DOCSLIB.ORG

On the Calculation of Molecular Properties of Heavy Element Systems with Ab Initio Approaches: from Gas-Phase to Complex Systems André Severo Pereira Gomes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
On the Calculation of Molecular Properties of Heavy Element Systems with Ab Initio Approaches: from Gas-Phase to Complex Systems André Severo Pereira Gomes On the calculation of molecular properties of heavy element systems with ab initio approaches: from gas-phase to complex systems André Severo Pereira Gomes To cite this version: André Severo Pereira Gomes. On the calculation of molecular properties of heavy element systems with ab initio approaches: from gas-phase to complex systems. Theoretical and/or physical chemistry. Universite de Lille, 2016. tel-01960393 HAL Id: tel-01960393 https://hal.archives-ouvertes.fr/tel-01960393 Submitted on 19 Dec 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. M´emoirepr´esent´epour obtenir le dipl^omed' Habilitation `adiriger des recherches { Sciences Physiques de l'Universit´ede Lille (Sciences et Technologies) ANDRE´ SEVERO PEREIRA GOMES Universit´ede Lille - CNRS Laboratoire PhLAM UMR 8523 On the calculation of molecular properties of heavy element systems with ab initio approaches: from gas-phase to complex systems M´emoirepr´esent´epour obtenir le dipl^omed' Habilitation `adiriger des recherches { Sciences Physiques de l'Universit´ede Lille (Sciences et Technologies) ANDRE´ SEVERO PEREIRA GOMES Universit´ede Lille - CNRS Laboratoire PhLAM UMR 8523 On the calculation of molecular properties of heavy element systems with ab initio approaches: from gas-phase to complex systems Soutenue publiquement le 16/12/2016, Membres du jury Rapporteur Hans Jørgen Aagaard Jensen Assistant Professor, Department of Chemistry and Physics, University of Southern Denmark, Odense, Denmark Rapporteur Nikolas Kaltsoyannis Professor and Head of Computational Chemistry, School of Chemistry, The University of Manchester, Manchester, UK Rapporteur Octavio Roncero Investigador Cient´ıfico,Dept. Fisica Atomica, Molecular y de Agregados, Instituto de Fisica Fundamental (C.S.I.C.), Madrid, Spain Examinateur Sylvain Cristol Professeur, Universit´ede Lille (Sciences et Technologies), Villeneuve d'Ascq, France Garant de l'habilitation Val´erieVallet Directrice de recherche au CNRS, Universit´ede Lille (Sciences et Technologies), Villeneuve d'Ascq, France c Andr´eSevero Pereira Gomes, April 11, 2017 Contents Contents 5 1 Abstract 1 2 Sommaire 3 3 Preface 5 4 Background and Motivation 7 4.1 Heavy elements from the perspective of \goal-driven" research . 7 4.2 Heavy elements from the perspective of \curiosity-driven" research . 11 4.3 This manuscript . 12 5 Electronic Structure Methods 13 5.1 Electronic structure methods for excited states . 13 5.2 The molecular Hamiltonian in the relativistic framework . 27 5.3 A comparison of IHFSCC to experiment for heavy elements . 33 5.4 Benchmaking approximate methods for small systems . 39 5.5 Towards large systems with TDDFT . 44 6 Frozen Density Embedding Methods 47 6.1 Basic Ideas and Exact Theory . 47 6.2 Approximate Embedding Methods . 54 6.3 Actinyls in Cs2UO2Cl4 .................................... 61 6.4 The shortcomings of the kinetic energy density functionals: CUO-Ng complexes . 65 6.5 FDE Second-order magnetic properties: formalism and first applications . 67 7 Perspectives 77 7.1 The treatment of electron correlation for open-shell ground and excited states . 77 7.2 The calculation of molecular properties with coupled cluster approaches . 79 7.3 Generalizing molecular properties for DFT-in-DFT and CC-in-DFT embedding . 79 7.4 Improving the accuracy of embedding approaches for strongly interacting systems . 80 7.5 Combining a molecular description of properties with a periodic description of the environment . 81 Bibliography 83 A Curriculum Vitae 107 B List of Publications 113 C Calculations on Gas-phase species 117 C.1 Paper I . 118 C.2 Paper II . 128 C.3 Paper III . 141 5 6 Contents C.4 Paper IV . 150 C.5 Paper V . 162 C.6 Paper VI . 168 C.7 Paper VI . 180 D Development of FDE and Applications to Heavy Elements 195 D.1 Paper VIII . 196 D.2 Paper IX . 207 D.3 Paper X . 219 D.4 Paper XI . 236 D.5 Paper XII . 249 D.6 Paper XIII . 263 D.7 Paper XIV . 274 List of Figures 291 List of Tables 292 Chapter 1 Abstract This work discusses theoretical approaches to model the electronic structure of species containing heavy elements { that is, those from the fifth row onwards on the periodic table { with a special emphasis on lanthanides and actinides, due to their importance in a number of technological issues and applications in fields as diverse as consumer electronics and nuclear energy. The three key ingredients which should be addressed in modeling of such systems are: (i) relativistic effects, arising from the speeds close to that of the light to which inner electrons are accelerated for heavy nuclei; (ii) electron correlation effects, due to the instantaneous interactions between the electrons as well as due to quasi-degeneracies in the electronic states in heavy element species that often possess unpaired d or f electrons; and (iii) environment effects arising from the interaction of the heavy element species with surrounding molecules, since these are often found in the condensed phase. We begin by briefly reviewing the approaches used to describe electron correlation and relativis- tic effects before turning our attention to the four-component intermediate Hamiltonian Fock-space coupled cluster (4c-IHFSCC) method in order to first establish its accuracy with respect to available experimental results and later show how served as a reference method to which more approximate ones were assessed. From this assessment it is then possible to pick the most suitable approaches to, for instance, treat treat large molecular systems which are beyond the reach of very accurate (and therefore computationally very costly) approaches. Next we briefly review the frozen density embedding (FDE) method, a formally exact approach that myself and others use as a framework to devise computationally efficient schemes to account for environment effects on the aforementioned electronic structure approaches. Application of these approximate schemes to heavy element systems are discussed in order to show that FDE can be quite accurate describe environment effects (notably in the absence of strong interactions such as covalent bonds between subsystems), thus allowing one to use approaches such as 4c-IHFSCC to obtain electronic spectra or ionization energies. 1 Chapter 2 Sommaire Cet ouvrage pr´esente des approches th´eoriquesapplicables `ala mod´elisationde la structure ´electronique d'esp`ecescontenant des ´el´ements lourds { c'est `adire, ceux qui se situent au-del`ade la cinqui`eme p´eriode de la classification p´eriodique { avec un int´er^etparticulier port´eaux lanthanides et actinides `acause de leur importance dans des domaines si vari´esque les appareils ´electroniquesou l'´energie nucl´eaire. La mod´elisationde la structure ´electroniquepour tels syst`emes requiert la prise en compte de trois ingr´edients : (i) des effets relativistes d^uaux vitesses tr`es´elev´eesdes ´electronsdu cœur, caus´ees par la forte attraction des noyaux lourds ; (ii) des effets de corr´elation´electronique issus non seulement de l'interaction instantan´eeentre ´electronsmais aussi de la quasi-d´eg´en´erescencessouvent pr´esentes dans des ´el´ements lourds poss´edant des couches ´electroniques d et f partiellement remplies ; et (iii) des effets de l'environnement sur les propri´et´esdes mol´eculescontenant les ´el´ements lourds, car celles-ci se trouvent en g´en´eralen phase condens´ee. Nous commen¸conspar une br`eve r´evisiondes approches utilis´eespour d´ecrirela corr´elation ´electroniqueet les effets relativistes avant de nous pencher sur la m´ethode intermediate Hamiltonian Fock-space coupled cluster `aquatre composantes (4c-IHFSCC), de fa¸con`a´etablirsa pr´ecisionpar rapport `ades r´esultatsexp´erimentaux et ensuite montrer comment celle-ci peut ^etreutilis´eecomme m´ethode de r´ef´erencepour l'´evaluation d'approches plus approxim´ees. Ces comparaisons nous ont permis ensuite de choisir les approches les plus ad´equatespour le traitement de syst`emesmol´eculaires plus ´etendus,qui seraient impossibles `atraiter avec des m´ethodes plus pr´ecises(et par cons´equent plus co^uteuses). Ensuite nous pr´esentons la m´ethode frozen density embedding (FDE), une approche formelle- ment exacte que moi-m^emeet d'autres utilisons comme point de d´epartpour concevoir des m´ethodes efficaces du point de vue computationnel afin de d´ecrireles effets de l'environnement dans le cadre des calculs de structure ´electronique. Nous discutons aussi de l'application de ces m´ethodes com- putationnelles `ades syst`emescontenant des ´el´ements lourds pour montrer qu'elles sont capables de tr`esbien d´ecrireles effets de l'environnement (notamment dans l'absence de interactions fortes telles que des liaisons chimiques entre sous-syst`emes),permettant ainsi l'utilisation d'approches telles que 4c-IHFSCC pour obtenir des spectres ´electroniquesou des ´energiesd'ionisation. 3 Chapter 3 Preface This manuscript describes my scientific activities on the calculation of molecular properties for systems containing heavy elements such as actinides, lanthanides and transition metals, carried out during my time as Postdoctoral researcher at the Free University (VU) Amsterdam under the supervision of Lucas Visscher (2005-2006, 2007-2009), at the Universit´ede Strasbourg (2006-2007) under the supervision of Trond Saue, and at the Universit´ede Lille 1 (2009), and following my appointment at CNRS as researcher (charg´ede recherche) in 2009. The main focus of my first year as postdoc in Amsterdam was on exploring how to execute computational chemistry codes in grid environments, but I profited from this period to start exploring with Ivan Infante the use of accurate, wavefunction-based (WFT) electronic structure methods such as Fock-space coupled cluster (FSCC) to obtain the electronic states of actinyl ions.
Load more

Recommended publications
  • Modern Quantum Chemistry with [Open]Molcas
    Modern quantum chemistry with [Open]Molcas Cite as: J. Chem. Phys. 152, 214117 (2020); https://doi.org/10.1063/5.0004835 Submitted: 17 February 2020 . Accepted: 11 May 2020 . Published Online: 05 June 2020 Francesco Aquilante , Jochen Autschbach , Alberto Baiardi , Stefano Battaglia , Veniamin A. Borin , Liviu F. Chibotaru , Irene Conti , Luca De Vico , Mickaël Delcey , Ignacio Fdez. Galván , Nicolas Ferré , Leon Freitag , Marco Garavelli , Xuejun Gong , Stefan Knecht , Ernst D. Larsson , Roland Lindh , Marcus Lundberg , Per Åke Malmqvist , Artur Nenov , Jesper Norell , Michael Odelius , Massimo Olivucci , Thomas B. Pedersen , Laura Pedraza-González , Quan M. Phung , Kristine Pierloot , Markus Reiher , Igor Schapiro , Javier Segarra-Martí , Francesco Segatta , Luis Seijo , Saumik Sen , Dumitru-Claudiu Sergentu , Christopher J. Stein , Liviu Ungur , Morgane Vacher , Alessio Valentini , and Valera Veryazov J. Chem. Phys. 152, 214117 (2020); https://doi.org/10.1063/5.0004835 152, 214117 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp Modern quantum chemistry with [Open]Molcas Cite as: J. Chem. Phys. 152, 214117 (2020); doi: 10.1063/5.0004835 Submitted: 17 February 2020 • Accepted: 11 May 2020 • Published Online: 5 June 2020 Francesco Aquilante,1,a) Jochen Autschbach,2,b) Alberto Baiardi,3,c) Stefano Battaglia,4,d) Veniamin A. Borin,5,e) Liviu F. Chibotaru,6,f) Irene Conti,7,g) Luca De Vico,8,h) Mickaël Delcey,9,i) Ignacio Fdez. Galván,4,j) Nicolas Ferré,10,k) Leon Freitag,3,l) Marco Garavelli,7,m) Xuejun Gong,11,n) Stefan Knecht,3,o) Ernst D. Larsson,12,p) Roland Lindh,4,q) Marcus Lundberg,9,r) Per Åke Malmqvist,12,s) Artur Nenov,7,t) Jesper Norell,13,u) Michael Odelius,13,v) Massimo Olivucci,8,14,w) Thomas B.
    [Show full text]
  • Charge-Transfer Biexciton Annihilation in a Donor-Acceptor
    Electronic Supplementary Material (ESI) for Chemical Science. This journal is © The Royal Society of Chemistry 2020 Supporting Information for Charge-Transfer Biexciton Annihilation in a Donor-Acceptor Co-crystal yields High-Energy Long-Lived Charge Carriers Itai Schlesinger, Natalia E. Powers-Riggs, Jenna L. Logsdon, Yue Qi, Stephen A. Miller, Roel Tempelaar, Ryan M. Young, and Michael R. Wasielewski* Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113 Contents 1. Single crystal X-ray structure data. ..................................................................................................2 2. Crystal structure determination and refinement.............................................................................3 3. Additional Steady-state absorption Spectra.....................................................................................4 4. Pump and probe spot sizes.................................................................................................................5 5. Excitation density and fraction of molecules excited calculations ..................................................6 6. Calculation of the fraction of CT excitons adjacent to one another ...............................................7 7. Calculation of reorganization energies and charge transfer rates..................................................9 8. Model Hamiltonian for calculating polarization-dependent steady-state absorption
    [Show full text]
  • FORCE FIELDS and CRYSTAL STRUCTURE PREDICTION Contents
    FORCE FIELDS AND CRYSTAL STRUCTURE PREDICTION Bouke P. van Eijck ([email protected]) Utrecht University (Retired) Department of Crystal and Structural Chemistry Padualaan 8, 3584 CH Utrecht, The Netherlands Originally written in 2003 Update blind tests 2017 Contents 1 Introduction 2 2 Lattice Energy 2 2.1 Polarcrystals .............................. 4 2.2 ConvergenceAcceleration . 5 2.3 EnergyMinimization .......................... 6 3 Temperature effects 8 3.1 LatticeVibrations............................ 8 4 Prediction of Crystal Structures 9 4.1 Stage1:generationofpossiblestructures . .... 9 4.2 Stage2:selectionoftherightstructure(s) . ..... 11 4.3 Blindtests................................ 14 4.4 Beyondempiricalforcefields. 15 4.5 Conclusions............................... 17 4.6 Update2017............................... 17 1 1 Introduction Everybody who looks at a crystal structure marvels how Nature finds a way to pack complex molecules into space-filling patterns. The question arises: can we understand such packings without doing experiments? This is a great challenge to theoretical chemistry. Most work in this direction uses the concept of a force field. This is just the po- tential energy of a collection of atoms as a function of their coordinates. In principle, this energy can be calculated by quantumchemical methods for a free molecule; even for an entire crystal computations are beginning to be feasible. But for nearly all work a parameterized functional form for the energy is necessary. An ab initio force field is derived from the abovementioned calculations on small model systems, which can hopefully be generalized to other related substances. This is a relatively new devel- opment, and most force fields are empirical: they have been developed to reproduce observed properties as well as possible. There exists a number of more or less time- honored force fields: MM3, CHARMM, AMBER, GROMOS, OPLS, DREIDING..
    [Show full text]
  • Generating Gaussian Basis Sets for CRYSTAL and Qwalk Lucas K
    Generating Gaussian basis sets for CRYSTAL and QWalk Lucas K. Wagner The point of a basis set is to describe a (generally unknown) function efficiently. That is, we are going to approximate some general function f(x) by a sum over known basis functions (in this case χ(x)): X f(x) = ciχi(x): (1) i We will usually choose χi(x) such that they are convenient to work with. Perhaps integrals are easy to do with them, or perhaps they very closely approximate the function f(x), so that we don’t need too many elements in the sum of Eqn1. One basis set expansion that you may be familiar with is the Fourier expansion, which uses plane waves as the χi’s. In many-body quantum systems, we typically start our description of the many-body wave function Ψ(r1; r2;:::) with a Slater determinant. This is written as follows: 0 1 φ1(r1) φ1(r2) φ1(r3) ::: B φ2(r1) φ2(r2) φ2(r3) ::: C ΨS(r1; r2;:::) = Det B C (2) @ φ3(r1) φ3(r2) φ3(r3) ::: A :::::::::::: where ri is the position of the ith electron and φi(r) is called a molecular or crystalline orbital (MO/CO). The Slater determinant is the simplest possible many-electron wave function that satisfies fermion antisymmetry [Ψ(r1; r2;:::) = Ψ(r2; r1;:::)]. There also − exist algorithms to evaluate properties of the Slater determinant efficiently. Note that these one-particle functions φi have not yet been specified, and we will have to come up with a way to represent them within the computer.
    [Show full text]
  • The Molpro Quantum Chemistry Package
    The Molpro Quantum Chemistry package Hans-Joachim Werner,1, a) Peter J. Knowles,2, b) Frederick R. Manby,3, c) Joshua A. Black,1, d) Klaus Doll,1, e) Andreas Heßelmann,1, f) Daniel Kats,4, g) Andreas K¨ohn,1, h) Tatiana Korona,5, i) David A. Kreplin,1, j) Qianli Ma,1, k) Thomas F. Miller, III,6, l) Alexander Mitrushchenkov,7, m) Kirk A. Peterson,8, n) Iakov Polyak,2, o) 1, p) 2, q) Guntram Rauhut, and Marat Sibaev 1)Institut f¨ur Theoretische Chemie, Universit¨at Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany 2)School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom 3)School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom 4)Max-Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany 5)Faculty of Chemistry, University of Warsaw, L. Pasteura 1 St., 02-093 Warsaw, Poland 6)Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States 7)MSME, Univ Gustave Eiffel, UPEC, CNRS, F-77454, Marne-la- Vall´ee, France 8)Washington State University, Department of Chemistry, Pullman, WA 99164-4630 1 Molpro is a general purpose quantum chemistry software package with a long devel- opment history. It was originally focused on accurate wavefunction calculations for small molecules, but now has many additional distinctive capabilities that include, inter alia, local correlation approximations combined with explicit correlation, highly efficient implementations of single-reference correlation methods, robust and efficient multireference methods for large molecules, projection embedding and anharmonic vibrational spectra.
    [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]
  • 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]
  • Molecular Modeling in Undergraduate Chemical Education
    Molecular Modeling in Undergraduate Chemical Education Summer 2005 Dr. Thomas Gardner Sean Ohlinger Wavefunction, Inc. 18401 Von Karman, Suite 370 Irvine, CA 92612 [email protected] www.wavefun.com A Workshop featuring A World of Molecular Visualization Possibilities! What are we going to do today? • Introduce you to molecular modeling with Spartan software and show how you can use this in teaching • Give you plenty of time to have fun working with the software • Demonstrate the Cambridge Crystal Structure Database (CCSD) and its interface with Spartan • Introduce Odyssey, the new Wavefunction courseware • Exchange ideas • Address your needs The Plan Part I Part II • Introduction to modeling • Discussion of Odyssey, and Spartan SpartanModel, and • Build some molecules Spartan Student Edition • Overview of • Hands-on with Odyssey computational chemistry • Animations in Spartan • An examination of PABA • Modeling reaction • Lunch chemistry • Stump the band What we won’t do today • Overwhelm you • Teach you the full intricacies of Spartan • Teach you all about computational chemistry What can you do with molecular modeling in your classroom and laboratory? • Enhance teaching of selected concepts and content • Move from two dimensions into three • Chemistry is about molecules, and the behavior of electrons • Prepare course material and WWW images • Computational experiments in place of selected wet labs • Motivate students to be excited about chemistry • Research, enrichment and special projects • Advanced courses • Better prepare students for graduate school and careers The Modeling Experiment • Build Structures Spartan allows the rapid construction of virtually any structure in three dimensions. • Perform Calculations Classical and quantum mechanical models offer sophisticated descriptions of both known and hypothetical molecules.
    [Show full text]
  • Ncomms1451.Pdf
    ARTICLE Received 29 Jun 2011 | Accepted 21 Jul 2011 | Published 16 Aug 2011 DOI: 10.1038/ncomms1451 From computational discovery to experimental characterization of a high hole mobility organic crystal Anatoliy N. Sokolov1,*, Sule Atahan-Evrenk2,*, Rajib Mondal1,*, Hylke B. Akkerman1, Roel S. Sánchez-Carrera2, Sergio Granados-Focil3, Joshua Schrier4, Stefan C.B. Mannsfeld5, Arjan P. Zoombelt1, Zhenan Bao1 & Alán Aspuru-Guzik2 For organic semiconductors to find ubiquitous electronics applications, the development of new materials with high mobility and air stability is critical. Despite the versatility of carbon, exploratory chemical synthesis in the vast chemical space can be hindered by synthetic and characterization difficulties. Here we show that in silico screening of novel derivatives of the dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]thiophene semiconductor with high hole mobility and air stability can lead to the discovery of a new high-performance semiconductor. On the basis of estimates from the Marcus theory of charge transfer rates, we identified a novel compound expected to demonstrate a theoretic twofold improvement in mobility over the parent molecule. Synthetic and electrical characterization of the compound is reported with single-crystal field- effect transistors, showing a remarkable saturation and linear mobility of 12.3 and 16 cm2 V − 1 s − 1, respectively. This is one of the very few organic semiconductors with mobility greater than 10 cm2 V − 1 s − 1 reported to date. 1 Department of Chemical Engineering, Stanford University, Stauffer III, 381 North-South Mall, Stanford, California 94305, USA. 2 Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.
    [Show full text]
  • Learning Avogadro - the Molecular Editor
    Learning Avogadro - The Molecular Editor Table of Contents 1. Preface 2. Getting Started i. Introduction ii. Drawing Molecules iii. Making Selections 3. Building Molecules i. Importing Molecules by Name ii. Importing from the Protein Data Bank (PDB) iii. Building a Peptide iv. Building DNA or RNA v. Building Carbon Nanotubes vi. Insert Molecular Fragments vii. Building with SMILES 4. Building Materials i. Building a Supercell ii. Making a Crystal Surface Slab iii. Building a Polymer Unit Cell iv. Perceiving Crystall Symmetry v. Reducing Crystals to a Primitive Unit Cell vi. Scaling Crystal Cell Volume vii. Building Molecule-Surface Interactions 5. Tools i. Draw Tool ii. Navigate Tool iii. Bond-Centric Manipulate Tool iv. Manipulate Tool v. Selection Tool vi. Auto-Rotate Tool vii. Auto-Optimize Tool viii. Measure Tool ix. Align Tool 6. Display Types i. Different Display Styles ii. Coloring Part of a Molecules 7. Menus i. File Menu ii. Edit Menu iii. View Menu iv. Build Menu v. Select Menu vi. Extension Menu 8. Optimizing Geometry i. Introduction to Molecular Mechanics ii. Finding Conformers of Molecules iii. Geometry Constraints 9. Extensions i. ABINIT Input Generator ii. LAMMPS Input 10. Tutorials 2 Learning Avogadro - The Molecular Editor i. Using QTAIM (Atoms in Molecules) Analysis ii. Viewing Vibrations iii. Viewing Vibrational Spectra Calculations iv. Viewing Molecular Orbitals v. Viewing Electrostatic Potential Maps vi. Naming a Molecule 3 Learning Avogadro - The Molecular Editor Avogadro: Molecular Editor and Visualization Avogadro is a free, open source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
    [Show full text]
  • Efficient Evaluation of Exact Exchange for Periodic Systems Via
    Efficient Evaluation of Exact Exchange for Periodic Systems via Concentric Atomic Density Fitting Xiao Wang,1, 2 Cannada A. Lewis,1 and Edward F. Valeev1, a) 1)Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA 2)Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA (Dated: 9 June 2020) The evaluation of exact (Hartree{Fock, HF) exchange operator is a crucial ingredi- ent for the accurate description of electronic structure in periodic systems through ab initio and hybrid density functional approaches. An efficient formulation of peri- odic HF exchange in LCAO representation presented here is based on the concentric atomic density fitting (CADF) approximation, a domain-free local density fitting ap- proach in which the product of two atomic orbitals (AOs) is approximated using a linear combination of fitting basis functions centered at the same nuclei as the AOs in that product. Significant reduction in the computational cost of exact exchange is demonstrated relative to the conventional approach due to avoiding the need to evaluate four-center two-electron integrals, with sub-millihartree/atom errors in abso- lute Hartree-Fock energies and good cancellation of fitting errors in relative energies. Novel aspects of the evaluation of the Coulomb contribution to the Fock operator, such as the use of real two-center multipole expansions and spheropole-compensated unit cell densities are also described. arXiv:2006.03999v1 [physics.chem-ph] 6 Jun 2020 a)Electronic mail: [email protected] 1 I. Introduction There has been dramatic recent progress in reduced-scaling many-body formalisms for molecular electronic structure problem.1{11 Such approaches allow robust simulation of elec- tronic structure of large systems that surpasses the accuracy of mainstream methods, i.e.
    [Show full text]
  • Release65:Nwchem Documentation 1 Release65:Nwchem Documentation
    Release65:NWChem Documentation 1 Release65:NWChem Documentation __NOTITLE__ NWChem 6. 5 User Documentation Overview __NOTITLE__ • Comprehensive Suite of Scalable Capabilities • Compiling NWChem • Getting Started • Top-level Directives • NWChem Architecture • Running NWChem System Description __NOTITLE__ • Charge • Geometry • Basis Sets • Effective Core Potentials • Relativistic All-electron Approximations Quantum Mechanical Methods __NOTITLE__ • Hartree-Fock (HF) Theory • Density Functional Theory (DFT) • Excited-State Calculations (CIS, TDHF, TDDFT) • Real-time TDDFT • Plane-Wave Density Functional Theory (plane-wave DFT) • Tensor Contraction Engine: CI, MBPT, and CC • MP2 • Coupled Cluster Calculations • Multiconfiguration SCF • Selected CI Classical Methods __NOTITLE__ • Prepare • Molecular Dynamics • Analysis Hybrid Approaches __NOTITLE__ • COSMO Solvation Model • Solvation Model Based on Density (SMD) Model • Vertical Excitation or Emission (VEM) Model • Hybrid Calculations with ONIOM • Combined Quantum and Molecular Mechanics (QM/MM) Release65:NWChem Documentation 2 • External Charges (Bq) Potential Energy Surface Analysis __NOTITLE__ • Constraints for Optimization • Geometry Optimization (Minimization & Transition State Search) • Hessians & Vibrational Frequencies • Nudged Elastic Band (NEB) and Zero Temperature String Methods Electronic Structure Analysis __NOTITLE__ • Molecular Properties • Electrostatic Potential Charges • DPLOT Other Capabilities __NOTITLE__ • Electron Transfer Calculations • VSCF • Dynamical Nucleation Theory
    [Show full text]