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Paterson MJ, Townsend D. Rydberg-to-valence evolution in excited state molecular dynamics. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1815389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Dave Townsend
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, UK
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Larsen MAB, Sølling TI, Forbes R, Boguslavskiy AE, Makhija V, Veyrinas K, Lausten R, Stolow A, Zawadzki MM, Saalbach L, Kotsina N, Paterson MJ, Townsend D. Vacuum ultraviolet excited state dynamics of small amides. J Chem Phys 2019; 150:054301. [DOI: 10.1063/1.5079721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Martin A. B. Larsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Theis I. Sølling
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Ruaridh Forbes
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
| | - Andrey E. Boguslavskiy
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
- National Research Council Canada,
100 Sussex Drive, Ottawa, Ontario K1N 5A2, Canada
| | - Varun Makhija
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
| | - Kévin Veyrinas
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
| | - Rune Lausten
- National Research Council Canada,
100 Sussex Drive, Ottawa, Ontario K1N 5A2, Canada
| | - Albert Stolow
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5,
Canada
- National Research Council Canada,
100 Sussex Drive, Ottawa, Ontario K1N 5A2, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5,
Canada
| | - Magdalena M. Zawadzki
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Lisa Saalbach
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Nikoleta Kotsina
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Martin J. Paterson
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
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Spinlove KE, Richings GW, Robb MA, Worth GA. Curve crossing in a manifold of coupled electronic states: direct quantum dynamics simulations of formamide. Faraday Discuss 2018; 212:191-215. [PMID: 30238103 DOI: 10.1039/c8fd00090e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Quantum dynamics simulations are an important tool to evaluate molecular behaviour including the, often key, quantum nature of the system. In this paper we present an algorithm that is able to simulate the time evolution of a molecule after photo-excitation into a manifold of states. The direct dynamics variational multi-configurational Gaussian (DD-vMCG) method circumvents the computational bottleneck problems of traditional grid-based methods by computing the potential energy functions on-the-fly, i.e. only where required. Unlike other commonly used direct dynamics methods, DD-vMCG is fully quantum mechanical. Here, the method is combined with a novel on-the-fly diabatisation scheme to simulate the short-time dynamics of the key molecule formamide and its acid analogue formimidic acid. This is a challenging test system due to the nature and large number of excited states, and eight coupled states are included in the calculations. It is shown that the method is able to provide unbiased information on the product channels open after excitation at different energies and demonstrates the potential to be a practical scheme, limited mainly by the quality of the quantum chemistry used to describe the excited states.
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Affiliation(s)
- K Eryn Spinlove
- Dept. of Chemistry, University College London, 20 Gordon St., London, UK. and School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK and Dept. of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - Gareth W Richings
- Dept. of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Michael A Robb
- Dept. of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - Graham A Worth
- Dept. of Chemistry, University College London, 20 Gordon St., London, UK.
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Tukachev NV, Bataev VA, Abramenkov AV, Godunov IA. Structure and conformational dynamics of formamide molecule in the ground and lowest excited electronic states. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation. Proc Natl Acad Sci U S A 2015; 112:E2746-55. [PMID: 25870268 DOI: 10.1073/pnas.1422225112] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Liquid formamide has been irradiated by high-energy proton beams in the presence of powdered meteorites, and the products of the catalyzed resulting syntheses were analyzed by mass spectrometry. Relative to the controls (no radiation, or no formamide, or no catalyst), an extremely rich, variegate, and prebiotically relevant panel of compounds was observed. The meteorites tested were representative of the four major classes: iron, stony iron, chondrites, and achondrites. The products obtained were amino acids, carboxylic acids, nucleobases, sugars, and, most notably, four nucleosides: cytidine, uridine, adenosine, and thymidine. In accordance with theoretical studies, the detection of HCN oligomers suggests the occurrence of mechanisms based on the generation of radical cyanide species (CN·) for the synthesis of nucleobases. Given that many of the compounds obtained are key components of extant organisms, these observations contribute to outline plausible exogenous high-energy-based prebiotic scenarios and their possible boundary conditions, as discussed.
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Zámečníková M, Nachtigallová D. Photodynamic behavior of electronic coupling in a N-methylformamide dimer. Phys Chem Chem Phys 2015; 17:12356-64. [DOI: 10.1039/c4cp04573d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.
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Antol I, Glasovac Z, Crespo-Otero R, Barbatti M. Guanidine and guanidinium cation in the excited state--theoretical investigation. J Chem Phys 2014; 141:074307. [PMID: 25149786 DOI: 10.1063/1.4892569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Diverse ab initio and density-functional-theory methods were used to investigate geometries, energies, and electronic absorption spectra of guanidine and its protonated form, as well as their photo-deactivation processes. It was shown that the guanidine is a weakly absorbing species with the excitation spectrum consisting mostly of transitions to the Rydberg excited states and one valence n-π4 state. The lowest energy band has a maximum at ca. 6.9 eV (∼180 nm). The protonation of guanidine affects its excitation spectrum substantially. A major shift of the Rydberg states to higher energies is clearly visible and strongly absorbing transitions from the ground state to the π3-π4 and π2-π4 states appears at 7.8 eV (∼160 nm). Three low-lying conical intersections (two for guanidine and one for protonated guanidine) between the ground state and the first excited singlet state were located. They are accessible from the Franck-Condon region through amino N-H stretching and out-of-plane deformations in guanidine and protonated guanidine, respectively. The relaxation of the π3-3s Rydberg state via amino N-H bond stretching was hindered by a barrier. The nondissociated conical intersection in protonated guanidine mediates the radiationless deactivation of the compound after excitation into the π3-π4 state. This fact is detrimental for the photostability of guanidine, since its conjugate acid is stable in aqueous solution over a wide pH range and in protein environment, where guanidinium moiety in arginine is expected to be in a protonated form.
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Affiliation(s)
- Ivana Antol
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia
| | - Zoran Glasovac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia
| | - Rachel Crespo-Otero
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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Eckert-Maksić M, Antol I, Vazdar M. Acetamide as the model of the peptide bond: Nonadiabatic photodynamical simulations in the gas phase and in the argon matrix. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nguyen HT, Nguyen VS, Trung NT, Havenith RWA, Nguyen MT. Decomposition pathways of the neutral and protonated formamide in some lower-lying excited states. J Phys Chem A 2013; 117:7904-17. [PMID: 23889466 DOI: 10.1021/jp405657y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unimolecular decompositions of neutral (NH2CHO) and protonated (NH3CHO(+)) formamide, an active precursor of biomolecules in prebiotic chemistry, are investigated in the ground (S0) and first triplet (T1) and singlet (S1) excited states. Different decomposition channels including the homolytic bond dissociations, dehydration, decarbonylation, dehydrogenation, etc., are explored using coupled-cluster theory (CCSD(T)/CBS method) for both S0 and T1 states and RASPT2(18,15)/6-31G(d,p) computations for the S1 state. On S1 and T1 energy surfaces, formamide preferentially follows C-N homolytic bond cleavages forming NH2 + HCO radical pairs. Formation of HCN and HNC from dehydration of neutral and protonated formamide via formimic acid and aminohydroxymethylene isomers has higher energy barriers. A strong stabilization upon triplet excitation of the two latter isomers significantly facilitates the interconversions between isomers, and thus considerably reduces the energy barriers for dehydration pathways. The most probable pathways for HCN and HNC generation are found to be dehydration of formamide in the T1 state. Dehydration pathways from the neutral S1 and protonated T1 forms lead to stable complexes of HCN and HNC with water but are associated with large energy barriers. Overall, in the lower-lying excited states of either neutral or protonated formamide, dehydration is not competitive with homolytic C-N bond cleavages, which finally lead to formation of CO.
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Affiliation(s)
- Huyen Thi Nguyen
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
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Antol I, Eckert-Maksić M, Vazdar M, Ruckenbauer M, Lischka H. QM/MM non-adiabatic decay dynamics of formamide in polar and non-polar solvents. Phys Chem Chem Phys 2012; 14:13262-72. [DOI: 10.1039/c2cp41830d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Eckert-Maksić M, Vazdar M, Ruckenbauer M, Barbatti M, Müller T, Lischka H. Matrix-controlled photofragmentation of formamide: dynamics simulation in argon by nonadiabatic QM/MM method. Phys Chem Chem Phys 2010; 12:12719-26. [DOI: 10.1039/c0cp00174k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Eckert-Maksić M, Antol I. Study of the Mechanism of the N−CO Photodissociation in N,N-Dimethylformamide by Direct Trajectory Surface Hopping Simulations. J Phys Chem A 2009; 113:12582-90. [DOI: 10.1021/jp9046177] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mirjana Eckert-Maksić
- Rudjer Bošković Institute, Division of Organic Chemistry and Biochemistry, POB 180, HR-10002 Zagreb, Croatia
| | - Ivana Antol
- Rudjer Bošković Institute, Division of Organic Chemistry and Biochemistry, POB 180, HR-10002 Zagreb, Croatia
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