical Study ◽  
Molecular Geometry ◽  
Intramolecular Hydrogen Bonding ◽  
Intramolecular Hydrogen

Problems in Structural Inorganic Chemistry

2018 ◽  
Author(s):  
Wai-Kee Li ◽  
Hung Kay Lee ◽  
Dennis Kee Pui Ng ◽  
Yu-San Cheung ◽  
Kendrew Kin Wah Mak ◽  
...  
Keyword(s):  
Inorganic Chemistry ◽  
Molecular Geometry ◽  
Orbital Theory ◽  
Crystal Field Theory ◽  
Structure Transition ◽  
Oxford University ◽  
Chinese University ◽  
Peking University ◽  
The Subject ◽  
Hybrid Orbitals

The First Edition of this book, which appeared in 2013, serves as a problem text for Part I (Fundamentals of Chemical Bonding) and Part II (Symmetry in Chemistry) of the book Advanced Structural Inorganic Chemistry published by Oxford University Press in 2008. A Chinese edition was published by Peking University Press in August in the same year. Since then the authors have received much feedback from users and reviewers, which prompted them to prepare a Second Edition for students ranging from freshmen to senior undergraduates who aspire to attend graduate school after finishing their first degree in Chemistry. Four new chapters are added to this expanded Second Edition, which now contains over 400 problems and their solutions. The topics covered in 13 chapters follow the sequence: electronic states and configurations of atoms and molecules, introductory quantum chemistry, atomic orbitals, hybrid orbitals, molecular symmetry, molecular geometry and bonding, crystal field theory, molecular orbital theory, vibrational spectroscopy, crystal structure, transition metal chemistry, metal clusters: bonding and reactivity, and bioinorganic chemistry. The problems collected in this volume originate from examination papers and take-home assignments that have been part of the teaching program conducted by senior authors at The Chinese University of Hong Kong over nearly a half-century. Whenever appropriate, source references in the chemical literature are given for readers who wish to delve deeper into the subject. Eight Appendices and a Bibliography listing 157 reference books are provided to students and teachers who wish to look up comprehensive presentations of specific topics.

Disazo (Bishydrazone) pigments based on acetoacetanilides

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Robert Christie ◽  
Adrian Abel
Keyword(s):  
Crystal Packing ◽  
Molecular Geometry ◽  
Coupling Reactions ◽  
Dominant Group ◽  
Color Strength ◽  
Decomposition Products ◽  
Organic Pigments ◽  
Yellow Pigments ◽  
Structure Investigations ◽  
Coupling Components

Abstract Disazoacetoacetanilide pigments, more commonly known as diarylide yellows, are the most important group of yellow classical organic pigments. They were commercialized in the early 20th century many years after the introduction of the structurally related monazoacetoacetanilides (Hansa yellows). The molecules adopt the bis-ketohydrazone tautomeric form. X-ray single crystal structure investigations have provided an insight into the influence of the molecular geometry and crystal packing arrangements in the solid state on the properties of the pigments in application. The synthesis of diarylide pigments is relatively straightforward, the conditions essentially following those used for the corresponding monoazo pigments, so that the products are economically priced. In the case of these disazo pigments, suitable aromatic amines (1 mol) are bis-diazotized and the resulting bis-diazonium salts reacted with acetoacetanilide coupling components (2 mol), the two azo coupling reactions occurring at the same time. They are by far the dominant group of yellow pigments used in printing inks, well-suited for most standard process yellow inks. They were formerly important in the coloration of plastics but are no longer recommended for polymers processed above 200 °C, under which conditions toxic decomposition products are formed. Diarylide yellow pigments are characterized by high color strength, good to excellent solvent fastness, and good chemical stability, although they generally show inferior lightfastness.

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