1
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Xiong M, Kong C, Yang Z, Yang T. Superhalogens inside fullerenes X@C 2n (X = BO 2, BeF 3; 2 n = 60, 70). Phys Chem Chem Phys 2024; 26:21282-21289. [PMID: 39078036 DOI: 10.1039/d4cp02082k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The exploration of endohedral fullerenes has garnered significant attention recently due to their distinctive chemical, electrochemical, and optoelectronic properties. Charge transfer, which usually occurs from encapsulated species to fullerenes, importantly affects the structures and properties of endohedral fullerenes. In this study, we theoretically investigated endohedral superhalogen fullerenes X@C2n (X = BO2, BeF3; 2n = 60, 70), in which the charge is reversely transferred from the fullerene to the superhalogen, by using density functional theory calculations and ab initio molecular dynamics simulations. Both natural population analysis and the quantum theory of atoms in molecules confirm about one electron transfer from the fullerene to the superhalogen, resulting in the formal valence state of X-@C2n+. Energy decomposition analysis on the interaction between the superhalogen and fullerene revealed that electrostatic energy contributes predominantly to the total interaction energy. These endohedral superhalogen fullerenes with cationic fullerenes were predicted to be able to serve as building blocks for one dimensional fullerene-based nanowires when combined with endohedral alkali-metallofullerenes with anionic fullerenes.
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Affiliation(s)
- Mo Xiong
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Chuncai Kong
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Zhimao Yang
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Tao Yang
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
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2
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Tyrcha B, Brzęk F, Żuchowski PS. Second quantization-based symmetry-adapted perturbation theory: Generalizing exchange beyond single electron pair approximation. J Chem Phys 2024; 160:044118. [PMID: 38295062 DOI: 10.1063/5.0184750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
This paper presents a general second-quantized form of a permutation operator interchanging n pairs of electrons between interacting subsystems in the framework of the symmetry-adapted perturbation theory (SAPT). We detail the procedure for constructing this operator through the consecutive multiplication of single-pair permutation operators. This generalized form of the permutation operator has enabled the derivation of universal formulas for S2n approximations of the exchange energies in the first and second order of the interaction operator. We present expressions for corrections of S4 approximations and assess its efficacy on a selection of systems anticipated to exhibit a slowly converging overlap expansion. Additionally, we outline a method to sum the overlap expansion series to infinity in second-quantization, up to the second order in V. This new approach offers an alternative to the existing formalism based on density-matrix formulations. When combined with a symbolic algebra program for automated derivations, it paves the way for advancements in SAPT theory, particularly for intricate wavefunction theories.
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Affiliation(s)
- Bartosz Tyrcha
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5/7, 87-100 Toruń, Poland
| | - Filip Brzęk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5/7, 87-100 Toruń, Poland
| | - Piotr S Żuchowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5/7, 87-100 Toruń, Poland
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3
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Żuchowski PS, Moszynski R. Dispersion Energy from the Time-Independent Coupled-Cluster Polarization Propagator. J Chem Theory Comput 2023; 19:1177-1185. [PMID: 36734970 PMCID: PMC9979596 DOI: 10.1021/acs.jctc.2c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We present a new method of calculation of the dispersion energy in the second-order symmetry-adapted perturbation theory. Using the Longuet-Higgins integral and time-independent coupled-cluster response theory, one shows that the general expression for the dispersion energy can be written in terms of cluster amplitudes and the excitation operators σ, which can be obtained by solving a linear equation. We introduced an approximate scheme dubbed CCPP2(T) for the dispersion energy accurate to the second order of intramonomer correlation, which includes certain classes to be summed to infinity. Assessment of the accuracy of the CCPP2(T) dispersion energy against the FCI dispersion for He2 demonstrates its high accuracy. For more complex systems, CCPP2(T) matches the accuracy of the best methods introduced for calculations of dispersion so far. The method can be extended to higher-order levels of excitations, providing a systematically improvable theory of dispersion interaction.
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Affiliation(s)
- Piotr S. Żuchowski
- Faculty
of Physics, Astronomy and Applied Informatics, Institute of Physics, Nicolas Copernicus University in Torun, Grudziadzka 5/7, Torun87-100, Poland,E-mail:
| | - Robert Moszynski
- Quantum
Chemistry Laboratory, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw02-093, Poland,E-mail:
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4
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Hapka M, Przybytek M, Pernal K. Symmetry-Adapted Perturbation Theory Based on Multiconfigurational Wave Function Description of Monomers. J Chem Theory Comput 2021; 17:5538-5555. [PMID: 34517707 PMCID: PMC8444344 DOI: 10.1021/acs.jctc.1c00344] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We present a formulation
of the multiconfigurational (MC) wave
function symmetry-adapted perturbation theory (SAPT). The method is
applicable to noncovalent interactions between monomers which require
a multiconfigurational description, in particular when the interacting
system is strongly correlated or in an electronically excited state.
SAPT(MC) is based on one- and two-particle reduced density matrices
of the monomers and assumes the single-exchange approximation for
the exchange energy contributions. Second-order terms are expressed
through response properties from extended random phase approximation
(ERPA). The dispersion components of SAPT(MC) have been introduced
in our previous works [HapkaM.2019, 15, 1016−102730525591; HapkaM.2019, 15, 6712–672331670950]. SAPT(MC) is applied either with generalized valence
bond perfect pairing (GVB) or with complete active space self-consistent
field (CASSCF) treatment of the monomers. We discuss two model multireference
systems: the H2 ··· H2 dimer
in out-of-equilibrium geometries and interaction between the argon
atom and excited state of ethylene. Using the C2H4* ··· Ar complex as an example, we examine second-order
terms arising from negative transitions in the linear response function
of an excited monomer. We demonstrate that the negative-transition
terms must be accounted for to ensure qualitative prediction of induction
and dispersion energies and develop a procedure allowing for their
computation. Factors limiting the accuracy of SAPT(MC) are discussed
in comparison with other second-order SAPT schemes on a data set of
small single-reference dimers.
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Affiliation(s)
- Michał Hapka
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland.,Faculty of Chemistry, University of Warsaw, ul. L. Pasteura 1, 02-093 Warsaw, Poland
| | - Michał Przybytek
- Faculty of Chemistry, University of Warsaw, ul. L. Pasteura 1, 02-093 Warsaw, Poland
| | - Katarzyna Pernal
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland
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5
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González-Veloso I, Figueiredo NM, Cordeiro MNDS. Unravelling the Interactions of Magnetic Ionic Liquids by Energy Decomposition Schemes: Towards a Transferable Polarizable Force Field. Molecules 2021; 26:molecules26185526. [PMID: 34576997 PMCID: PMC8466702 DOI: 10.3390/molecules26185526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
This work aims at unravelling the interactions in magnetic ionic liquids (MILs) by applying Symmetry-Adapted Perturbation Theory (SAPT) calculations, as well as based on those to set-up a polarisable force field model for these liquids. The targeted MILs comprise two different cations, namely: 1-butyl-3-methylimidazolium ([Bmim]+) and 1-ethyl-3-methylimidazolium ([Emim]+), along with several metal halides anions such as [FeCl4]−, [FeBr4]−, [ZnCl3]− and [SnCl4]2− To begin with, DFT geometry optimisations of such MILs were performed, which in turn revealed that the metallic anions prefer to stay close to the region of the carbon atom between the nitrogen atoms in the imidazolium fragment. Then, a SAPT study was carried out to find the optimal separation of the monomers and the different contributions for their interaction energy. It was found that the main contribution to the interaction energy is the electrostatic interaction component, followed by the dispersion one in most of the cases. The SAPT results were compared with those obtained by employing the local energy decomposition scheme based on the DLPNO-CCSD(T) method, the latter showing slightly lower values for the interaction energy as well as an increase of the distance between the minima centres of mass. Finally, the calculated SAPT interaction energies were found to correlate well with the melting points experimentally measured for these MILs.
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6
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Madajczyk K, Żuchowski PS, Brzȩk F, Rajchel Ł, Kȩdziera D, Modrzejewski M, Hapka M. Dataset of noncovalent intermolecular interaction energy curves for 24 small high-spin open-shell dimers. J Chem Phys 2021; 154:134106. [PMID: 33832261 DOI: 10.1063/5.0043793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a dataset of 24 interaction energy curves of open-shell noncovalent dimers, referred to as the O24 × 5 dataset. The dataset consists of high-spin dimers up to 11 atoms selected to assure diversity with respect to interaction types: dispersion, electrostatics, and induction. The benchmark interaction energies are obtained at the restricted open-shell CCSD(T) level of theory with complete basis set extrapolation (from aug-cc-pVQZ to aug-cc-pV5Z). We have analyzed the performance of selected wave function methods MP2, CCSD, and CCSD(T) as well as the F12a and F12b variants of coupled-cluster theory. In addition, we have tested dispersion-corrected density functional theory methods based on the PBE exchange-correlation model. The O24 × 5 dataset is a challenge to approximate methods due to the wide range of interaction energy strengths it spans. For the dispersion-dominated and mixed-type subsets, any tested method that does not include the triples contribution yields errors on the order of tens of percent. The electrostatic subset is less demanding with errors that are typically an order of magnitude smaller than the mixed and dispersion-dominated subsets.
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Affiliation(s)
- Katarzyna Madajczyk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudzia̧dzka 5, 87-100 Toruń, Poland
| | - Piotr S Żuchowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudzia̧dzka 5, 87-100 Toruń, Poland
| | - Filip Brzȩk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudzia̧dzka 5, 87-100 Toruń, Poland
| | - Łukasz Rajchel
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudzia̧dzka 5, 87-100 Toruń, Poland
| | - Dariusz Kȩdziera
- Faculty of Chemistry, Nicolaus Copernicus University, ul. Gagarina 7, Toruń, Poland
| | - Marcin Modrzejewski
- Faculty of Chemistry, University of Warsaw, ul. L. Pasteura 1, 02-093 Warsaw, Poland
| | - Michał Hapka
- Faculty of Chemistry, University of Warsaw, ul. L. Pasteura 1, 02-093 Warsaw, Poland
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7
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Quintas-Sánchez E, Dawes R. Spectroscopy and Scattering Studies Using Interpolated Ab Initio Potentials. Annu Rev Phys Chem 2021; 72:399-421. [PMID: 33503385 DOI: 10.1146/annurev-physchem-090519-051837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Born-Oppenheimer potential energy surface (PES) has come a long way since its introduction in the 1920s, both conceptually and in predictive power for practical applications. Nevertheless, nearly 100 years later-despite astonishing advances in computational power-the state-of-the-art first-principles prediction of observables related to spectroscopy and scattering dynamics is surprisingly limited. For example, the water dimer, (H2O)2, with only six nuclei and 20 electrons, still presents a formidable challenge for full-dimensional variational calculations of bound states and is considered out of reach for rigorous scattering calculations. The extremely poor scaling of the most rigorous quantum methods is fundamental; however, recent progress in development of approximate methodologies has opened the door to fairly routine high-quality predictions, unthinkable 20 years ago. In this review, in relation to the workflow of spectroscopy and/or scattering studies, we summarize progress and challenges in the component areas of electronic structure calculations, PES fitting, and quantum dynamical calculations.
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Affiliation(s)
- Ernesto Quintas-Sánchez
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA;
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA;
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8
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Interactions of CO
2
with cluster models of
metal–organic
frameworks. J Comput Chem 2020; 41:2066-2083. [DOI: 10.1002/jcc.26377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/12/2020] [Accepted: 06/13/2020] [Indexed: 11/07/2022]
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9
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Mao Y, Levine DS, Loipersberger M, Horn PR, Head-Gordon M. Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals. Phys Chem Chem Phys 2020; 22:12867-12885. [PMID: 32510096 DOI: 10.1039/d0cp01933j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H2O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H2O) and ˙OH(H2O)2), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH3CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
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10
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Garcia J, Podeszwa R, Szalewicz K. SAPT codes for calculations of intermolecular interaction energies. J Chem Phys 2020; 152:184109. [PMID: 32414261 DOI: 10.1063/5.0005093] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Symmetry-adapted perturbation theory (SAPT) is a method for calculations of intermolecular (noncovalent) interaction energies. The set of SAPT codes that is described here, the current version named SAPT2020, includes virtually all variants of SAPT developed so far, among them two-body SAPT based on perturbative, coupled cluster, and density functional theory descriptions of monomers, three-body SAPT, and two-body SAPT for some classes of open-shell monomers. The properties of systems governed by noncovalent interactions can be predicted only if potential energy surfaces (force fields) are available. SAPT is the preferred approach for generating such surfaces since it is seamlessly connected to the asymptotic expansion of interaction energy. SAPT2020 includes codes for automatic development of such surfaces, enabling generation of complete dimer surfaces with a rigid monomer approximation for dimers containing about one hundred atoms. These codes can also be used to obtain surfaces including internal degrees of freedom of monomers.
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Affiliation(s)
- Javier Garcia
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Rafał Podeszwa
- Institute of Chemistry, University of Silesia at Katowice, Szkolna 9, Katowice, Poland
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
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11
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Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, Schriber JB, Xie Y, Glick ZL, Sirianni DA, O’Brien JS, Waldrop JM, Kumar A, Hohenstein EG, Pritchard BP, Brooks BR, Schaefer HF, Sokolov AY, Patkowski K, DePrince AE, Bozkaya U, King RA, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.4: Open-source software for high-throughput quantum chemistry. J Chem Phys 2020; 152:184108. [PMID: 32414239 PMCID: PMC7228781 DOI: 10.1063/5.0006002] [Citation(s) in RCA: 337] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
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Affiliation(s)
| | - Lori A. Burns
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew C. Simmonett
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Robert M. Parrish
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Matthew C. Schieber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | | | - Peter Kraus
- School of Molecular and Life Sciences, Curtin
University, Kent St., Bentley, Perth, Western Australia 6102,
Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of
Sciences, Královopolská 135, 612 65 Brno, Czech
Republic
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical
and Computational Chemistry, UiT, The Arctic University of Norway, N-9037
Tromsø, Norway
| | - Asem Alenaizan
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew M. James
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Susi Lehtola
- Department of Chemistry, University of
Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki,
Finland
| | - Jonathon P. Misiewicz
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific
Computing, Heidelberg University, D-69120 Heidelberg,
Germany
| | - Robert A. Shaw
- ARC Centre of Excellence in Exciton Science,
School of Science, RMIT University, Melbourne, VIC 3000,
Australia
| | - Jeffrey B. Schriber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Yi Xie
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Zachary L. Glick
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Dominic A. Sirianni
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Joseph Senan O’Brien
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Jonathan M. Waldrop
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - Ashutosh Kumar
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Edward G. Hohenstein
- SLAC National Accelerator Laboratory, Stanford
PULSE Institute, Menlo Park, California 94025,
USA
| | | | - Bernard R. Brooks
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and Biochemistry, The
Ohio State University, Columbus, Ohio 43210, USA
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry,
Florida State University, Tallahassee, Florida 32306-4390,
USA
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe
University, Ankara 06800, Turkey
| | - Rollin A. King
- Department of Chemistry, Bethel
University, St. Paul, Minnesota 55112, USA
| | | | - Justin M. Turney
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | | | - C. David Sherrill
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
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12
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Pawlak M, Żuchowski PS, Moiseyev N, Jankowski P. Evidence of Nonrigidity Effects in the Description of Low-Energy Anisotropic Molecular Collisions of Hydrogen Molecules with Excited Metastable Helium Atoms. J Chem Theory Comput 2020; 16:2450-2459. [PMID: 32150402 PMCID: PMC7497643 DOI: 10.1021/acs.jctc.0c00183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Cold collisions serve
as a sensitive probe of the interaction potential.
In the recent study of Klein et al. (Nature Phys.2017, 13, 35–38), the one-parameter
scaling of the interaction potential was necessary to obtain agreement
between theoretical and observed patterns of the orbiting resonances
for excited metastable helium atoms colliding with hydrogen molecules.
Here, we show that the effect of nonrigidity of the H2 molecule
on the resonant structure, absent in the previous study, is critical
to predict the correct positions of the resonances in that case. We
have complemented the theoretical description of the interaction potential
and revised reaction rate coefficients by proper inclusion of the
flexibility of the molecule. The calculated reaction rate coefficients
are in remarkable agreement with the experimental data without empirical
adjustment of the interaction potential. We have shown that even state-of-the-art
calculations of the interaction energy cannot ensure agreement with
the experiment if such an important physical effect as flexibility
of the interacting molecule is neglected. Our findings about the significance
of the nonrigidity effects can be especially crucial in cold chemistry,
where the quantum nature of molecules is pronounced.
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Affiliation(s)
- Mariusz Pawlak
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
| | - Piotr S Żuchowski
- Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry and Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Piotr Jankowski
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
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13
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Hapka M, Przybytek M, Pernal K. Second-Order Exchange-Dispersion Energy Based on a Multireference Description of Monomers. J Chem Theory Comput 2019; 15:6712-6723. [PMID: 31670950 DOI: 10.1021/acs.jctc.9b00925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a method for calculation of the second-order exchange-dispersion energy in the framework of the symmetry-adapted perturbation theory (SAPT) for weakly interacting monomers described with multiconfigurational wave functions. The proposed formalism is based on response properties obtained from extended random phase approximation (ERPA) equations and assumes the single-exchange (S2) approximation. The approach is applicable to closed shell systems where static correlation cannot be neglected or to systems in nondegenerate excited states. We examine the new method in combination with either generalized valence bond perfect pairing (GVB) or complete active space self-consistent field (CASSCF) description of the interacting monomers. For model multireference dimers in ground states (H2···H2, Be···Be, He···H2), exchange-dispersion energies are reproduced accurately. For the interaction between the excited hydrogen molecule and the helium atom we found unacceptably large errors which is attributed to the neglect of diagonal double excitations in the employed approximation to the linear response function.
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Affiliation(s)
- Michał Hapka
- Institute of Physics , Lodz University of Technology , ul. Wolczanska 219 , 90-924 Lodz , Poland.,Faculty of Chemistry , University of Warsaw , ul. L. Pasteura 1 , 02-093 Warsaw , Poland
| | - Michał Przybytek
- Faculty of Chemistry , University of Warsaw , ul. L. Pasteura 1 , 02-093 Warsaw , Poland
| | - Katarzyna Pernal
- Institute of Physics , Lodz University of Technology , ul. Wolczanska 219 , 90-924 Lodz , Poland
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14
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Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
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15
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Bistoni G. Finding chemical concepts in the Hilbert space: Coupled cluster analyses of noncovalent interactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1442] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Giovanni Bistoni
- Max‐Planck‐Institut für Kohlenforschung Mülheim an der Ruhr Germany
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16
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Waldrop JM, Patkowski K. Spin splittings from first-order symmetry-adapted perturbation theory without single-exchange approximation. J Chem Phys 2019; 150:074109. [PMID: 30795682 DOI: 10.1063/1.5086079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The recently proposed spin-flip symmetry-adapted perturbation theory (SF-SAPT) first-order exchange energy [Patkowski et al., J. Chem. Phys. 148, 164110 (2018)] enables the standard open-shell SAPT approach to treat arbitrary spin states of the weakly interacting complex. Here, we further extend first-order SF-SAPT beyond the single-exchange approximation to a complete treatment of the exchanges of electrons between monomers. This new form of the exchange correction replaces the single-exchange approximation with a more moderate single-spin-flip approximation. The newly developed expressions are applied to a number of small test systems to elucidate the quality of both approximations. They are also applied to the singlet-triplet splittings in pancake bonded dimers. The accuracy of the single-exchange approximation deteriorates at short intermolecular separations, especially for systems with few electrons and for the high-spin state of the complex. In contrast, the single-spin-flip approximation is exact for interactions involving a doublet molecule and remains highly accurate for any number of unpaired electrons. Because the single-exchange approximation affects the high-spin and low-spin states of pancake bonded complexes evenly, the resulting splitting values are of similar accuracy to those produced by the formally more accurate single-spin-flip approximation.
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Affiliation(s)
- Jonathan M Waldrop
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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17
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Altun A, Saitow M, Neese F, Bistoni G. Local Energy Decomposition of Open-Shell Molecular Systems in the Domain-Based Local Pair Natural Orbital Coupled Cluster Framework. J Chem Theory Comput 2019; 15:1616-1632. [PMID: 30702888 PMCID: PMC6728066 DOI: 10.1021/acs.jctc.8b01145] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Local
energy decomposition (LED) analysis decomposes the interaction
energy between two fragments calculated at the domain-based local
pair natural orbital CCSD(T) (DLPNO-CCSD(T)) level of theory into
a series of chemically meaningful contributions and has found widespread
applications in the study of noncovalent interactions. Herein, an
extension of this scheme that allows for the analysis of interaction
energies of open-shell molecular systems calculated at the UHF-DLPNO-CCSD(T)
level is presented. The new scheme is illustrated through applications
to the CH2···X (X = He, Ne, Ar, Kr, and
water) and heme···CO interactions in the low-lying
singlet and triplet spin states. The results are used to discuss the
mechanism that governs the change in the singlet–triplet energy
gap of methylene and heme upon adduct formation.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Masaaki Saitow
- Department of Chemistry, Graduate School of Science , Nagoya University , 1-5 Chikusa-ku , 464-8602 Nagoya , Japan
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
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18
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Patkowski K, Żuchowski PS, Smith DGA. First-order symmetry-adapted perturbation theory for multiplet splittings. J Chem Phys 2018; 148:164110. [PMID: 29716224 DOI: 10.1063/1.5021891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a symmetry-adapted perturbation theory (SAPT) for the interaction of two high-spin open-shell molecules (described by their restricted open-shell Hartree-Fock determinants) resulting in low-spin states of the complex. The previously available SAPT formalisms, except for some system-specific studies for few-electron complexes, were restricted to the high-spin state of the interacting system. Thus, the new approach provides, for the first time, a SAPT-based estimate of the splittings between different spin states of the complex. We have derived and implemented the lowest-order SAPT term responsible for these splittings, that is, the first-order exchange energy. We show that within the so-called S2 approximation commonly used in SAPT (neglecting effects that vanish as fourth or higher powers of intermolecular overlap integrals), the first-order exchange energies for all multiplets are linear combinations of two matrix elements: a diagonal exchange term that determines the spin-averaged effect and a spin-flip term responsible for the splittings between the states. The numerical factors in this linear combination are determined solely by the Clebsch-Gordan coefficients: accordingly, the S2 approximation implies a Heisenberg Hamiltonian picture with a single coupling strength parameter determining all the splittings. The new approach is cast into both molecular-orbital and atomic-orbital expressions: the latter enable an efficient density-fitted implementation. We test the newly developed formalism on several open-shell complexes ranging from diatomic systems (Li⋯H, Mn⋯Mn, …) to the phenalenyl dimer.
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Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
| | - Piotr S Żuchowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, Torun 87-100, Poland
| | - Daniel G A Smith
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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19
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Pastorczak E, Corminboeuf C. Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions. J Chem Phys 2018; 146:120901. [PMID: 28388098 DOI: 10.1063/1.4978951] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized.
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Affiliation(s)
- Ewa Pastorczak
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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20
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Lao KU, Herbert JM. Atomic Orbital Implementation of Extended Symmetry-Adapted Perturbation Theory (XSAPT) and Benchmark Calculations for Large Supramolecular Complexes. J Chem Theory Comput 2018; 14:2955-2978. [DOI: 10.1021/acs.jctc.8b00058] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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21
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Holzer C, Klopper W. Communication: Symmetry-adapted perturbation theory with intermolecular induction and dispersion energies from the Bethe–Salpeter equation. J Chem Phys 2017; 147:181101. [DOI: 10.1063/1.5007929] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christof Holzer
- Institute of Physical Chemistry, Theoretical Chemistry Group, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Theoretical Chemistry Group, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, D-76049 Karlsruhe, Germany
- Centre for Advanced Study (CAS) at The Norwegian Academy of Science and Letters, Drammensveien 78, N-0271 Oslo, Norway
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22
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Pastorczak E, Shen J, Hapka M, Piecuch P, Pernal K. Intricacies of van der Waals Interactions in Systems with Elongated Bonds Revealed by Electron-Groups Embedding and High-Level Coupled-Cluster Approaches. J Chem Theory Comput 2017; 13:5404-5419. [DOI: 10.1021/acs.jctc.7b00797] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ewa Pastorczak
- Institute
of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland
| | - Jun Shen
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Michał Hapka
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Piotr Piecuch
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Katarzyna Pernal
- Institute
of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland
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23
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Parrish RM, Burns LA, Smith DGA, Simmonett AC, DePrince AE, Hohenstein EG, Bozkaya U, Sokolov AY, Di Remigio R, Richard RM, Gonthier JF, James AM, McAlexander HR, Kumar A, Saitow M, Wang X, Pritchard BP, Verma P, Schaefer HF, Patkowski K, King RA, Valeev EF, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. J Chem Theory Comput 2017; 13:3185-3197. [PMID: 28489372 PMCID: PMC7495355 DOI: 10.1021/acs.jctc.7b00174] [Citation(s) in RCA: 758] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Daniel G A Smith
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Andrew C Simmonett
- National Institutes of Health , National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - A Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306-4390, United States
| | - Edward G Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University , Ankara 06800, Turkey
| | - Alexander Yu Sokolov
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Ryan M Richard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Jérôme F Gonthier
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Andrew M James
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Harley R McAlexander
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Masaaki Saitow
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University , 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Xiao Wang
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Benjamin P Pritchard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Prakash Verma
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| | - Rollin A King
- Department of Chemistry, Bethel University , St. Paul, Minnesota 55112, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | | | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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24
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Sladek V, Tvaroška I. First-Principles Interaction Analysis Assessment of the Manganese Cation in the Catalytic Activity of Glycosyltransferases. J Phys Chem B 2017; 121:6148-6162. [DOI: 10.1021/acs.jpcb.7b03714] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Vladimir Sladek
- Institute
of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
- Department
of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Tokyo 171-8501, Japan
| | - Igor Tvaroška
- Institute
of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
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25
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Gonthier JF, Sherrill CD. Density-fitted open-shell symmetry-adapted perturbation theory and application to π-stacking in benzene dimer cation and ionized DNA base pair steps. J Chem Phys 2017; 145:134106. [PMID: 27782424 DOI: 10.1063/1.4963385] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Symmetry-Adapted Perturbation Theory (SAPT) is one of the most popular approaches to energy component analysis of non-covalent interactions between closed-shell systems, yielding both accurate interaction energies and meaningful interaction energy components. In recent years, the full open-shell equations for SAPT up to second-order in the intermolecular interaction and zeroth-order in the intramolecular correlation (SAPT0) were published [P. S. Zuchowski et al., J. Chem. Phys. 129, 084101 (2008); M. Hapka et al., ibid. 137, 164104 (2012)]. Here, we utilize density-fitted electron repulsion integrals to produce an efficient computational implementation. This approach is used to examine the effect of ionization on π-π interactions. For the benzene dimer radical cation, comparison against reference values indicates a good performance for open-shell SAPT0, except in cases with substantial charge transfer. For π stacking between hydrogen-bonded pairs of nucleobases, dispersion interactions still dominate binding, in spite of the creation of a positive charge.
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Affiliation(s)
- Jérôme F Gonthier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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26
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Kłos J, Hapka M, Chałasiński G, Halvick P, Stoecklin T. Theoretical study of the buffer-gas cooling and trapping of CrH(X6Σ+) by3He atoms. J Chem Phys 2016; 145:214305. [DOI: 10.1063/1.4968529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jacek Kłos
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021, USA
| | - Michał Hapka
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Grzegorz Chałasiński
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Philippe Halvick
- Institut des Sciences Moléculaires, Université de Bordeaux, CNRS-UMR 5255, 33405 Talence, France
| | - Thierry Stoecklin
- Institut des Sciences Moléculaires, Université de Bordeaux, CNRS-UMR 5255, 33405 Talence, France
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27
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Levine DS, Horn PR, Mao Y, Head-Gordon M. Variational Energy Decomposition Analysis of Chemical Bonding. 1. Spin-Pure Analysis of Single Bonds. J Chem Theory Comput 2016; 12:4812-4820. [DOI: 10.1021/acs.jctc.6b00571] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel S. Levine
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul R. Horn
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yuezhi Mao
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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28
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Jachymski K, Hapka M, Jankunas J, Osterwalder A. Experimental and Theoretical Studies of Low‐Energy Penning Ionization of NH
3
, CH
3
F, and CHF
3. Chemphyschem 2016; 17:3776-3782. [DOI: 10.1002/cphc.201600608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/02/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Krzysztof Jachymski
- Faculty of Physics University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Institute for Theoretical Physics III and Center for Integrated Quantum Science and Technology University of Stuttgart Pfaffenwaldring 57 70550 Stuttgart Germany
| | - Michał Hapka
- Faculty of Chemistry University of Warsaw Pasteura 1 02-093 Warsaw Poland
| | - Justin Jankunas
- Institute for Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- Deceased
| | - Andreas Osterwalder
- Institute for Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
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29
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Jankunas J, Jachymski K, Hapka M, Osterwalder A. Communication: Importance of rotationally inelastic processes in low-energy Penning ionization of CHF3. J Chem Phys 2016; 144:221102. [DOI: 10.1063/1.4953908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Justin Jankunas
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Krzysztof Jachymski
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Institute for Theoretical Physics III and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | - Michał Hapka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andreas Osterwalder
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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30
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Lao KU, Herbert JM. Energy Decomposition Analysis with a Stable Charge-Transfer Term for Interpreting Intermolecular Interactions. J Chem Theory Comput 2016; 12:2569-82. [PMID: 27049750 DOI: 10.1021/acs.jctc.6b00155] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many schemes for decomposing quantum-chemical calculations of intermolecular interaction energies into physically meaningful components can be found in the literature, but the definition of the charge-transfer (CT) contribution has proven particularly vexing to define in a satisfactory way and typically depends strongly on the choice of basis set. This is problematic, especially in cases of dative bonding and for open-shell complexes involving cation radicals, for which one might expect significant CT. Here, we analyze CT interactions predicted by several popular energy decomposition analyses and ultimately recommend the definition afforded by constrained density functional theory (cDFT), as it is scarcely dependent on basis set and provides results that are in accord with chemical intuition in simple cases, and in quantitative agreement with experimental estimates of the CT energy, where available. For open-shell complexes, the cDFT approach affords CT energies that are in line with trends expected based on ionization potentials and electron affinities whereas some other definitions afford unreasonably large CT energies in large-gap systems, which are sometimes artificially offset by underestimation of van der Waals interactions by density functional theory. Our recommended energy decomposition analysis is a composite approach, in which cDFT is used to define the CT component of the interaction energy and symmetry-adapted perturbation theory (SAPT) defines the electrostatic, polarization, Pauli repulsion, and van der Waals contributions. SAPT/cDFT provides a stable and physically motivated energy decomposition that, when combined with a new implementation of open-shell SAPT, can be applied to supramolecular complexes involving molecules, ions, and/or radicals.
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Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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31
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Frey JA, Holzer C, Klopper W, Leutwyler S. Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes. Chem Rev 2016; 116:5614-41. [DOI: 10.1021/acs.chemrev.5b00652] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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32
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Shagam Y, Klein A, Skomorowski W, Yun R, Averbukh V, Koch CP, Narevicius E. Molecular hydrogen interacts more strongly when rotationally excited at low temperatures leading to faster reactions. Nat Chem 2015; 7:921-6. [DOI: 10.1038/nchem.2359] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/25/2015] [Indexed: 11/09/2022]
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33
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Parrish RM, Sherrill CD. Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition. J Chem Phys 2015; 141:044115. [PMID: 25084889 DOI: 10.1063/1.4889855] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Jankunas J, Jachymski K, Hapka M, Osterwalder A. Observation of orbiting resonances in He(3S1) + NH3Penning ionization. J Chem Phys 2015; 142:164305. [DOI: 10.1063/1.4919369] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Justin Jankunas
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Michał Hapka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andreas Osterwalder
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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35
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Jankunas J, Bertsche B, Jachymski K, Hapka M, Osterwalder A. Dynamics of gas phase Ne* + NH3 and Ne* + ND3 Penning ionisation at low temperatures. J Chem Phys 2014; 140:244302. [PMID: 24985633 DOI: 10.1063/1.4883517] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Justin Jankunas
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Benjamin Bertsche
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Michał Hapka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andreas Osterwalder
- Institute for Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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36
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Soydaş E, Bozkaya U. Accurate Open-Shell Noncovalent Interaction Energies from the Orbital-Optimized Møller–Plesset Perturbation Theory: Achieving CCSD Quality at the MP2 Level by Orbital Optimization. J Chem Theory Comput 2013; 9:4679-83. [DOI: 10.1021/ct4008124] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emine Soydaş
- Department of Chemistry, Atatürk University, Erzurum 25240, Turkey
| | - Uğur Bozkaya
- Department of Chemistry, Atatürk University, Erzurum 25240, Turkey
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37
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Jansen G. Symmetry‐adapted perturbation theory based on density functional theory for noncovalent interactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1164] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Georg Jansen
- Theoretical Organic Chemistry, Department of ChemistryUniversity Duisburg‐EssenEssenGermany
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Hapka M, Chałasiński G, Kłos J, Żuchowski PS. First-principle interaction potentials for metastable He(3S) and Ne(3P) with closed-shell molecules: Application to Penning-ionizing systems. J Chem Phys 2013; 139:014307. [DOI: 10.1063/1.4812182] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Horn PR, Sundstrom EJ, Baker TA, Head-Gordon M. Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: Theory and applications to intermolecular interactions involving radicals. J Chem Phys 2013; 138:134119. [DOI: 10.1063/1.4798224] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Wu J, Chai Z, Wang D. A benchmark study of DFT methods on the electronic properties of lanthanofullerenes: a case study of Ce@C2v(9)-C82 anion. RSC Adv 2013. [DOI: 10.1039/c3ra43085e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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