Postmodern Electronic Structure Theory by Joonho Lee A
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Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
Identification of a Spin-Coupled Mo (III) in the Nitrogenase Iron
Identification of a spin-coupled Mo(III) in the nitrogenase iron-molybdenum cofactor Ragnar Bjornsson, Frederico A. Lima, Thomas Spatzal, Thomas Weyhermueller, Pieter Glatzel, Eckhard Bill, Oliver Einsle, Frank Neese, Serena Debeer To cite this version: Ragnar Bjornsson, Frederico A. Lima, Thomas Spatzal, Thomas Weyhermueller, Pieter Glatzel, et al.. Identification of a spin-coupled Mo(III) in the nitrogenase iron-molybdenum cofactor. Chemical Science , The Royal Society of Chemistry, 2014, 5 (8), pp.3096-3103. 10.1039/c4sc00337c. hal- 01572851 HAL Id: hal-01572851 https://hal.archives-ouvertes.fr/hal-01572851 Submitted on 8 Aug 2017 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. Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Identification of a spin-coupled Mo(III)inthe nitrogenase iron–molybdenum cofactor† Cite this: Chem. Sci.,2014,5,3096 a a b a Ragnar Bjornsson,‡ Frederico A. Lima,‡§ Thomas Spatzal,{ Thomas Weyhermuller,¨ Pieter Glatzel,c Eckhard Bill,a Oliver Einsle,*b Frank Neese*a and Serena DeBeer*ad Nitrogenase is a complex enzyme that catalyzes the formation of ammonia utilizing a MoFe7S9C cluster. The presence of a central carbon atom was recently revealed, finally completing the atomic level description of the active site. -
A Model for Dinitrogen Binding in the E4 State of Nitrogenase† Cite This: Chem
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue A model for dinitrogen binding in the E4 state of nitrogenase† Cite this: Chem. Sci.,2019,10, 11110 ab a ab All publication charges for this article Albert Th. Thorhallsson, Bardi Benediktsson and Ragnar Bjornsson * have been paid for by the Royal Society of Chemistry Molybdenum nitrogenase is one of the most intriguing metalloenzymes in nature, featuring an exotic iron– molybdenum–sulfur cofactor, FeMoco, whose mode of action remains elusive. In particular, the molecular and electronic structure of the N2-binding E4 state is not known. In this study we present theoretical QM/ MM calculations of new structural models of the E4 state of molybdenum-dependent nitrogenase and compare to previously suggested models for this enigmatic redox state. We propose two models as possible candidates for the E4 state. Both models feature two hydrides on the FeMo cofactor, bridging atoms Fe2 and Fe6 with a terminal sulfhydryl group on either Fe2 or Fe6 (derived from the S2B bridge) and the change in coordination results in local lower-spin electronic structure at Fe2 and Fe6. These structures appear consistent with the bridging hydride proposal put forward from ENDOR studies and are calculated to be lower in energy than other proposed models for E4 at the TPSSh-QM/MM level of Creative Commons Attribution 3.0 Unported Licence. theory. We critically analyze the DFT method dependency in calculations of FeMoco that has resulted in strikingly different proposals for this state. Importantly, dinitrogen binds exothermically to either Fe2 or Fe6 in our models, contrary to others, an effect rationalized via the unique ligand field (from the hydrides) at the Fe with an empty coordination site. -
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program Start: Sunday, May 7, 2017 afternoon. Resort check-in at 4:00 pm. Finish: Wednesday, May 10, noon Lectures are in Scripps, posters are in Heather. Sunday 6:00-7:00: Dinner 7:30-9:00 Opening session 7:30–7:45 Anna Krylov (USC): “MolSSI and some lessons from previous workshop, goals of the workshop” 7:45-8:00 Theresa Windus (Iowa): “Mission of the Molecular Science Consortium” 8:00-9:00 Introduction of participants: 2 min presentation, can have one slide (send in advance) 9:00-10:30 Reception and posters Monday Breakfast: 7:30-9:00 9:00-11:45 Session I: Overview of tensors projects and current developments (moderator Daniel Smith) 9:00-9:10 Daniel Smith (MolSSI): Overview of tensor projects 9:10-9:30 Evgeny Epifanovsky (Q-Chem): Overview of Libtensor 9:30-9:50 Ed Solomonik: "An Overview of Cyclops Tensor Framework" 9:50-10:10 Ed Valeev (VT): "TiledArray: A composable massively parallel block-sparse tensor framework" 10:10-10:30 Coffee break 10:30-10:50 Devin Matthews (UT Austin): "Aquarius and TBLIS: Orthogonal Axes in Multilinear Algebra" 10:50-11:10 Karol Kowalskii (PNNL, NWChem): "NWChem, NWChemEX , and new tensor algebra systems for many-body methods" 11:10-11:30 Peng Chong (VT): "Many-body toolkit in re-designed Massively Parallel Quantum Chemistry package" 11:30-11:55 Moderated discussion: "What problems are we *still* solving?” Lunch: 12:00-1:00 Free time for unstructured discussions 5:00 Posters (coffee/tea) Dinner: 6-7:00 7:15-9:00 Session II: Computer -
The Mysterious Central Atom in the Nitrogenase Femo Cofactor
The mysterious central atom in the nitrogenase FeMo cofactor Kevin Hwang Literature Seminar December 6, 2011 The reduction of dinitrogen remains one of the biggest challenges in chemistry today. While industrial-scale production of ammonia has been made possible by the Haber- Bosch process, this process requires harsh conditions, with very high temperatures and pressures necessary in order to break the extremely robust N-N triple bond. In contrast, certain bacteria have evolved enzymes capable of catalytically reducing nitrogen to ammonia under ambient conditions (Eq. 1), a feat thus far unmatched by human ingenuity.1 As a result, substantial effort has been applied towards understanding the mechanism of bacterial nitrogenases, and in particular one of the most studied is the molybdenum- containing nitrogenase (Mo-nitrogenase).2 This review will cover recent work elucidating the structure of the iron-molybdenum cofactor, which in Mo-nitrogenase is believed to be the site of nitrogen binding and reduction. The structure of nitrogenase from Azotobacter vinelandii was first reported in 1992 by Kim and Rees.3 From this structure, the overall organization of nitrogenase was described. Nitrogenase contains two proteins - an iron-containing protein, with a [4Fe:4S] cluster used for electron transfer; and an iron-molybdenum protein, which contains a [8Fe:7S] cluster (the P cluster), also used for electron transfer, and an iron-molybdenum cluster known alternatively as the M cluster or the iron- molybdenum cofactor (FeMoco). The assigned structure contained a unique arrangement of seven iron atoms and one molybdenum atom, bridged by sulfur atoms, surrounding a cavity with diameter approximately 4Å (Figure 1).3 Investigation of MoFe-deficient variants of nitrogenase have suggested that this cluster is the site of nitrogen fixation, Figure 1. -
Pyscf: the Python-Based Simulations of Chemistry Framework
PySCF: The Python-based Simulations of Chemistry Framework Qiming Sun∗1, Timothy C. Berkelbach2, Nick S. Blunt3,4, George H. Booth5, Sheng Guo1,6, Zhendong Li1, Junzi Liu7, James D. McClain1,6, Elvira R. Sayfutyarova1,6, Sandeep Sharma8, Sebastian Wouters9, and Garnet Kin-Lic Chany1 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA 2Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA 3Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA 4Department of Chemistry, University of California, Berkeley, California 94720, USA 5Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom 6Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA 7Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P. R. China 8Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80302, USA 9Brantsandpatents, Pauline van Pottelsberghelaan 24, 9051 Sint-Denijs-Westrem, Belgium arXiv:1701.08223v2 [physics.chem-ph] 2 Mar 2017 Abstract PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, so as to facilitate new method development and enable flexible ∗[email protected] [email protected] 1 computational workflows. The package provides a wide range of tools to support simulations of finite-size systems, extended systems with periodic boundary conditions, low-dimensional periodic systems, and custom Hamiltonians, using mean-field and post-mean-field methods with standard Gaussian basis functions. To ensure ease of extensibility, PySCF uses the Python language to implement almost all of its features, while computationally critical paths are implemented with heavily optimized C routines. -
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 -
Femo Cofactor Maturation on Nifen SPECIAL FEATURE
FeMo cofactor maturation on NifEN SPECIAL FEATURE Yilin Hu*, Mary C. Corbett†, Aaron W. Fay*, Jerome A. Webber*, Keith O. Hodgson†‡§, Britt Hedman‡§, and Markus W. Ribbe*§ *Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; †Department of Chemistry, Stanford University, Stanford, CA 94305; and ‡Stanford Synchrotron Radiation Laboratory, Stanford Linear Accellerator Center, Stanford University, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025-7015 Edited by Douglas C. Rees, California Institute of Technology, Pasadena, CA, and approved May 10, 2006 (received for review March 31, 2006) FeMo cofactor (FeMoco) biosynthesis is one of the most compli- Unlike the P cluster, FeMoco, which contains additional hetero- cated processes in metalloprotein biochemistry. Here we show that metal (Mo) and organic moiety (homocitrate), is first assembled on Mo and homocitrate are incorporated into the Fe͞S core of the a scaffold protein (17, 18) and then inserted into its destined FeMoco precursor while it is bound to NifEN and that the resulting location in MoFe protein (‘‘ex situ’’ assembly). Biosynthesis of fully complemented, FeMoco-like cluster is transformed into a FeMoco presumably starts with the production of the Fe͞Scoreby mature FeMoco upon transfer from NifEN to MoFe protein through NifB (encoded by nifB) (19, 20), which is then transferred to, and direct protein–protein interaction. Our findings not only clarify the further processed on, the ␣22 tetrameric NifEN protein (17, 21). process of FeMoco -
Trends in Atomistic Simulation Software Usage [1.3]
A LiveCoMS Perpetual Review Trends in atomistic simulation software usage [1.3] Leopold Talirz1,2,3*, Luca M. Ghiringhelli4, Berend Smit1,3 1Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques, Valais, École Polytechnique Fédérale de Lausanne, CH-1951 Sion, Switzerland; 2Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l’Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 3National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 4The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany This LiveCoMS document is Abstract Driven by the unprecedented computational power available to scientific research, the maintained online on GitHub at https: use of computers in solid-state physics, chemistry and materials science has been on a continuous //github.com/ltalirz/ rise. This review focuses on the software used for the simulation of matter at the atomic scale. We livecoms-atomistic-software; provide a comprehensive overview of major codes in the field, and analyze how citations to these to provide feedback, suggestions, or help codes in the academic literature have evolved since 2010. An interactive version of the underlying improve it, please visit the data set is available at https://atomistic.software. GitHub repository and participate via the issue tracker. This version dated August *For correspondence: 30, 2021 [email protected] (LT) 1 Introduction Gaussian [2], were already released in the 1970s, followed Scientists today have unprecedented access to computa- by force-field codes, such as GROMOS [3], and periodic tional power. -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape. Permalink https://escholarship.org/uc/item/4sm897jh Journal Chemical reviews, 121(8) ISSN 0009-2665 Authors Kowalski, Karol Bair, Raymond Bauman, Nicholas P et al. Publication Date 2021-04-01 DOI 10.1021/acs.chemrev.0c00998 Peer reviewed eScholarship.org Powered by the California Digital Library University of California From NWChem to NWChemEx: Evolving with the computational chemistry landscape Karol Kowalski,y Raymond Bair,z Nicholas P. Bauman,y Jeffery S. Boschen,{ Eric J. Bylaska,y Jeff Daily,y Wibe A. de Jong,x Thom Dunning, Jr,y Niranjan Govind,y Robert J. Harrison,k Murat Keçeli,z Kristopher Keipert,? Sriram Krishnamoorthy,y Suraj Kumar,y Erdal Mutlu,y Bruce Palmer,y Ajay Panyala,y Bo Peng,y Ryan M. Richard,{ T. P. Straatsma,# Peter Sushko,y Edward F. Valeev,@ Marat Valiev,y Hubertus J. J. van Dam,4 Jonathan M. Waldrop,{ David B. Williams-Young,x Chao Yang,x Marcin Zalewski,y and Theresa L. Windus*,r yPacific Northwest National Laboratory, Richland, WA 99352 zArgonne National Laboratory, Lemont, IL 60439 {Ames Laboratory, Ames, IA 50011 xLawrence Berkeley National Laboratory, Berkeley, 94720 kInstitute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794 ?NVIDIA Inc, previously Argonne National Laboratory, Lemont, IL 60439 #National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373 @Department of Chemistry, Virginia Tech, Blacksburg, VA 24061 4Brookhaven National Laboratory, Upton, NY 11973 rDepartment of Chemistry, Iowa State University and Ames Laboratory, Ames, IA 50011 E-mail: [email protected] 1 Abstract Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. -
Openmolcas: from Source Code to Insight Ignacio Fdez
Article Cite This: J. Chem. Theory Comput. XXXX, XXX, XXX−XXX pubs.acs.org/JCTC OpenMolcas: From Source Code to Insight Ignacio Fdez. Galvan,́ 1,2 Morgane Vacher,1 Ali Alavi,3 Celestino Angeli,4 Francesco Aquilante,5 Jochen Autschbach,6 Jie J. Bao,7 Sergey I. Bokarev,8 Nikolay A. Bogdanov,3 Rebecca K. Carlson,7,9 Liviu F. Chibotaru,10 Joel Creutzberg,11,12 Nike Dattani,13 Mickael̈ G. Delcey,1 Sijia S. Dong,7,14 Andreas Dreuw,15 Leon Freitag,16 Luis Manuel Frutos,17 Laura Gagliardi,7 Fredé rić Gendron,6 Angelo Giussani,18,19 Leticia Gonzalez,́ 20 Gilbert Grell,8 Meiyuan Guo,1,21 Chad E. Hoyer,7,22 Marcus Johansson,12 Sebastian Keller,16 Stefan Knecht,16 Goran Kovacevič ,́ 23 Erik Kallman,̈ 1 Giovanni Li Manni,3 Marcus Lundberg,1 Yingjin Ma,16 Sebastian Mai,20 Joaõ Pedro Malhado,24 Per Åke Malmqvist,12 Philipp Marquetand,20 Stefanie A. Mewes,15,25 Jesper Norell,11 Massimo Olivucci,26,27,28 Markus Oppel,20 Quan Manh Phung,29 Kristine Pierloot,29 Felix Plasser,30 Markus Reiher,16 Andrew M. Sand,7,31 Igor Schapiro,32 Prachi Sharma,7 Christopher J. Stein,16,33 Lasse Kragh Sørensen,1,34 Donald G. Truhlar,7 Mihkel Ugandi,1,35 Liviu Ungur,36 Alessio Valentini,37 Steven Vancoillie,12 Valera Veryazov,12 Oskar Weser,3 Tomasz A. Wesołowski,5 Per-Olof Widmark,12 Sebastian Wouters,38 Alexander Zech,5 J. Patrick Zobel,12 and Roland Lindh*,2,39 1Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. -
Electronic Structure Calculations in Quantum Chemistry
Electronic Structure Calculations in Quantum Chemistry Alexander B. Pacheco User Services Consultant LSU HPC & LONI [email protected] HPC Training Louisiana State University Baton Rouge Nov 16, 2011 Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 1 / 55 Outline 1 Introduction 2 Ab Initio Methods 3 Density Functional Theory 4 Semi-empirical Methods 5 Basis Sets 6 Molecular Mechanics 7 Quantum Mechanics/Molecular Mechanics (QM/MM) 8 Computational Chemistry Programs 9 Exercises 10 Tips for Quantum Chemical Calculations Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 2 / 55 Introduction What is Computational Chemistry? Computational Chemistry is a branch of chemistry that uses computer science to assist in solving chemical problems. Incorporates the results of theoretical chemistry into efficient computer programs. Application to single molecule, groups of molecules, liquids or solids. Calculates the structure and properties of interest. Computational Chemistry Methods range from 1 Highly accurate (Ab-initio,DFT) feasible for small systems 2 Less accurate (semi-empirical) 3 Very Approximate (Molecular Mechanics) large systems Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 3 / 55 Introduction Theoretical Chemistry can be broadly divided into two main categories 1 Static Methods ) Time-Independent Schrödinger Equation H^ Ψ = EΨ ♦ Quantum Chemical/Ab Initio /Electronic Structure Methods ♦ Molecular Mechanics 2 Dynamical Methods ) Time-Dependent Schrödinger Equation @ { Ψ = H^ Ψ ~@t ♦ Classical Molecular Dynamics ♦ Semi-classical and Ab-Initio Molecular Dynamics Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 4 / 55 Tutorial Goals Provide a brief introduction to Electronic Structure Calculations in Quantum Chemistry.