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Liang J, Feng X, Hait D, Head-Gordon M. Revisiting the Performance of Time-Dependent Density Functional Theory for Electronic Excitations: Assessment of 43 Popular and Recently Developed Functionals from Rungs One to Four. J Chem Theory Comput 2022; 18:3460-3473. [PMID: 35533317 DOI: 10.1021/acs.jctc.2c00160] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this paper, the performance of more than 40 popular or recently developed density functionals is assessed for the calculation of 463 vertical excitation energies against the large and accurate QuestDB benchmark set. For this purpose, the Tamm-Dancoff approximation offers a good balance between computational efficiency and accuracy. The functionals ωB97X-D and BMK are found to offer the best performance overall with a root-mean square error (RMSE) of around 0.27 eV, better than the computationally more demanding CIS(D) wave function method with a RMSE of 0.36 eV. The results also suggest that Jacob's ladder still holds for time-dependent density functional theory excitation energies, though hybrid meta generalized-gradient approximations (meta-GGAs) are not generally better than hybrid GGAs. Effects of basis set convergence, gauge invariance correction to meta-GGAs, and nonlocal correlation (VV10) are also studied, and practical basis set recommendations are provided.
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Affiliation(s)
- Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Xintian Feng
- Q-Chem Inc., Pleasanton, California 94588, United States
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Raczyńska ED, Makowski M. Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine. J Phys Chem A 2018; 122:7863-7879. [PMID: 30192141 DOI: 10.1021/acs.jpca.8b07539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC+•), and negative ionization, called one-electron reduction (iC + e → iC-•), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC+• is close to that of the iC conjugate acid, and basicity of iC-• is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC+•, iC-•, U, U+•, U-•, C, C+•, and C-• are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry , Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c , 02-776 Warszawa , Poland
| | - Mariusz Makowski
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
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Raeber AE, Wong BM. The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs. J Chem Theory Comput 2016; 11:2199-209. [PMID: 26574420 DOI: 10.1021/acs.jctc.5b00105] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.
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Affiliation(s)
- Alexandra E Raeber
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program, University of California, Riverside , Riverside, California 92521, United States
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program, University of California, Riverside , Riverside, California 92521, United States
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Benda Z, Szalay PG. Characterization of the excited states of DNA building blocks: a coupled cluster computational study. Phys Chem Chem Phys 2016; 18:23596-606. [PMID: 27506397 DOI: 10.1039/c6cp02969h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DNA building blocks consisting of up to four nucleobases are investigated using the EOM-CCSD and CC2-LR methods in two B-DNA-like arrangements of a poly-adenine:poly-thymine (poly-A:poly-T) system. Excitation energies and oscillator strengths are presented and the characteristics of the excited states are discussed. Excited states of single-stranded poly-A systems are highly delocalized, especially the spectroscopically bright states, where delocalization over up to four fragments can be observed. In the case of poly-T systems, the states are somewhat less delocalized, extending to maximally about three fragments. A single A:T Watson-Crick pair has highly localized states, while delocalization over base pairs can be observed for some excited states of the (A)2:(T)2 system, but intrastrand delocalization is more pronounced in this case, as well. As for the characteristics of the simulated UV absorption spectra, a significant decrease of intensity can be observed in the case of single strands with increasing chain length; this is due to the stacking interactions and is in accordance with previous results. On the other hand, the breaking of H-bonds between the two strands does not alter the spectral intensity considerably, it only causes a redshift of the absorption band, thus it is unable to explain the experimentally observed DNA hyperchromism on its own, and stacking interactions need to be considered for the description of this effect as well.
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Affiliation(s)
- Zsuzsanna Benda
- Institute of Chemistry, Eötvös University, H-1518 Budapest, P.O. Box 32, Hungary.
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Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies. J Mol Model 2016; 22:146. [PMID: 27259531 PMCID: PMC4893064 DOI: 10.1007/s00894-016-3020-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023]
Abstract
Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.
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Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Raczyńska ED, Kamińska B. Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM). J Mol Model 2013; 19:3947-60. [PMID: 23832652 PMCID: PMC3744648 DOI: 10.1007/s00894-013-1926-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 06/16/2013] [Indexed: 11/25/2022]
Abstract
Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. PCM hydration influences geometries, π-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Live Science (SGGW), 02-776, Warszawa, Poland.
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8
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Gedik M, Brown A. Computational study of the excited state properties of modified RNA nucleobases. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Szalay PG, Watson T, Perera A, Lotrich V, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 3. Watson–Crick and Stacked Base Pairs. J Phys Chem A 2013; 117:3149-57. [DOI: 10.1021/jp3100975] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Péter G. Szalay
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Victor Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
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Raczyńska ED, Makowski M, Zientara-Rytter K, Kolczyńska K, Stępniewski TM, Hallmann M. Quantum-Chemical Studies on the Favored and Rare Tautomers of Neutral and Redox Adenine. J Phys Chem A 2013; 117:1548-59. [DOI: 10.1021/jp3081029] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ewa D. Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska
159 c, 02-776 Warszawa, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, Univeristy of Gdańsk, ul. Sobieskiego 18, 80-952
Gdańsk, Poland
| | - Katarzyna Zientara-Rytter
- Interdisciplinary
Department of
Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland
| | - Katarzyna Kolczyńska
- Interdisciplinary
Department of
Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland
| | - Tomasz M. Stępniewski
- Interdisciplinary
Department of
Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland
| | - Małgorzata Hallmann
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska
159 c, 02-776 Warszawa, Poland
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Szalay PG, Watson T, Perera A, Lotrich V, Fogarasi G, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 2. Effect of Biological Environment on the Electronic Excitation Spectrum of Nucleobases. J Phys Chem A 2012; 116:8851-60. [DOI: 10.1021/jp305130q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Péter G. Szalay
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Victor Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Géza Fogarasi
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
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Yamazaki S, Taketsugu T. Photoreaction channels of the guanine-cytosine base pair explored by long-range corrected TDDFT calculations. Phys Chem Chem Phys 2012; 14:8866-77. [PMID: 22596076 DOI: 10.1039/c2cp23867e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoinduced processes in the Watson-Crick guanine-cytosine base pair are comprehensively studied by means of long-range corrected (LC) TDDFT calculations of potential energy profiles using the LC-BLYP and CAM-B3LYP functionals. The ab initio CC2 method and the conventional TDDFT method with the B3LYP functional are also employed to assess the reliability of the LC-TDDFT method. The present approach allows us to compare the potential energy profiles at the same computational level for excited-state reactions of the base pair, including single and double proton transfer between the bases and nonradiative decay via ring puckering in each base. In particular, long-range correction to the TDDFT method is critical for a qualitatively correct description of the proton transfer reactions. The calculated energy profiles exhibit low barriers for out-of-plane deformation of the guanine moiety in the locally-excited state, which is expected to lead to a conical intersection with the ground state, as well as for single proton transfer from guanine to cytosine with the well-known electron-driven proton transfer mechanism. Thus the present results suggest that both processes can compete in hydrogen-bonded base pairs and play a significant role in the mechanism of photostability.
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Affiliation(s)
- Shohei Yamazaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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López-Pérez DE, Revilla-López G, Jacquemin D, Zanuy D, Palys B, Sek S, Alemán C. Intermolecular interactions in electron transfer through stretched helical peptides. Phys Chem Chem Phys 2012; 14:10332-44. [DOI: 10.1039/c2cp40761b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Cerón-Carrasco JP, Jacquemin D, Cauët E. Cisplatin cytotoxicity: a theoretical study of induced mutations. Phys Chem Chem Phys 2012; 14:12457-64. [DOI: 10.1039/c2cp40515f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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