401
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Cook C, Beran GJO. Reduced-cost supercell approach for computing accurate phonon density of states in organic crystals. J Chem Phys 2020; 153:224105. [PMID: 33317313 DOI: 10.1063/5.0032649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Phonon contributions to organic crystal structures and thermochemical properties can be significant, but computing a well-converged phonon density of states with lattice dynamics and periodic density functional theory (DFT) is often computationally expensive due to the need for large supercells. Using semi-empirical methods like density functional tight binding (DFTB) instead of DFT can reduce the computational costs dramatically, albeit with noticeable reductions in accuracy. This work proposes approximating the phonon density of states via a relatively inexpensive DFTB supercell treatment of the phonon dispersion that is then corrected by shifting the individual phonon modes according to the difference between the DFT and DFTB phonon frequencies at the Γ-point. The acoustic modes are then computed at the DFT level from the elastic constants. In several small-molecule crystal test cases, this combined approach reproduces DFT thermochemistry with kJ/mol accuracy and 1-2 orders of magnitude less computational effort. Finally, this approach is applied to computing the free energy differences between the five crystal polymorphs of oxalyl dihydrazide.
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Affiliation(s)
- Cameron Cook
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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402
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Nieman R, Spezia R, Jayee B, Minton TK, Hase WL, Guo H. Exploring reactivity and product formation in N(4S) collisions with pristine and defected graphene with direct dynamics simulations. J Chem Phys 2020; 153:184702. [DOI: 10.1063/5.0028253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Reed Nieman
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 4 Place Jussieu, 75005 Paris, France
| | - Bhumika Jayee
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Timothy K. Minton
- Ann and H. J. Smead Department of Aerospace Engineering Sciences, University of Colorado, Boulder, Colorado 80303, USA
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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403
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Jenness GR, Bresnahan CG, Shukla MK. Adventures in DFTB: Toward an Automatic Parameterization Scheme. J Chem Theory Comput 2020; 16:6894-6903. [PMID: 33119287 DOI: 10.1021/acs.jctc.0c00842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As we push forward on understanding the fate of chemicals in the environment, we need a method that will allow for the simulation of the inherent heterogeneity. Density functional tight binding (DFTB) is a methodology that allows for a detailed electronic description and would be ideal for this problem. While many parameters can be derived directly from DFT, empirical parameters still exist in the confinement and repulsion potentials. In this manuscript, we examine these potentials and present solutions that will minimize the degree of empiricism. Our results show that it is possible to construct confinement potentials from examining the atomic radial wavefunctions. Moreover, we found that the heterogeneous repulsion potentials can be derived from using only homogeneous repulsion curves.
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Affiliation(s)
- Glen R Jenness
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, Mississippi 39180, United States
| | - Caitlin G Bresnahan
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, Mississippi 39180, United States
| | - Manoj K Shukla
- Environmental Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, Mississippi 39180, United States
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404
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Vuong VQ, Madridejos JML, Aradi B, Sumpter BG, Metha GF, Irle S. Density-functional tight-binding for phosphine-stabilized nanoscale gold clusters. Chem Sci 2020; 11:13113-13128. [PMID: 34094493 PMCID: PMC8163209 DOI: 10.1039/d0sc04514d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/21/2020] [Indexed: 12/19/2022] Open
Abstract
We report a parameterization of the second-order density-functional tight-binding (DFTB2) method for the quantum chemical simulation of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces. Our parameterization extends the previously released DFTB2 "auorg" parameter set by connecting it to the electronic parameter of phosphorus in the "mio" parameter set. Although this connection could technically simply be accomplished by creating only the required additional Au-P repulsive potential, we found that the Au 6p and P 3d virtual atomic orbital energy levels exert a strong influence on the overall performance of the combined parameter set. Our optimized parameters are validated against density functional theory (DFT) geometries, ligand binding and cluster isomerization energies, ligand dissociation potential energy curves, and molecular orbital energies for relevant phosphine-ligated Au n clusters (n = 2-70), as well as selected experimental X-ray structures from the Cambridge Structural Database. In addition, we validate DFTB simulated far-IR spectra for several phosphine- and thiolate-ligated gold clusters against experimental and DFT spectra. The transferability of the parameter set is evaluated using DFT and DFTB potential energy surfaces resulting from the chemisorption of a PH3 molecule on the gold (111) surface. To demonstrate the potential of the DFTB method for quantum chemical simulations of metalloid gold clusters that are challenging for traditional DFT calculations, we report the predicted molecular geometry, electronic structure, ligand binding energy, and IR spectrum of Au108S24(PPh3)16.
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Affiliation(s)
- Van Quan Vuong
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville TN USA
| | | | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen Bremen Germany
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory Oak Ridge TN USA
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory Oak Ridge TN USA
| | - Gregory F Metha
- Department of Chemistry, The University of Adelaide South Australia 5005 Australia
| | - Stephan Irle
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville TN USA
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory Oak Ridge TN USA
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405
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Kondo T, Sasaki T, Ruiz-Barragan S, Ribas-Ariño J, Shiga M. Refined metadynamics through canonical sampling using time-invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions. J Comput Chem 2020; 42:156-165. [PMID: 33124054 DOI: 10.1002/jcc.26443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022]
Abstract
We propose a canonical sampling method to refine metadynamics simulations a posteriori, where the hills obtained from metadynamics are used as a time-invariant bias potential. In this way, the statistical error in the computed reaction barriers is reduced by an efficient sampling of the collective variable space at the free energy level of interest. This simple approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high-temperature aqueous solutions. It was found that the reaction proceeds consistently via an SN 2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species. Although demonstration is shown for a specific problem, the computational method suggested herein could be generally used for simulations of complex reactions in the condensed phase.
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Affiliation(s)
- Tomomi Kondo
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Sergi Ruiz-Barragan
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
| | - Jordi Ribas-Ariño
- Departament de Ciència dels Materials i Química Física and IQTCUB, Universitat de Barcelona, Barcelona, Spain
| | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Chiba, Japan
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406
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Dekkiche H, Gemma A, Tabatabaei F, Batsanov AS, Niehaus T, Gotsmann B, Bryce MR. Electronic conductance and thermopower of single-molecule junctions of oligo(phenyleneethynylene) derivatives. NANOSCALE 2020; 12:18908-18917. [PMID: 32902546 DOI: 10.1039/d0nr04413j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report the synthesis and the single-molecule transport properties of three new oligo(phenyleneethynylene) (OPE3) derivatives possessing terminal dihydrobenzo[b]thiophene (DHBT) anchoring groups and various core substituents (phenylene, 2,5-dimethoxyphenylene and 9,10-anthracenyl). Their electronic conductance and their Seebeck coefficient have been determined using scanning tunneling microscopy-based break junction (STM-BJ) experiments between gold electrodes. The transport properties of the molecular junctions have been modelled using DFT-based computational methods which reveal a specific binding of the sulfur atom of the DHBT anchor to the electrodes. The experimentally determined Seebeck coefficient varies between -7.9 and -11.4 μV K-1 in the series and the negative sign is consistent with charge transport through the LUMO levels of the molecules.
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Affiliation(s)
- Hervé Dekkiche
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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407
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Morante S, La Penna G, Rossi G, Stellato F. SARS-CoV-2 Virion Stabilization by Zn Binding. Front Mol Biosci 2020; 7:222. [PMID: 33195401 PMCID: PMC7533540 DOI: 10.3389/fmolb.2020.00222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
Zinc plays a crucial role in the process of virion maturation inside the host cell. The accessory Cys-rich proteins expressed in SARS-CoV-2 by genes ORF7a and ORF8 are likely involved in zinc binding and in interactions with cellular antigens activated by extensive disulfide bonds. In this report we provide a proof of concept for the feasibility of a structural study of orf7a and orf8 proteins. A conceivable hypothesis is that lack of cellular zinc, or substitution thereof, might lead to a significant slowing down of viral maturation.
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Affiliation(s)
- Silvia Morante
- Dipartimento di Fisica, Università di Roma "Tor Vergata", Rome, Italy.,INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - Giovanni La Penna
- INFN, Sezione di Roma Tor Vergata, Rome, Italy.,CNR, Insitute of Chemistry of Organometallic Compounds, Firenze, Italy
| | - Giancarlo Rossi
- Dipartimento di Fisica, Università di Roma "Tor Vergata", Rome, Italy.,INFN, Sezione di Roma Tor Vergata, Rome, Italy.,Centro Fermi - Museo Storico della Fisica e Centro Studi e Ricerche "Enrico Fermi", Rome, Italy
| | - Francesco Stellato
- Dipartimento di Fisica, Università di Roma "Tor Vergata", Rome, Italy.,INFN, Sezione di Roma Tor Vergata, Rome, Italy
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408
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Řezáč J. Non-Covalent Interactions Atlas Benchmark Data Sets 2: Hydrogen Bonding in an Extended Chemical Space. J Chem Theory Comput 2020; 16:6305-6316. [DOI: 10.1021/acs.jctc.0c00715] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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409
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Elapolu MSR, Tabarraei A. An Atomistic Study of the Stress Corrosion Cracking in Graphene. J Phys Chem A 2020; 124:7060-7070. [PMID: 32786986 DOI: 10.1021/acs.jpca.0c04758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using molecular dynamics (MD) simulations, we study the mechanism of stress corrosion cracking in graphene. Two sets of modelings are conducted. In the first one, large graphene sheets with cracks in the armchair and zigzag directions are exposed to oxygen molecules. The crack growth as a result of chemical reactions between carbon radicals and oxygen molecules at different mechanical tensile stress levels is studied. In the second set of simulations, MD simulations are combined with the density functional-based tight bonding method to enhance the accuracy. This set of modelings focuses on a smaller zone in the vicinity of the crack tip. The impact of initial crack orientation on corrosion is studied by investigating corrosion of cracks in both armchair and zigzag directions. We investigate the subcritical crack propagation occurring as a result of the combined effects of both mechanical loading and chemical reactions. Our results show that cracks in graphene can grow due to chemical reactions with the environmental molecules. The MD modelings also predict that reaction of carbon atoms with oxygen molecules might lead to a stress relaxation at the crack tip, hence preventing further crack propagation. The results show that subcritical crack growth can happen by two mechanisms, which include the failure of C-C bonds or by removing the carbon atoms from graphene sheets in the form of CO or CO2 molecules.
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Affiliation(s)
- Mohan S R Elapolu
- Department of Mechanical Engineering & Engineering Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Alireza Tabarraei
- Department of Mechanical Engineering & Engineering Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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410
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Sherrill CD, Manolopoulos DE, Martínez TJ, Michaelides A. Electronic structure software. J Chem Phys 2020; 153:070401. [DOI: 10.1063/5.0023185] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
30332-0400, USA
| | - David E. Manolopoulos
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, Oxford University, South Parks Road, Oxford OX1
3QZ, United Kingdom
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305,
USA
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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411
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Stöhr M, Medrano Sandonas L, Tkatchenko A. Accurate Many-Body Repulsive Potentials for Density-Functional Tight Binding from Deep Tensor Neural Networks. J Phys Chem Lett 2020; 11:6835-6843. [PMID: 32787209 DOI: 10.1021/acs.jpclett.0c01307] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We combine density-functional tight binding (DFTB) with deep tensor neural networks (DTNN) to maximize the strengths of both approaches in predicting structural, energetic, and vibrational molecular properties. The DTNN is used to construct a nonlinear model for the localized many-body interatomic repulsive energy, which so far has been treated in an atom-pairwise manner in DFTB. Substantially improving upon standard DFTB and DTNN, the resulting DFTB-NNrep model yields accurate predictions of atomization and isomerization energies, equilibrium geometries, vibrational frequencies, and dihedral rotation profiles for a large variety of organic molecules compared to the hybrid DFT-PBE0 functional. Our results highlight the potential of combining semiempirical electronic-structure methods with physically motivated machine learning approaches for predicting localized many-body interactions. We conclude by discussing future advancements of the DFTB-NNrep approach that could enable chemically accurate electronic-structure calculations for systems with tens of thousands of atoms.
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Affiliation(s)
- Martin Stöhr
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
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412
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Bannwarth C, Caldeweyher E, Ehlert S, Hansen A, Pracht P, Seibert J, Spicher S, Grimme S. Extended
tight‐binding
quantum chemistry methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1493] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christoph Bannwarth
- Department of Chemistry and The PULSE Institute Stanford University Stanford California USA
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
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413
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Oliveira MJT, Papior N, Pouillon Y, Blum V, Artacho E, Caliste D, Corsetti F, de Gironcoli S, Elena AM, García A, García-Suárez VM, Genovese L, Huhn WP, Huhs G, Kokott S, Küçükbenli E, Larsen AH, Lazzaro A, Lebedeva IV, Li Y, López-Durán D, López-Tarifa P, Lüders M, Marques MAL, Minar J, Mohr S, Mostofi AA, O'Cais A, Payne MC, Ruh T, Smith DGA, Soler JM, Strubbe DA, Tancogne-Dejean N, Tildesley D, Torrent M, Yu VWZ. The CECAM electronic structure library and the modular software development paradigm. J Chem Phys 2020; 153:024117. [PMID: 32668924 DOI: 10.1063/5.0012901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.
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Affiliation(s)
- Micael J T Oliveira
- Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany
| | - Nick Papior
- DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yann Pouillon
- Departamento CITIMAC, Universidad de Cantabria, Santander, Spain
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | | | - Damien Caliste
- Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - Fabiano Corsetti
- Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Alin M Elena
- Scientific Computing Department, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
| | - Alberto García
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain
| | | | - Luigi Genovese
- Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - William P Huhn
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Georg Huhs
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - Emine Küçükbenli
- Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | | | - Alfio Lazzaro
- Department of Chemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | | | - Yingzhou Li
- Department of Mathematics, Duke University, Durham, North Carolina 27708-0320, USA
| | | | - Pablo López-Tarifa
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, 20018 San Sebastián, Spain
| | - Martin Lüders
- Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jan Minar
- New Technologies Research Centre, University of West Bohemia, 301 00 Plzen, Czech Republic
| | - Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Arash A Mostofi
- Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alan O'Cais
- Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Mike C Payne
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Thomas Ruh
- Institute of Materials Chemistry, TU Wien, 1060 Vienna, Austria
| | - Daniel G A Smith
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - José M Soler
- Departamento e Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David A Strubbe
- Department of Physics, University of California, Merced, California 95343, USA
| | | | - Dominic Tildesley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | | | - Victor Wen-Zhe Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
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414
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Bonafé FP, Aradi B, Hourahine B, Medrano CR, Hernández FJ, Frauenheim T, Sánchez CG. A Real-Time Time-Dependent Density Functional Tight-Binding Implementation for Semiclassical Excited State Electron–Nuclear Dynamics and Pump–Probe Spectroscopy Simulations. J Chem Theory Comput 2020; 16:4454-4469. [DOI: 10.1021/acs.jctc.9b01217] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Franco P. Bonafé
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universitát Bremen, Bremen, Germany
| | - Ben Hourahine
- SUPA, Department of Physics, John Anderson Building, The University of Strathclyde, 107 Rottenrow, Glasgow G15 6QN, United Kingdom
| | - Carlos R. Medrano
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - Federico J. Hernández
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
- Department of Physics, Universidad de Santiago de Chile, Av. Ecuador 3493, Santiago, Chile
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, Universitát Bremen, Bremen, Germany
- Computational Science Research Center (CSRC) Beijing and Computational Science and Applied Research (CSAR) Institute, Shenzhen, China
| | - Cristián G. Sánchez
- Instituto Interdisciplinario de Ciencias Básicas, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
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415
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Niklasson AMN. Density-Matrix Based Extended Lagrangian Born–Oppenheimer Molecular Dynamics. J Chem Theory Comput 2020; 16:3628-3640. [DOI: 10.1021/acs.jctc.0c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Anders M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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416
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Mazurek AH, Szeleszczuk Ł, Pisklak DM. Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences. Pharmaceutics 2020; 12:E415. [PMID: 32369915 PMCID: PMC7284980 DOI: 10.3390/pharmaceutics12050415] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.
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Affiliation(s)
| | - Łukasz Szeleszczuk
- Chair and Department of Physical Pharmacy and Bioanalysis, Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 str., 02-093 Warsaw, Poland; (A.H.M.); (D.M.P.)
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Villegas-Lelovsky L, Paupitz R. Graphenylene-based nanoribbons for novel molecular electronic devices. Phys Chem Chem Phys 2020; 22:28365-28375. [PMID: 33300921 DOI: 10.1039/d0cp04188b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the last decade, graphene has been frequently cited as one of the most promising materials for nanoelectronics. However, despite its outstanding mechanical and electronic properties, its use in the production of real nanoelectronic devices usually imposes some practical difficulties. This happens mainly due to the fact that, in its pristine form, graphene is a gapless material. We investigate theoretically the possibility of obtaining rectifying nanodevices using another carbon based two dimensional material, namely the graphenylene. This material has the advantage of being an intrinsic semiconductor, posing as a promising material for nanoelectronics. By doping graphenylene, one could obtain 2-dimensional p-n junctions, which can be useful for the construction of low dimensional electronic devices. We propose 2-dimensional diodes in which a clear rectification effect was demonstrated, with a conducting threshold of approximately 1.5 eV in direct bias and current blocking with opposite bias. During these investigations were found specific configurations that could result in devices with Zener-like behavior. Also, one unexpected effect was identified, which was the existence of transmission dips in electronic conductance plots. This result is discussed as a related feature to what was found in graphene nanoribbon systems under external magnetic fields, even though the external field was not a necessary ingredient to obtain such effect in the present case.
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