Electron Correlation Effects in Molecules
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Density Functional Theory
Density Functional Approach Francesco Sottile Ecole Polytechnique, Palaiseau - France European Theoretical Spectroscopy Facility (ETSF) 22 October 2010 Density Functional Theory 1. Any observable of a quantum system can be obtained from the density of the system alone. < O >= O[n] Hohenberg, P. and W. Kohn, 1964, Phys. Rev. 136, B864 Density Functional Theory 1. Any observable of a quantum system can be obtained from the density of the system alone. < O >= O[n] 2. The density of an interacting-particles system can be calculated as the density of an auxiliary system of non-interacting particles. Hohenberg, P. and W. Kohn, 1964, Phys. Rev. 136, B864 Kohn, W. and L. Sham, 1965, Phys. Rev. 140, A1133 Density Functional ... Why ? Basic ideas of DFT Importance of the density Example: atom of Nitrogen (7 electron) 1. Any observable of a quantum Ψ(r1; ::; r7) 21 coordinates system can be obtained from 10 entries/coordinate ) 1021 entries the density of the system alone. 8 bytes/entry ) 8 · 1021 bytes 4:7 × 109 bytes/DVD ) 2 × 1012 DVDs 2. The density of an interacting-particles system can be calculated as the density of an auxiliary system of non-interacting particles. Density Functional ... Why ? Density Functional ... Why ? Density Functional ... Why ? Basic ideas of DFT Importance of the density Example: atom of Oxygen (8 electron) 1. Any (ground-state) observable Ψ(r1; ::; r8) 24 coordinates of a quantum system can be 24 obtained from the density of the 10 entries/coordinate ) 10 entries 8 bytes/entry ) 8 · 1024 bytes system alone. 5 · 109 bytes/DVD ) 1015 DVDs 2. -
Theoretical Methods That Help Understanding the Structure and Reactivity of Gas Phase Ions
International Journal of Mass Spectrometry 240 (2005) 37–99 Review Theoretical methods that help understanding the structure and reactivity of gas phase ions J.M. Merceroa, J.M. Matxaina, X. Lopeza, D.M. Yorkb, A. Largoc, L.A. Erikssond,e, J.M. Ugaldea,∗ a Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Euskadi, Spain b Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA c Departamento de Qu´ımica-F´ısica, Universidad de Valladolid, Prado de la Magdalena, 47005 Valladolid, Spain d Department of Cell and Molecular Biology, Box 596, Uppsala University, 751 24 Uppsala, Sweden e Department of Natural Sciences, Orebro¨ University, 701 82 Orebro,¨ Sweden Received 27 May 2004; accepted 14 September 2004 Available online 25 November 2004 Abstract The methods of the quantum electronic structure theory are reviewed and their implementation for the gas phase chemistry emphasized. Ab initio molecular orbital theory, density functional theory, quantum Monte Carlo theory and the methods to calculate the rate of complex chemical reactions in the gas phase are considered. Relativistic effects, other than the spin–orbit coupling effects, have not been considered. Rather than write down the main equations without further comments on how they were obtained, we provide the reader with essentials of the background on which the theory has been developed and the equations derived. We committed ourselves to place equations in their own proper perspective, so that the reader can appreciate more profoundly the subtleties of the theory underlying the equations themselves. Finally, a number of examples that illustrate the application of the theory are presented and discussed. -
Camcasp 5.9 Alston J. Misquitta† and Anthony J
CamCASP 5.9 Alston J. Misquittay and Anthony J. Stoneyy yDepartment of Physics and Astronomy, Queen Mary, University of London, 327 Mile End Road, London E1 4NS yy University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW September 1, 2015 Abstract CamCASP is a suite of programs designed to calculate molecular properties (multipoles and frequency- dependent polarizabilities) in single-site and distributed form, and interaction energies between pairs of molecules, and thence to construct atom–atom potentials. The CamCASP distribution also includes the programs Pfit, Casimir,Gdma 2.2, Cluster, and Process. Copyright c 2007–2014 Alston J. Misquitta and Anthony J. Stone Contents 1 Introduction 1 1.1 Authors . .1 1.2 Citations . .1 2 What’s new? 2 3 Outline of the capabilities of CamCASP and other programs 5 3.1 CamCASP limits . .7 4 Installation 7 4.1 Building CamCASP from source . .9 5 Using CamCASP 10 5.1 Workflows . 10 5.2 High-level scripts . 10 5.3 The runcamcasp.py script . 11 5.4 Low-level scripts . 13 6 Data conventions 13 7 CLUSTER: Detailed specification 14 7.1 Prologue . 15 7.2 Molecule definitions . 15 7.3 Geometry manipulations and other transformations . 16 7.4 Job specification . 18 7.5 Energy . 23 7.6 Crystal . 25 7.7 ORIENT ............................................... 26 7.8 Finally, . 29 8 Examples 29 8.1 A SAPT(DFT) calculation . 29 8.2 An example properties calculation . 30 8.3 Dispersion coefficients . 34 8.4 Using CLUSTER to obtain the dimer geometry . 36 9 CamCASP program specification 39 9.1 Global data . -
Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C
Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C. All rights reserved. Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QSite, and QikProp are trademarks of Schrödinger, L.L.C. MacroModel is a registered trademark of Schrödinger, L.L.C. To the maximum extent permitted by applicable law, this publication is provided “as is” without warranty of any kind. This publication may contain trademarks of other companies. October 2003 Contents Chapter 1: Introduction.......................................................................................1 1.1 Conventions Used in This Manual.......................................................................2 1.2 Citing Jaguar in Publications ...............................................................................3 Chapter 2: The Maestro Graphical User Interface...........................................5 2.1 Starting Maestro...................................................................................................5 2.2 The Maestro Main Window .................................................................................7 2.3 Maestro Projects ..................................................................................................7 2.4 Building a Structure.............................................................................................9 2.5 Atom Selection ..................................................................................................10 2.6 Toolbar Controls ................................................................................................11 -
Thomas–Fermi–Dirac–Von Weizsäcker Models in Finite Systems Garnet Kin-Lic Chan, Aron J
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Caltech Authors - Main Thomas–Fermi–Dirac–von Weizsäcker models in finite systems Garnet Kin-Lic Chan, Aron J. Cohen, and Nicholas C. Handy Citation: 114, (2001); doi: 10.1063/1.1321308 View online: http://dx.doi.org/10.1063/1.1321308 View Table of Contents: http://aip.scitation.org/toc/jcp/114/2 Published by the American Institute of Physics JOURNAL OF CHEMICAL PHYSICS VOLUME 114, NUMBER 2 8 JANUARY 2001 Thomas–Fermi–Dirac–von Weizsa¨cker models in finite systems Garnet Kin-Lic Chan,a) Aron J. Cohen, and Nicholas C. Handy Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom ͑Received 7 June 2000; accepted 8 September 2000͒ To gain an understanding of the variational behavior of kinetic energy functionals, we perform a numerical study of the Thomas–Fermi–Dirac–von Weizsa¨cker theory in finite systems. A general purpose Gaussian-based code is constructed to perform energy and geometry optimizations on polyatomic systems to high accuracy. We carry out benchmark studies on atomic and diatomic systems. Our results indicate that the Thomas–Fermi–Dirac–von Weizsa¨cker theory can give an approximate description of matter, with atomic energies, binding energies, and bond lengths of the correct order of magnitude, though not to the accuracy required of a qualitative chemical theory. We discuss the implications for the development of new kinetic functionals. © 2001 American Institute of Physics. ͓DOI: 10.1063/1.1321308͔ I. INTRODUCTION -
The Size-Consistency Problem in Configuration Interaction Calculation
The Size-Consistency Problem in Configuration Interaction calculation P´eter G. Szalay E¨otv¨osLor´and University Institute of Chemistry H-1518 Budapest, P.O.Box 32, Hungary [email protected] P.G. Szalay: Size-consistency corrected CI Rio de Janeiro, Nov. 27 - Dec. 2, 2005 Size-consistency Consider two subsystems at infinite separation. We have two choices: • treat the two system separately; • consider only a super-system. Provided that there is no interaction between the two systems, the two treatments should give the same result, a basic physical requirement. E¨otv¨osLor´and University, Institute of Chemistry 1 P.G. Szalay: Size-consistency corrected CI Rio de Janeiro, Nov. 27 - Dec. 2, 2005 Size-consistency Let us use the CID wave function to describe this system! For the super − system we have : ΨCID = ΦHF + ΦD (1) ΦD is the sum all double excitations out of ΦHF (including coefficients). For the subsystems we can write: A A A ΨCID = ΦHF + ΦD (2) B B B ΨCID = ΦHF + ΦD (3) The product of these two wave functions gives the other choice for the wave function of the super-system: A+B A B ΨCID = ΨCID ΨCID (4) A B A B B A A B = ΦHF ΦHF + ΦHF ΦD + ΦHF ΦD + ΦD ΦD A B = ΦHF + ΦD + ΦD ΦD E¨otv¨osLor´and University, Institute of Chemistry 2 P.G. Szalay: Size-consistency corrected CI Rio de Janeiro, Nov. 27 - Dec. 2, 2005 Size-consistency This simple model enables us to identify the origin of the size-consistency error: The difference of the two super-system wave functions: A B A B ΨCID ΨCID − ΨCID = ΦD ΦD (5) i.e. -
Quantum Chemical Calculations of NMR Parameters
Quantum Chemical Calculations of NMR Parameters Tatyana Polenova University of Delaware Newark, DE Winter School on Biomolecular NMR January 20-25, 2008 Stowe, Vermont OUTLINE INTRODUCTION Relating NMR parameters to geometric and electronic structure Classical calculations of EFG tensors Molecular properties from quantum chemical calculations Quantum chemistry methods DENSITY FUNCTIONAL THEORY FOR CALCULATIONS OF NMR PARAMETERS Introduction to DFT Software Practical examples Tutorial RELATING NMR OBSERVABLES TO MOLECULAR STRUCTURE NMR Spectrum NMR Parameters Local geometry Chemical structure (reactivity) I. Calculation of experimental NMR parameters Find unique solution to CQ, Q, , , , , II. Theoretical prediction of fine structure constants from molecular geometry Classical electrostatic model (EFG)- only in simple ionic compounds Quantum mechanical calculations (Density Functional Theory) (EFG, CSA) ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL EFG TENSOR IS DETERMINED BY THE COMBINED ELECTRONIC AND NUCLEAR WAVEFUNCTION, NO ANALYTICAL EXPRESSION IN THE GENERAL CASE THE SIMPLEST APPROXIMATION: CLASSICAL POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 ATOMS CONTRIBUTING TO THE EFG TENSOR ARE TREATED AS POINT CHARGES, THE RESULTING EFG TENSOR IS THE SUM WITH RESPECT TO ALL ATOMS VERY CRUDE MODEL, WORKS QUANTITATIVELY ONLY IN SIMPLEST IONIC SYSTEMS, BUT YIELDS QUALITATIVE TRENDS AND GENERAL UNDERSTANDING OF THE SYMMETRY AND MAGNITUDE OF THE EXPECTED TENSOR ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 2Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 3 Ze V = ; V = 0; V = 0 2,0 2 d 3 2,±1 2,±2 V2,0 = 0; V2,±1 = 0; V2,±2 = 0 MOLECULAR PROPERTIES FROM QUANTUM CHEMICAL CALCULATIONS H = E See for example M. -
Use of Mo”Ller-Plesset Perturbation Theory in Molecular Calculations: Spectroscopic Constants of First Row Diatomic Molecules
JOURNAL OF CHEMICAL PHYSICS VOLUME 108, NUMBER 12 22 MARCH 1998 Use of Mo”ller-Plesset perturbation theory in molecular calculations: Spectroscopic constants of first row diatomic molecules Thom H. Dunning, Jr. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 Kirk A. Peterson Department of Chemistry, Washington State University and the Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 ~Received 9 December 1997; accepted 17 December 1997! The convergence of Mo”ller–Plesset perturbation expansions ~MP2–MP4/MP5! for the spectroscopic constants of a selected set of diatomic molecules ~BH, CH, HF, N2, CO, and F2! has been investigated. It was found that the second-order perturbation contributions to the spectroscopic constants are strongly dependent on basis set, more so for HF and CO than for BH. The MP5 contributions for HF were essentially zero for the cc-pVDZ basis set, but increased significantly with basis set illustrating the difficulty of using small basis sets as benchmarks for correlated calculations. The convergence behavior of the exact Mo”ller–Plesset perturbation expansions were investigated using estimates of the complete basis set limits obtained using large correlation consistent basis sets. For BH and CH, the perturbation expansions of the spectroscopic constants converge monotonically toward the experimental values, while for HF, N2, CO, and F2, the expansions oscillate about the experimental values. The perturbation expansions are, in general, only slowly converging and, for HF, N2, CO, and F2, appear to be far from convergence at MP4. In fact, for HF, N2, and CO, the errors in the calculated spectroscopic constants for the MP4 method are larger than those for the MP2 method ~the only exception is De!. -
Virt&L-Comm.3.2012.1
Virt&l-Comm.3.2012.1 A MODERN APPROACH TO AB INITIO COMPUTING IN CHEMISTRY, MOLECULAR AND MATERIALS SCIENCE AND TECHNOLOGIES ANTONIO LAGANA’, DEPARTMENT OF CHEMISTRY, UNIVERSITY OF PERUGIA, PERUGIA (IT)* ABSTRACT In this document we examine the present situation of Ab initio computing in Chemistry and Molecular and Materials Science and Technologies applications. To this end we give a short survey of the most popular quantum chemistry and quantum (as well as classical and semiclassical) molecular dynamics programs and packages. We then examine the need to move to higher complexity multiscale computational applications and the related need to adopt for them on the platform side cloud and grid computing. On this ground we examine also the need for reorganizing. The design of a possible roadmap to establishing a Chemistry Virtual Research Community is then sketched and some examples of Chemistry and Molecular and Materials Science and Technologies prototype applications exploiting the synergy between competences and distributed platforms are illustrated for these applications the middleware and work habits into cooperative schemes and virtual research communities (part of the first draft of this paper has been incorporated in the white paper issued by the Computational Chemistry Division of EUCHEMS in August 2012) INTRODUCTION The computational chemistry (CC) community is made of individuals (academics, affiliated to research institutions and operators of chemistry related companies) carrying out computational research in Chemistry, Molecular and Materials Science and Technology (CMMST). It is to a large extent registered into the CC division (DCC) of the European Chemistry and Molecular Science (EUCHEMS) Society and is connected to other chemistry related organizations operating in Chemical Engineering, Biochemistry, Chemometrics, Omics-sciences, Medicinal chemistry, Forensic chemistry, Food chemistry, etc. -
Ab Initio Investigation of the Ground State Properties of PO, PO + , and PO − Aristophanes Metropoulos, Aristotle Papakondylis, and Aristides Mavridis
Ab initio investigation of the ground state properties of PO, PO + , and PO − Aristophanes Metropoulos, Aristotle Papakondylis, and Aristides Mavridis Citation: The Journal of Chemical Physics 119, 5981 (2003); doi: 10.1063/1.1599341 View online: http://dx.doi.org/10.1063/1.1599341 View Table of Contents: http://scitation.aip.org/content/aip/journal/jcp/119/12?ver=pdfcov Published by the AIP Publishing Articles you may be interested in Correlated ab initio investigations on the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O 2 − ( X Π g 2 ) − HF ( X Σ + 1 ) complex J. Chem. Phys. 138, 014304 (2013); 10.1063/1.4772653 Molecular geometry of OCAgI determined by broadband rotational spectroscopy and ab initio calculations J. Chem. Phys. 136, 064306 (2012); 10.1063/1.3683221 Ab initio properties of Li-group-II molecules for ultracold matter studies J. Chem. Phys. 135, 164108 (2011); 10.1063/1.3653974 Calculation of the structure, potential energy surface, vibrational dynamics, and electric dipole properties for the Xe:HI van der Waals complex J. Chem. Phys. 134, 174302 (2011); 10.1063/1.3583817 Potential curves and spectroscopic properties for the ground state of ClO and for the ground and various excited states of ClO − J. Chem. Phys. 117, 9703 (2002); 10.1063/1.1516803 This article is copyrighted as indicated in the article. Reuse of AIP content is subject to the terms at: http://scitation.aip.org/termsconditions. Downloaded to IP: 128.240.225.44 On: Sat, 20 Dec 2014 03:10:02 JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 12 22 SEPTEMBER 2003 Ab initio investigation of the ground state properties of PO, PO¿, and POÀ Aristophanes Metropoulosa) Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vass. -
Computational Chemistry: a Practical Guide for Applying Techniques to Real-World Problems
Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc. ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic) COMPUTATIONAL CHEMISTRY COMPUTATIONAL CHEMISTRY A Practical Guide for Applying Techniques to Real-World Problems David C. Young Cytoclonal Pharmaceutics Inc. A JOHN WILEY & SONS, INC., PUBLICATION New York . Chichester . Weinheim . Brisbane . Singapore . Toronto Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or all capital letters. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Copyright ( 2001 by John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax (212) 850-6008, E-Mail: PERMREQ @ WILEY.COM. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold with the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional person should be sought. -
A PILOT INITIATIVE for EGI-XSEDE COLLABORATION Laganà A
A PILOT INITIATIVE FOR EGI-XSEDE COLLABORATION Laganà A. Dept of Chemistry, Biology & Biotechnologies, PG, IT A PROPOSAL FROM THE CMMST (Chemistry, Molecular, Materials Science and Technologies) COMMUNITY: implement a Synergistic High- Throughput&Performance Universal Molecular Simulator as a service for scientists and technologists 1 EGI-InSPIRE RI-261323 www.egi.eu The goals of the EGI-CMMST community THE GOALS wImplement a SYNERGISTIC (collaborative/competitive) HW, SW, MW work-model for molecular sciences & technologies computing wOffer a SERVICE for new discoveries by means of extremely accurate (quantum), efficient and versatile multiscale real-like SIMULATOR operating on distributed platforms FOR THIS PURPOSE IN EGI WE ARE STRUCTURING theEuropean CMMST (Chemistry, Molecular, Materials Sciences & Techno-logies) VRC (Virtual Research Community) based on: - EGI National Grid infrastructures, resources and operations - EGI and COMMUNITY user support, tools and services 2 EGI-InSPIRE RI-261323 www.egi.eu 1st target: A WORLDWIDE DISTRIBUTED PLATFORM • CONNECT EGI distributed operations platform to XSEDE (PRACE, etc.) network and consortia of resource providers by placing allocation requests in an appropriate form 3 EGI-InSPIRE RI-261323 www.egi.eu 2nd TARGET: A WORLDWIDE RESEARCH FEDERATION • FEDERATE CMMST communities around the world (EU, US, CANADA, PACIFIC ASIA, …) for reciprocal collaboration, support and servicing 4 EGI-InSPIRE RI-261323 www.egi.eu 3rd TARGET: QUALITY EVALUATION • IMPLEMENT proper quality evaluation criteria in