1
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Rogers DM, Do H, Hirst JD. Electronic circular dichroism of proteins computed using a diabatisation scheme. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2133748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering and Key Laboratory of Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
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2
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Bertram L, Roberts SJ, Powner MW, Szabla R. Photochemistry of 2-thiooxazole: a plausible prebiotic precursor to RNA nucleotides. Phys Chem Chem Phys 2022; 24:21406-21416. [PMID: 36047336 PMCID: PMC7613695 DOI: 10.1039/d2cp03167a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potentially prebiotic chemical reactions leading to RNA nucleotides involve periods of UV irradiation, which are necessary to promote selectivity and destroy biologially irrelevant side products. Nevertheless, UV light has only been applied to promote specific stages of prebiotic reactions and its effect on complete prebiotic reaction sequences has not been extensively studied. Here, we report on an experimental and computational investigation of the photostability of 2-thiooxazole (2-TO), a potential precursor of pyrimidine and 8-oxopurine nucleotides on early Earth. Our UV-irradiation experiments resulted in rapid decomposition of 2-TO into unidentified small molecule photoproducts. We further clarify the underlying photochemistry by means of accurate ab initio calculations and surface hopping molecular dynamics simulations. Overall, the computational results show efficient rupture of the aromatic ring upon the photoexcitation of 2-TO via breaking of the C-O bond. Consequently, the initial stage of the divergent prebiotic synthesis of pyrimidine and 8-oxopurine nucleotides would require periodic shielding from UV light either with sun screening chromophores or through a planetary scenario that would protect 2-TO until it is transformed into a more stable intermediate compound, e.g. oxazolidinone thione.
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Affiliation(s)
- Lauren Bertram
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Samuel J Roberts
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Rafał Szabla
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.,Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.
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3
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Hirata K, Kasai KI, Yoshizawa K, Grégoire G, Ishiuchi SI, Fujii M. Excited state dynamics of protonated dopamine: hydration and conformation effects. Phys Chem Chem Phys 2022; 24:10737-10744. [PMID: 35389419 DOI: 10.1039/d2cp00543c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic and vibrational spectroscopy in a cryogenic ion trap has been applied to protonated dopamine water clusters and assigned with the help of quantum chemistry calculations performed in the ground and electronic excited states. A dramatic hydration effect is observed when dopamine is solvated by three water molecules. The broad electronic spectra recorded for the bare and small water clusters containing protonated dopamine turn to sharp, well-resolved vibronic transitions in the 1-3 complex. This reflects the change induced by hydration in the photodynamics of protonated dopamine which is initially controlled by an excited state proton transfer (ESPT) reaction from the ammonium group toward the catechol ring. Interestingly, conformer selectivity is revealed in the 1-3 complex which shows two low lying energy conformers for which the ESPT reaction is prevented or not depending on the H-bond network formed between the dopamine and water molecules.
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Affiliation(s)
- Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Ken-Ichi Kasai
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Koki Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Gilles Grégoire
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, F-91405 Orsay, France
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
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4
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Feng JY, Lee YP, Zhu CY, Hsu PJ, Kuo JL, Ebata T. IR-VUV spectroscopy of pyridine dimers, trimers and pyridine-ammonia complexes in a supersonic jet. Phys Chem Chem Phys 2020; 22:21520-21534. [PMID: 32955537 DOI: 10.1039/d0cp03197f] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The infrared spectra of the C-H stretching vibrations of (pyridine)m, m = 1-3, and the N-H stretching vibrations of (pyridine)m-(NH3)n, m = 1, 2; n = 1-4, complexes were investigated by infrared (IR)-vacuum ultraviolet (VUV) spectroscopy under jet-cooled conditions. The ionization potential (IP0) of the pyridine monomer was determined to be 74 546 cm-1 (9.242 eV), while its complexes showed only smooth curves of the ionization thresholds at ∼9 eV, indicating large structural changes in the ionic form. The pyridine monomer exhibits five main features with several satellite bands in the C-H stretching region at 3000-3200 cm-1. Anharmonic calculations including Fermi-resonance were carried out to analyze the candidates of the overtone and combination bands which can couple to the C-H stretching fundamentals. For (pyridine)2 and (pyridine)3, most C-H bands are blue-shifted by 3-5 cm-1 from those of the monomer. The structures revealed by random searching algorithms with density functional methods indicate that the π-stacked structure is most stable for (pyridine)2, while (pyridine)3 prefers the structures stabilized by dipole-dipole and C-Hπ interactions. For the (pyridine)m-(NH3)n complexes, the mass spectrum exhibited a wide range distribution of the complexes. The observed IR spectra in the N-H stretching vibrations of the complexes showed four main bands in the 3200-3450 cm-1 region. These features are very similar to those of (NH3)n complexes, and the bands are assigned to the anti-symmetric N-H stretching band (ν3), the symmetric N-H stretching (ν1) band, and the first overtone bands of the N-H bending vibrations (2ν4). The anharmonic calculations including the Fermi-resonance between ν1 and 2ν4 well reproduced the observed spectra.
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Affiliation(s)
- Jun-Ying Feng
- Department of Applied Chemistry and Institute for Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan.
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5
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Kochman MA, Durbeej B. Theoretical Study of Ground- and Excited-State Charge Transfer in Fulvene-Based Donor–Acceptor Systems. J Phys Chem A 2019; 123:6660-6673. [DOI: 10.1021/acs.jpca.9b02962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michał Andrzej Kochman
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Bo Durbeej
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
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6
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Dimić D. The importance of specific solvent–solute interactions for studying UV–vis spectra of light-responsive molecular switches. CR CHIM 2018. [DOI: 10.1016/j.crci.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Loos PF, Scemama A, Blondel A, Garniron Y, Caffarel M, Jacquemin D. A Mountaineering Strategy to Excited States: Highly Accurate Reference Energies and Benchmarks. J Chem Theory Comput 2018; 14:4360-4379. [DOI: 10.1021/acs.jctc.8b00406] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France
| | - Anthony Scemama
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France
| | - Aymeric Blondel
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Yann Garniron
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France
| | - Michel Caffarel
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France
| | - Denis Jacquemin
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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8
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Hršak D, Nørby MS, Coriani S, Kongsted J. One-Photon Absorption Properties from a Hybrid Polarizable Density Embedding/Complex Polarization Propagator Approach for Polarizable Solutions. J Chem Theory Comput 2018; 14:2145-2154. [DOI: 10.1021/acs.jctc.8b00155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Morten Steen Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800 Kongens Lyngby, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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9
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Szabla R, Kruse H, Stadlbauer P, Šponer J, Sobolewski AL. Sequential electron transfer governs the UV-induced self-repair of DNA photolesions. Chem Sci 2018; 9:3131-3140. [PMID: 29732095 PMCID: PMC5916108 DOI: 10.1039/c8sc00024g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/22/2018] [Indexed: 01/09/2023] Open
Abstract
Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors repairing CpDs, the intrinsic self-repairing capabilities of the GAT 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order [ADC(2)] method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the T 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T dimer. Consequently, the molecular mechanism of GAT 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S1 potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S1/S0 state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.
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Affiliation(s)
- Rafał Szabla
- Institute of Physics , Polish Academy of Sciences , Al. Lotników 32/46 , PL-02668 Warsaw , Poland.,Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , 61265 Brno , Czech Republic .
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , 61265 Brno , Czech Republic .
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , 61265 Brno , Czech Republic . .,Regional Centre of Advanced Technologies and Materials , Department of Physical Chemistry , Faculty of Science , Palacký University , 17. Listopadu 1192/12 , 77146 Olomouc , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , 61265 Brno , Czech Republic .
| | - Andrzej L Sobolewski
- Institute of Physics , Polish Academy of Sciences , Al. Lotników 32/46 , PL-02668 Warsaw , Poland
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10
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Hršak D, Olsen JMH, Kongsted J. Polarizable Density Embedding Coupled Cluster Method. J Chem Theory Comput 2018; 14:1351-1360. [DOI: 10.1021/acs.jctc.7b01153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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11
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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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12
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Xu J, Tsanakopoulou M, Magnani CJ, Szabla R, Šponer JE, Šponer J, Góra RW, Sutherland JD. A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization. Nat Chem 2016; 9:303-309. [PMID: 28338689 DOI: 10.1038/nchem.2664] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
Previous research has identified ribose aminooxazoline as a potential intermediate in the prebiotic synthesis of the pyrimidine nucleotides with remarkable properties. It crystallizes spontaneously from reaction mixtures, with an enhanced enantiomeric excess if initially enantioenriched, which suggests that reservoirs of this compound might have accumulated on the early Earth in an optically pure form. Ribose aminooxazoline can be converted efficiently into α-ribocytidine by way of 2,2'-anhydroribocytidine, although anomerization to β-ribocytidine by ultraviolet irradiation is extremely inefficient. Our previous work demonstrated the synthesis of pyrimidine β-ribonucleotides, but at the cost of ignoring ribose aminooxazoline, using arabinose aminooxazoline instead. Here we describe a long-sought route through ribose aminooxazoline to the pyrimidine β-ribonucleosides and their phosphate derivatives that involves an extraordinarily efficient photoanomerization of α-2-thioribocytidine. In addition to the canonical nucleosides, our synthesis accesses β-2-thioribouridine, a modified nucleoside found in transfer RNA that enables both faster and more-accurate nucleic acid template-copying chemistry.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Maria Tsanakopoulou
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher J Magnani
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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13
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Nåbo LJ, Olsen JMH, Holmgaard List N, Solanko LM, Wüstner D, Kongsted J. Embedding beyond electrostatics—The role of wave function confinement. J Chem Phys 2016; 145:104102. [DOI: 10.1063/1.4962367] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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14
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Chattopadhyaya M, Murugan NA, Rinkevicius Z. Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study. J Phys Chem A 2016; 120:7175-82. [DOI: 10.1021/acs.jpca.6b07660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M. Chattopadhyaya
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish
e-Science Research Center (SeRC), KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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15
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Ramos ML, Justino LLG, Abreu PE, Fonseca SM, Burrows HD. Oxocomplexes of Mo(VI) and W(VI) with 8-hydroxyquinoline-5-sulfonate in solution: structural studies and the effect of the metal ion on the photophysical behaviour. Dalton Trans 2015; 44:19076-89. [PMID: 26498366 DOI: 10.1039/c5dt03473f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multinuclear ((1)H, (13)C, (95)Mo and (183)W) NMR spectroscopy, combined with DFT calculations, provides detailed information on the complexation between the Mo(VI) and W(VI) oxoions and 8-hydroxyquinoline-5-sulfonate (8-HQS) in aqueous solution. Over the concentration region studied, Mo(VI) and W(VI) oxoions form three homologous complexes with 8-HQS in water in the pH range 2-8. Two of these, detected at pH < 6, are mononuclear 1 : 2 (metal : ligand) isomers, with the metal centre (MO2(2+)) coordinated to two 8-HQS ligands. An additional complex, dominant at slightly higher pH values (5-8) for solutions with a 1 : 1 metal : ligand molar ratio, has a binuclear M2O5(2+) centre coordinated to two 8-HQS ligands. The two metal atoms are bridged by three oxygen atoms, two coming from 8-HQS, together with the M-O-M bridge of the bimetallic centre. We show that the long-range exchange corrected BOP functional with local response dispersion (LCBOPLRD), together with explicit solvent molecules, leads to geometries that readily converge to equilibrium structures having realistic bridging O8-HQS-M bonds. Previous attempts to calculate the structures of such binuclear complexes using DFT with the B3LYP functional have failed due to difficulties in treating the weak interaction in these bridged structures. We believe that the LCBOPLRD method may be of more general application in theoretical studies in related binuclear metal complexes. UV/visible absorption and luminescence spectra of all the complexes have also been recorded. The complex between Mo(vi) and 8-HQS is only weakly luminescent, in contrast to what has been observed with this ligand and many other metal ions. We suggest that this is due to the presence of low-lying ligand-to-metal charge transfer (LMCT) states close to the emitting ligand-based level which quench the emission. However, with W(VI), DFT calculations show that the LMCT states are now much higher in energy than the ligand based levels, leading to a marked increase in fluorescence.
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Affiliation(s)
- M Luísa Ramos
- Centro de Química and Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
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16
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Dipeptides containing N-terminal threonine residues: quantum chemical structural studies on nonionic, zwitterionic and water-clustered systems. Struct Chem 2015. [DOI: 10.1007/s11224-015-0564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Mandal S, Das G, Askari H. Physicochemical properties of the ternary complexes of Pt(ii) with uracil and small peptide moieties: an experimental and computational study. NEW J CHEM 2015. [DOI: 10.1039/c5nj00120j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactions of Pt(Ura)(GL) with DNA.
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Affiliation(s)
- Shilpi Mandal
- Centre of Advanced Study and Department of Chemistry
- North-Eastern Hill University
- Shillong-793022
- India
| | - Gunajyoti Das
- Department of Chemistry
- Central Institute of Technology
- India
| | - Hassan Askari
- Centre of Advanced Study and Department of Chemistry
- North-Eastern Hill University
- Shillong-793022
- India
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18
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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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Murugan NA, Schrader S, Ågren H. Role of Protonation State and Solvation on the pH Dependent Optical Properties of Bromocresol Green. J Chem Theory Comput 2014; 10:3958-68. [DOI: 10.1021/ct500375x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Arul Murugan
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Sigurd Schrader
- Technische Hochschule Wildau, Hochschulring
1, 15745 Wildau, Brandenburg, Germany
| | - Hans Ågren
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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20
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Murugan NA. Solvatochromism in a Pyridinium Cyclopentadienylide: Insights from a Sequential Car–Parrinello QM/MM and TD-DFT/Semicontinuum Approach. J Phys Chem B 2014; 118:7358-66. [DOI: 10.1021/jp410854b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- N. Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691, Stockholm, Sweden
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21
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Morzan UN, Ramírez FF, Oviedo MB, Sánchez CG, Scherlis DA, Lebrero MCG. Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework. J Chem Phys 2014; 140:164105. [DOI: 10.1063/1.4871688] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Li J, Ren HS, Ma JY, Li XY. Spectral Shift of π→π* Transition forp-Nitroaniline Based on a New Expression of Nonequilibrium Solvation Energy. CHINESE J CHEM PHYS 2014. [DOI: 10.1063/1674-0068/27/02/181-188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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23
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Influence of C-terminal residues on the structural and molecular properties of dipeptides: a theoretical study in a vacuum and implicit and explicit aqueous environments. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-013-1093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Das G, Mandal S. Quantum mechanical investigations on the role of C-terminal residue in influencing the structural features of dipeptides containing N-terminal proline. J Mol Graph Model 2014; 49:1-10. [PMID: 24468791 DOI: 10.1016/j.jmgm.2013.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/18/2022]
Abstract
This study investigates the influence of the side chain moiety of C-terminal residue on the structural and molecular properties of seven dipeptides having proline at their N-terminal positions. The C-terminal component of the dipeptides is varied with seven different combinations viz. Ala, Leu, Asp, Thr, Asn, Arg and Sec. The calculations are carried out using B3LYP/6-311++G(d,p) level of theory in gas and implicit aqueous phase. Effects of explicit aqueous environment on the dipeptide structures are also investigated for two systems. The results furnished by this DFT study provide valuable information regarding the role of the side chain groups of C-terminal residues in determining the structural features of the amide planes, values of the ψ and ф dihedrals, geometry about the α-carbon atoms, theoretical IR spectra as well as the number and type of intramolecular H-bond interactions existing in the dipeptides, and extend a fine corroboration to the earlier theoretical and experimental observations. In aqueous phase the dipeptide geometries exhibit larger values of total dipole moments, greater HOMO-LUMO energy gaps and enhanced thermodynamic stability than those in gas phase. The explicit water molecules are found to modify the geometrical parameters related to the amide planes and vibrational spectra of the dipeptides.
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Affiliation(s)
- Gunajyoti Das
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India.
| | - Shilpi Mandal
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India
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25
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De Silva N, Willow SY, Gordon MS. Solvent induced shifts in the UV spectrum of amides. J Phys Chem A 2013; 117:11847-55. [PMID: 23758065 DOI: 10.1021/jp402999p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and πnb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides.
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Affiliation(s)
- Nuwan De Silva
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
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26
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Nguyen VS, Orlando TM, Leszczynski J, Nguyen MT. Theoretical Study of the Decomposition of Formamide in the Presence of Water Molecules. J Phys Chem A 2013; 117:2543-55. [DOI: 10.1021/jp312853j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vinh Son Nguyen
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
| | - Thomas M. Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity,
Department of Chemistry, Jackson State University, Jackson, Mississippi 39217-0510, United States
| | - Minh Tho Nguyen
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
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27
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Time-Dependent Density Functional Theory Study on Hydrogen and Dihydrogen Bonding in Electronically Excited State of 2-Pyridone–Borane–Trimethylamine Cluster. J CLUST SCI 2013. [DOI: 10.1007/s10876-013-0572-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Ramos ML, Justino LLG, Salvador AIN, de Sousa ARE, Abreu PE, Fonseca SM, Burrows HD. NMR, DFT and luminescence studies of the complexation of Al(III) with 8-hydroxyquinoline-5-sulfonate. Dalton Trans 2013; 41:12478-89. [PMID: 22955198 DOI: 10.1039/c2dt31381b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Multinuclear ((1)H, (13)C and (27)Al) magnetic resonance spectroscopy (1D and 2D), DFT calculations and fluorescence have been used to study the complexation of 8-hydroxyquinoline-5-sulfonate (8-HQS) with Al(III). The study combines the high sensitivity of luminescence techniques, the selectivity of multinuclear NMR spectroscopy with the structural details accessible through DFT calculations, and aims to provide a detailed understanding of the complexation between the Al(3+) ion and 8-HQS. A full speciation study has been performed and over the concentration region studied, the Al(3+) ion forms complexes with 8-HQS in an aqueous solution in the pH range 2-6. At higher pH, the extensive hydrolysis of the metal limits complexation. Using Job's method, three complexes were detected, with 1 : 1, 1 : 2 and 1 : 3 (metal : ligand) stoichiometries. These results are in agreement with those previously reported using potentiometric and electrochemical techniques. The geometries of the complexes are proposed based on the combination of NMR results with optimized DFT calculations. All the complexes in aqueous solutions at 25 °C are mononuclear species, and have an approximately octahedral geometry with the metal coordinated to one molecule of 8-HQS and four molecules of water (1 : 1 complex), two molecules of 8-HQS and two molecules of water mutually cis (1 : 2 complex), and to three molecules of 8-HQS in non-symmetrical arrangement (mer-isomer), for the 1 : 3 (metal : ligand) complex. On binding to Al(III), 8-HQS shows a more marked fluorescence than the weakly fluorescent free ligand. In addition, as previously noted, there are marked changes in the absorption spectra, which support the use of 8-HQS as a sensitive optical sensor to detect Al(3+) metal ions in surface waters and biological fluids. These complexes also show potential for applications in organic light emitting diodes (OLEDs).
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Affiliation(s)
- M Luísa Ramos
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
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29
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Ramos ML, de Sousa ARE, Justino LLG, Fonseca SM, Geraldes CFGC, Burrows HD. Structural and photophysical studies on gallium(iii) 8-hydroxyquinoline-5-sulfonates. Does excited state decay involve ligand photolabilisation? Dalton Trans 2013; 42:3682-94. [PMID: 23299787 DOI: 10.1039/c2dt32587j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- M Luísa Ramos
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
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30
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Garbuio V, Cascella M, Sole RD, Marsili M, Pulci O. Excited state properties of formamide in water solution: An ab initio study. J Chem Phys 2012; 137:164317. [DOI: 10.1063/1.4763980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Liu T, Yu Z, Han L, Wang X, Liu C. Experimental and theoretical study on the 1:1 supramolecular complexes of formamide with adrenaline. Gene 2012; 496:136-40. [DOI: 10.1016/j.gene.2012.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 01/18/2012] [Indexed: 11/30/2022]
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32
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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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33
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Ren HS, Li YK, Zhu Q, Zhu J, Li XY. Spectral shifts of the n → π* and π → π* transitions of uracil based on a modified form of solvent reorganization energy. Phys Chem Chem Phys 2012; 14:13284-91. [DOI: 10.1039/c2cp41047h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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34
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Sok S, Willow SY, Zahariev F, Gordon MS. Solvent-Induced Shift of the Lowest Singlet π → π* Charge-Transfer Excited State of p-Nitroaniline in Water: An Application of the TDDFT/EFP1 Method. J Phys Chem A 2011; 115:9801-9. [DOI: 10.1021/jp2045564] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sarom Sok
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Soohaeng Y. Willow
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
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35
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Lu JF, Wu YF, Yu ZY, Lin XJ. DFT study of ionization potentials and electron affinities of formamide and its methylation derivatives. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2011. [DOI: 10.1134/s003602441108019x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Gaigeot MP, Besley NA, Hirst JD. Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide. J Phys Chem B 2011; 115:5526-35. [PMID: 21344909 DOI: 10.1021/jp111140f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory based molecular dynamics simulations are used to study the structure, infrared (IR) spectroscopy, circular dichroism (CD) spectroscopy, and coupling between the amide I vibrations of a bridged cyclic diamide in the gas phase and in aqueous solution. IR spectra computed via the dipole moment time correlation function show a large red-shift of 30 cm(-1) in the amide I vibration in solution compared to the gas phase, and are in good agreement with experiment. Conformationally averaged CD spectra computed using the CIS(D) method are highly sensitive to the structures used, and structures sampled in the aqueous phase simulation are required to obtain qualitatively correct CD spectra. Analysis of the coupling between the amide I modes shows that in the aqueous phase there is an increased localization of the vibrations on the individual peptide groups and a reduction in the mode coupling parameter compared to the gas phase. Overall, the results illustrate the significance of incorporating molecular dynamics in the simulation of IR and CD spectra.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry Val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environment, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France
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37
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Murugan NA. Modeling Solvatochromism of a Quinolinium Betaine Dye in Water Solvent Using Sequential Hybrid QM/MM and Semicontinuum Approach. J Phys Chem B 2011; 115:1056-61. [DOI: 10.1021/jp1049342] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- N. Arul Murugan
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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38
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Sada M, Komagawa S, Uchiyama M, Kobata M, Mizuno T, Utimoto K, Oshima K, Matsubara S. Reaction Pathway of Methylenation of Carbonyl Compounds with Bis(iodozincio)methane. J Am Chem Soc 2010; 132:17452-8. [DOI: 10.1021/ja104439w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mutsumi Sada
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Shinsuke Komagawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Masanobu Uchiyama
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Masami Kobata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Tsuyoshi Mizuno
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Kiitiro Utimoto
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Koichiro Oshima
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
| | - Seijiro Matsubara
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoudai-katsura, Nishikyo, Kyoto 615-8510, Japan, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8510, Japan
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39
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Nagaraju M, Narahari Sastry G. Effect of alkyl substitution on H-bond strength of substituted amide-alcohol complexes. J Mol Model 2010; 17:1801-16. [DOI: 10.1007/s00894-010-0886-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/20/2010] [Indexed: 11/28/2022]
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40
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Arora P, Slipchenko LV, Webb SP, DeFusco A, Gordon MS. Solvent-Induced Frequency Shifts: Configuration Interaction Singles Combined with the Effective Fragment Potential Method. J Phys Chem A 2010; 114:6742-50. [DOI: 10.1021/jp101780r] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pooja Arora
- Department Of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, Department Of Chemistry, Purdue University, West Lafayette, Indiana 47907, and VeraChem LLC, PO Box 2206, Germantown, Maryland 20875
| | - Lyudmila V. Slipchenko
- Department Of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, Department Of Chemistry, Purdue University, West Lafayette, Indiana 47907, and VeraChem LLC, PO Box 2206, Germantown, Maryland 20875
| | - Simon P. Webb
- Department Of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, Department Of Chemistry, Purdue University, West Lafayette, Indiana 47907, and VeraChem LLC, PO Box 2206, Germantown, Maryland 20875
| | - Albert DeFusco
- Department Of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, Department Of Chemistry, Purdue University, West Lafayette, Indiana 47907, and VeraChem LLC, PO Box 2206, Germantown, Maryland 20875
| | - Mark S. Gordon
- Department Of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, Department Of Chemistry, Purdue University, West Lafayette, Indiana 47907, and VeraChem LLC, PO Box 2206, Germantown, Maryland 20875
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41
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Duan CS, Fu H, You JM, Ma KS, Zhou ZY. Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2010. [DOI: 10.1134/s0036024410130169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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42
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Chen A, Pu X, He S, Guo Y, Wen Z, Li M, Wong NB, Tian A. Solvent effects on isolated formamide and its monohydrated complex: observations from PCM study. NEW J CHEM 2009. [DOI: 10.1039/b902149c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Su CF, Li YM, Zhou ZY, Wang XX, Ma KS. The density functional theory study on the ionization potentials and electron affinities of cytosine-formamide complexes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409030200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Asmuruf FA, Besley NA. Time dependent density functional theory study of the near-edge x-ray absorption fine structure of benzene in gas phase and on metal surfaces. J Chem Phys 2008; 129:064705. [DOI: 10.1063/1.2967190] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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45
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Zhang AG, Qin M, Zhou ZY, Jia ZK, Hou RY. A density functional theory study of interaction between formamide and guanine. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2008. [DOI: 10.1134/s0036024408070169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Panuszko A, Gojło E, Zielkiewicz J, Śmiechowski M, Krakowiak J, Stangret J. Hydration of Simple Amides. FTIR Spectra of HDO and Theoretical Studies. J Phys Chem B 2008; 112:2483-93. [PMID: 18247601 DOI: 10.1021/jp7099509] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Emilia Gojło
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Jan Zielkiewicz
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Joanna Krakowiak
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
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47
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Alves WA, Antunes OAC. Lewis acid-base adducts: a quantitative Raman analysis of formamide and dimethylsulfoxide mixtures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2007; 67:847-51. [PMID: 17023198 DOI: 10.1016/j.saa.2006.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 08/31/2006] [Indexed: 05/12/2023]
Abstract
Raman spectra of pure liquid dimethylsulfoxide (DMSO) and of binary mixtures of formamide (FA) and DMSO in different compositions were obtained. The vibrations involving the SO functional group in the band envelope at ca. 1050 cm(-1) of pure liquid DMSO are assigned to monomers, dimers and higher aggregates of DMSO. The appearance of a new band at 1024 cm(-1), whose intensity shows large dependence on the FA concentration, is assigned to a FA-DMSO adduct. This has been possible due to the two H-bond donor sites of FA and the strong donor character of DMSO that become the environment propitious for the donor-acceptor reaction. Quantitative analysis performed in the SO stretching region in the binary mixtures gives a 1:1 stoichiometry in this adduct in the limit of infinite dilution. This proportion is in full agreement with our previous determination for the FA-ACN adduct. The experimental evidence of the 1:1 FA-DMSO adduct is presented for the first time using Raman spectroscopy. The results described here open new possibilities to study the acid-base reactions nature of FA adducts.
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Affiliation(s)
- Wagner A Alves
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465/Km 7, Seropédica, RJ 23890-000, Brazil.
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Abstract
The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense pi-->pi* transition for formamide upon solvation undergoes a redshift of 0.3 eV, compared with the experimental data (0.40-0.5 eV).
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Affiliation(s)
- Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, USA.
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