1
|
Valverde D, de Araújo AVS, Borin AC. Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil. Molecules 2021; 26:5191. [PMID: 34500625 PMCID: PMC8434193 DOI: 10.3390/molecules26175191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning's cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.
Collapse
Affiliation(s)
- Danillo Valverde
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
| | | | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
| |
Collapse
|
2
|
Green JA, Improta R. Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study. Phys Chem Chem Phys 2020; 22:5509-5522. [PMID: 32104818 DOI: 10.1039/c9cp06373k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.
Collapse
Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
| |
Collapse
|
3
|
Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| |
Collapse
|
4
|
Zentel T, Kühn O. Hydrogen bonding in the protic ionic liquid triethylammonium nitrate explored by density functional tight binding simulations. J Chem Phys 2016; 145:234504. [DOI: 10.1063/1.4972006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tobias Zentel
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Oliver Kühn
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| |
Collapse
|
5
|
Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
Collapse
Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
| |
Collapse
|
6
|
Brela M, Stare J, Pirc G, Sollner-Dolenc M, Boczar M, Wójcik MJ, Mavri J. Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide. J Phys Chem B 2012; 116:4510-8. [PMID: 22429110 DOI: 10.1021/jp2094559] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.
Collapse
Affiliation(s)
- Mateusz Brela
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | | | | | | | | |
Collapse
|
7
|
Stare J, Mavri J, Grdadolnik J, Zidar J, Maksić ZB, Vianello R. Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study. J Phys Chem B 2011; 115:5999-6010. [DOI: 10.1021/jp111175e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jernej Zidar
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | | | - Robert Vianello
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| |
Collapse
|
8
|
Yan YA, Kühn O. Unraveling the Correlated Dynamics of the Double Hydrogen Bonds of Nucleic Acid Base Pairs in Solution. J Phys Chem B 2011; 115:5254-9. [DOI: 10.1021/jp108521g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yun-an Yan
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| |
Collapse
|