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Juarez G, Alonso ER, Aguado R, León I. Rotational Spectroscopy as a Tool to Characterize Sweet Taste: The Study of Dulcin. ChemistryOpen 2024:e202400159. [PMID: 39051712 DOI: 10.1002/open.202400159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/06/2024] [Indexed: 07/27/2024] Open
Abstract
According to old theories of sweetness, the perception of sweet substances is closely linked to the arrangement of atoms within them. To assess the validity of these theories, we conducted an analysis of the structure of the artificial sweetener dulcin for the first time, utilizing microwave spectroscopy and a laser ablation source. These techniques have enabled the identification of two conformers, which are stabilized by an intramolecular hydrogen bond between the amino group and the phenyl ring. The observed conformations were examined in light of the Shallenberger-Acree-Kier molecular theory of sweet taste, and they align with the hypothesized criteria. Furthermore, the study illustrates how conformational relaxation can alter the equilibrium conformational distribution, resulting in the absence of certain conformers in the conformational landscape.
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Affiliation(s)
- Gabriela Juarez
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Raúl Aguado
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
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2
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Cormanich RA, da Silva GD. Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations. J Chem Inf Model 2024; 64:3322-3331. [PMID: 38536765 DOI: 10.1021/acs.jcim.4c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
This work reports on new software for automatic conformer energy benchmarking calculations for flexible molecules. The software workflow consists of four parts: conformational search, preoptimization, optimization, and frequency calculations at a higher level and last calculations using several theoretical levels. The software was written to be user-friendly and versatile to be used by nonexperts in computational chemistry. Any theoretical levels available in either Gaussian 16 or ORCA 5 may be applied in the benchmarking study. The workflow will automatically run conformational search calculations and deal with conformers that converge to the same minimum and those that show a negative frequency. At the end of the workflow, the user will have the mean absolute deviations and the most accurate method/DFT functional and basis set in comparison to the benchmark to be applied for the molecular system of interest. Case examples are given at the end of the paper that may help users to get insight into the software's main features.
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Affiliation(s)
- Rodrigo A Cormanich
- Instituto de Química, Departamento de Química Orgânica, Universidade Estadual de Campinas, PO Box 6154, Campinas 13083-970, São Paulo, Brazil
| | - Gabriel D da Silva
- Instituto de Química, Departamento de Química Orgânica, Universidade Estadual de Campinas, PO Box 6154, Campinas 13083-970, São Paulo, Brazil
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3
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Sanz-Novo M, Kolesniková L, Insausti A, Alonso JL, León I, Alonso ER. A journey across dopamine Metabolism: A rotational study of DOPAC. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122303. [PMID: 36608514 DOI: 10.1016/j.saa.2022.122303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
DOPAC, a relevant scaffold in dopamine metabolism, was probed in the gas phase and interrogated by high-resolution rotational spectroscopy. Herein, three distinct conformers were isolated in a supersonic jet and identified for the first time through an examination of the trend of the rotational constants and the dipole moment selection rules. Additionally, we examined the plausible relaxation pathways of the low-energy conformers of DOPAC, which helped us to claim the indirect detection of two additional conformers, providing conclusive experimental evidence of the flexible nature of this biomolecule. The current investigation sheds some light on the differences between jet-cooled rotational experiments and matrix-isolation infrared spectroscopy.
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Affiliation(s)
- Miguel Sanz-Novo
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Lucie Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic
| | - Aran Insausti
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/ EHU), 48940 Leioa, Spain
| | - José L Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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4
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León I, Fusè M, Alonso ER, Mata S, Mancini G, Puzzarini C, Alonso JL, Barone V. Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry and artificial intelligence: the puzzling case of homocysteine. J Chem Phys 2022; 157:074107. [DOI: 10.1063/5.0102841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the ``surviving' conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic alpha-amino acid. The synergism of the integrated strategy allowed the characterization of five conformers stabilized by bifurcated N-H-O=C hydrogen bonds, together with an additional conformer involving a more conventional HNH-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.
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Affiliation(s)
- Iker León
- Universidad de Valladolid - Campus Miguel Delibes, Spain
| | | | - Elena R. Alonso
- Química Física y Química Inorgánica, Universidad de Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM). Edificio Quifima. Laboratorios de Espectroscopia y Bioespectroscopia. Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Spain
| | | | | | - Jose L. Alonso
- Grupo de Espectroscopia Molecular (GEM). Edificio Quifima. Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid Departamento Química Física y Química Inorgánica, Spain
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5
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Wang Y, Gu Z, Deng X, Zhang B. Ultraviolet-light-triggered isomerization of Rydberg-excited propanal: Real-time capture of ultrafast structural evolution and dynamics investigation. J Chem Phys 2021; 154:054301. [PMID: 33557549 DOI: 10.1063/5.0039802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Structure rearrangement processes, such as isomerization, are attracting extensive interest as a potential carrier in molecular scale electronics design. UV-light-triggered isomerization of Rydberg-excited propanal with two UV photons has been investigated with time-resolved photoelectron spectroscopy. By following the photoionization from 3s Rydberg states in the time domain, the ultrafast structural evolution and the corresponding photoisomerization dynamics are observed and tracked in real-time. The conversion barrier for isomerization from cis-propanal to gauche isomer is estimated to be about 1500 ± 100 cm-1 experimentally. Both the photoisomerization yield and the conversion rate have shown strong dependence on the excitation energy. It is observed that whether vibration modes are selectively excited or not, cis-to-gauche photoisomerization of propanal in 3s Rydberg state occurs once the excitation energy is higher than the conversion barrier without any vibrational excitation specificity. This yields a powerful approach to studying structural evolution dynamics in large molecules, which may have applications in molecular devices.
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Affiliation(s)
- Yanmei Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Zhenfei Gu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Xulan Deng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Bing Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
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6
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Martínez-Flores C, Domínguez-Gutiérrez F, Cabrera-Trujillo R. Rotational and vibrational effects on the energy loss of hydrogen colliding on glycine at low irradiation energies. Radiat Phys Chem Oxf Engl 1993 2020. [DOI: 10.1016/j.radphyschem.2019.108513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Sanz-Novo M, Alonso ER, León I, Alonso JL. The Shape of the Archetypical Oxocarbon Squaric Acid and Its Water Clusters. Chemistry 2019; 25:10748-10755. [PMID: 31283059 DOI: 10.1002/chem.201901916] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Indexed: 12/15/2022]
Abstract
Herein, a full structural description is presented for the archetypical supramolecular synthone squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione), placed in the gas phase by laser ablation and characterized by chirped pulse Fourier transform microwave technique. Free from natural environmental disturbances, two different anti-anti and syn-anti planar forms and the corresponding water clusters have been revealed in a supersonic expansion. The substitution structure of the most stable anti-anti conformer has also been extracted from the analysis of the rotational spectra of the 13 C and 18 O isotopic species in their natural abundance. The interplay between inter- and intramolecular interactions involving hydroxy and carbonyl groups has been analyzed by QTAIM (quantum theory of atoms in molecules) methods for squaric acid and its water clusters to understand their chemical behavior and further rationalize their role in the stabilization of these molecular systems.
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Affiliation(s)
- Miguel Sanz-Novo
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Iker León
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
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8
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches. J Phys Chem A 2019; 123:862-872. [DOI: 10.1021/acs.jpca.8b10881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Ranim Mallat
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Tim Gorn
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M. Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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9
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Competition between folded and extended structures of alanylalanine (Ala-Ala) in a molecular beam. Phys Chem Chem Phys 2019; 21:14126-14132. [DOI: 10.1039/c9cp00140a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural analysis of the neutral dipeptide Ala-Ala by action spectroscopy using IRMPD-VUV spectroscopy reveals predominance of extended structure.
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Affiliation(s)
- Vasyl Yatsyna
- University of Gothenburg
- Department of Physics
- Sweden
- Radboud University
- Institute for Molecules and Materials
| | - Ranim Mallat
- University of Gothenburg
- Department of Physics
- Sweden
| | - Tim Gorn
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | - Michael Schmitt
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | | | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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10
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Quantum scattering theory for collisional energy transfer. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/b978-0-444-64207-3.00002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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Neeman EM, León I, Alonso ER, Kolesniková L, Mata S, Alonso JL. The effect of N-methylation on the conformational landscape of alanine: the case of N-methyl-l-alanine. Phys Chem Chem Phys 2018; 20:29159-29165. [PMID: 30426989 DOI: 10.1039/c8cp06043f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-proteinogenic amino acid N-methyl-l-alanine has been brought into the gas phase using laser ablation techniques and studied by high resolution chirped pulse and molecular-beam Fourier transform microwave spectroscopies coupled to supersonic expansion. Four conformers showing the three types of hydrogen bond interactions I (NHO[double bond, length as m-dash]C), II (OHN) and III (N-HO-H) have been unambiguously identified, based on the comparison of the experimental rotational and 14N nuclear quadrupole constants with the calculated ab initio values. The observation of a type III conformer evidences the role of methyl groups in both sides to impose the steric hindrance, precluding the relaxation from type III to type I conformers and explains the responsibility for the unique conformational landscape observed in the case of NMA.
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Affiliation(s)
- E M Neeman
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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12
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Chang X, Chen Z, Su P, Wu W. The C O rotation in the gaseous glycine. An energy decomposition analysis study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Barone V, Biczysko M, Bloino J, Puzzarini C. Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine. Phys Chem Chem Phys 2013; 15:10094-111. [PMID: 23599122 DOI: 10.1039/c3cp50439e] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized using a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within the chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ mol(-1) accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ mol(-1). Regarding molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm(-1). Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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14
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Bazsó G, Magyarfalvi G, Tarczay G. Tunneling Lifetime of the ttc/VIp Conformer of Glycine in Low-Temperature Matrices. J Phys Chem A 2012; 116:10539-47. [DOI: 10.1021/jp3076436] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
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15
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Bazsó G, Magyarfalvi G, Tarczay G. Near-infrared laser induced conformational change and UV laser photolysis of glycine in low-temperature matrices: Observation of a short-lived conformer. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.04.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Jiménez AI, Vaquero V, Cabezas C, López JC, Cativiela C, Alonso JL. The Singular Gas-Phase Structure of 1-Aminocyclopropanecarboxylic Acid (Ac3c). J Am Chem Soc 2011; 133:10621-8. [DOI: 10.1021/ja2033603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana I. Jiménez
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - Vanesa Vaquero
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cabezas
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Juan C. López
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cativiela
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - José L. Alonso
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
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17
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Rahaman O, van Duin AC, Goddard WA, Doren DJ. Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization. J Phys Chem B 2011; 115:249-61. [PMID: 21166434 PMCID: PMC3042430 DOI: 10.1021/jp108642r] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF → ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.
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Affiliation(s)
- Obaidur Rahaman
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, USA
| | - Adri C.T. van Duin
- Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - William A. Goddard
- Material and Process Simulation Center, California Institute of Technology, Pasadena CA 91125, USA
| | - Douglas J. Doren
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, USA
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18
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Yamakita Y, Ohno K. Collision-Energy-Resolved Penning Ionization Electron Spectroscopy of Glycine with He(23S) Metastable Atoms: Conformational Isomers in Collisional Ionization. J Phys Chem A 2009; 113:10779-86. [DOI: 10.1021/jp9038978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yoshihiro Yamakita
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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Deb N, Bagchi S, Mukherjee AK. Fluorimetric study of water-ethanol interaction and its effect on the micellisation of sodium dodecyl sulphate in the presence of bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 73:370-373. [PMID: 19328034 DOI: 10.1016/j.saa.2009.02.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Revised: 02/13/2009] [Accepted: 02/20/2009] [Indexed: 05/27/2023]
Abstract
The model for self-association of ethanol in water which was established earlier by compressibility and infrared absorption measurements, has been further supported in the present work by monitoring fluorimetrically the variation of the solvatochromic Kamlet-Taft pi* parameter of ethanol-water mixtures over the entire mole fraction range. This model has been used to interpret the variation of the critical micellisation concentration (cmc) of sodium dodecyl sulphate in the presence of bovine serum albumin (BSA) in aqueous ethanol mixtures (as obtained from the tryptophan fluorescence intensity of BSA) in low ethanol mole fraction range.
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Affiliation(s)
- Nipamanjari Deb
- Department of Chemistry, The University of Burdwan, Golapbag, Burdwan 713104, India
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20
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Kim HM, Han KY, Park J, Kim SK, Kim ZH. Conformational study of jet-cooled L-phenylglycine. J Chem Phys 2008; 128:184313. [DOI: 10.1063/1.2918344] [Citation(s) in RCA: 3] [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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21
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Baquero EE, James WH, Choi SH, Gellman SH, Zwier TS. Single-Conformation Ultraviolet and Infrared Spectroscopy of Model Synthetic Foldamers: β-Peptides Ac-β3-hPhe-β3-hAla-NHMe and Ac-β3-hAla-β3-hPhe-NHMe. J Am Chem Soc 2008; 130:4795-807. [PMID: 18345673 DOI: 10.1021/ja078272q] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Esteban E. Baquero
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1322
| | - William H. James
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1322
| | - Soo Hyuk Choi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1322
| | - Samuel H. Gellman
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1322
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1322
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22
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Shubert VA, Baquero EE, Clarkson JR, James WH, Turk JA, Hare AA, Worrel K, Lipton MA, Schofield DP, Jordan KD, Zwier TS. Entropy-driven population distributions in a prototypical molecule with two flexible side chains: O-(2-acetamidoethyl)-N-acetyltyramine. J Chem Phys 2007; 127:234315. [DOI: 10.1063/1.2803076] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Erlekam U, Frankowski M, von Helden G, Meijer G. Cold collisions catalyse conformational conversion. Phys Chem Chem Phys 2007; 9:3786-9. [PMID: 17622413 DOI: 10.1039/b703571c] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have determined the abundance of two different conformational structures of the mixed benzene dimer (C(6)H(6))(C(6)D(6)) in a molecular beam, with various carrier gases. These two T-shaped conformers have a subtle zero-point energy difference of only a few cm(-1), and a transition state barrier of about 64 cm(-1). Nevertheless, depending on the carrier gas, the lowest energy conformer can exclusively be prepared in the molecular beam. Low-energy two-body collisions of the benzene-dimers with the carrier gas atoms are concluded to be responsible for this.
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Affiliation(s)
- Undine Erlekam
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195, Berlin, Germany.
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Miller TF, Clary DC. Quantum Simulation of a Hydrated Noradrenaline Analog with the Torsional Path Integral Method. J Phys Chem A 2005; 110:731-40. [PMID: 16405347 DOI: 10.1021/jp055108l] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An extended version of the torsional path integral Monte Carlo (TPIMC) method is presented and shown to be useful for studying the conformation of flexible molecules in solvated clusters. The new technique is applied to the hydrated clusters of the 2-amino-1-phenyl-ethanol (APE) molecule. APE + nH2O clusters with n = 0-4 are studied at 100 and 300 K using both classical and quantum simulations. Only at the lower temperature is the hydration number n found to impact the conformational distribution of the APE molecule. This is shown to be a result of the temperature-dependent balance between the internal energy and entropy contributions to the relative conformer free energies. Furthermore, at 100 K, large quantum effects are observed in the calculated conformer populations. A particularly large quantum shift of 30% of the total population is calculated for the APE + 2H2O cluster, which is explained in terms of the relative zero point energy of the lowest-energy hydrated structures for this cluster. Finally, qualitative agreement is found between the reported calculations and recent spectroscopy experiments on the hydrated clusters of APE, including an entropically driven preference for the formation of AG-type hydrated structures and the formation of a water "droplet" in the APE + 4H2O cluster.
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Affiliation(s)
- Thomas F Miller
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
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Sturdy YK, Skylaris CK, Clary DC. Torsional Anharmonicity in the Conformational Analysis of β-d-Galactose. J Phys Chem B 2005; 110:3485-92. [PMID: 16494402 DOI: 10.1021/jp053225a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Schemes to include a treatment of torsional anharmonicity in the conformational analysis of biological molecules are introduced. The approaches combine ab initio electronic energies and harmonic frequencies with anharmonic torsional partition functions calculated using the torsional path integral Monte Carlo method on affordable potential energy surfaces. The schemes are applied to the conformational study of the monosaccharide beta-d-galactose in the gas phase. The global minimum structure is almost exclusively populated at 100 K, but a large number of conformers are present at ambient and higher temperatures. Both quantum mechanical and anharmonic effects in the torsional modes have little effect on the populations at all temperatures considered, and it is, therefore, expected that standard harmonic treatments are satisfactory for the conformational study of monosaccharides.
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Affiliation(s)
- Yvette K Sturdy
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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