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Masumian E, Boese AD. Benchmarking Swaths of Intermolecular Interaction Components with Symmetry-Adapted Perturbation Theory. J Chem Theory Comput 2024; 20:30-48. [PMID: 38117939 PMCID: PMC10782453 DOI: 10.1021/acs.jctc.3c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
A benchmark database for interaction energy components of various noncovalent interactions (NCIs) along their dissociation curve is one of the essential needs in theoretical chemistry, especially for the development of force fields and machine-learning methods. We utilize DFT-SAPT or SAPT(DFT) as one of the most accurate methods to generate an extensive stock of the energy components, including dispersion energies extrapolated to the complete basis set limit (CBS). Precise analyses of the created data, and benchmarking the total interaction energies against the best available CCSD(T)/CBS values, reveal different aspects of the methodology and the nature of NCIs. For example, error cancellation effects between the S2 approximation and nonexact xc-potentials occur, and large charge transfer energies in some systems, including heavy atoms, can explain the lower accuracy of DFT-SAPT. This method is perfect for neutral complexes containing light nonmetals, while other systems with heavier atoms should be treated carefully. In the last part, a representative data set for all NCIs is extracted from the original data.
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Affiliation(s)
- Ehsan Masumian
- Physical and Theoretical Chemistry,
Department of Chemistry, University of Graz, 8010 Graz, Austria
| | - A. Daniel Boese
- Physical and Theoretical Chemistry,
Department of Chemistry, University of Graz, 8010 Graz, Austria
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Sierański T. Energy, orbital and structural stacking landscape of a purine homodimer system. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02668-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe multidimensional study, combining the extensive calculations of potential energy surfaces for the parallel-displaced configurations and methods such as energy decomposition and natural bond orbital analysis, has been carried out. The resulted data give an energy, orbital and structural landscapes of this biologically essential system. The balance of the two energy sources, electrostatic and dispersion, is clearly visible. The obtained results, taken as a whole, provide an insight into the hierarchy of intermolecular interactions in the purine system, together with their sources.
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Sylvetsky N, Kesharwani MK, Martin JML. The aug-cc-pVnZ-F12 basis set family: Correlation consistent basis sets for explicitly correlated benchmark calculations on anions and noncovalent complexes. J Chem Phys 2017; 147:134106. [DOI: 10.1063/1.4998332] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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Byrd JN, Lutz JJ, Jin Y, Ranasinghe DS, Montgomery JA, Perera A, Duan XF, Burggraf LW, Sanders BA, Bartlett RJ. Predictive coupled-cluster isomer orderings for some SinCm(m,n≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks. J Chem Phys 2016; 145:024312. [DOI: 10.1063/1.4955196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jason N. Byrd
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940, USA
| | - Jesse J. Lutz
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Yifan Jin
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | | | - John A. Montgomery
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Ajith Perera
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Xiaofeng F. Duan
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
- Air Force Research Laboratory DoD Supercomputing Resource Center, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Larry W. Burggraf
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Beverly A. Sanders
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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Brauer B, Kesharwani MK, Kozuch S, Martin JML. The S66x8 benchmark for noncovalent interactions revisited: explicitly correlated ab initio methods and density functional theory. Phys Chem Chem Phys 2016; 18:20905-25. [DOI: 10.1039/c6cp00688d] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of CCSD(F12*)(T), DFT, and SAPT methods.
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Affiliation(s)
- Brina Brauer
- Department of Organic Chemistry
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
| | - Manoj K. Kesharwani
- Department of Organic Chemistry
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
| | - Sebastian Kozuch
- Department of Chemistry
- Ben-Gurion University of the Negev
- 84105 Beer-Sheva
- Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
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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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Byrd JN, Bartlett RJ, Montgomery JA. At what chain length do unbranched alkanes prefer folded conformations? J Phys Chem A 2014; 118:1706-12. [PMID: 24524689 DOI: 10.1021/jp4121854] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Short unbranched alkanes are known to prefer linear conformations, whereas long unbranched alkanes are folded. It is not known with certainty at what chain length the linear conformation is no longer the global minimum. To clarify this point, we use ab initio and density functional methods to compute the relative energies of the linear and hairpin alkane conformers for increasing chain lengths. Extensive electronic structure calculations are performed to obtain optimized geometries, harmonic frequencies, and accurate single point energies for the selected alkane conformers from octane through octadecane. Benchmark CCSD(T)/cc-pVTZ single point calculations are performed for chains through tetradecane, whereas approximate methods are required for the longer chains up to octadecane. Using frozen natural orbitals to unambiguously truncate the virtual orbital space, we are able to compute composite CCSD FNO(T) single point energies for all the chain lengths. This approximate composite method has significant computational savings compared to full CCSD(T) while retaining ∼0.15 kcal/mol accuracy compared to the benchmark results. More approximate dual-basis resolution-of-the-identity double-hybrid DFT calculations are also performed and shown to have reasonable 0.2-0.4 kcal/mol errors compared with our benchmark values. After including contributions from temperature dependent internal energy shifts, we find the preference for folded conformations to lie between hexadecane and octadecane, in excellent agreement with recent experiments [ Lüttschwager , N. O. ; Wassermann , T. N. ; Mata , R. A. ; Suhm , M. A. Angew. Chem. Int. Ed. 2013 , 52 , 463 ].
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Affiliation(s)
- Jason N Byrd
- Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States
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Grant Hill J, Das A. Interaction in the indole⋯imidazole heterodimer: structure, Franck–Condon analysis and energy decomposition. Phys Chem Chem Phys 2014; 16:11754-62. [DOI: 10.1039/c4cp01360c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Nagels N, Hauchecorne D, Herrebout WA. Exploring the C-X…π halogen bonding motif: an infrared and Raman study of the complexes of CF₃X (X = Cl, Br and I) with the aromatic model compounds benzene and toluene. Molecules 2013; 18:6829-51. [PMID: 23752468 PMCID: PMC6270472 DOI: 10.3390/molecules18066829] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/29/2013] [Accepted: 05/31/2013] [Indexed: 11/16/2022] Open
Abstract
The formation of halogen bonded complexes formed between the trifluorohalomethanes CF₃Cl, CF₃Br and CF₃I and the Lewis bases benzene and toluene at temperatures below 150K was investigated using FTIR and Raman spectroscopy. Experiments using liquid krypton as solvent show that for both CF₃Br and CF₃I substantial fractions of the monomers can be involved in 1:1 complexes. In addition, weak absorptions illustrating the formation of 2:1 complexes between CF₃I and benzene are observed. Using spectra recorded at temperatures between 120 and 140 K, observed information on the relative stability was obtained for all complexes by determining the complexation enthalpies in solution. The resulting values for CF₃Br.benzene, CF₃I.benzene and (CF₃I)₂.benzene are -6.5(3), -7.6(2) and -14.5(9) kJ mol⁻¹. The values for CF₃Br.toluene and CF₃I.toluene are -6.2(5) and -7.4(5) kJ mol⁻¹. The experimental complexation enthalpies are compared with theoretical data obtained by combining results from MP2/aug-cc-pVDZ(-PP) and MP2/aug-cc-pVTZ(-PP) ab initio calculations, from statistical thermodynamical calculations and from Monte Carlo Free Energy Perturbation simulations. The data are also compared with results derived for other C-X···π halogen bonded complexes involving unsaturated Lewis bases such as ethene and ethyne.
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Affiliation(s)
| | | | - Wouter A. Herrebout
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +32-3-265-3373; FAX: +32-3-265-3205
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