Application of Hartree-Fock Method for Modeling of Bioactive Molecules Using SAR and QSPR
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Quantitative Structure–Activity Relationships (Qsar) Study on Novel 4-Amidinoquinoline and 10- Amidinobenzonaphthyridine Derivatives As Potent Antimalaria Agent
JCECThe Journal of Engineering and Exact Sciences – JCEC, Vol. 05 N. 03 (2019) journal homepage: https://periodicos.ufv.br/ojs/jcec doi: 10.18540/jcecvl5iss3pp0271-0282 OPEN ACCESS – ISSN: 2527-1075 QUANTITATIVE STRUCTURE–ACTIVITY RELATIONSHIPS (QSAR) STUDY ON NOVEL 4-AMIDINOQUINOLINE AND 10- AMIDINOBENZONAPHTHYRIDINE DERIVATIVES AS POTENT ANTIMALARIA AGENT A. W. MAHMUD1, G. A. SHALLANGWA1 and A. UZAIRU1 1Ahmadu Bello University, Department of Chemistry, Zaria, Kaduna, Nigeria. A R T I C L E I N F O A B S T R A C T Article history: Quantitative structure–activity relationships (QSAR) has been a reliable study in the Received 2019-02-16 development of models that predict biological activities of chemical substances based on Accepted 2019-06-27 Available online 2019-06-30 their structures for the development of novel chemical entities. This study was carried out on 44 compounds of 4-amidinoquinoline and 10-amidinobenzonaphthyridine derivatives to p a l a v r a s - c h a v e develop a model that relates their structures to their activities against Plasmodium QSAR falciparum. Density Functional Theory (DFT) with basis set B3LYP/6-31G was used to ∗ Antimalaria optimize the compounds. Genetic Function Algorithm (GFA) was employed in selecting Plasmodium falciparum descriptors and building the model. Four models were generated and the model with best 4-Amidinoquinolina internal and external validation has internal squared correlation coefficient ( 2) of 0.9288, k e y w o r d s adjusted squared correlation coefficient ( adj) of 0.9103, leave-one-out (LOO) cross- 2 2 QSAR validation coefficient ( cv) value of 0.8924 and external squared correlation coefficient ( ) Antimalaria value of 0.8188. -
Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extracts and Flavonoids from Pistacia Integerrima
DOI:http://dx.doi.org/10.7314/APJCP.2016.17.1.51 Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extract and Flavonoids from Pistacia integerrima RESEARCH ARTICLE Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extracts and Flavonoids from Pistacia integerrima Abdur Rauf1*, Ghias Uddin2, Muslim Raza3, Bashir Ahmad4, Noor Jehan1, Bina S Siddiqui5, Joseph Molnar6, Akos Csonka6, Diana Szabo6 Abstract Phytochemical investigation of Pistacia integerrima has highlighted isolation of two known compounds naringenin (1) and dihydrokaempferol (2). A crude extract and these isolated compounds were here evaluated for their effects on reversion of multidrug resistance (MDR) mediated by P-glycoprotein (P-gp). The multidrug resistance P-glycoprotein is a target for chemotherapeutic drugs from cancer cells. In the present study rhodamine- 123 exclusion screening test on human mdr1 gene transfected mouse gene transfected L5178 and L5178Y mouse T-cell lymphoma cells showed excellent MDR reversing effects in a dose dependent manner. In-silico molecular docking investigations demonstrated a common binding site for Rhodamine123, and compounds naringenin and dihydrokaempferol. Our results showed that the relative docking energies estimated by docking softwares were in satisfactory correlation with the experimental activities. Preliminary interaction profile of P-gp docked complexes were also analysed in order to understand the nature of binding modes of these compounds. Our computational investigation suggested that the compounds interactions with the hydrophobic pocket of P-gp are mainly related to the inhibitory activity. Moreover this study s a platform for the discovery of novel natural compounds from herbal origin, as inhibitor molecules against the P-glycoprotein for the treatment of cancer. -
The Norbornene Mystery Revealed
Supplementary Material (ESI) for Chemical Communications This journal is (c) The Royal Society of Chemistry 2010 Electronic Supporting Information The Norbornene Mystery Revealed Stephan N. Steinmann, Pierre Vogel, Yirong Mo, and Clémence Corminboeuf* To be published in Chemical Communication. The supplementary Data were prepared on June 22, 2010 and contains 14 pages. Contents: Method Section Figure S1: Molecules used for the comparisons between known experimental 1 Jcc-coupling constants (in Hertz) and the computed values. 1 Table S1 JCC-coupling comparison between experiment and computation. 1 Table S2: JCC-coupling constants for all compounds considered. Cartesian coordinates: B3LYP/6-311+G(d,p) (BLW and canonical) optimized structures for all compounds considered in the article. Contents: Computational Details 1 Table S1: JCC-coupling constants for all compounds considered. 1 Figure S1: Molecules for JCC-coupling comparison between experiment and computation. 1 Table S2: JCC-coupling comparison between experiment and computation. B3LYP/6-311+G(d,p) (BLW and canonical) optimized structures for all compounds considered in the article. Computational Details Standard geometries were optimized at the B3LYP1, 2/6-311+G** level using Gaussian 09.3 The BLW- constrained B3LYP/6-311+G** geometries (‘loc’) were optimized using a modified version of GAMESS-US (release 2008)4interfaced with the BLW-module.5, 6 Both the density and the J-coupling constants have been computed at the PBE7/IGLO-III level in Dalton 2.0.8 The BLW-eigenvalues and eigenvectors were optimized at the given DFT level with the SCF module of Dalton, SIRIUS, that has been interfaced with the BLW- module. -
Computational Chemistry for Chemistry Educators Shawn C
Volume 1, Issue 1 Journal Of Computational Science Education Computational Chemistry for Chemistry Educators Shawn C. Sendlinger Clyde R. Metz North Carolina Central University College of Charleston Department of Chemistry Department of Chemistry and Biochemistry 1801 Fayetteville Street, 66 George Street, Durham, NC 27707 Charleston, SC 29424 919-530-6297 843-953-8097 [email protected] [email protected] ABSTRACT 1. INTRODUCTION In this paper we describe an ongoing project where the goal is to The majority of today’s students are technologically savvy and are develop competence and confidence among chemistry faculty so often more comfortable using computers than the faculty who they are able to utilize computational chemistry as an effective teach them. In order to harness the student’s interest in teaching tool. Advances in hardware and software have made technology and begin to use it as an educational tool, most faculty research-grade tools readily available to the academic community. members require some level of instruction and training. Because Training is required so that faculty can take full advantage of this chemistry research increasingly utilizes computation as an technology, begin to transform the educational landscape, and important tool, our approach to chemistry education should reflect attract more students to the study of science. this. The ability of computer technology to visualize and manipulate objects on an atomic scale can be a powerful tool to increase both student interest in chemistry as well as their level of Categories and Subject Descriptors understanding. Computational Chemistry for Chemistry Educators (CCCE) is a project that seeks to provide faculty the J.2 [Physical Sciences and Engineering]: Chemistry necessary knowledge, experience, and technology access so that they can begin to design and incorporate computational approaches in the courses they teach. -
Organi &C Biomolecular Chemistry
Organic Biomolecular& Chemistry INDEXED IN MEDLINE Incorporating Acta Chemica Scandinavica Instructions for Authors (2004) Also see www.rsc.org/illustrations and www.rsc.org/electronicfiles CONTENTS 1.0 General Policy 1.0 General Policy Organic & Biomolecular Chemistry is a bimonthly journal 1.1 Articles for the publication of original research papers (articles), 1.2 Communications communications, Emerging Areas and Perspectives focusing on 1.3 Emerging Areas all aspects of synthetic, physical and biomolecular organic 1.4 Perspective Articles chemistry. 1.5 Submission of Articles Authors should note that papers that mainly emphasise the novel properties, applications or potential applications of 2.0 Administration materials may be more suited for submission to Journal of Materials Chemistry. (http://www.rsc.org/materials). 3.0 Notes on the Preparation of Papers There is no page charge for papers published in Organic & 3.1 Organisation of Material Biomolecular Chemistry. 3.2 Artwork Guidelines 3.3 Nomenclature Scope of the Journal 3.4 Deposition of Supplementary Data Organic & Biomolecular Chemistry brings together molecular 3.5 Guidelines on submitting files for proof preparation design, synthesis, structure, function and reactivity in one journal. It publishes fundamental work on synthetic, physical 4.0 Experimental and Characterisation Requirements and biomolecular organic chemistry as well as all organic 4.1 Physical Characteristics of Compounds aspects of: chemical biology, medicinal chemistry, natural 4.2 Characterisation of New Compounds -
Molecular Dynamics Simulations of Tight Junction Proteins
Molecular Dynamics Simulations of Tight Junction Proteins Eleni Fitsiou This dissertation is submitted for the degree of Doctor of Philosophy August 2020 Department of Chemistry I would like to dedicate this dissertation to my husband Antonios and sons Dimitrios and Ioannis. ii “Wisdom begins in wonder” Socrates iii Declaration I, Eleni Fitsiou, declare that this thesis titled ‘Molecular Dynamics Simulations of Tight Junction Proteins’ has not been submitted in support of an application for another degree at this or any other university. It is the result of my own work and includes nothing that is the outcome of work done in collaboration except where specifically indicated. Where I have quoted from the work of others, the source is always given. Lancaster University, UK iv Abstract Tight junctions (TJs) are specialised cell-cell structures that serve primarily as a barrier to molecular transport through the intercellular space between the cells. The claudin family of proteins are the main structural and functional components of the TJ strands that circumscribe the cells. The detailed molecular organisation at the TJs is not entirely resolved, being relatively inaccessible by current experimental methods. Here, we have employed molecular dynamics simulations using both atomistic and coarse-grained models to investigate the TJ structure formed by claudin-1 using self-assembly coupled with free energy calculations and enhanced sampling techniques. A feature of the studies is that the self-assembly simulations have been carried out using atomistic detail (a first) by simulating only the extracellular domains of claudin-1 in an implied membrane. The results show that the cis-interaction can occur in the absence of trans-interacting partners and that a claudin dimer is the smallest stable unit. -
Interpretation of Molecule Conformations from Drawn Diagrams” by Dana Tenneson, Ph.D., Brown University, May 2008
Abstract of \Interpretation of Molecule Conformations from Drawn Diagrams" by Dana Tenneson, Ph.D., Brown University, May 2008. In chemistry, molecules are drawn on paper and chalkboards as diagrams consisting of lines, letters, and symbols which represent not only the atoms and bonds in the molecules but concisely encode cues to the 3D geometry of the molecules. Recent efforts into pen-based input methods for chemistry software have made progress at allowing chemists to input 2D diagrams of molecules into a computer simply by drawing them on a digitizer tablet. However, the task of interpreting these parsed sketches into proper 3D models has been largely unsolved due to the difficulty in making the models satisfy both the natural properties of molecule structure and the geometric cues made explicit in the drawing. This dissertation presents a set of techniques developed to solve this model construction problem within the context of an educational application for chemistry students. Our primary contribution is a framework for combining molecular structure knowledge and molecule diagram understanding via augmenting molecular mechanics equations to include drawing-based penalty terms. Additionally, we present an algorithm for generating molecule models from drawn diagrams which leverages domain- specific and diagram-driven heuristics. These heuristics make our process fast and accurate enough for molecule diagram drawing to be used as an interactive technique for model construction on modern Tablet PC computers. Interpretation of Molecule Conformations -
Car-Parrinello Molecular Dynamics
CPMD Car-Parrinello Molecular Dynamics An ab initio Electronic Structure and Molecular Dynamics Program The CPMD consortium WWW: http://www.cpmd.org/ Mailing list: [email protected] E-mail: [email protected] January 29, 2019 Send comments and bug reports to [email protected] This manual is for CPMD version 4.3.0 CPMD 4.3.0 January 29, 2019 Contents I Overview3 1 About this manual3 2 Citation 3 3 Important constants and conversion factors3 4 Recommendations for further reading4 5 History 5 5.1 CPMD Version 1.....................................5 5.2 CPMD Version 2.....................................5 5.2.1 Version 2.0....................................5 5.2.2 Version 2.5....................................5 5.3 CPMD Version 3.....................................5 5.3.1 Version 3.0....................................5 5.3.2 Version 3.1....................................5 5.3.3 Version 3.2....................................5 5.3.4 Version 3.3....................................6 5.3.5 Version 3.4....................................6 5.3.6 Version 3.5....................................6 5.3.7 Version 3.6....................................6 5.3.8 Version 3.7....................................6 5.3.9 Version 3.8....................................6 5.3.10 Version 3.9....................................6 5.3.11 Version 3.10....................................7 5.3.12 Version 3.11....................................7 5.3.13 Version 3.12....................................7 5.3.14 Version 3.13....................................7 5.3.15 Version 3.14....................................7 5.3.16 Version 3.15....................................8 5.3.17 Version 3.17....................................8 5.4 CPMD Version 4.....................................8 5.4.1 Version 4.0....................................8 5.4.2 Version 4.1....................................8 5.4.3 Version 4.3....................................9 6 Installation 10 7 Running CPMD 11 8 Files 12 II Reference Manual 15 9 Input File Reference 15 9.1 Basic rules........................................ -
Ab Initio Search for Novel Bxhy Building Blocks with Potential for Hydrogen Storage
Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 12-2010 Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage Jared K. Olson Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Physical Chemistry Commons Recommended Citation Olson, Jared K., "Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage" (2010). All Graduate Theses and Dissertations. 844. https://digitalcommons.usu.edu/etd/844 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. AB INITIO SEARCH FOR NOVEL BXHY BUILDING BLOCKS WITH POTENTIAL FOR HYDROGEN STORAGE by Jared K. Olson A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry (Physical Chemistry) Approved: Dr. Alexander I. Boldyrev Dr. Steve Scheiner Major Professor Committee Member Dr. David Farrelly Dr. Stephen Bialkowski Committee Member Committee Member Dr. T.C. Shen Byron Burnham Committee Member Dean of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2010 ii Copyright © Jared K. Olson 2010 All Rights Reserved iii ABSTRACT Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage by Jared K. Olson, Doctor of Philosophy Utah State University, 2010 Major Professor: Dr. Alexander I. Boldyrev Department: Chemistry and Biochemistry On-board hydrogen storage presents a challenging barrier to the use of hydrogen as an energy source because the performance of current storage materials falls short of platform requirements. -
Introduction to Bioinformatics (Elective) – SBB1609
SCHOOL OF BIO AND CHEMICAL ENGINEERING DEPARTMENT OF BIOTECHNOLOGY Unit 1 – Introduction to Bioinformatics (Elective) – SBB1609 1 I HISTORY OF BIOINFORMATICS Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biologicaldata. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques. Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine. Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. "Classical" bioinformatics: "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.” The National Center for Biotechnology Information (NCBI 2001) defines bioinformatics as: "Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. -
Surface Modification of Mgni by Perylene
Materials Transactions, Vol. 43, No. 11 (2002) pp. 2711 to 2716 Special Issue on Protium New Function in Materials c 2002 The Japan Institute of Metals Surface Modification of MgNi by Perylene Tiejun Ma, Yuji Hatano, Takayuki Abe and Kuniaki Watanabe Hydrogen Isotope Research Center, Toyama University, Toyama 930-8555, Japan Amorphous MgNi was modified by ball milling with perylene and its effects on the charge/discharge capacity were examined by using a conventional two-electrode cell. It was found that both the ball milling time and perylene/MgNi ratio had great influence on the discharge capacity and cycle life of MgNi. Three types of effects were identified, depending on ball-milling conditions. One of them was the increase in the discharge capacity at the first cycle, the second type was the deceleration of the degradation of the discharge capacity with charge/discharge cycle, and the last type was the reduction in the charge/discharge capacity. Chemical states of modified surfaces were analyzed by Auger electron spectroscopy (AES) as well as ab-inito calculation. Both AES and ab-initio calculations indicated that carbon atoms can form bonding with both magnesium and nickel atoms, but bonding with magnesium atoms is most preferable. The change in the charge/discharge capacity is attributed to such kind of reactions, and the three distinct effects are ascribed to the presence of different MgNi-perylene composites, formed during the ball milling on the surface, resulting in the retardation or acceleration of Mg(OH)2 formation on the electrode. (Received May 20, 2002; Accepted July 16, 2002) Keywords: magnesium, nickel, aromatic compound, surface modification, battery, electrode 1. -
Titelei 1..30
Johann Gasteiger, Thomas Engel (Eds.) Chemoinformatics Chemoinformatics: A Textbook. Edited by Johann Gasteiger and Thomas Engel Copyright 2003 Wiley-VCH Verlag GmbH & Co. KGaA. ISBN: 3-527-30681-1 Related Titles from WILEY-VCH Hans-Dieter HoÈltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers Molecular Modeling 2003 ISBN 3-527-30589-0 Helmut GuÈnzler, Hans-Ulrich Gremlich IR Spectroscopy An Introduction 2002 ISBN 3-527-28896-1 Jure Zupan, Johann Gasteiger Neural Networks in Chemistry and Drug Design An Introduction 1999 ISBN 3-527-29778-2 (HC) ISBN 3-527-29779-0 (SC) Siegmar Braun, Hans-Otto Kalinowski, Stefan Berger 150 and More Basic NMR Experiments A Practical Course 1998 ISBN 3-527-29512-7 Johann Gasteiger, Thomas Engel (Eds.) Chemoinformatics A Textbook Editors: This book was carefully produced. Never- theless, editors, authors and publisher do Prof. Dr. Johann Gasteiger not warrant the information contained Computer-Chemie-Centrum and Institute therein to be free of errors. Readers are ofOrganic Chemistry advised to keep in mind that statements, University ofErlangen-NuÈrnberg data, illustrations, procedural details or NaÈgelsbachstraûe 25 other items may inadvertently be inaccurate. 91052 Erlangen Germany Library of Congress Card No.: applied for A catalogue record for this book is available from the British Library. Dr. Thomas Engel Computer-Chemie-Centrum and Institute Bibliographic information published by ofOrganic Chemistry Die Deutsche Bibliothek University ofErlangen-NuÈrnberg Die Deutsche Bibliothek lists this publica- NaÈgelsbachstraûe 25 tion in the Deutsche Nationalbibliografie; 91052 Erlangen detailed bibliographic data is available in the Germany Internet at http://dnb.ddb.de ISBN 3-527-30681-1 c 2003 WILEY-VCH Verlag GmbH & Co.