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Bernhardt B, Dressler F, Eckhardt AK, Becker J, Schreiner PR. Characterization of the Simplest Thiolimine: The Higher Energy Tautomer of Thioformamide. Chemistry 2021; 27:6732-6739. [PMID: 33496350 PMCID: PMC8252572 DOI: 10.1002/chem.202005188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/21/2021] [Indexed: 12/21/2022]
Abstract
As sulfur‐containing organic molecules thioamides and their isomers are conceivable intermediates in prebiotic chemistry, for example, in the formation of amino acids and thiazoles and resemble viable candidates for detection in interstellar media. Here, we report the characterization of parent thioformamide in the solid state via single‐crystal X‐ray diffraction and its photochemical interconversion to its hitherto unreported higher energy tautomer thiolimine in inert argon and dinitrogen matrices. Upon photogeneration, four conformers of thiolimine form, whose ratio depends on the employed wavelength. One of these conformers interconverts due to quantum mechanical tunneling with a half‐life of 30–45 min in both matrix materials at 3 and 20 K. A spontaneous reverse reaction from thiolimine to thioformamide is not observed. To support our experimental findings, we explored the potential energy surface of the system at the AE‐CCSD(T)/aug‐cc‐pCVTZ level of theory and computed tunneling half‐lives with the CVT/SCT approach applying DFT methods.
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Affiliation(s)
- Bastian Bernhardt
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35390, Giessen, Germany
| | - Friedemann Dressler
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35390, Giessen, Germany
| | - André K Eckhardt
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35390, Giessen, Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35390, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35390, Giessen, Germany
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Largely reduced grid densities in a vibrational self-consistent field treatment do not significantly impact the resultingwavenumbers. Molecules 2014; 19:21253-75. [PMID: 25525825 PMCID: PMC6270979 DOI: 10.3390/molecules191221253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/25/2014] [Accepted: 12/09/2014] [Indexed: 11/16/2022] Open
Abstract
Especially for larger molecules relevant to life sciences, vibrational self-consistent field (VSCF) calculations can become unmanageably demanding even when only first and second order potential coupling terms are considered. This paper investigates to what extent the grid density of the VSCF’s underlying potential energy surface can be reduced without sacrificing accuracy of the resulting wavenumbers. Including single-mode and pair contributions, a reduction to eight points per mode did not introduce a significant deviation but improved the computational efficiency by a factor of four. A mean unsigned deviation of 1.3% from the experiment could be maintained for the fifteen molecules under investigation and the approach was found to be applicable to rigid, semi-rigid and soft vibrational problems likewise. Deprotonated phosphoserine, stabilized by two intramolecular hydrogen bonds, was investigated as an exemplary application.
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Lutz OMD, Rode BM, Bonn GK, Huck CW. The impact of highly correlated potential energy surfaces on the anharmonically corrected IR spectrum of acetonitrile. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 131:545-555. [PMID: 24840497 DOI: 10.1016/j.saa.2014.04.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/20/2014] [Accepted: 04/13/2014] [Indexed: 06/03/2023]
Abstract
This paper discusses the quality and feasibility of highly correlated ab initio techniques in a vibrational self-consistent field (VSCF) approach using acetonitrile as a model system. The topical renormalized coupled-cluster technique exploiting the similarity-transformed Hamiltonian's left eigenstates (i.e. CR-CC(2,3)) is investigated alongside the well-known Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2) and coupled cluster (CCSD(T)) methods. The inclusion of mode triple interactions is discussed and it is found that the use of an effective core potential (ECP) serves as a viable compromise during the highly demanding task of computing such contributions, thus enabling a grid-based evaluation of three mode interaction terms with coupled cluster techniques also for larger molecules. In this context, a previously proposed reduced coupling scheme [1] is investigated, confirming the applicability of this technique to a system exhibiting a rather complex electronic structure. A combination of Ahlrichs' triple-ζ valence polarized (TZVP) basis set with Dunning's set of core-valence correlation functions is found to deliver results in good agreement with experiment while being computationally very feasible. Since CH3CN exhibits four degenerate vibrational degrees of freedom, it serves as an ideal model system for critically assessing the qualities of the degenerate second-order perturbation theory corrected (DPT2) VSCF technique. Besides fundamental vibrations, a thorough investigation of overtone transitions and combination bands is conducted by means of comparing the results to both available and newly recorded experimental data.
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Affiliation(s)
- Oliver M D Lutz
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Bernd M Rode
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Günther K Bonn
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
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Meng K, Wang J. Anharmonic overtone and combination states of glycine and two model peptides examined by vibrational self-consistent field theory. Phys Chem Chem Phys 2011; 13:2001-13. [DOI: 10.1039/c0cp01177k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kowal AT. Ab initio molecular geometry and anharmonic vibrational spectra of thiourea and thiourea-d4. J Comput Chem 2010; 32:718-29. [DOI: 10.1002/jcc.21665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 07/07/2010] [Accepted: 08/07/2010] [Indexed: 11/10/2022]
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Rasheed T, Ahmad S. Approximate solution of the mode-mode coupling integral: Application to cytosine and its deuterated derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:446-456. [PMID: 20638327 DOI: 10.1016/j.saa.2010.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 05/30/2010] [Accepted: 06/11/2010] [Indexed: 05/29/2023]
Abstract
Ab initio Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset (MP2) methods were used to perform harmonic and anharmonic calculations for the biomolecule cytosine and its deuterated derivative. The anharmonic vibrational spectra were computed using the vibrational self-consistent field (VSCF) and correlation-corrected vibrational self-consistent field (CC-VSCF) methods. Calculated anharmonic frequencies have been compared with the argon matrix spectra reported in literature. The results were analyzed with focus on the properties of anharmonic couplings between pair of modes. A simple and easy to use formula for calculation of mode-mode coupling magnitudes has been derived. The key element in present approach is the approximation that only interactions between pairs of normal modes have been taken into account, while interactions of triples or more are neglected. FTIR and Raman spectra of solid state cytosine have been recorded in the regions 400-4000 cm(-1) and 60-4000 cm(-1), respectively. Vibrational analysis and assignments are based on calculated potential energy distribution (PED) values.
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Affiliation(s)
- Tabish Rasheed
- Department of Physics, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
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Bouteiller Y, Gillet JC, Grégoire G, Schermann JP. Transferable Specific Scaling Factors for Interpretation of Infrared Spectra of Biomolecules from Density Functional Theory. J Phys Chem A 2008; 112:11656-60. [DOI: 10.1021/jp805854q] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yves Bouteiller
- Laboratoire de Physique des Lasers, UMR CNRS 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Jean-Christophe Gillet
- Laboratoire de Physique des Lasers, UMR CNRS 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Gilles Grégoire
- Laboratoire de Physique des Lasers, UMR CNRS 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Jean Pierre Schermann
- Laboratoire de Physique des Lasers, UMR CNRS 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
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Bounouar M, Scheurer C. The impact of approximate VSCF schemes and curvilinear coordinates on the anharmonic vibrational frequencies of formamide and thioformamide. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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