DOCSLIB.ORG

Adfbrochure2012.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Adfbrochure2012.Pdf Quality Software. Quantum Science. ADF www.scm.com Contents Key benefits of ADF package ............................................ 3 Our DFT programs ADF and BAND .............................. 5 Spectroscopic properties .................................................... 6 Structure and reactivity ...................................................... 9 Model Hamiltonians ...........................................................10 Chemical analysis ................................................................ 12 Accuracy and efficiency .................................................... 14 DFTB and MOPAC .............................................................. 16 ReaxFF ..................................................................................... 17 COSMO-RS ...........................................................................18 Integrated Graphical User Interface .............................. 19 Background information ................................................... 21 Feature list ..............................................................................22 Quality Software. Quantum Science. Heavy elements & spectroscopy Molecules, surfaces & crystals Understand & predict Accurate & efficient User-friendly & expert support The Amsterdam Density Functional software suite for chemistry and materials science: ● ADF: accurate DFT for molecules in gas and solution ● BAND: periodic DFT for solids, surfaces and polymers ● DFTB, MOPAC: fast approximate quantum methods (0-3D) ● ReaxFF: reactive MD of complex chemical systems ● COSMO-RS: quantum-based fluid thermodynamics ● GUI: easy preparation, execution and analysis Key benefits of ADF package Excels in modeling transition metals Spectroscopy and heavy elements ADF is a popular tool to predict and understand To treat molecules with heavy elements magnetic, electric, optical and vibrational accurately, relativistic effects need to be spectroscopy, in particular in systems with taken into account. ADF and BAND feature transition metals where relativistic effects play scalar relativistic and full spin-orbit coupling a defining role. The long list of available Hamiltonians through the zeroth-order regular spectroscopic properties, most of which can approximation (ZORA) of the Dirac equation. be calculated efficiently in parallel, continues All-electron basis sets for the entire periodic to expand. We provide the latest exchange- table remove the need for pseudopotentials/ correlation (xc) functionals, including model effective core potentials. Our modern SCF potentials specifically targeted at improved algorithms converge even for difficult systems, optical and magnetic spectra. such as open-shell transition metal compounds. 3 Structure & Reactivity Accurate, robust, fast, and easy to use ADF and BAND have an efficient and stable ADF has an accurate and tunable integration geometry optimizer for both minima and scheme and flexible and stable SCF convergence transitions states (TSs). Even notoriously difficult algorithms. Our software developers follow the TSs can be located with a properly defined TS latest trends in xc functionals, ensuring the reaction coordinate (TSRC). Nudged elastic availability of modern as well as old-time favorite band and IRC are available to trace full reaction xc functionals, including hybrids, metaGGAs and paths. Analytical second derivatives yield normal dispersion corrections. All-electron and frozen- modes and IR spectra, while Raman intensities core basis sets are available up to quadruple-zeta can be calculated for selected modes. Modern for the entire periodic table (H - Uuo). ADF’s meta-GGA, dispersion-corrected, and hybrid Slater-type basis sets resemble the true atomic functionals give excellent results for reaction orbitals more closely than commonly used barrier heights and various chemical analysis Gaussian functions, and are more efficient than tools provide unprecedented insight in structure plane waves for 1D, 2D, and empty 3D periodic and reactivity. structures. Linear scaling techniques and good parallelism up to hundreds of processor Molecules, clusters, polymers, cores makes ADF a very fast program. All our surfaces, solids, liquids programs and the easy graphical user interface The molecular ADF code treats molecules and run out of the box on Mac, Windows or Linux/ clusters in the gas phase or embedded in a UNIX. solvent or protein environment. Our periodic BAND program with localized orbitals deals Expert staff and support with solids as well as with periodic systems SCM provides expert technical and scientific in one (polymers) or two (slabs or surfaces) support by our highly trained team of theoretical dimensions, without resorting to an artificial chemists and physicists with many decades of and inefficient slab-gap approach. The DFTB combined experience in ADF development and and MOPAC programs are fast approximate applications. Active collaborations with a large quantum programs to calculate molecules or number of academic development groups and periodic systems (1D, 2D or 3D) while ReaxFF interactions with users ensure a rapid growth of is a reactive force field approach to study the ADF functionality at the forefront of research. chemical reaction dynamics of large 3D periodic boxes of complex systems (e.g. gas mixtures, solutions, liquid-surface interactions). Going beyond the atomistic level, the COSMO-RS module enables prediction of thermodynamic properties of solutions and mixed fluids (liquids and gases). 4 Our DFT programs: ADF and BAND Key benefits for our molecular ADF and periodic BAND programs are summarized on the previous pages. Below we highlight a few of the ever-expanding list of capabilities. ADF is an efficiently parallelized, powerful computational chemistry program to model, comprehend, and predict chemical structure and reactivity (p. 9). A vast range of spectroscopic properties can be calculated (p. 6), with inclusion of relativistic effects across the entire electromagnetic spectrum from radio waves (NMR) to γ-rays (Mössbauer spectroscopy). ADF can also optimize excited states and calculate phosphorescence with TDDFT, and calculate All-electric single-molecule motor calculated with ADF. electronic transport properties through Green’s See www.scm.com/News/Seldenthuis. functions. Modern xc functionals (dispersion corrections, BAND shares a lot of functionality with the (hybrid) metaGGAs) as well as established molecular ADF code, including chemical analysis functionals (PBE0, B3LYP, BP86) are available (p. 12) and spectroscopic properties: NMR, EPR, and environment effects of solvents, electric and Electric Field Gradients (p. 6). BAND is the fields and large non-reactive parts (e.g. proteins, perfect companion to ADF for surface science, catalysts) can be accounted for in various ways featuring a true 2D approach for molecule- (p. 10). An extensive amount of comprehensive surface interactions, homogeneous electric analysis tools (p. 12) afford precious in-depth field, and local density of state (LDOS) for understanding in chemical structure and STM images. The analysis of molecule-surface reactivity. interactions is facilitated by a consistent accurate description of molecules and surfaces alike, with the same algorithms as ADF for explicit relativity, modern xc functionals, dispersion corrections, and solvent effects via COSMO. Specific properties for periodic systems include: phonon spectra and smooth band structures which can be visualized in our GUI with accompanying points and paths in the Brillouin zone, and frequency-dependent dielectric functions. Solvated Ru complex on a TiO2 surface calculated with the COSMO model in BAND. 5 Spectroscopic properties One of ADF’s strong points is the enormous IR, (resonance) Raman, VROA, VCD breadth of properties, which can be calculated Analytic and numerical second derivatives with high accuracy (basis sets, relativistic effects, yield IR frequencies and intensities. Raman modern functionals) and efficiency (linear scattering intensities and depolarization ratios scaling techniques, parallel implementation). may be calculated for all or for selected vibrations. ADF also features resonance Raman spectra, vibrational (resonance) Raman optical activities (VR(R)OAs), and vibrational circular dichroism (VCD) spectra. The IR spectrum of Cr(CO)6 with animation of the vibrational modes. (Vibrationally resolved) UV/Vis or X-ray spectra; (hyper)polarizabilities, vdW coefficients Excitation energies, oscillator strengths, for vibrationally resolved UV/Vis and X-ray frequency-dependent (hyper)polarizabilities spectra. X-ray structure factors for crystals can (nonlinear optics), and van der Waals dispersion be computed with BAND. Excitation energies coefficients, are all available in ADF as may be calculated state-selectively for open- applications of time-dependent DFT (TDDFT). and closed-shell systems. Unique to ADF, with self-consistent spin-orbit coupling TDDFT Dynamic polarizabilities are available through phosphorescence lifetimes can be calculated, calculated lifetimes at or near resonance. TDDFT important for Organic Light Emitting Diodes gradients allow excited state optimization (OLEDs), see http://www.scm.com/News/ and the calculation of Franck-Condon factors OLEDs.html. 6 Calculated vibronic fine structure of OLED emitter Pt(4,6-dFppy)(acac) in excellent agreement with experiment. CD, ORD, MCD, Verdet constant, magnetizabilities Circular dichroism (CD) and optical rotatory dispersion (ORD) spectra of chiral molecules are
Load more

Recommended publications
  • 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.
    [Show full text]
  • GROMACS: Fast, Flexible, and Free
    GROMACS: Fast, Flexible, and Free DAVID VAN DER SPOEL,1 ERIK LINDAHL,2 BERK HESS,3 GERRIT GROENHOF,4 ALAN E. MARK,4 HERMAN J. C. BERENDSEN4 1Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden 2Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-10691 Stockholm, Sweden 3Max-Planck Institut fu¨r Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany 4Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands Received 12 February 2005; Accepted 18 March 2005 DOI 10.1002/jcc.20291 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simula- tions. The package includes about 100 utility and analysis programs.
    [Show full text]
  • Chem3d 17.0 User Guide Chem3d 17.0
    Chem3D 17.0 User Guide Chem3D 17.0 Table of Contents Recent Additions viii Chapter 1: About Chem3D 1 Additional computational engines 1 Serial numbers and technical support 3 About Chem3D Tutorials 3 Chapter 2: Chem3D Basics 5 Getting around 5 User interface preferences 9 Background settings 10 Sample files 10 Saving to Dropbox 10 Chapter 3: Basic Model Building 12 Default settings 12 Selecting a display mode 12 Using bond tools 13 Using the ChemDraw panel 15 Using other 2D drawing packages 15 Building from text 16 Adding fragments 18 Selecting atoms and bonds 18 Atom charges 21 Object position 23 Substructures 24 Refining models 27 Copying and printing 29 Finding structures online 32 Chapter 4: Displaying Models 35 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. ii Chem3D 17.0 Display modes 35 Atom and bond size 37 Displaying dot surfaces 38 Serial numbers 38 Displaying atoms 39 Atom symbols 40 Rotating models 41 Atom and bond properties 44 Showing hydrogen bonds 45 Hydrogens and lone pairs 46 Translating models 47 Scaling models 47 Aligning models 47 Applying color 49 Model Explorer 52 Measuring molecules 59 Comparing models by overlay 62 Molecular surfaces 63 Using stereo pairs 72 Stereo enhancement 72 Setting view focus 73 Chapter 5: Building Advanced Models 74 Dummy bonds and dummy atoms 74 Substructures 75 Bonding by proximity 78 Setting measurements 78 Atom and building types 81 Stereochemistry 85 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. iii Chem3D 17.0 Building with Cartesian
    [Show full text]
  • CHEM 743 “Quantum Chemistry” S'15
    CHEM 743 \Quantum Chemistry" S'15 Instructor: Sophya Garashchuk∗ Dept of Chemistry and Biochemistry, University of South Carolina, Columbia y (Dated: January 7, 2015) Syllabus • Learning outcomes: (i) the students will gain theoretical knowledge in quantum mechanics and computer skills enabling them to use modern electronic structure codes and simulations with confidence and intelligence to better understand chemical processes; (ii) the students will be able to set up their own input files and interpret/visualize output files for standard quantum chemistry programs/packages that might be relevant to their research; (iii) the students will improve general critical thinking and problem-solving skills as well as improve their skills of independent computer-aided research through extensive use of electronically available resources. • Prerequisites: CHEM 542 or equivalent, i. e. Physical Chemistry - Quantum Mechanics and Spectroscopy • Classes will take place MW 9:40-10:55 AM at PSC 101. We will work with Maple, Q-Chem, Spartan, ADF Class materials and assignments or links to them will be posted on Blackboard Computer and software support: Jun Zhou [email protected] Ph: (803) 777-5492 College of Arts & Sciences Sumwalt College 228 • Office hours: Tue 10-11 am, GSRC 407. I am generally available Mon-Fri 9:00 AM { 5PM. You can just drop by, call or e-mail to check if I am available, or if you have difficulty reaching me, make an appointment. • The suggested general quantum chemistry textbook is \Introduction to Quantum Mechanics in Chemistry", by M. A. Ratner and G. C. Schatz, Prentice-Hall, New Jersey, 2001. Used copies are available through BN.com.
    [Show full text]
  • RMG-Py and Cantherm Documentation ⇌Release 2.0.0
    RMG RMG-Py and CanTherm Documentation ⇌Release 2.0.0 William H. Green, Richard H. West, and the RMG Team Sep 16, 2016 CONTENTS 1 RMG User’s Guide 3 1.1 Introduction...............................................3 1.2 Release Notes..............................................4 1.3 Overview of Features...........................................6 1.4 Installation................................................7 1.5 Creating Input Files........................................... 20 1.6 Example Input Files........................................... 29 1.7 Running a Job.............................................. 36 1.8 Analyzing the Output Files........................................ 37 1.9 Species Representation.......................................... 38 1.10 Group Representation.......................................... 39 1.11 Databases................................................. 39 1.12 Thermochemistry Estimation...................................... 58 1.13 Kinetics Estimation........................................... 63 1.14 Liquid Phase Systems.......................................... 65 1.15 Guidelines for Building a Model..................................... 72 1.16 Standalone Modules........................................... 73 1.17 Frequently Asked Questions....................................... 81 1.18 Credits.................................................. 82 1.19 How to Cite................................................ 82 2 CanTherm User’s Guide 83 2.1 Introduction..............................................
    [Show full text]
  • Mercury Binding to the Chelation Therapy Agents DMSA and DMPS
    Mercury Binding to the Chelation Therapy Agents DMSA and DMPS, and the Rational Design of Custom Chelators for Mercury. Graham N. George,*,† Roger C. Prince,‡ Jürgen Gailer,§ Gavin A. Buttigieg,¶ M. Bonner Denton,¶ Hugh H. Harris⊥ and Ingrid J. Pickering† Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada, ExxonMobil Research and Engineering Company, Annandale, New Jersey 08801, Boehringer Ingelheim Austria GmbH, Dr. Boehringer Gasse 5-11, 1120 Vienna, Austria, Department of Chemistry, The University of Arizona, Tucson, Arizona 85721, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia. AUTHOR EMAIL ADDRESS: [email protected] RECEIVED DATE (to be automatically inserted after your manuscript is accepted if required according to the journal that you are submitting your paper to) TITLE RUNNING HEAD: Mercury Binding to DMSA and DMPS * To whom correspondence should be addressed at Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK, S7N 5E2, Canada. Phone: 306-966-5722, Fax: 306- 966-8593, E-mail: [email protected] † University of Saskatchewan ‡ ExxonMobil Research and Engineering § Boehringer Ingelheim Austria ¶ University of Arizona ⊥ University of Sydney 1 ABSTRACT Clinical chelation therapy of mercury poisoning generally uses one or both of two drugs – meso- dimercaptosuccinic acid (DMSA), and dimercaptopropanesulfonic acid (DMPS), commercially sold as ® ® Chemet and Dimaval , respectively. We have used a combination of mercury LIII-edge X-ray absorption spectroscopy and density functional theory calculations to investigate the chemistry of interaction of mercuric ions with each of these chelation therapy drugs. We show that neither DMSA nor DMPS forms a true chelate complex with mercuric ions, and that these drugs should be considered sub-optimal for their clinical task of binding mercuric ions.
    [Show full text]
  • Teaching with SCIGRESS
    Teaching with SCIGRESS Exercises on Molecular Modeling in Chemistry Crispin Wong and James Currie, eds. Pacific University Teaching with SCIGRES Molecular Modeling in Chemistry Crispin Wong and James Currie Editors Pacific University Forest Grove, Oregon 2 Copyright statement © 2001 - 2012 Fujitsu Limited. All rights reserved. This document may not be used, sold, transferred, copied or reproduced, in any manner or form, or in any medium, to any person other than with the prior written consent of Fujitsu Limited. Published by Fujitsu Limited. All possible care has been taken in the preparation of this publication. Fujitsu Limited does not accept liability for any inaccuracies that may be found. Fujitsu Limited reserves the right to make changes without notice both to this publication and to the product it describes. 3 Table of Contents Exercises 7 Part 1: General Chemistry Experiment 1 Calculating the Geometry of Molecules and Ions 16 Experiment 2 Kinetics of Substitution Reactions 29 Experiment 3 Sunscreen and Ultraviolet Absorption 38 Part 2: Organic Chemistry Experiment 4 Evaluations of Conformations of Menthone and Isomenthone 46 Experiment 5 The Evelyn Effect 52 Part 3: Physical Chemistry Experiment 6 Investigating the Resonance Stabilization of Benzene 63 Experiment 7 Investigation of the Rotational Barrier in N-N-dimethylacetamide 68 Part 4: Inorganic Chemistry Experiment 8 Polarities of Small Molecules 75 Experiment 9 Structures of Molecules Which Exceed the Octet Rule. 77 Experiment 10 Comparison of Gas Phase Acidities of Binary
    [Show full text]
  • Automated Calculation of Reaction Kinetics Via Transition State Theory
    AUTOMATED CALCULATION OF REACTION KINETICS VIA TRANSITION STATE THEORY A Dissertation Presented By Pierre Lennox Bhoorasingh to The Department of Chemical Engineering In partial fulfillment of the requirements for the degree of Doctor of Philosophy in the field of Chemical Engineering Northeastern University Boston, Massachusetts August 2016 Dedication I dedicate this thesis to AMT. i Acknowledgments I have been able to complete this thesis work due to the help I have received from those who have found time in their busy schedules. This is my attempt to express my profound gratitude to those who have helped me during my thesis work. Thanks to my advisor, Prof. Richard West, for the guidance over the 5 years. You also gave me the freedom to explore and that has only enhanced my thesis work, and it has been a pleasure to be your first graduate student. I would also like to thank my thesis committee members, Dr. David Budil, Dr. Hicham Fenniri, Dr. C. Franklin Goldsmith, and Dr. Reza Sheikhi. They made the time to have engaging discussions that impacted this thesis, and were also very generous with their professional advice. Thanks to the Computational Modeling group. Fariba Seyedzadeh Khanshan and Be- linda Slakman, you were always helpful in our discussions and made the laboratory a fun working environment. I’d also like to thank Jason Cain for being a super helpful under- graduate who assumed nothing in pursuit of the right approach. I want to also thank Sean Troiano, Victor Lambert, Jacob Barlow, and Elliot Nash for their contributions to laboratory discussions.
    [Show full text]
  • Winmostar™ User Manual Release 10.7.0
    Winmostar™ User Manual Release 10.7.0 X-Ability Co., Ltd. Sep 30, 2021 Contents 1 Introduction 2 2 Installation Guide 26 3 Main Window 30 4 Basic Operation Flow 33 5 Structure Building 36 6 Main Menu and Subwindows 43 7 Remote job 183 8 Add-On 191 9 Integration with other software 200 10 Other topics 202 11 Known problems 208 12 Frequently asked questions · Troubleshooting 212 Bibliography 242 i Winmostar™ User Manual, Release 10.7.0 This manual describes the operation method of each function of Winmostar (TM). The latest version of this document is available from Official site. If you are using Winmostar (TM) for the first time, please refer to Quick Manual. If there is an uncertain point or it does not move as expected, please confirm Frequently asked questions · Troubleshooting which is updated from time to time. For specific operational procedures for each purpose, such as chemical reaction analysis and calculation of specific physical properties, see various tutorials. Contents 1 CHAPTER 1 Introduction Winmostar (TM) provides a graphical user interface that can efficiently manipulate quantum chemical calculations, first principles calculations, and molecular dynamics calculations. From the creation of the initial structure, from the calculation execution to the result analysis, you can carry out the one operation required for the simulation on Winmostar (TM). For molecular modeling function it has been confirmed to operate up to 100,000 atoms. The function of MD calculation has been confirmed in a larger system. 1.1 About quotation When announcing data created using Winmostar (TM) in academic presentations, articles, etc., please describe the Winmostar (TM) main body as follows, for example.
    [Show full text]
  • Jorge Kohanoff
    DNA damage from first principles Jorge Kohanoff Atomistic Simulation Centre School of Maths and Physics Queen’s University Belfast Northern Ireland UK CP2K UK Users Meeting London, 29th January 2014 Queen’s University Belfast Northern Ireland The Atomistic Simulation Centre Queen’s University Belfast, Northern Ireland Tchavdar Todorov Daniel Dundas Myrta Grüning Gareth Tribello Lorenzo Stella Jorge Kohanoff Contents • Introduction • Low-energy electrons • Electronic capture • C-O bond cleavage in nucleotides • Strand breaks in polynucleotides • Electronic capture in aminoacid-DNA • Conclusions • (Shock waves) Radiation damage of biological systems Radiation causes lesions to any biomolecule, especially DNA Directly Types of DNA Damage Ionization (X-rays, UV) • Base Damage Impact fragmentation • Single Strand Breaks Indirectly by generating reactive species Low-energy electrons by ionization • Double Strand Breaks free radicals: e.g. OH˙ from water • Clustered Damage Thermo-mechanically Strand Breaks Low-energy electrons (1-20 eV) cause SSB and DSB in plasmid DNA B. Boudaïffa et al, Science 287, 1659 (2000) P. Swiderek, Angew. Chem. Int.. Ed. 45, 4056 (2006) SSB DSB The irradiation process projectile ρ(r,t) ρ(r,t’) ) ρρ((r,t’r,t’’) ) ρ(r,t=0) V*(r,t) V*(r,t)’ ) V*V((r,tr,t’’’)) Secondary electron Electronic (heat) transport Phonon emission generation Inelastic electron transport Multiscale phenomenon Secondary electron generation (TDDFT-Ehrenfest) A. A. Correa, J. Kohanoff, E. Artacho, D. Sánchez-Portal, and A. Caro, Non- adiabatic forces in ion-solid interactions: the initial stages of radiation damage, Phys. Rev. Lett. 108, 213201 (2012). M. Ahsan Zeb, J. Kohanoff, D. Sánchez-Portal, A. Arnau, J.
    [Show full text]
  • MOPAC Manual (Seventh Edition)
    MOPAC Manual (Seventh Edition) Dr James J. P. Stewart PUBLIC DOMAIN COPY (NOT SUITABLE FOR PRODUCTION WORK) January 1993 This document is intended for use by developers of semiempirical programs and software. It is not intended for use as a guide to MOPAC. All the new functionalities which have been donated to the MOPAC project during the period 1989-1993 are included in the program. Only minimal checking has been done to ensure confor- mance with the donors' wishes. As a result, this program should not be used to judge the quality of programming of the donors. This version of MOPAC-7 is not supported, and no attempt has been made to ensure reliable performance. This program and documentation have been placed entirely in the public domain, and can be used by anyone for any purpose. To help developers, the donated code is packaged into files, each file representing one donation. In addition, some notes have been added to the Manual. These may be useful in understanding the donations. If you want to use MOPAC-7 for production work, you should get the copyrighted copy from the Quantum Chemistry Program Exchange. That copy has been carefully written, and allows the donors' contributions to be used in a full, production-quality program. Contents CONTENTS New Functionalities: • { Michael B. Coolidge, The Frank J. Seiler Research Laboratory, U.S. Air Force Academy, CO 80840, and James J. P. Stewart, Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO 80921-2512. (The Air Force code was obtained under the Freedom of Information Act) Symmetry is used to speed up FORCE calculations, and to facilitate the analysis of molecular vibrations.
    [Show full text]
  • Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis
    nanomaterials Article Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis Vladimir Bystrov 1,* , Jose Coutinho 2, Pavel Zelenovskiy 3,4 , Alla Nuraeva 3, Svitlana Kopyl 5 , Olga Zhulyabina 6 and Vsevolod Tverdislov 6 1 Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, Pushchino, Moscow 142290, Russia 2 Department of Physics & I3N, University of Aveiro, Campus Santiago, 3810-193 Aveiro, Portugal; [email protected] 3 School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia; [email protected] (P.Z.); [email protected] (A.N.) 4 Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal 5 Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal; [email protected] 6 Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (O.Z.); [email protected] (V.T.) * Correspondence: [email protected] Received: 11 August 2020; Accepted: 27 September 2020; Published: 10 October 2020 Abstract: The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT.
    [Show full text]