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Martín-Fernández C, Elguero J, Alkorta I. Beryllium as a Base: Complexes of Be(CO) 3 with HX (X=F, Cl, Br, CN, NC, CCH, OH). Chemphyschem 2024:e202400608. [PMID: 38950128 DOI: 10.1002/cphc.202400608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
Beryllium chemistry is typically governed by its electron deficient character, but in some compounds it can act as a base. In order to understand better the unusual basicity of Be, we have systematically explored the complexes of one such compound, Be(CO)3, towards several hydrogen bond donors HX (X=F, Cl, Br, CN, NC, CCH, OH). For all complexes we find three different minima, two hydrogen bonded minima (to the Be or O atoms), and one weak beryllium bonded minimum. Further characterization of the interactions using a topological analysis of the electron density and Symmetry Adapted Perturbation Theory (SAPT) provide insight into the nature of these interactions. Overall these results highlight the capability of certain beryllium compounds to act as either a weak Lewis acid or, unconventionally, a Lewis base whose basicity towards hydrogen bonding is comparable to that of π systems.
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Affiliation(s)
| | - José Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006, Madrid, Spain
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2
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Kumawat RL, Sherrill CD. High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs. J Chem Inf Model 2023; 63:3150-3157. [PMID: 37125692 DOI: 10.1021/acs.jcim.3c00428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase pairs [adenine:thymine (A:T) and guanine:cytosine (G:C)] and non-natural Hachimoji nucleobase pairs [isoguanine:1-methylcytosine (B:S) and 2-aminoimidazo[1,2a][1,3,5]triazin-4(1H)-one:6-amino-5-nitropyridin-2-one (P:Z)] to see how the intermolecular interaction energies and their energetic components (electrostatics, exchange-repulsion, induction/polarization, and London dispersion interactions) vary among the base pairs. We examined the Hoogsteen (HG) geometries in addition to the traditional Watson-Crick (WC) geometries. Coupled-cluster theory through perturbative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit and high-order symmetry-adapted perturbation theory (SAPT) at the SAPT2+(3)(CCD)δMP2/aug-cc-pVTZ level are used to estimate highly accurate noncovalent interaction energies. Electrostatic interactions are the most attractive component of the interaction energies, but the sum of induction/polarization and London dispersion is nearly as large, for all base pairs and geometries considered. Interestingly, the non-natural Hachimoji base pairs interact more strongly than the corresponding natural base pairs, by -21.8 (B:S) and -0.3 (P:Z) kcal mol-1 in the WC geometries, according to CCSD(T)/CBS. This is consistent with the H-bond distances being generally shorter in the non-natural base pairs. The natural base pairs are energetically more stabilized in their Hoogsteen geometries than in their WC geometries. The Hoogsteen geometry makes the A:T base pair slightly more stable, by -0.8 kcal mol-1, and it greatly stabilizes the G:C+ base pair, by -15.3 kcal mol-1. The G:C+ stabilization is mainly due to the fact that C has typically added a proton when found in Hoogsteen geometries. By contrast, Hoogsteen geometries are substantially less favorable than WC geometries for non-natural Hachimoji base pairs, by 17.3 (B:S) and 13.8 (P:Z) kcal mol-1.
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Affiliation(s)
- Rameshwar L Kumawat
- 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
| | - 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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3
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Perkins MA, Tschumper GS. Characterization of competing halogen-bonding and hydrogen-bonding motifs in the acetonitrile/hydrogen iodide dimer. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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4
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Arathala P, Tangtartharakul CB, Sinha A. Atmospheric Ring-Closure and Dehydration Reactions of 1,4-Hydroxycarbonyls in the Gas Phase: The Impact of Catalysts. J Phys Chem A 2021; 125:5963-5975. [PMID: 34191509 DOI: 10.1021/acs.jpca.1c02331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1,4-Hydroxycarbonyls can potentially undergo sequential reactions involving cyclization followed by dehydration to form dihydrofurans. As dihydrofurans contain a double bond, they are highly reactive toward atmospheric oxidants such as OH, O3, and NO3. In the present study, we use ab initio calculations to examine the impact of various atmospheric catalysts on the energetics and kinetics of the gas-phase cyclization and dehydration reaction steps associated with 4-hydroxybutanal, a prototypical 1,4-hydroxycarbonyl molecule. The cyclization step transforms 4-hydroxybutanal into 2-hydroxytetrahydrofuran, which can subsequently undergo dehydration to form 2,3-dihydrofuran. As the barriers associated with the cyclization and dehydration steps for 4-hydroxybutanal are, respectively, 34.8 and 63.0 kcal/mol in the absence of a catalyst, both reaction steps are inaccessible under atmospheric conditions in the gas phase. However, the presence of a suitable catalyst can significantly reduce the reaction barriers, and we have examined the impact of a single molecule of H2O, HO2 radical, HC(O)OH, HNO3, and H2SO4 on these reactions. We find that H2SO4 reduces the reaction barriers the greatest, with the barrier for the cyclization step being reduced to -13.1 kcal/mol and that for the dehydration step going down to 9.2 kcal/mol, measured relative to their respective separated starting reactants. Interestingly, our kinetic study shows that HNO3 gives the fastest rate due to the combined effects of a larger atmospheric concentration and a reduced barrier. Thus, our study suggests that, with acid catalysis, the cyclization reaction step can readily occur for 1,4-hydroxycarbonyls in the gas phase. Because the dehydration step exhibits a significant barrier even with acid catalysis, the 2-hydroxytetrahydrofuran products, once formed, are likely lost through their reaction with OH radicals in the atmosphere. We have investigated the reaction pathways and the rate constant for this bimolecular reaction in the presence of excess molecular oxygen (3O2), as it would occur under tropospheric conditions, using computational chemistry over the 200-300 K temperature range. We find that the main products from these OH-initiated oxidation reactions are succinaldehyde + HO2 and 2,3-dihydro-2-furanol + HO2.
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Affiliation(s)
- Parandaman Arathala
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - Chanin B Tangtartharakul
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - Amitabha Sinha
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
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5
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Irmler A, Gallo A, Grüneis A. Focal-point approach with pair-specific cusp correction for coupled-cluster theory. J Chem Phys 2021; 154:234103. [PMID: 34241257 DOI: 10.1063/5.0050054] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a basis set correction scheme for the coupled-cluster singles and doubles (CCSD) method. The scheme is based on employing frozen natural orbitals (FNOs) and diagrammatically decomposed contributions to the electronic correlation energy, which dominate the basis set incompleteness error (BSIE). As recently discussed in the work of Irmler et al. [Phys. Rev. Lett. 123, 156401 (2019)], the BSIE of the CCSD correlation energy is dominated by the second-order Møller-Plesset (MP2) perturbation energy and the particle-particle ladder term. Here, we derive a simple approximation to the BSIE of the particle-particle ladder term that effectively corresponds to a rescaled pair-specific MP2 BSIE, where the scaling factor depends on the spatially averaged correlation hole depth of the coupled-cluster and first-order pair wavefunctions. The evaluation of the derived expressions is simple to implement in any existing code. We demonstrate the effectiveness of the method for the uniform electron gas. Furthermore, we apply the method to coupled-cluster theory calculations of atoms and molecules using FNOs. Employing the proposed correction and an increasing number of FNOs per occupied orbital, we demonstrate for a test set that rapidly convergent closed and open-shell reaction energies, atomization energies, electron affinities, and ionization potentials can be obtained. Moreover, we show that a similarly excellent trade-off between required virtual orbital basis set size and remaining BSIEs can be achieved for the perturbative triples contribution to the CCSD(T) energy employing FNOs and the (T*) approximation.
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Affiliation(s)
- Andreas Irmler
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Alejandro Gallo
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Andreas Grüneis
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
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6
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Carrell EJ, Thorne CM, Tschumper GS. Erratum: “Basis set dependence of higher-order correlation effects in π-type interactions” [J. Chem. Phys. 136, 014103 (2012)]. J Chem Phys 2020; 153:069901. [DOI: 10.1063/5.0021960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Emily J. Carrell
- Department of Chemistry and Biochemistry University of Mississippi, University, Mississippi 38677-1848, USA
| | - Cara M. Thorne
- Department of Chemistry and Biochemistry University of Mississippi, University, Mississippi 38677-1848, USA
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi, University, Mississippi 38677-1848, USA
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7
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Ohno K, Oki T, Yamakado H. Quantum Chemical Exploration of Intermolecular Reactions of Acetylene. J Comput Chem 2020; 41:687-697. [PMID: 31793029 DOI: 10.1002/jcc.26120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 11/09/2022]
Abstract
Quantum chemical explorations of potential energy surfaces showed that acetylene produces various products starting from molecular arrays in short distances of 1.3-2.5 Å. Arrays of (C2 H2 )2 gave cyclobutadiene, tetrahedrane, and acetylene dimers. Arrays of (C2 H2 )3 gave benzene, prismane, benzvalene, Dewar benzene, and acetylene trimers. Arrays of (C2 H2 )4 gave cubane, cyclooctatetranene, and acetylene tetramers. Different forms of initial arrays yielded different sets of products; a parallel array of two monomers gave cyclobutadiene, whereas a cross array gave tetrahedrane. Initial molecular arrays with unusually close contacts were estimated to require local forces of 1-9 × 10-8 N. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Konan 1-9-36, Minato-ku, Tokyo, 108-0075, Japan.,Tohoku University, Graduate School of Science, Aramaki Aza-Aoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Takuto Oki
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
| | - Hideo Yamakado
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
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8
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Arzuaga X, Smith MT, Gibbons CF, Skakkebæk NE, Yost EE, Beverly BEJ, Hotchkiss AK, Hauser R, Pagani RL, Schrader SM, Zeise L, Prins GS. Proposed Key Characteristics of Male Reproductive Toxicants as an Approach for Organizing and Evaluating Mechanistic Evidence in Human Health Hazard Assessments. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:65001. [PMID: 31199676 PMCID: PMC6792367 DOI: 10.1289/ehp5045] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/22/2019] [Accepted: 05/30/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Assessing chemicals for their potential to cause male reproductive toxicity involves the evaluation of evidence obtained from experimental, epidemiological, and mechanistic studies. Although mechanistic evidence plays an important role in hazard identification and evidence integration, the process of identifying, screening and analyzing mechanistic studies and outcomes is a challenging exercise due to the diversity of research models and methods and the variety of known and proposed pathways for chemical-induced toxicity. Ten key characteristics of carcinogens provide a valuable tool for organizing and assessing chemical-specific data by potential mechanisms for cancer-causing agents. However, such an approach has not yet been developed for noncancer adverse outcomes. OBJECTIVES The objective in this study was to identify a set of key characteristics that are frequently exhibited by exogenous agents that cause male reproductive toxicity and that could be applied for identifying, organizing, and summarizing mechanistic evidence related to this outcome. DISCUSSION The identification of eight key characteristics of male reproductive toxicants was based on a survey of known male reproductive toxicants and established mechanisms and pathways of toxicity. The eight key characteristics can provide a basis for the systematic, transparent, and objective organization of mechanistic evidence relevant to chemical-induced effects on the male reproductive system. https://doi.org/10.1289/EHP5045.
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Affiliation(s)
- Xabier Arzuaga
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Martyn T. Smith
- University of California, Berkeley, School of Public Health, Berkeley, California, USA
| | - Catherine F. Gibbons
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Niels E. Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Erin E. Yost
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Brandiese E. J. Beverly
- Office of Health Assessment and Translation, National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Andrew K. Hotchkiss
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Russ Hauser
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Rodrigo L. Pagani
- Department of Urology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Steven M. Schrader
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA (retired)
| | - Lauren Zeise
- Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Sacramento, California, USA
| | - Gail S. Prins
- Department of Urology, University of Illinois at Chicago, Chicago, Illinois, USA
- School of Public Health, University of Illinois at Chicago, Chicago, Illinois, USA
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9
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Sirianni DA, Alenaizan A, Cheney DL, Sherrill CD. Assessment of Density Functional Methods for Geometry Optimization of Bimolecular van der Waals Complexes. J Chem Theory Comput 2018; 14:3004-3013. [PMID: 29763302 DOI: 10.1021/acs.jctc.8b00114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We explore the suitability of three popular density functionals (B97-D3, B3LYP-D3, M05-2X) for producing accurate equilibrium geometries of van der Waals (vdW) complexes with diverse binding motifs. For these functionals, optimizations using Dunning's aug-cc-pVDZ basis set best combine accuracy and a reasonable computational expense. Each DFT/aug-cc-pVDZ combination produces optimized equilibrium geometries for 21 small vdW complexes of organic molecules (up to four non-hydrogen atoms total) that agree with high-level CCSD(T)/CBS reference geometries to within ±0.1 Å for the averages of the center-of-mass displacement and the mean least root-mean-squared displacement. The DFT/aug-cc-pVDZ combinations are also able to reproduce the optimal center-of-mass displacements interpolated from CCSD(T)/CBS radial potential energy surfaces in both NBC7x and HBC6 test sets to within ±0.1 Å. We therefore conclude that each of these denisty functional methods, together with the aug-cc-pVDZ basis set, is suitable for producing equilibrium geometries of generic nonbonded complexes.
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Affiliation(s)
- Dominic A Sirianni
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Daniel L Cheney
- Molecular Structure and Design , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - 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 , United States
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10
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Richard RM, Bakr BW, Sherrill CD. Understanding the Many-Body Basis Set Superposition Error: Beyond Boys and Bernardi. J Chem Theory Comput 2018; 14:2386-2400. [DOI: 10.1021/acs.jctc.7b01232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan M. Richard
- 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, United States
| | - Brandon W. Bakr
- 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, United States
| | - 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, United States
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11
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Temelso B, Klein KL, Mabey JW, Pérez C, Pate BH, Kisiel Z, Shields GC. Exploring the Rich Potential Energy Surface of (H2O)11 and Its Physical Implications. J Chem Theory Comput 2018; 14:1141-1153. [DOI: 10.1021/acs.jctc.7b00938] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Berhane Temelso
- Provost’s
Office and Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Katurah L. Klein
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Joel W. Mabey
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Cristóbal Pérez
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chausse 149, D-22761 Hamburg, Germany
| | - Brooks H. Pate
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Zbigniew Kisiel
- Institute
of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warszawa, Poland
| | - George C. Shields
- Provost’s
Office and Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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12
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Elm J, Kristensen K. Basis set convergence of the binding energies of strongly hydrogen-bonded atmospheric clusters. Phys Chem Chem Phys 2017; 19:1122-1133. [DOI: 10.1039/c6cp06851k] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the first binding energy benchmark set at the CBS limit of strongly hydrogen bonded atmospheric molecular clusters.
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Affiliation(s)
- Jonas Elm
- Division of Atmospheric Sciences
- Department of Physics
- University of Helsinki
- Finland
| | - Kasper Kristensen
- qLEAP Center for Theoretical Chemistry
- Department of Chemistry
- Aarhus University
- Denmark
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13
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Sirianni DA, Burns LA, Sherrill CD. Comparison of Explicitly Correlated Methods for Computing High-Accuracy Benchmark Energies for Noncovalent Interactions. J Chem Theory Comput 2016; 13:86-99. [DOI: 10.1021/acs.jctc.6b00797] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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, 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
| | - 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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14
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Van Dornshuld E, Tschumper GS. Big Changes for Small Noncovalent Dimers: Revisiting the Potential Energy Surfaces of (P2)2 and (PCCP)2 with CCSD(T) Optimizations and Vibrational Frequencies. J Chem Theory Comput 2016; 12:1534-41. [PMID: 26999433 DOI: 10.1021/acs.jctc.5b01105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article details the re-examination of low-lying stationary points on the potential energy surfaces (PESs) of two challenging noncovalent homogeneous dimers, (P2)2 and (PCCP)2. The work was motivated by the rather large differences between MP2 and CCSD(T) energetics that were recently reported for these systems (J. Comput. Chem. 2014, 35, 479-487). The current investigation reveals significant qualitative and quantitative changes when the CCSD(T) method is used to characterize the stationary points instead of MP2. For example, CCSD(T) optimizations and harmonic vibrational frequency computations with the aug-cc-pVTZ basis set indicate that the parallel-slipped (PS) structure is the only P2 dimer stationary point examined that is a minimum (zero imaginary frequencies, ni = 0), whereas prior MP2 computations indicated that it was a transition state (ni = 1). Furthermore, the L-shaped structure of (P2)2 was the only minimum according to MP2 computations, but it collapses to the PS structure on the CCSD(T)/aug-cc-pVTZ PES. For the larger PCCP dimer, the CCSD(T) computations reveal that four rather than just two of the six stationary points characterized are minima. A series of explicitly correlated single-point energies were computed for all of the optimized structures to estimate the MP2 and CCSD(T) electronic energies at the complete basis set limit. CCSDT(Q) computations were also performed to assess the effects of dynamical electron correlation beyond the CCSD(T) level. For both (P2)2 and (PCCP)2, dispersion remains the dominant attractive component to the interaction energy according to symmetry-adapted perturbation theory analyses, and it is also the most challenging component to accurately evaluate.
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Affiliation(s)
- Eric Van Dornshuld
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677-1848, United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677-1848, United States
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15
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Richard RM, Marshall MS, Dolgounitcheva O, Ortiz JV, Brédas JL, Marom N, Sherrill CD. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules I. Reference Data at the CCSD(T) Complete Basis Set Limit. J Chem Theory Comput 2016; 12:595-604. [PMID: 26731487 DOI: 10.1021/acs.jctc.5b00875] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates.
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Affiliation(s)
- Ryan M Richard
- 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, United States
| | - Michael S Marshall
- 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, United States
| | - O Dolgounitcheva
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
| | - J V Ortiz
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
| | - Jean-Luc Brédas
- Solar & Photovoltaics Engineering Research Center, Physical Science and Engineering Division King Abdullah University of Science and Technology , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Noa Marom
- Department of Physics, Tulane University , New Orleans, Louisiana 70118-5645, United States
| | - 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, United States
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16
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Temelso B, Renner CR, Shields GC. Importance and Reliability of Small Basis Set CCSD(T) Corrections to MP2 Binding and Relative Energies of Water Clusters. J Chem Theory Comput 2015; 11:1439-48. [DOI: 10.1021/ct500944v] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Carla R. Renner
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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17
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Van Dornshuld E, Tschumper GS. Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P2 )2 and (PCCP)2. J Comput Chem 2014; 35:479-87. [PMID: 24403058 DOI: 10.1002/jcc.23522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 01/19/2023]
Abstract
This work characterizes eight stationary points of the P2 dimer and six stationary points of the PCCP dimer, including a newly identified minimum on both potential energy surfaces. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with the second-order Møller-Plesset (MP2) electronic structure method and six different basis sets: aug-cc-pVXZ, aug-cc-pV(X+d)Z, and aug-cc-pCVXZ where X = T, Q. A new L-shaped structure with C2 symmetry is the only minimum for the P2 dimer at the MP2 level of theory with these basis sets. The previously reported parallel-slipped structure with C2 h symmetry and a newly identified cross configuration with D2 symmetry are the only minima for the PCCP dimer. Single point energies were also computed using the canonical MP2 and CCSD(T) methods as well as the explicitly correlated MP2-F12 and CCSD(T)-F12 methods and the aug-cc-pVXZ (X = D, T, Q, 5) basis sets. The energetics obtained with the explicitly correlated methods were very similar to the canonical results for the larger basis sets. Extrapolations were performed to estimate the complete basis set (CBS) limit MP2 and CCSD(T) binding energies. MP2 and MP2-F12 significantly overbind the P2 and PCCP dimers relative to the CCSD(T) and CCSD(T)-F12 binding energies by as much as 1.5 kcal mol(-1) for the former and 5.0 kcal mol(-1) for the latter at the CBS limit. The dominant attractive component of the interaction energy for each dimer configuration was dispersion according to several symmetry-adapted perturbation theory analyses.
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Affiliation(s)
- Eric Van Dornshuld
- Department of Chemistry and Biochemistry, University of Mississippi, MS 38677-1848
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18
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Burns LA, Marshall MS, Sherrill CD. Comparing Counterpoise-Corrected, Uncorrected, and Averaged Binding Energies for Benchmarking Noncovalent Interactions. J Chem Theory Comput 2013; 10:49-57. [PMID: 26579890 DOI: 10.1021/ct400149j] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lori A Burns
- 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, United States
| | - Michael S Marshall
- 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, United States
| | - 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, United States
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19
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Copeland KL, Pellock SJ, Cox JR, Cafiero ML, Tschumper GS. Examination of tyrosine/adenine stacking interactions in protein complexes. J Phys Chem B 2013; 117:14001-8. [PMID: 24171662 DOI: 10.1021/jp408027j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.
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Affiliation(s)
- Kari L Copeland
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
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20
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Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Howard JC, Tschumper GS. Wavefunction methods for the accurate characterization of water clusters. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1168] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi, University Mississippi USA
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22
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Patkowski K. Basis set converged weak interaction energies from conventional and explicitly correlated coupled-cluster approach. J Chem Phys 2013; 138:154101. [DOI: 10.1063/1.4800981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Copeland KL, Tschumper GS. Effects of Heterogeneity in Small π-Type Dimers: Homogeneous and Mixed Dimers of Diacetylene and Cyanogen. J Chem Theory Comput 2012; 8:4279-84. [DOI: 10.1021/ct300644a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kari L. Copeland
- Department of Chemistry
and Biochemistry, University of Mississippi, University, Mississippi
38677-1848, United States
| | - Gregory S. Tschumper
- Department of Chemistry
and Biochemistry, University of Mississippi, University, Mississippi
38677-1848, United States
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24
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Patkowski K. On the accuracy of explicitly correlated coupled-cluster interaction energies — have orbital results been beaten yet? J Chem Phys 2012; 137:034103. [DOI: 10.1063/1.4734597] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Husar DE, Temelso B, Ashworth AL, Shields GC. Hydration of the Bisulfate Ion: Atmospheric Implications. J Phys Chem A 2012; 116:5151-63. [DOI: 10.1021/jp300717j] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Devon E. Husar
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Berhane Temelso
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Alexa L. Ashworth
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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