1
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Jensen F. Basis Set Superposition Errors Are Partly Basis Set Imbalances. J Chem Theory Comput 2024; 20:767-774. [PMID: 38174405 DOI: 10.1021/acs.jctc.3c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
When calculating fragment interaction energies by electronic structure methods employing medium-sized atom-centered basis sets, it is often observed that the effect is systematically overestimated. The common interpretation is that the systematic error arises because the basis set for the complex is more complete than for the isolated fragments, and this is denoted basis set superposition errors. It has been observed, however, that the interaction energy in some cases is underestimated, which defies the interpretation in terms of basis set completeness, and instead suggests that the effect partly is due to basis set imbalance. The imbalance can be removed by explicit optimization of the basis sets for each structure, and it is shown that this to a significant extent reduces the systematic overestimation attributed to basis set superposition error.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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2
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Pitteloud Q, Wind P, Jensen SR, Frediani L, Jensen F. Quantifying Intramolecular Basis Set Superposition Errors. J Chem Theory Comput 2023; 19:5863-5871. [PMID: 37595013 DOI: 10.1021/acs.jctc.3c00693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
We show that medium-sized Gaussian basis sets lead to significant intramolecular basis set superposition errors at Hartree-Fock and density functional levels of theory, with artificial stabilization of compact over extended conformations for a 186 atom deca-peptide. Errors of ∼80 and ∼10 kJ/mol are observed, with polarized double zeta and polarized triple zeta quality basis sets, respectively. Two different procedures for taking the basis set superposition error into account are tested. While both reduce the error, it appears that polarized quadruple zeta basis sets are required to reduce the error below a few kJ/mol. Alternatively, the basis set superposition error can be eliminated using multiresolution methods based on Multiwavelets.
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Affiliation(s)
- Quentin Pitteloud
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Peter Wind
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Stig Rune Jensen
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Luca Frediani
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Aarhus DK-8000, Denmark
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3
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Štejfa V, Fulem M, Růžička K. First-principles calculation of ideal-gas thermodynamic properties of long-chain molecules by R1SM approach—Application to n-alkanes. J Chem Phys 2019; 150:224101. [DOI: 10.1063/1.5093767] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Květoslav Růžička
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
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4
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Hameed R, Khan A, van Mourik T. Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1418029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rabia Hameed
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Afsar Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Tanja van Mourik
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
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5
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Jensen F. Using valence bond methods to estimate intramolecular basis set superposition errors. J Chem Phys 2017. [DOI: 10.1063/1.4983229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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6
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Liu C, McGivern WS, Manion JA, Wang H. Theory and Experiment of Binary Diffusion Coefficient of n-Alkanes in Dilute Gases. J Phys Chem A 2016; 120:8065-8074. [DOI: 10.1021/acs.jpca.6b08261] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Changran Liu
- Stanford University, Stanford, California 94304, United States
| | - W. Sean McGivern
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jeffrey A Manion
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Hai Wang
- Stanford University, Stanford, California 94304, United States
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7
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Eremin RA, Kholmurodov KT, Petrenko VI, Rosta L, Grigoryeva NA, Avdeev MV. On the microstructure of organic solutions of mono-carboxylic acids: Combined study by infrared spectroscopy, small-angle neutron scattering and molecular dynamics simulations. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Ashouri M, Maghari A, Karimi-Jafari MH. Hydrogen bonding motifs in a hydroxy-bisphosphonate moiety: revisiting the problem of hydrogen bond identification. Phys Chem Chem Phys 2015; 17:13290-300. [DOI: 10.1039/c5cp00693g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relative energy of conformers are highly correlated with their sum of local density of potential energy at H-bond critical points.
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Affiliation(s)
- Mitra Ashouri
- Department of Physical Chemistry
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
| | - Ali Maghari
- Department of Physical Chemistry
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
| | - M. H. Karimi-Jafari
- Department of Bioinformatics
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
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9
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Sladek V, Holka F, Tvaroška I. Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE. Phys Chem Chem Phys 2015; 17:18501-13. [DOI: 10.1039/c5cp02191j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxygen substitution in 2-methoxytetrahydropyran by sulphur in 2-methoxythiane approximately doubles the anomeric effect, which slows down enzymatic processing of 2-methoxythiane.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Filip Holka
- Faculty of Materials Science and Technology in Trnava
- Slovak University of Technology in Bratislava
- SK-917 24 Trnava
- Slovakia
| | - Igor Tvaroška
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
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10
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Terashima Y, Takeda K, Honda M. Raman and density functional theory studies of solvation structure and ion association of NaClO4 in 1,2-propanediamine. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2013.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Fadda E, Woods RJ. Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations. CAN J CHEM 2013; 91:859-865. [PMID: 25418993 PMCID: PMC4239032 DOI: 10.1139/cjc-2012-0542] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work we analyze the effect of the inclusion of an empirical dispersion term to standard DFT (DFT-D) in the prediction of the conformational energy of the alanine dipeptide (Ala2) and in assessing the relative stabilities of short polyala-nine peptides in helical conformations, i.e., α and 310 helices, from Ala4 to Ala16. The Ala2 conformational energies obtained with the dispersion-corrected GGA functional B97-D are compared to previously published high level MP2 data. Meanwhile, the B97-D performance on larger polyalanine peptides is compared to MP2, B3LYP and RHF calculations obtained at a lower level of theory. Our results show that electron correlation affects the conformational energies of short peptides with a weight that increases with the peptide length. Indeed, while the contribution of vdW forces is significant for larger peptides, in the case of Ala2 it is negligible when compared to solvent effects. Even for short peptides, the inclusion of an empirical dispersion term greatly improves accuracy of DFT methods, providing results that correlate very well with the MP2 reference at no additional computational cost.
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Affiliation(s)
- Elisa Fadda
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Robert J Woods
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland; Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
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12
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Kim JY, Won GY, Lee S. Effects of Microsolvation on the Stability of Zwitterionic Valine. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.11.3797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Bagdi K, Molnár K, Kállay M, Schön P, Vancsó JG, Pukánszky B. Quantitative estimation of the strength of specific interactions in polyurethane elastomers, and their effect on structure and properties. Eur Polym J 2012. [DOI: 10.1016/j.eurpolymj.2012.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Assessment of density functionals on intramolecular dispersion interaction in large normal alkanes. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Deuterium-labelled N-acyl-L-homoserine lactones (AHLs)--inter-kingdom signalling molecules--synthesis, structural studies, and interactions with model lipid membranes. Anal Bioanal Chem 2012; 403:473-82. [PMID: 22367286 DOI: 10.1007/s00216-012-5839-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 01/31/2012] [Accepted: 02/03/2012] [Indexed: 10/28/2022]
Abstract
N-Acyl-L-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-L-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum's acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein.
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16
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Faver JC, Zheng Z, Merz KM. Statistics-based model for basis set superposition error correction in large biomolecules. Phys Chem Chem Phys 2012; 14:7795-9. [DOI: 10.1039/c2cp23715f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Wang X, He X, Huang G, Wu J. Correlations between alkyl side chain length and dynamic mechanical properties of poly(n-alkyl acrylates) and poly(n-alkyl methacrylates). POLYMER 2012. [DOI: 10.1016/j.polymer.2011.11.059] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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18
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Balabin RM. Experimental thermodynamics of free glycine conformations: the first Raman experiment after twenty years of calculations. Phys Chem Chem Phys 2012; 14:99-103. [DOI: 10.1039/c1cp20805e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Pele L, Šebek J, Potma EO, Benny Gerber R. Raman and IR spectra of butane: Anharmonic calculations and interpretation of room temperature spectra. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Hua S, Xu L, Li W, Li S. Cooperativity in Long α- and 310-Helical Polyalanines: Both Electrostatic and van der Waals Interactions Are Essential. J Phys Chem B 2011; 115:11462-9. [DOI: 10.1021/jp203423w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shugui Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Lina Xu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
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