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Maciejczyk M, Pyrka M. Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:545-557. [PMID: 37507591 PMCID: PMC10618388 DOI: 10.1007/s00249-023-01672-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.
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Affiliation(s)
- Maciej Maciejczyk
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719, Olsztyn, Poland.
| | - Maciej Pyrka
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719, Olsztyn, Poland
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2
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Sadiq S, Park W, Mironov V, Lee S, Filatov Gulak M, Choi CH. Prototropically Controlled Dynamics of Cytosine Photodecay. J Phys Chem Lett 2023; 14:791-797. [PMID: 36652675 DOI: 10.1021/acs.jpclett.2c03340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The effect of the existence of several prototropic tautomers of cytosine on its UV/vis spectra and the excited state decay dynamics is studied by spectral and nonadiabatic molecular dynamics (NAMD) simulations in connection with the mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. Simulated UV/vis spectra provide a strong indication that the H3N keto-amino cytosine tautomer (the least anticipated species) may be present under experimental conditions. The NAMD simulations yield a wide range of excited state decay constants for various tautomers of cytosine, ranging from ∼1.3 ps for the biologically relevant H1N keto-amino tautomer to ∼0.1 ps for the keto-imino tautomer. The slowness of the H1N decay dynamics follows from the presence of a barrier on the excited state energy surface separating the Franck-Condon structure from the major decay funnel, the conical intersection seam. It is suggested that the experimentally observed photodecay dynamics may result from a combination of the decay processes of various tautomers (H3N in particular) present simultaneously under the experimental conditions.
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Affiliation(s)
- Saima Sadiq
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Vladimir Mironov
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
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3
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Mehta N, Martin JML. Explicitly Correlated Double-Hybrid DFT: A Comprehensive Analysis of the Basis Set Convergence on the GMTKN55 Database. J Chem Theory Comput 2022; 18:5978-5991. [PMID: 36099641 PMCID: PMC9558368 DOI: 10.1021/acs.jctc.2c00426] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Double-hybrid density functional theory (DHDFT) offers
a pathway
to accuracy approaching composite wavefunction approaches such as
G4 theory. However, the Görling–Levy second-order perturbation
theory (GLPT2) term causes them to partially inherit the slow ∝L–3 (with L the maximum
angular momentum) basis set convergence of correlated wavefunction
methods. This could potentially be remedied by introducing F12 explicit
correlation: we investigate the basis set convergence of both DHDFT
and DHDFT-F12 (where GLPT2 is replaced by GLPT2-F12) for the large
and chemically diverse general main-group thermochemistry, kinetics,
and noncovalent interactions (GMTKN55) benchmark suite. The B2GP-PLYP-D3(BJ)
and revDSD-PBEP86-D4 DHDFs are investigated as test cases, together
with orbital basis sets as large as aug-cc-pV5Z and F12 basis sets
as large as cc-pVQZ-F12. We show that F12 greatly accelerates basis
set convergence of DHDFs, to the point that even the modest cc-pVDZ-F12
basis set is closer to the basis set limit than cc-pV(Q+d)Z or def2-QZVPPD
in orbital-based approaches, and in fact comparable in quality to
cc-pV(5+d)Z. Somewhat surprisingly, aug-cc-pVDZ-F12 is not required
even for the anionic subsets. In conclusion, DHDF-F12/VDZ-F12 eliminates
concerns about basis set convergence in both the development and applications
of double-hybrid functionals. Mass storage and I/O bottlenecks for
larger systems can be circumvented by localized pair natural orbital
approximations, which also exhibit much gentler system size scaling.
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Affiliation(s)
- Nisha Mehta
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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4
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Roque JPL, Nunes CM, Fausto R. Matrix Isolation in Heterocyclic Chemistry. HETEROCYCLES 2022. [DOI: 10.1002/9783527832002.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Feng M, Dong Q, Wu N, Wen JJ, Wang QY, Tong YC. Adsorption of CO, O2, and H2O by Iron Confined in B-Doped Carbon Nanotubes: Theoretical Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422140102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Wang QY, Nan G, Chen YY, Tong YC, Xu XJ, Bai QL. Theoretical Study on the Structures of Single-Atom M (M = Fe, Co, and Ni) Adsorption Outside and Inside the Defect Carbon Nanotubes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422140254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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8
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Gould T, Dale SG. Poisoning density functional theory with benchmark sets of difficult systems. Phys Chem Chem Phys 2022; 24:6398-6403. [PMID: 35244641 DOI: 10.1039/d2cp00268j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Large benchmark sets like GMTKN55 [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] let us analyse the performance of density functional theory over a diverse range of systems and bonding types. However, assessing over a large and diverse set can miss cases where approaches fail badly, and can give a misleading sense of security. To this end we introduce a series of 'poison' benchmark sets, P30-5, P30-10 and P30-20, comprising systems with up to 5, 10 and 20 atoms, respectively. These sets represent the most difficult-to-model systems in GMTKN55. We expect them to be useful in developing new approximations, identifying weak points in existing ones, and to aid in selecting appropriate DFAs for computational studies involving difficult physics, e.g. catalysis.
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Affiliation(s)
- Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University, Nathan, Qld 4111, Australia.
| | - Stephen G Dale
- Qld Micro- and Nanotechnology Centre, Griffith University, Nathan, Qld 4111, Australia.
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9
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Szatylowicz H, Stasyuk OA, Solà M, Krygowski TM. Aromaticity of nucleic acid bases. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry Warsaw University of Technology, Noakowskiego 3, 00‐664 Warsaw Poland
| | - Olga A. Stasyuk
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/ Maria Aurélia Capmany 69, 17003 Girona Spain
| | - Miquel Solà
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/ Maria Aurélia Capmany 69, 17003 Girona Spain
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10
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Mehta N, Goerigk L. Assessing the Applicability of the Geometric Counterpoise Correction in B2PLYP/Double-ζ Calculations for Thermochemistry, Kinetics, and Noncovalent Interactions. Aust J Chem 2021. [DOI: 10.1071/ch21133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a proof-of-concept study of the suitability of Kruse and Grimme’s geometric counterpoise correction (gCP) for basis set superposition errors (BSSEs) in double-hybrid density functional calculations with a double-ζ basis set. The gCP approach only requires geometrical information as an input and no orbital/density information is needed. Therefore, this correction is practically free of any additional cost. gCP is trained against the Boys and Bernardi counterpoise correction across a set of 528 noncovalently bound dimers. We investigate the suitability of the approach for the B2PLYP/def2-SVP level of theory, and reveal error compensation effects—missing London dispersion and the BSSE—associated with B2PLYP/def2-SVP calculations, and present B2PLYP-gCP-D3(BJ)/def2-SVP with the reparametrised DFT-D3(BJ) and gCP corrections as a more balanced alternative. Benchmarking results on the S66x8 benchmark set for noncovalent interactions and the GMTKN55 database for main-group thermochemistry, kinetics, and noncovalent interactions show a statistical improvement of the B2PLYP-gCP-D3(BJ) scheme over plain B2PLYP and B2PLYP-D3(BJ). B2PLYP-D3(BJ) shows significant overestimation of interaction energies, barrier heights with larger deviations from the reference values, and wrong relative stabilities in conformers, all of which can be associated with BSSE. We find that the gCP-corrected method represents a significant improvement over B2PLYP-D3(BJ), particularly for intramolecular noncovalent interactions. These findings encourage future developments of efficient double-hybrid DFT strategies that can be applied when double-hybrid calculations with large basis sets are not feasible due to system size.
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11
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Melandri S, Evangelisti L, Canola S, Sa'adeh H, Calabrese C, Coreno M, Grazioli C, Prince KC, Negri F, Maris A. Chlorination and tautomerism: a computational and UPS/XPS study of 2-hydroxypyridine ⇌ 2-pyridone equilibrium. Phys Chem Chem Phys 2020; 22:13440-13455. [PMID: 32519689 DOI: 10.1039/d0cp02304c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The prototropic tautomeric equilibrium in 2-hydroxypyridine serves as a prototype model for the study of nucleobases' behaviour. The position of such an equilibrium in parent and chlorine monosubstituted 2-hydroxypyridine compounds in the gas phase was determined using synchrotron based techniques. The lactim tautomer is dominant for the 5- and 6-substituted compounds, whereas the parent, 3- and 4-substituted isomers have comparable populations for both tautomers. Information was obtained by measuring valence band and core level photoemission spectra at the chlorine L-edge and carbon, nitrogen, and oxygen K-edges. The effect of chlorine on the core ionization potentials of the atoms in the heterocycle was evaluated and reasonable agreement with a simple model was obtained. Basic considerations of resonance structures correctly predicts the tautomeric equilibrium for the 5- and 6-substituted compounds. The vibrationally resolved structure of the low energy portion of the valence band photoionization spectra is assigned based on quantum-chemical calculations of the neutral and charged species followed by simulation of the vibronic structure. It is shown that the first ionization occurs from a π orbital of similar shape for both tautomers. In addition, the highly distinctive vibronic structure observed just above the first ionization of the lactim, for three of the five species investigated, is assigned to the second ionization of the lactam.
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Affiliation(s)
- Sonia Melandri
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Luca Evangelisti
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Sofia Canola
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Hanan Sa'adeh
- Department of Physics, The University of Jordan, Amman, JO-11942, Jordan
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, E-48080 Bilbao, Spain and Basque Centre for Biophysics (CSIC, UPV/EHU), Barrio Sarriena, E-48940 Leioa, Spain
| | - Marcello Coreno
- CNR-ISM, Trieste LD2 Unit, Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Cesare Grazioli
- CNR-ISM, Trieste LD2 Unit, Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra Sincrotrone Trieste, Area Science Park, I-34149 Basovizza, Trieste, Italy. and Centre for Translational Atomaterials, Swinburne University of Technology, Melbourne, Australia
| | - Fabrizia Negri
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Assimo Maris
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
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12
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Rostkowska H, Luchowska A, Lapinski L, Nowak MJ. Photochemical transformations of 4,6-dihydroxypyrimidine and 2-methyl-4,6-dihydroxypyrimidine isolated in low-temperature Ar, Ne and H2 matrices. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Bomzon B, Khunger Y, Subramanian R. A dielectric and spectrophotometric study of the tautomerization of 2-hydroxypyridine and 2-mercaptopyridine in water. RSC Adv 2020; 10:2389-2395. [PMID: 35494609 PMCID: PMC9048638 DOI: 10.1039/c9ra08392h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 11/21/2022] Open
Abstract
The basic ionization (pk1) and acidic ionization (pk2) constants and equilibrium constant (KT) of 2HPy and 2MPy were determined. The pk1(s) of their N- and X-methyl derivatives (X = O, S) were also determined. The equilibrium constant of 2MPy is approximately 60 times greater than its oxygen analog, 2HPy. The micro-ionization constants of the functional groups, –NH (pkA and pkC) and –XH (pkB and pkD), were determined to provide further insights into the ionization equilibria of these N-heteroaromatic XH compounds (2HPy and 2MPy). The relaxation time of water (τ) in aqueous solutions of 2HPy and 2MPy are collectively used with the KT values to determine the forward (kf) and backward (kb) rate constants of tautomerization. Subsequently, the kf and kb are used to provide the rationale for the KT and τ values. The basic ionization (pk1) and acidic ionization (pk2) constants and equilibrium constant (KT) of 2HPy and 2MPy were determined.![]()
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Affiliation(s)
- Biswadeep Bomzon
- Department of Chemistry, Indian Institute of Technology Patna 801106 India
| | - Yashita Khunger
- Department of Chemistry, Indian Institute of Technology Patna 801106 India
| | - Ranga Subramanian
- Department of Chemistry, Indian Institute of Technology Patna 801106 India
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14
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Dral PO, Wu X, Thiel W. Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections. J Chem Theory Comput 2019; 15:1743-1760. [PMID: 30735388 PMCID: PMC6416713 DOI: 10.1021/acs.jctc.8b01265] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/31/2022]
Abstract
We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E ABC for Axilrod-Teller-Muto dispersion interactions as integral parts. Heats of formation are determined by adding explicitly computed zero-point vibrational energy and thermal corrections, in contrast to standard MNDO-type and OM x methods. We report ODM x parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine that are optimized with regard to a wide range of carefully chosen state-of-the-art reference data. Extensive benchmarks show that the ODM x methods generally perform better than the available MNDO-type and OM x methods for ground-state and excited-state properties, while they describe noncovalent interactions with similar accuracy as OM x methods with a posteriori dispersion corrections.
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Affiliation(s)
- Pavlo O. Dral
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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15
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Karton A. Thermochemistry of Guanine Tautomers Re-Examined by Means of High-Level CCSD(T) Composite Ab Initio Methods. Aust J Chem 2019. [DOI: 10.1071/ch19276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We obtained accurate gas-phase tautomerization energies for a set of 14 guanine tautomers by means of high-level thermochemical procedures approximating the CCSD(T) energy at the complete basis set (CBS) limit. For the five low-lying tautomers, we use the computationally demanding W1-F12 composite method for obtaining the tautomerization energies. The relative W1-F12 tautomerization enthalpies at 298K are: 0.00 (1), 2.37 (2), 2.63 (3), 4.03 (3′), and 14.31 (4) kJmol−1. Thus, as many as four tautomers are found within a small energy window of less than 1.0kcalmol−1 (1kcalmol−1=4.184kJmol−1). We use these highly accurate W1-F12 tautomerization energies to evaluate the performance of a wide range of lower-level composite ab initio procedures. The Gn composite procedures (G4, G4(MP2), G4(MP2)-6X, G3, G3B3, G3(MP2), and G3(MP2)B3) predict that the enol tautomer (3) is more stable than the keto tautomer (2) by amounts ranging from 0.36 (G4) to 1.28 (G3(MP2)) kJmol−1. We also find that an approximated CCSD(T)/CBS energy calculated as HF/jul-cc-pV{D,T}Z+CCSD/jul-cc-pVTZ+(T)/jul-cc-pVDZ results in a root-mean-square deviation (RMSD) of merely 0.11kJmol−1 relative to the W1-F12 reference values. We use this approximated CCSD(T)/CBS method to obtain the tautomerization energies of 14 guanine tautomers. The relative tautomerization enthalpies at 298K are: 0.00 (1), 2.20 (2), 2.51 (3), 4.06 (3′), 14.30 (4), 25.65 (5), 43.78 (4′), 53.50 (6′), 61.58 (6), 77.37 (7), 82.52 (8′), 86.02 (9), 100.70 (10), and 121.01 (8) kJmol−1. Using these tautomerization enthalpies, we evaluate the performance of standard and composite methods for the entire set of 14 guanine tautomers. The best-performing procedures emerge as (RMSDs are given in parentheses): G4(MP2)-6X (0.51), CCSD(T)+ΔMP2/CBS (0.52), and G4(MP2) (0.64kJmol−1). The worst performers are CCSD(T)/AVDZ (1.05), CBS-QB3 (1.24), and CBS-APNO (1.38kJmol−1).
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16
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Morgante P, Peverati R. ACCDB: A collection of chemistry databases for broad computational purposes. J Comput Chem 2018; 40:839-848. [DOI: 10.1002/jcc.25761] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 11/11/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Pierpaolo Morgante
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
| | - Roberto Peverati
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
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17
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Wang QY, Tong YC, Yan PJ, Xu XJ, Li Z. Attachment of CO to a (6, 6) CNT with a Sc adsorbate atom. Struct Chem 2018. [DOI: 10.1007/s11224-018-1202-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Najibi A, Goerigk L. The Nonlocal Kernel in van der Waals Density Functionals as an Additive Correction: An Extensive Analysis with Special Emphasis on the B97M-V and ωB97M-V Approaches. J Chem Theory Comput 2018; 14:5725-5738. [DOI: 10.1021/acs.jctc.8b00842] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Asim Najibi
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
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19
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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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20
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Mehta N, Casanova-Páez M, Goerigk L. Semi-empirical or non-empirical double-hybrid density functionals: which are more robust? Phys Chem Chem Phys 2018; 20:23175-23194. [PMID: 30062343 DOI: 10.1039/c8cp03852j] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of non-empirical double-hybrid density functionals (DHDFs) is a very active research area with the number of approaches in this field having increased rapidly. At the same time, there is a lack of published work that provides a fair assessment and comparison between non-empirical and semi-empirical DHDFs on an equal footing. Herein, we close this gap and present a thorough analysis of both classes of DHDFs on the large GMTKN55 benchmark database for general main-group thermochemistry, kinetics, and noncovalent interactions [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184-32215]. In total, 115 variations of dispersion-corrected and -uncorrected DHDFs are tested, which will be condensed to an in-depth assessment of 31 methods: 19 non-empirical and 12 semi-empirical DHDFs. As such, our study represents the largest DHDF study ever conducted and can serve as an important benchmark informing method developers and users alike. Our results show that semi-empirical DHDFs are the most robust density functional approximations and more reliable and accurate than non-empirical ones. In fact, some non-empirical approaches are even outperformed by hybrid approaches or even dispersion-corrected and -uncorrected MP2 and SCS-MP2. SOS0-PBE0-2-D3(BJ) is the only exception and the only non-empirical DHDF that we can safely recommend for general applicability. However, it is still outperformed by six semi-empirical DHDFs, of which we would like to particularly recommend the following five: ωB97X-2-D3(BJ), DSD-BLYP-D3(BJ), DSD-PBEP86-D3(BJ), B2NC-PLYP-D3(BJ), and B2GPPLYP-D3(BJ). Our findings seriously question current trends in the field and they highlight that novel strategies have to be found in order to outperform the currently best density functional theory methods on the market. We hope that our study can function as an important cornerstone inspiring such a change of direction in the field.
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Affiliation(s)
- Nisha Mehta
- School of Chemistry, The University of Melbourne, Parkville, Australia.
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21
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Lapinski L, Reva I, Gerega A, Nowak MJ, Fausto R. UV-induced transformations of matrix-isolated 6-azacytosine. J Chem Phys 2018; 149:104301. [DOI: 10.1063/1.5045735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Anna Gerega
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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22
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Joksch M, Agarwala H, Spannenberg A, Beweries T. Halogen Bonding in Ring‐Substituted Group 10 POCOP Iodido Complexes with Iodine and Its Possible Role in Oxidative Addition. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Markus Joksch
- Leibniz‐Institut für Katalyse e.V. an der Universität Rostock Albert‐Einstein‐Str. 29a 18059 Rostock Germany
| | - Hemlata Agarwala
- Leibniz‐Institut für Katalyse e.V. an der Universität Rostock Albert‐Einstein‐Str. 29a 18059 Rostock Germany
- Laboratoire de Chimie des Processus Biologiques Collège de France 11 Place Marcelin Berthelot 75005 Paris France
| | - Anke Spannenberg
- Leibniz‐Institut für Katalyse e.V. an der Universität Rostock Albert‐Einstein‐Str. 29a 18059 Rostock Germany
| | - Torsten Beweries
- Leibniz‐Institut für Katalyse e.V. an der Universität Rostock Albert‐Einstein‐Str. 29a 18059 Rostock Germany
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23
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Zhao HY, Lau KC, Garcia GA, Nahon L, Carniato S, Poisson L, Schwell M, Al-Mogren MM, Hochlaf M. Unveiling the complex vibronic structure of the canonical adenine cation. Phys Chem Chem Phys 2018; 20:20756-20765. [PMID: 29989120 DOI: 10.1039/c8cp02930j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.
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Affiliation(s)
- Hong Yan Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
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24
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Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives. PHYSICAL SCIENCES REVIEWS 2017. [DOI: 10.1515/psr-2016-0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Computational chemistry can be applied to vibrational spectroscopy in different ways, such as for a better characterization and assignment of all the bands of the experimental spectra, as a tool in the identification of the tautomers present in the gas phase and in the solid state through their spectra and for the simulation of the solid and liquid phase of a compound and the consequent simulation and interpretation of their spectra. In the present study, as an example of the applicability of computational chemistry, the structure and spectra of cytosine and uracil nucleic acid bases and two cytosine derivatives are shown. The FTIR and Raman spectra were analysed with the support of ab initio (Hartree-Fock (HF), MP2) and density functional theory (DFT) (B3LYP, PBE, B-P, etc.) calculations using several basis sets and several scaling equations. The calculations predict an easier tautomerization of cytosine than uracil molecule, but the tautomerization is hindered in the 5-bromocytosine molecule. Thus, in the solid state, this molecule only exists in the amino-oxo tautomeric form.
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25
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Maximoff SN, Kamerlin SCL, Florián J. DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study. J Phys Chem B 2017; 121:7813-7822. [PMID: 28732447 DOI: 10.1021/acs.jpcb.7b04874] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.
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Affiliation(s)
- Sergey N Maximoff
- Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
| | | | - Jan Florián
- Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
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26
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Goerigk L, Hansen A, Bauer C, Ehrlich S, Najibi A, Grimme S. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys Chem Chem Phys 2017; 19:32184-32215. [DOI: 10.1039/c7cp04913g] [Citation(s) in RCA: 854] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.
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Affiliation(s)
- Lars Goerigk
- School of Chemistry
- The University of Melbourne
- Parkville
- Australia
| | - Andreas Hansen
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Christoph Bauer
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Stephan Ehrlich
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Asim Najibi
- School of Chemistry
- The University of Melbourne
- Parkville
- Australia
| | - Stefan Grimme
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
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27
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Calabrese C, Maris A, Uriarte I, Cocinero EJ, Melandri S. Effects of Chlorination on the Tautomeric Equilibrium of 2‐Hydroxypyridine: Experiment and Theory. Chemistry 2016; 23:3595-3604. [DOI: 10.1002/chem.201604891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Camilla Calabrese
- Dipartimento di Chimica “G. Ciamician” Università degli Studi di Bologna Via Selmi 2 40126 Bologna Italy
| | - Assimo Maris
- Dipartimento di Chimica “G. Ciamician” Università degli Studi di Bologna Via Selmi 2 40126 Bologna Italy
| | - Iciar Uriarte
- Dpto. Química Física Universidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
| | - Emilio J. Cocinero
- Dpto. Química Física Universidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
| | - Sonia Melandri
- Dipartimento di Chimica “G. Ciamician” Università degli Studi di Bologna Via Selmi 2 40126 Bologna Italy
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28
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Pyrka M, Maciejczyk M. Theoretical investigations of tautomeric equilibrium of 9-methyl-8-aza-iso-Guanine and its electrostatic properties. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Asami H, Tokugawa M, Masaki Y, Ishiuchi SI, Gloaguen E, Seio K, Saigusa H, Fujii M, Sekine M, Mons M. Effective Strategy for Conformer-Selective Detection of Short-Lived Excited State Species: Application to the IR Spectroscopy of the N1H Keto Tautomer of Guanine. J Phys Chem A 2016; 120:2179-84. [DOI: 10.1021/acs.jpca.6b01194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroya Asami
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Munefumi Tokugawa
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Shun-ichi Ishiuchi
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-15,
Nagatsuta-cho Midori, Yokohama 226-8503, Japan
| | - Eric Gloaguen
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Kohji Seio
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Hiroyuki Saigusa
- Graduate
School of Bio- and Nanosystem Science, Yokohama City University, Yokohama 236-0027, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-15,
Nagatsuta-cho Midori, Yokohama 226-8503, Japan
| | - Mitsuo Sekine
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Michel Mons
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
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30
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Dral P, Wu X, Spörkel L, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties. J Chem Theory Comput 2016; 12:1097-120. [PMID: 26771261 PMCID: PMC4785506 DOI: 10.1021/acs.jctc.5b01047] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 11/30/2022]
Abstract
The semiempirical orthogonalization-corrected OMx methods (OM1, OM2, and OM3) go beyond the standard MNDO model by including additional interactions in the electronic structure calculation. When augmented with empirical dispersion corrections, the resulting OMx-Dn approaches offer a fast and robust treatment of noncovalent interactions. Here we evaluate the performance of the OMx and OMx-Dn methods for a variety of ground-state properties using a large and diverse collection of benchmark sets from the literature, with a total of 13035 original and derived reference data. Extensive comparisons are made with the results from established semiempirical methods (MNDO, AM1, PM3, PM6, and PM7) that also use the NDDO (neglect of diatomic differential overlap) integral approximation. Statistical evaluations show that the OMx and OMx-Dn methods outperform the other methods for most of the benchmark sets.
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Affiliation(s)
- Pavlo
O. Dral
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Lasse Spörkel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
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31
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Power B, Haldys V, Salpin JY, Fridgen TD. Structures of [M(Ura-H)(H2 O)n ](+) (M = Mg, Ca, Sr, Ba; n = 1-3) complexes in the gas phase by IRMPD spectroscopy and theoretical studies. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:236-244. [PMID: 26956390 DOI: 10.1016/j.ijms.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/17/2023]
Abstract
The structures of singly and doubly (and for Mg, triply) hydrated group 2 metal dications bound to deprotonated uracil were explored in the gas phase using infrared multiple photon dissociation spectroscopy in the mid-infrared region (1000-1900 cm(-1) ) and the O-H/N-H stretching region (2700-3800 cm(-1) ) in a Fourier transform ion cyclotron resonance mass spectrometer. The infrared multiple photon dissociation spectra were then compared with the computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31 + G(d,p) basis set for all atoms except Ba(2+) and Sr(2+) , for which the LANL2DZ or the def2-TZVPP basis sets with relativistic core potentials were used. Atoms-in-molecules analysis was conducted for all lowest energy structures. The lowest energy isomers in all cases are those in which the one uracil is deprotonated at the N3 position, and the metal is coordinated to the N3 and O4 of uracil. Regardless of the degree of solvation, all water molecules are bound to the metal ion and participate in a hydrogen bond with a carbonyl of the uracil moiety.
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Affiliation(s)
- Barry Power
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
| | - Violette Haldys
- Université d'Evry Val d'Essonne - Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Bâtiment Maupertuis, Boulevard François Mitterrand, 91025, Evry, France
- CNRS UMR 8587
| | - Jean-Yves Salpin
- Université d'Evry Val d'Essonne - Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Bâtiment Maupertuis, Boulevard François Mitterrand, 91025, Evry, France
- CNRS UMR 8587
| | - Travis D Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
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32
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Goryachkovskaya TN, Kozlov AS, Popik VM, Kolchanov NA, Peltek SE. Dependence of a DNA globule size in a gas phase on the chain length. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s2079059715040061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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McCann BW, McFarland S, Acevedo O. Benchmarking Continuum Solvent Models for Keto–Enol Tautomerizations. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b04116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Billy W. McCann
- Department
of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Stuart McFarland
- Department
of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department
of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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34
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Chan B, Goerigk L, Radom L. On the inclusion of post-MP2 contributions to double-Hybrid density functionals. J Comput Chem 2015; 37:183-93. [DOI: 10.1002/jcc.23972] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Bun Chan
- School of Chemistry; The University of Sydney and Centre of Excellence for Free Radical Chemistry and Biotechnology; Sydney New South Wales 2006 Australia
| | - Lars Goerigk
- School of Chemistry; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Leo Radom
- School of Chemistry; The University of Sydney and Centre of Excellence for Free Radical Chemistry and Biotechnology; Sydney New South Wales 2006 Australia
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35
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Theoretical study of tautomeric equilibria of 2,6-diamino-8-azapurine and 8-aza-iso-Guanine. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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36
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Grimme S, Bauer CA. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:125-140. [PMID: 26307693 DOI: 10.1255/ejms.1313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich- Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany. - bonn.de
| | - Christopher Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany.
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37
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Bousquet D, Brémond E, Sancho-García JC, Ciofini I, Adamo C. Non-parametrized functionals with empirical dispersion corrections: A happy match? Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1602-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Bauer CA, Grimme S. Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics. J Phys Chem A 2014; 118:11479-84. [DOI: 10.1021/jp5096618] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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39
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Galstyan G, Knapp EW. Computing pK(A) values of hexa-aqua transition metal complexes. J Comput Chem 2014; 36:69-78. [PMID: 25328033 DOI: 10.1002/jcc.23764] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/24/2014] [Accepted: 10/09/2014] [Indexed: 01/13/2023]
Abstract
Aqueous pKA values for 15 hexa-aqua transition metal complexes were computed using a combination of quantum chemical and electrostatic methods. Two different structure models were considered optimizing the isolated complexes in vacuum or in presence of explicit solvent using a QM/MM approach. They yield very good agreement with experimentally measured pKA values with an overall root mean square deviation of about 1 pH unit, excluding a single but different outlier for each of the two structure models. These outliers are hexa-aqua Cr(III) for the vacuum and hexa-aqua Mn(III) for the QM/MM structure model. Reasons leading to the deviations of the outlier complexes are partially explained. Compared to previous approaches from the same lab the precision of the method was systematically improved as discussed in this study. The refined methods to obtain the appropriate geometries of the complexes, developed in this work, may allow also the computation of accurate pKA values for multicore transition metal complexes in different oxidation states.
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Affiliation(s)
- Gegham Galstyan
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, D-14195, Berlin, Germany
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40
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Das T, Ghosh D. Ionization-Induced Tautomerization in Cytosine and Effect of Solvation. J Phys Chem A 2014; 118:5323-32. [DOI: 10.1021/jp503947d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamal Das
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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41
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Yurdakul S, Yurdakul M. FT-IR, FT-Raman spectra, and DFT computations of the vibrational spectra and molecular geometry of chlorzoxazone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 126:339-348. [PMID: 24684869 DOI: 10.1016/j.saa.2014.02.156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 06/03/2023]
Abstract
Far-IR, mid-IR, and FT-Raman spectra of the chlorzoxazone (CZX) were recorded. The observed vibrational wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. Density functional calculations were performed to support wavenumber assignments of the observed bands. The equilibrium geometry and harmonic wavenumbers of CZX were calculated by the DFT B3LYP method. All tautomeric forms and dimer form of CZX were determined and optimized. Additionally, experimental FT-IR spectrum in ethanol solution was recorded and compared with solid phase experimental data for the first time. The combination of the DFT B3LYP with polarized continuum model (PCM) was employed to characterize the solvent effects in ethanol solution.
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Affiliation(s)
- Senay Yurdakul
- Department of Physics, Faculty of Sciences, Gazi University, Teknikokullar 06500, Ankara, Turkey.
| | - Murat Yurdakul
- Department of Mathematics, Faculty of Arts and Sciences, Middle East Technical University, Çankaya 06800, Ankara, Turkey
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42
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Kim M, Lee M, Lee H. Adsorption Selectivities between Hydroxypyridine and Pyridone Adsorbed on the Ge(100) Surface: Conjugation and Geometric Configuration Effects on Adsorption Structures. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.2.581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Ali ST, Antonov L, Fabian WMF. Phenol-quinone tautomerism in (arylazo)naphthols and the analogous Schiff bases: benchmark calculations. J Phys Chem A 2014; 118:778-89. [PMID: 24417622 DOI: 10.1021/jp411502u] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tautomerization energies of a series of isomeric [(4-R-phenyl)azo]naphthols and the analogous Schiff bases (R = N(CH3)2, OCH3, H, CN, NO2) are calculated by LPNO-CEPA/1-CBS using the def2-TZVPP and def2-QZVPP basis sets for extrapolation. The performance of various density functionals (B3LYP, M06-2X, PW6B95, B2PLYP, mPW2PLYP, PWPB95) as well as MP2 and SCS-MP2 is evaluated against these results. M06-2X and SCS-MP2 yield results close to the LPNO-CEPA/1-CBS values. Solvent effects (CCl4, CHCl3, CH3CN, and CH3OH) are treated by a variety of bulk solvation models (SM8, IEFPCM, COSMO, PBF, and SMD) as well as explicit solvation (Monte Carlo free energy perturbation using the OPLSAA force field).
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Affiliation(s)
- S Tahir Ali
- Department of Chemistry, Federal Urdu University of Arts, Science & Technology , Karachi, Sindh, Pakistan
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44
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Schwell M, Hochlaf M. Photoionization Spectroscopy of Nucleobases and Analogues in the Gas Phase Using Synchrotron Radiation as Excitation Light Source. Top Curr Chem (Cham) 2014; 355:155-208. [DOI: 10.1007/128_2014_550] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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45
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Stasyuk OA, Szatylowicz H, Krygowski TM. Tautomerisation of thymine acts against the Hückel 4N + 2 rule. The effect of metal ions and H-bond complexations on the electronic structure of thymine. Org Biomol Chem 2014; 12:6476-83. [DOI: 10.1039/c4ob00964a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Not necessarily the π-electron delocalization is responsible for the stability of thymine tautomers.
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Affiliation(s)
- Olga A. Stasyuk
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw, Poland
| | - Halina Szatylowicz
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw, Poland
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46
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Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. From 2-Hydroxypyridine to 4(3H)-Pyrimidinone: Computational Study on the Control of the Tautomeric Equilibrium. J Phys Chem A 2013; 117:12668-74. [DOI: 10.1021/jp410004x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Inês M. Rocha
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
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47
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Bousquet D, Brémond E, Sancho-García JC, Ciofini I, Adamo C. Is There Still Room for Parameter Free Double Hybrids? Performances of PBE0-DH and B2PLYP over Extended Benchmark Sets. J Chem Theory Comput 2013; 9:3444-52. [DOI: 10.1021/ct400358f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Diane Bousquet
- Laboratoire d’Electrochimie,
Chimie des Interfaces et Modélisation pour l’Energie,
CNRS UMR-7575, Chimie ParisTech, 11 rue
P. et M. Curie, F-75231 Paris Cedex 05, France
| | - Eric Brémond
- Laboratoire d’Electrochimie,
Chimie des Interfaces et Modélisation pour l’Energie,
CNRS UMR-7575, Chimie ParisTech, 11 rue
P. et M. Curie, F-75231 Paris Cedex 05, France
| | | | - Ilaria Ciofini
- Laboratoire d’Electrochimie,
Chimie des Interfaces et Modélisation pour l’Energie,
CNRS UMR-7575, Chimie ParisTech, 11 rue
P. et M. Curie, F-75231 Paris Cedex 05, France
| | - Carlo Adamo
- Laboratoire d’Electrochimie,
Chimie des Interfaces et Modélisation pour l’Energie,
CNRS UMR-7575, Chimie ParisTech, 11 rue
P. et M. Curie, F-75231 Paris Cedex 05, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris,
France
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Affiliation(s)
- Susumu Kawauchi
- Tokyo Institute of Technology; Department of Organic and Polymeric Materials; 2-12-1 O-okayama, Meguro-ku Tokyo 152-8552 Japan
| | - Liudmil Antonov
- Tokyo Institute of Technology; Department of Organic and Polymeric Materials; 2-12-1 O-okayama, Meguro-ku Tokyo 152-8552 Japan
- Institute of Organic Chemistry with Centre of Phytochemistry; Bulgarian Academy of Sciences; Acad. G. Bonchev str., bl.9 Sofia 1113 Bulgaria
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49
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Lobsiger S, Trachsel MA, Frey HM, Leutwyler S. Excited-State Structure and Dynamics of Keto–Amino Cytosine: The 1ππ* State Is Nonplanar and Its Radiationless Decay Is Not Ultrafast. J Phys Chem B 2013; 117:6106-15. [DOI: 10.1021/jp401881b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Maria A. Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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50
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Alparone A. Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers. J Mol Model 2013; 19:3095-102. [PMID: 23605138 DOI: 10.1007/s00894-013-1838-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/21/2013] [Indexed: 11/29/2022]
Abstract
Dipole moments (μ), charge distributions, and static electronic first-order hyperpolarizabilities (β(μ)) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree-Fock, Møller-Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning's correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a μ value smaller than that of the 9H form by a factor of ca. 3.5. The β μ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the β(μ) (9H)/β(μ) (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the β(μ) values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.
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Affiliation(s)
- Andrea Alparone
- Department of Chemistry, University of Catania, viale A. Doria 6, Catania 95125, Italy.
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