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Šulka M, Dubecký M. Fragmentation of natural orbital occupation numbers-based diagnostic of differential multireference character in complexes with hydrogen bonds. J Comput Chem 2021; 42:475-483. [PMID: 33321553 DOI: 10.1002/jcc.26470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 11/06/2022]
Abstract
We explore the possible route to approximate natural orbital occupation numbers-based diagnostic of differential multireference character of noncovalent energy differences by techniques based on many-body expansion. It turns out that two-body fragmentation of monomers may lead to a reasonable approximation of such a diagnostic in hydrogen-bonded complexes. The results are useful, for example, for assessment of the expected bias cancellation in energy differences of larger systems obtained by single-reference methods.
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Affiliation(s)
- Martin Šulka
- Advanced Technologies Research Institute, Faculty of Materials Science and Technology in Trnava, Slovak University of Technology in Bratislava, Trnava, Slovakia.,Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matúš Dubecký
- Advanced Technologies Research Institute, Faculty of Materials Science and Technology in Trnava, Slovak University of Technology in Bratislava, Trnava, Slovakia.,Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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2
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Gonthier JF, Head-Gordon M. Assessing Electronic Structure Methods for Long-Range Three-Body Dispersion Interactions: Analysis and Calculations on Well-Separated Metal Atom Trimers. J Chem Theory Comput 2019; 15:4351-4361. [PMID: 31283231 DOI: 10.1021/acs.jctc.9b00050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three-body dispersion interactions are much weaker than their two-body counterpart. However, their importance grows quickly as the number of interacting monomers rises. To explore the numerical performance of correlation methods for long-range three-body dispersion, we performed calculations on eight very simple dispersion-dominated model metal trimers: Na3, Mg3, Zn3, Cd3, Hg3, Cu3, Ag3, and Au3. One encouraging aspect is that relatively small basis sets of augmented triple-ζ size appear to be adequate for three-body dispersion in the long-range. Coupled cluster calculations were performed at high levels to assess MP3, CCSD, CCSD(T), empirical density functional theory dispersion (D3), and the many-body dispersion (MBD) approach. We found that the accuracy of CCSD(T) was generally significantly lower than for two-body interactions, with errors sometimes reaching 20% in the investigated systems, while CCSD and particularly MP3 were generally more erratic. MBD is found to perform better than D3 at large distances, whereas the opposite is true at shorter distances. When computing reference numbers for three-body dispersion, care should be taken to appropriately represent the effect of the connected triple excitations, which are significant in most cases and incompletely approximated by CCSD(T).
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Affiliation(s)
- Jérôme F Gonthier
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , 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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3
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Maleki F, Salehzadeh S. Extension of the atom by atom scheme of counterpoise method and presentation of its new advantages. J Chem Phys 2018; 149:064116. [DOI: 10.1063/1.5037576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Farahnaz Maleki
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran
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4
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Karlický F, Otyepková E, Lo R, Pitoňák M, Jurečka P, Pykal M, Hobza P, Otyepka M. Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite. J Chem Theory Comput 2017; 13:1328-1340. [PMID: 28145699 PMCID: PMC5352977 DOI: 10.1021/acs.jctc.6b01130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Indexed: 11/28/2022]
Abstract
Understanding strength and nature of noncovalent binding to surfaces imposes significant challenge both for computations and experiments. We explored the adsorption of five small nonpolar organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate) to fluorographene and fluorographite using inverse gas chromatography and theoretical calculations, providing new insights into the strength and nature of adsorption of small organic molecules on these surfaces. The measured adsorption enthalpies on fluorographite range from -7 to -13 kcal/mol and are by 1-2 kcal/mol lower than those measured on graphene/graphite, which indicates higher affinity of organic adsorbates to fluorographene than to graphene. The dispersion-corrected functionals performed well, and the nonlocal vdW DFT functionals (particularly optB86b-vdW) achieved the best agreement with the experimental data. Computations show that the adsorption enthalpies are controlled by the interaction energy, which is dominated by London dispersion forces (∼70%). The calculations also show that bonding to structural features, like edges and steps, as well as defects does not significantly increase the adsorption enthalpies, which explains a low sensitivity of measured adsorption enthalpies to coverage. The adopted Langmuir model for fitting experimental data enabled determination of adsorption entropies. The adsorption on the fluorographene/fluorographite surface resulted in an entropy loss equal to approximately 40% of the gas phase entropy.
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Affiliation(s)
- František Karlický
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Eva Otyepková
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Rabindranath Lo
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166
10 Prague 6, Czech Republic
| | - Michal Pitoňák
- Department
of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, 842 15 Bratislava, Slovakia
- Computing Center
of the Slovak Academy of Sciences, Dúbravská cesta č. 9, 845 35 Bratislava, Slovakia
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Martin Pykal
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Pavel Hobza
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166
10 Prague 6, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
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5
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Aquilante F, Delcey MG, Pedersen TB, Fdez. Galván I, Lindh R. Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1284354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Francesco Aquilante
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
| | - Mickaël G. Delcey
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA, USA
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, Blindern, Oslo, Norway
| | - Ignacio Fdez. Galván
- Department of Chemistry – Ångström, The Theoretical Chemistry Programme, Uppsala University, Uppsala, Sweden
- Uppsala Center for Computational Chemistry – UC3, Uppsala University, Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry – Ångström, The Theoretical Chemistry Programme, Uppsala University, Uppsala, Sweden
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6
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Salehzadeh S, Maleki F. New equation for calculating total interaction energy in one noncyclic ABC triad and new insights into cooperativity of noncovalent bonds. J Comput Chem 2016; 37:2799-2807. [PMID: 27753119 DOI: 10.1002/jcc.24505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022]
Abstract
In this work, a new equation consist of A⋅⋅⋅B, B⋅⋅⋅C, A⋅⋅⋅BC, and AB⋅⋅⋅C interactions is proposed for calculating the total interaction energy of noncyclic ABC triads. New equations are also proposed for calculating the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions on the formation of triad from the corresponding dyads. The advantages of equations proposed here in comparison with many-body interaction energy approach are discussed. All proposed equations were tested in F3 MLi⋅⋅⋅NCH⋅⋅⋅HLH and F3 MLi⋅⋅⋅HLH⋅⋅⋅HCN (M = C, Si; L = Be, Mg) as well as H3 N⋅⋅⋅XY⋅⋅⋅HF (X, Y = F, Cl, Br) noncyclic A⋅⋅⋅B⋅⋅⋅C triads. The data show that the total cooperativity of triad correlates well with the sum of the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions calculated through new equations proposed here. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Farahnaz Maleki
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran
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7
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Otero-de-la-Roza A, DiLabio GA, Johnson ER. Exchange–Correlation Effects for Noncovalent Interactions in Density Functional Theory. J Chem Theory Comput 2016; 12:3160-75. [DOI: 10.1021/acs.jctc.6b00298] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Gino A. DiLabio
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Erin R. Johnson
- Department
of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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Sun CL, Ding F, Ding YL, Wang CS. The nonadditivity of stacking interactions in adenine–thymine and guanine–cytosine stacked structures: Study by MP2 and SCS-MP2 calculations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nonadditivity of stacking interactions in stacked structures of adenine–thymine and guanine–cytosine base pairs is investigated by MP2 and SCS-MP2 calculations with 6-311++G** and aug-cc-pvdz basis sets. The calculation results indicate that the intermolecular distances in the multi-stacked structures do not become shorter obviously as the stacked structure added. The middle stacking interaction energies in the multi-stacked structures also become weaker than that of dimer structures. It is found that the total stacking interaction energies of the trimer and tetramer stacked structures do not increase proportionally. Based on the results, we suggest that there is negative cooperativity of the stacking interactions in the adenine–thymine and guanine–cytosine stacked structures.
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Affiliation(s)
- Chang-Liang Sun
- Center of Physical Chemistry Test, Shenyang University of Chemical Technology, Shenyang 110142, P. R. China
| | - Fu Ding
- Center of Physical Chemistry Test, Shenyang University of Chemical Technology, Shenyang 110142, P. R. China
| | - Yan-Li Ding
- Department of Mathematics and Physics, Shenyang University of Chemical Technology Shenyang 110142, P. R. China
| | - Chang-Sheng Wang
- Department of Chemistry, Liaoning Normal University, Dalian 116029, P. R. China
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9
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10
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Haldar S, Gnanasekaran R, Hobza P. A comparison of ab initio quantum-mechanical and experimental D0 binding energies of eleven H-bonded and eleven dispersion-bound complexes. Phys Chem Chem Phys 2015; 17:26645-52. [DOI: 10.1039/c5cp04427h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dissociation energies (D0) of 11 H-bonded and 11 dispersion-bound complexes were calculated as the sum of interaction energies and the change of zero-point vibrational energies (ΔZPVE).
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Affiliation(s)
- Susanta Haldar
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6
- Czech Republic
- Department of Physical and Macromolecular Chemistry
| | - Ramachandran Gnanasekaran
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6
- Czech Republic
- Regional Center of Advanced Technologies and Materials
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11
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Sedlak R, Janowski T, Pitoňák M, Řezáč J, Pulay P, Hobza P. The accuracy of quantum chemical methods for large noncovalent complexes. J Chem Theory Comput 2013; 9:3364-3374. [PMID: 24098094 PMCID: PMC3789125 DOI: 10.1021/ct400036b] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable "accuracy/cost" ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent.
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Affiliation(s)
- Robert Sedlak
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Prague, Czech Republic
| | - Tomasz Janowski
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Michal Pitoňák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, 842 15 Bratislava, Slovak Republic
- Computing Center of the Slovak Academy of Sciences, Dúbravská cesta č. 9, 845 35 Bratislava, Slovak Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Peter Pulay
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
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12
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Šulka M, Pitoňák M, Černušák I, Urban M, Neogrády P. Ab initio study of many-body decomposition of the interaction energy in small beryllium clusters. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Boström J, Aquilante F, Pedersen TB, Lindh R. Analytical Gradients of Hartree–Fock Exchange with Density Fitting Approximations. J Chem Theory Comput 2012; 9:204-12. [DOI: 10.1021/ct200836x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jonas Boström
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124 S-221 00 Lund, Sweden
| | - Francesco Aquilante
- Center for Biomolecular Nanotechnologies @UNILE, Italian Institute of Technology (IIT), Via Barsanti, I-73010 Arnesano (LE), Italy
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Roland Lindh
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
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14
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Šimuneková M, Šimunek J, Chrappová J, Schwendt P, Žák Z, Pavelčík F. Dinucleating role of a strong hydrogen bond in crystal structure of [N(C4H9)4]{[VO(HO2)(O2)(phen)][VO(O2)2(phen)]}·3H2O2·H2O. INORG CHEM COMMUN 2012. [DOI: 10.1016/j.inoche.2012.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Rutledge LR, Wetmore SD. A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase. Phys Chem Chem Phys 2012; 14:2743-53. [PMID: 22270716 DOI: 10.1039/c2cp23600a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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16
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Marshall MS, Burns LA, Sherrill CD. Basis set convergence of the coupled-cluster correction, δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases. J Chem Phys 2011; 135:194102. [DOI: 10.1063/1.3659142] [Citation(s) in RCA: 263] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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17
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Langner KM, Janowski T, Góra RW, Dziekoński P, Sokalski WA, Pulay P. The Ethidium–UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State. J Chem Theory Comput 2011; 7:2600-9. [DOI: 10.1021/ct200121f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Karol M. Langner
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tomasz Janowski
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Paweł Dziekoński
- Wrocław Center for Networking and Supercomputing, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W. Andrzej Sokalski
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Peter Pulay
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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18
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Dom JJJ, van der Veken BJ, Michielsen B, Jacobs S, Xue Z, Hesse S, Loritz HM, Suhm MA, Herrebout WA. On the weakly C-H···π hydrogen bonded complexes of sevoflurane and benzene. Phys Chem Chem Phys 2011; 13:14142-52. [PMID: 21666925 DOI: 10.1039/c1cp20693a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A vibrational assignment of the anaesthetic sevoflurane, (CF(3))(2)CHOCH(2)F, is proposed and its interaction with the aromatic model compound benzene is studied using vibrational spectroscopy of supersonic jet expansions and of cryosolutions in liquid xenon. Ab initio calculations, at the MP2/cc-pVDZ and MP2/aug-cc-pVDZ levels, predict two isomers for the 1 : 1 complex, one in which the near-cis, gauche conformer of sevoflurane is hydrogen bonded through its isopropyl-hydrogen atom, the other in which the same conformer is bonded through a bifurcated hydrogen bond with the fluoromethyl hydrogen atoms. From the experiments it is shown that the two isomers are formed, however with a strong population dominance of the isopropyl-bonded species, both in the jet and liquid phase spectra. The experimental complexation enthalpy in liquid xenon, ΔH(o)(LXe), of this species equals -10.9(2) kJ mol(-1), as derived from the temperature dependent behaviour of the cryosolution spectra. Theoretical complexation enthalpies in liquid xenon were obtained by combining the complete basis set extrapolated complexation energies at the MP2/aug-cc-pVXZ (X = D,T) level with corrections derived from statistical thermodynamics and Monte Carlo Free Energy Perturbation calculations, resulting in a complexation enthalpy of -11.2(3) kJ mol(-1) for the isopropyl-bonded complex, in very good agreement with the experimental value, and of -11.4(4) kJ mol(-1), for the fluoromethyl-bonded complex. The Monte Carlo calculations show that the solvation entropy of the isopropyl-bonded species is considerably higher than that of the fluoromethyl-bonded complex, which assists in explaining its dominance in the liquid phase spectra.
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Affiliation(s)
- Johan J J Dom
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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Pitoňák M, Aquilante F, Hobza P, Neogrády P, Noga J, Urban M. Parallelized implementation of the CCSD(T) method in MOLCAS using optimized virtual orbitals space and Cholesky decomposed two-electron integrals. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011048] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Parallelized implementation of the coupled cluster singles doubles with non-iterative triples in the MOLCAS program suite is described. The code benefits from the Cholesky decomposition of two-electron integrals and the algorithm is particularly designed for calculations using reduced optimized virtual orbital space. Different aspects of parallelization and its efficiency are discussed based on our recent successful calculations for medium sized molecules involving more than 1000 basis functions.
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Přenosil O, Pitoňák M, Sedlák R, Kabeláč M, Hobza P. H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and Molecular Mechanics Study. ACTA ACUST UNITED AC 2011. [DOI: 10.1524/zpch.2011.0109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The cooperativity effects have been evaluated on three model systems, the formamide, (formylamino)acetamide and amyloidic-layer oligomers with an increasing size of the monomer units (6, 13 and 214 atoms). In the last model, each layer is a dimer of the amino-acid sequence GNNQQNY in one-letter amino-acid abbreviations. The series of oligomers for each model system of up to six monomers have been constructed. For the calculation of the strength of a particular H-bond formed between various sub-oligomers within an oligomer, different wave function, density functional and semi-empirical quantum mechanical methods as well as empirical force fields have been used. Semi-empirical methods are found to be a reasonable compromise between accuracy and computational cost. These methods are able to describe the cooperativity effects with an accuracy almost comparable to that of the ab initio methods. On the contrary, the empirical force-field methods for all of the model systems mostly failed to describe the H-bonding cooperativity effects properly. Based on the results obtained in this work, we recommend using semi-empirical methods. For the systems where this is impossible, we agree to use polarizable force fields with some reservations. Generally, the more flexible the oligomer chain is (the less steric the repulsion or rigid motifs are), the larger the cooperativity that can be achieved. With the increasing number of monomers in a sequence connected via H-bonds, the cooperativity effects appear to be growing, but relatively soon (at 3–4 monomer units) they tend to become saturated.
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Affiliation(s)
- Ondřej Přenosil
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, 166 10 Prague 6, Tschechische Republik
| | - Michal Pitoňák
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, 166 10 Prague 6, Tschechische Republik
| | - Robert Sedlák
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, 166 10 Prague 6, Tschechische Republik
| | - Martin Kabeláč
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, 166 10 Prague 6, Tschechische Republik
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Cholesky Decomposition Techniques in Electronic Structure Theory. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_13] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 562] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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Acosta-Silva C, Branchadell V, Bertran J, Oliva A. Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers. J Phys Chem B 2010; 114:10217-27. [PMID: 20684646 DOI: 10.1021/jp103850h] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193 Spain
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Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals. J Mol Model 2010; 16:1721-9. [PMID: 20449619 DOI: 10.1007/s00894-010-0722-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
Abstract
Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of thw 162 analyzed tetramers both three- and four-body contributions are negligible except for d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal mol(-1). This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.
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Michielsen B, Dom JJJ, Veken BJVD, Hesse S, Xue Z, Suhm MA, Herrebout WA. The complexes of halothane with benzene: the temperature dependent direction of the complexation shift of the aliphatic C–H stretching. Phys Chem Chem Phys 2010; 12:14034-44. [DOI: 10.1039/c0cp00771d] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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