Learning Avogadro - the Molecular Editor
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Olaseni Sode
Olaseni Sode Work Address: 5735 S. Ellis Ave. [email protected] Searle 231 +1 (314) 856-2373 The University of Chicago Chicago, IL 60615 Home Address: 1119 E Hyde Park Blvd [email protected] Apt. 3E +1 (314) 856-2373 Chicago, IL 60615 http://www.olaseniosode.com Education University of Illinois at Urbana-Champaign Urbana, IL Ph.D. in Chemistry September 2012 – Supervisor: Professor So Hirata – Thesis title: A Theoretical Study of Molecular Crystals – Transferred from the University of Florida in 2010 with Prof. Hirata Morehouse College Atlanta, GA B.S. & B.A. in Chemistry and French December 2006 – Studied at the Université de Nantes, Nantes, France (2004-2005) Research Experience The University of Chicago Chicago, IL Postdoctoral Research – research advisor: Dr. Gregory A. Voth 2012–present – Studied proposed proton transport minimum free-energy pathways in [FeFe]-hydrogenase via molecular dynamics simulations and the multistate empirical valence bond technique. – Collaborated to develop the multiscale string method to accelerate refinement of chemical reaction pathways of adenosine triphosphate (ATP) hydrolysis in globular and filamentous actin proteins. University of California, San Diego La Jolla, CA Visiting Scholar – research advisor: Dr. Francesco Paesani 2014, 2015 – Developed and implemented a reactive molecular dynamics scheme for condensed phase systems of the hydrated hydronium ions. University of Illinois at Urbana-Champaign Urbana, IL Doctoral Research – research advisor: Dr. So Hirata 2010-2012 – Characterized the vibrational structure of extended systems including infrared and Raman-active vibrations, as well as phonon dispersions and densities of states in the first Brillouin zone. – Developed zero-point vibrational energy analysis scheme for molecular clusters using a fragmented, local basis scheme. -
Pysimm: a Python Package for Simulation of Molecular Systems
SoftwareX 6 (2016) 7–12 Contents lists available at ScienceDirect SoftwareX journal homepage: www.elsevier.com/locate/softx pysimm: A python package for simulation of molecular systems Michael E. Fortunato a, Coray M. Colina a,b,∗ a Department of Chemistry, University of Florida, Gainesville, FL 32611, United States b Department of Materials Science and Engineering and Nuclear Engineering, University of Florida, Gainesville, FL 32611, United States article info a b s t r a c t Article history: In this work, we present pysimm, a python package designed to facilitate structure generation, simulation, Received 15 August 2016 and modification of molecular systems. pysimm provides a collection of simulation tools and smooth Received in revised form integration with highly optimized third party software. Abstraction layers enable a standardized 1 December 2016 methodology to assign various force field models to molecular systems and perform simple simulations. Accepted 5 December 2016 These features have allowed pysimm to aid the rapid development of new applications specifically in the area of amorphous polymer simulations. Keywords: ' 2016 The Authors. Published by Elsevier B.V. Amorphous polymers Molecular simulation This is an open access article under the CC BY license Python (http://creativecommons.org/licenses/by/4.0/). Code metadata Current code version v0.1 Permanent link to code/repository used for this code version https://github.com/ElsevierSoftwareX/SOFTX-D-16-00070 Legal Code License MIT Code versioning system used git Software code languages, tools, and services used python2.7 Compilation requirements, operating environments & Linux dependencies If available Link to developer documentation/manual http://pysimm.org/documentation/ Support email for questions [email protected] 1. -
Mercury 2.4 User Guide and Tutorials 2011 CSDS Release
Mercury 2.4 User Guide and Tutorials 2011 CSDS Release Copyright © 2010 The Cambridge Crystallographic Data Centre Registered Charity No 800579 Conditions of Use The Cambridge Structural Database System (CSD System) comprising all or some of the following: ConQuest, Quest, PreQuest, Mercury, (Mercury CSD and Materials module of Mercury), VISTA, Mogul, IsoStar, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the foregoing data files, documentation and command procedures (each individually a Component) is a database and copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its licensors and all rights are protected. Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary. When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence. All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence. In particular: • The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location. • The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re- distributed in any form, in whole or in part, to any third party. • Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al. -
Instructions on Making Pdf Files Containing 3D
Detailed Instructions for Creating an Embedded Virtual 3-D Image of a Molecule Creating the documents with embedded virtual three-dimensional images may be done fairly easily by repeating the following procedures. Once you have embedded your first image, the use of that image is limited only by your imagination. The following instructions are written in extreme detail with annotated screen shots of the four programs you will use throughout for clarification. Once you are familiar with the procedure embedding a structure of interest should take less than 20 min., limited only by the speed with which you can click a mouse. In practice most of our embedded 3-D images have been created by our undergraduate student collaborators. Step 1. Creating a 2-D image in ChemSketch Using ACD ChemSketch 11.0 Freeware (http://www.acdlabs.com/download/chemsk_download.html ) a two dimensional structure may be drawn as per your specific need (see Figure 1). Once the molecule is drawn, optimized it by clicking the 3-D optimization button then save as an MDL molfile (*.mol). Figure 1: A screen shot of acetone drawn with ChemSketch after 3-D optimization. Step 2. Converting the *.mol file to a *.pdb file using Open Babel The file can now be converted from a .mol file to a .pdb file, Protein Data Bank format, to be properly accessed with the Adobe Acrobat 3D Toolkit 8.1.0. The file conversion is done using Open Babel Graphical User Interface v2.2.0 (openbabel.sourceforge.net) under default settings. Step by step instructions: A. -
A Study on Cheminformatics and Its Applications on Modern Drug Discovery
Available online at www.sciencedirect.com Procedia Engineering 38 ( 2012 ) 1264 – 1275 Internatio na l Conference on Modeling Optimisatio n and Computing (ICMOC 2012) A Study on Cheminformatics and its Applications on Modern Drug Discovery B.Firdaus Begama and Dr. J.Satheesh Kumarb aResearch Scholar, Bharathiar University, Coimbatore, India, [email protected] bAssistant Professor, Bharathiar University, Coimbatore, India, [email protected] Abstract Discovering drugs to a disease is still a challenging task for medical researchers due to the complex structures of biomolecules which are responsible for disease such as AIDS, Cancer, Autism, Alzimear etc. Design and development of new efficient anti-drugs for the disease without any side effects are becoming mandatory in the recent history of human life cycle due to changes in various factors which includes food habit, environmental and migration in human life style. Cheminformaticds deals with discovering drugs based in modern drug discovery techniques which in turn rectifies complex issues in traditional drug discovery system. Cheminformatics tools, helps medical chemist for better understanding of complex structures of chemical compounds. Cheminformatics is a new emerging interdisciplinary field which primarily aims to discover Novel Chemical Entities [NCE] which ultimately results in design of new molecule [chemical data]. It also plays an important role for collecting, storing and analysing the chemical data. This paper focuses on cheminformatics and its applications on drug discovery and modern drug discovery techniques which helps chemist and medical researchers for finding solution to the complex disease. © 2012 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of Noorul Islam Centre for Higher Education. -
Electronic Supporting Information a New Class of Soluble and Stable Transition-Metal-Substituted Polyoxoniobates: [Cr2(OH)4Nb10o
Electronic Supplementary Material (ESI) for Dalton Transactions This journal is © The Royal Society of Chemistry 2012 Electronic Supporting Information A New Class of Soluble and Stable Transition-Metal-Substituted Polyoxoniobates: [Cr2(OH)4Nb10O30]8-. Jung-Ho Son, C. André Ohlin and William H. Casey* A) Computational Results The two most interesting aspects of this new polyoxoanion is the inclusion of a more redox active metal and the optical activity in the visible region. For these reasons we in particular wanted to explore whether it was possible to readily and routinely predict the location of the absorbance bands of this type of compound. Also, owing to the difficulty in isolating the oxidised and reduced forms of the central polyanion dichromate species, we employed computations at the density functional theory (DFT) level to get a better idea of the potential characteristics of these forms. Structures were optimised for anti-parallel and parallel electronic spin alignments, and for both high and low spin cases where relevant. Intermediate spin configurations were 8- II III also tested for [Cr2(OH)4Nb10O30] . As expected, the high spin form of the Cr Cr complex was favoured (Table S1, below). DFT overestimates the bond lengths in general, but gives a good picture of the general distortion of the octahedral chromium unit, and in agreement with the crystal structure predicts that the shortest bond is the Cr-µ2-O bond trans from the central µ6- oxygen in the Lindqvist unit, and that the (Nb-)µ2-O-Cr-µ4-O(-Nb,Nb,Cr) angle is smaller by ca 5˚ from the ideal 180˚. -
Computer-Assisted Catalyst Development Via Automated Modelling of Conformationally Complex Molecules
www.nature.com/scientificreports OPEN Computer‑assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands Sibo Lin1*, Jenna C. Fromer2, Yagnaseni Ghosh1, Brian Hanna1, Mohamed Elanany3 & Wei Xu4 Simulation of conformationally complicated molecules requires multiple levels of theory to obtain accurate thermodynamics, requiring signifcant researcher time to implement. We automate this workfow using all open‑source code (XTBDFT) and apply it toward a practical challenge: diphosphinoamine (PNP) ligands used for ethylene tetramerization catalysis may isomerize (with deleterious efects) to iminobisphosphines (PPNs), and a computational method to evaluate PNP ligand candidates would save signifcant experimental efort. We use XTBDFT to calculate the thermodynamic stability of a wide range of conformationally complex PNP ligands against isomeriation to PPN (ΔGPPN), and establish a strong correlation between ΔGPPN and catalyst performance. Finally, we apply our method to screen novel PNP candidates, saving signifcant time by ruling out candidates with non‑trivial synthetic routes and poor expected catalytic performance. Quantum mechanical methods with high energy accuracy, such as density functional theory (DFT), can opti- mize molecular input structures to a nearby local minimum, but calculating accurate reaction thermodynamics requires fnding global minimum energy structures1,2. For simple molecules, expert intuition can identify a few minima to focus study on, but an alternative approach must be considered for more complex molecules or to eventually fulfl the dream of autonomous catalyst design 3,4: the potential energy surface must be frst surveyed with a computationally efcient method; then minima from this survey must be refned using slower, more accurate methods; fnally, for molecules possessing low-frequency vibrational modes, those modes need to be treated appropriately to obtain accurate thermodynamic energies 5–7. -
Getting Started in Jmol
Getting Started in Jmol Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingResources/jmol/jmolTraining/started.html Introduction Physical models of proteins are powerful tools that can be used synergistically with computer visualizations to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own! At the MSOE Center for BioMolecular Modeling we use the molecular visualization program Jmol to explore protein and molecular structures in fully interactive 3-dimensional displays. Jmol a free, open source molecular visualization program used by students, educators and researchers internationally. The Jmol Training Guide from the MSOE Center for BioMolecular Modeling will provide the tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters. Examples of Proteins in Jmol Jmol allows users to rotate proteins and molecular structures in a fully interactive 3-dimensional display. Some sample proteins designed with Jmol are shown to the right. Hemoglobin Proteins Insulin Proteins Green Fluorescent safely carry oxygen in the help regulate sugar in Proteins create blood. the bloodstream. bioluminescence in animals like jellyfish. Downloading Jmol Jmol Can be Used in Two Ways: 1. As an independent program on a desktop - Jmol can be downloaded to run on your desktop like any other program. It uses a Java platform and therefore functions equally well in a PC or Mac environment. 2. As a web application - Jmol has a web-based version (oftern refered to as "JSmol") that runs on a JavaScript platform and therefore functions equally well on all HTML5 compatible browsers such as Firefox, Internet Explorer, Safari and Chrome. -
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department Name of FOSS Applications Employability GChemPaint GChemPaint is an editor for 2Dchem- GChemPaint is currently being developed ical structures with a multiple docu- as part of The Chemistry Development ment interface. Kit, and a Standard Widget Tool kit- based GChemPaint application is being developed, as part of Bioclipse. Jmol Jmol applet is used to explore the Jmol is a free, open source molecule viewer structure of molecules. Jmol applet is for students, educators, and researchers used to depict X-ray structures in chemistry and biochemistry. It is cross- platform, running on Windows, Mac OS X, and Linux/Unix systems. For PG Students LaTeX Document markup language and Value addition to academic Skills set. preparation system for Tex typesetting Essential for International paper presentation and scientific journals. For PG student for their project work Scilab Scientific Computation package for Value addition in technical problem numerical computations solving via use of computational methods for engineering problems, Applicable in Chemical, ECE, Electrical, Electronics, Civil, Mechanical, Mathematics etc. For PG student who are taking Physical Chemistry Avogadro Avogadro is a free and open source, Research and Development in Chemistry, advanced molecule editor and Pharmacist and University lecturers. visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc. Spoken Tutorial Project, IIT Bombay Brochure for Commerce and Commerce IT Name of FOSS Applications / Employability LibreOffice – Writer, Calc, Writing letters, documents, creating spreadsheets, tables, Impress making presentations, desktop publishing LibreOffice – Base, Draw, Managing databases, Drawing, doing simple Mathematical Math operations For Commerce IT Students Drupal Drupal is a free and open source content management system (CMS). -
Dalton2018.0 – Lsdalton Program Manual
Dalton2018.0 – lsDalton Program Manual V. Bakken, A. Barnes, R. Bast, P. Baudin, S. Coriani, R. Di Remigio, K. Dundas, P. Ettenhuber, J. J. Eriksen, L. Frediani, D. Friese, B. Gao, T. Helgaker, S. Høst, I.-M. Høyvik, R. Izsák, B. Jansík, F. Jensen, P. Jørgensen, J. Kauczor, T. Kjærgaard, A. Krapp, K. Kristensen, C. Kumar, P. Merlot, C. Nygaard, J. Olsen, E. Rebolini, S. Reine, M. Ringholm, K. Ruud, V. Rybkin, P. Sałek, A. Teale, E. Tellgren, A. Thorvaldsen, L. Thøgersen, M. Watson, L. Wirz, and M. Ziolkowski Contents Preface iv I lsDalton Installation Guide 1 1 Installation of lsDalton 2 1.1 Installation instructions ............................. 2 1.2 Hardware/software supported .......................... 2 1.3 Source files .................................... 2 1.4 Installing the program using the Makefile ................... 3 1.5 The Makefile.config ................................ 5 1.5.1 Intel compiler ............................... 5 1.5.2 Gfortran/gcc compiler .......................... 9 1.5.3 Using 64-bit integers ........................... 12 1.5.4 Using Compressed-Sparse Row matrices ................ 13 II lsDalton User’s Guide 14 2 Getting started with lsDalton 15 2.1 The Molecule input file ............................ 16 2.1.1 BASIS ................................... 17 2.1.2 ATOMBASIS ............................... 18 2.1.3 User defined basis sets .......................... 19 2.2 The LSDALTON.INP file ............................ 21 3 Interfacing to lsDalton 24 3.1 The Grand Canonical Basis ........................... 24 3.2 Basisset and Ordering .............................. 24 3.3 Normalization ................................... 25 i CONTENTS ii 3.4 Matrix File Format ................................ 26 3.5 The lsDalton library bundle .......................... 27 III lsDalton Reference Manual 29 4 List of lsDalton keywords 30 4.1 **GENERAL ................................... 31 4.1.1 *TENSOR ...............................