1
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Alberini A, Fornaro T, García-Florentino C, Biczysko M, Poblacion I, Aramendia J, Madariaga JM, Poggiali G, Vicente-Retortillo Á, Benison KC, Siljeström S, Biancalani S, Lorenz C, Cloutis EA, Applin DM, Gómez F, Steele A, Wiens RC, Hand KP, Brucato JR. Investigating the stability of aromatic carboxylic acids in hydrated magnesium sulfate under UV irradiation to assist detection of organics on Mars. Sci Rep 2024; 14:15945. [PMID: 38987581 PMCID: PMC11237158 DOI: 10.1038/s41598-024-66669-8] [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: 05/28/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
The Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) instrument onboard the Mars 2020 Perseverance rover detected so far some of the most intense fluorescence signals in association with sulfates analyzing abraded patches of rocks at Jezero crater, Mars. To assess the plausibility of an organic origin of these signals, it is key to understand if organics can survive exposure to ambient Martian UV after exposure by the Perseverance abrasion tool and prior to analysis by SHERLOC. In this work, we investigated the stability of organo-sulfate assemblages under Martian-like UV irradiation and we observed that the spectroscopic features of phthalic and mellitic acid embedded into hydrated magnesium sulfate do not change for UV exposures corresponding to at least 48 Martian sols and, thus, should still be detectable in fluorescence when the SHERLOC analysis takes place, thanks to the photoprotective properties of magnesium sulfate. In addition, different photoproduct bands diagnostic of the parent carboxylic acid molecules could be observed. The photoprotective behavior of hydrated magnesium sulfate corroborates the hypothesis that sulfates might have played a key role in the preservation of organics on Mars, and that the fluorescence signals detected by SHERLOC in association with sulfates could potentially arise from organic compounds.
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Affiliation(s)
- Andrew Alberini
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy.
- Department of Physics and Astronomy, University of Florence, Via Giovanni Sansone 1, Sesto Fiorentino, 50019, Florence, Italy.
| | - Teresa Fornaro
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy.
| | - Cristina García-Florentino
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy
- Department of Analytical Chemistry, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Malgorzata Biczysko
- College of Science, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Iratxe Poblacion
- Department of Analytical Chemistry, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Julene Aramendia
- Department of Analytical Chemistry, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Juan Manuel Madariaga
- Department of Analytical Chemistry, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Giovanni Poggiali
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy
- LESIA - Observatoire de Paris, CNRS, Université Paris Cité, Université PSL, Sorbonne Université, 5 Place Jules Janssen, 92190, Meudon, France
| | | | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV, USA
| | | | - Sole Biancalani
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy
- Department of Physics, University of Trento, Via Sommarive 14, 38123, Povo, Italy
- Italian Space Angency (ASI), Viale del Politecnico Snc, 00133, Rome, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121, Florence, Italy
| | - Christian Lorenz
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126, Naples, Italy
| | - Edward A Cloutis
- Centre for Terrestrial and Planetary Exploration, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada
| | - Dan M Applin
- Centre for Terrestrial and Planetary Exploration, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada
| | - Felipe Gómez
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
| | | | - Roger C Wiens
- Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA
| | - Kevin P Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - John R Brucato
- INAF- Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125, Firenze, Italy
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2
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Uribe L, Lazzari F, Di Grande S, Crisci L, Mendolicchio M, Barone V. Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS). J Chem Phys 2024; 161:014307. [PMID: 38958160 DOI: 10.1063/5.0216384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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3
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Torres-Boy A, Taccone MI, Kirschbaum C, Ober K, Stein T, Meijer G, von Helden G. Investigation of the Proton-Bound Dimer of Dihydrogen Phosphate and Formate Using Infrared Spectroscopy in Helium Droplets. J Phys Chem A 2024; 128:4456-4466. [PMID: 38771224 PMCID: PMC11163467 DOI: 10.1021/acs.jpca.4c01632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Understanding the structural and dynamic properties of proton-bound complexes is crucial for elucidating fundamental aspects of chemical reactivity and molecular interactions. In this work, the proton-bound complex between dihydrogen phosphate and formate, and its deuterated counterparts, is investigated using IR action spectroscopy in helium droplets. Contrary to the initial expectation that the stronger phosphoric acid would donate a proton to formate, both experiment and theory show that all exchangeable protons are located in the phosphate moiety. The experimental spectra show good agreement with both scaled harmonic and VPT2 anharmonic calculations, indicating that anharmonic effects are small. Some H-bending modes of the nondeuterated complex are found to be sensitive to the helium environment. In the case of the partially deuterated complexes, the experiments indicate that internal dynamics leads to isomeric interconversion upon IR excitation.
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Affiliation(s)
| | - Martín I. Taccone
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, 14195 Berlin, Germany
| | - Katja Ober
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Tamar Stein
- Institute
of Chemistry and Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Gerard Meijer
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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4
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McIntosh O, García-Florentino C, Fornaro T, Marabello D, Alberini A, Siljeström S, Biczysko M, Szopa C, Brucato J. Undecanoic Acid and L-Phenylalanine in Vermiculite: Detection, Characterization, and UV Degradation Studies for Biosignature Identification on Mars. ASTROBIOLOGY 2024; 24:518-537. [PMID: 38669050 DOI: 10.1089/ast.2023.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Solar radiation that arrives on the surface of Mars interacts with organic molecules present in the soil. The radiation can degrade or transform the organic matter and make the search for biosignatures on the planet's surface difficult. Therefore, samples to be analyzed by instruments on board Mars probes for molecular content should be selectively chosen to have the highest organic preservation content. To support the identification of organic molecules on Mars, the behavior under UV irradiation of two organic compounds, undecanoic acid and L-phenylalanine, in the presence of vermiculite and two chloride salts, NaCl and MgCl, was studied. The degradation of the molecule's bands was monitored through IR spectroscopy. Our results show that, while vermiculite acts as a photoprotective mineral with L-phenylalanine, it catalyzes the photodegradation of undecanoic acid molecules. On the other hand, both chloride salts studied decreased the degradation of both organic species acting as photoprotectors. While these results do not allow us to conclude on the preservation capabilities of vermiculite, they show that places where chloride salts are present could be good candidates for in situ analytic experiments on Mars due to their organic preservation capacity under UV radiation.
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Affiliation(s)
- Ophélie McIntosh
- LATMOS/IPSL, UVSQ Université Paris-Saclay, Sorbonne Université, CNRS, Guyancourt, France
- INAF - Astrophysical Observatory of Arcetri, Firenze, Italy
| | - Cristina García-Florentino
- INAF - Astrophysical Observatory of Arcetri, Firenze, Italy
- Department of Analytical Chemistry, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Teresa Fornaro
- INAF - Astrophysical Observatory of Arcetri, Firenze, Italy
| | - Domenica Marabello
- Department of Chemistry, University of Torino, Torino, Italy
- Interdepartmental Center for Crystallography, University of Torino, Torino, Italy
| | | | - Sandra Siljeström
- Department of Methodology, Textiles and Medical Technology, RISE Research Institutes of Sweden, Stockholm, Sweden
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, Shanghai, China
| | - Cyril Szopa
- LATMOS/IPSL, UVSQ Université Paris-Saclay, Sorbonne Université, CNRS, Guyancourt, France
| | - John Brucato
- INAF - Astrophysical Observatory of Arcetri, Firenze, Italy
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5
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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024. [PMID: 38682874 DOI: 10.1002/jcc.27377] [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: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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6
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Fusè M, Mazzeo G, Longhi G, Abbate S, Yang Q, Bloino J. Scaling-up VPT2: A feasible route to include anharmonic correction on large molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 311:123969. [PMID: 38330757 DOI: 10.1016/j.saa.2024.123969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Vibrational analysis plays a crucial role in the investigation of molecular systems. Though methodologies like second-order vibrational perturbation theory (VPT2) have paved the way to more accurate simulations, the computational cost remains a difficult barrier to overcome when the molecular size increases. Building upon recent advances in the identification of resonances, we propose an approach making anharmonic simulations possible for large-size systems, typically unreachable by standard means. This relies on the fact that, often, only portions of the whole spectra are of actual interest. Therefore, the anharmonic corrections can be included selectively on subsets of normal modes directly related to the regions of interest. Starting from the VPT2 equations, we evaluate rigorously and systematically the impact of the truncated anharmonic treatment onto simulations. The limit and feasibility of the reduced-dimensionality approach are detailed, starting on a smaller model system. The methodology is then challenged on the IR absorption and vibrational circular dichroism spectra of an organometallic complex in three different spectral ranges.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, 56125, Pisa, Italy.
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7
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Fusè M, Mazzeo G, Abbate S, Ruzziconi R, Bloino J, Longhi G. Mid-IR and CH stretching vibrational circular dichroism spectroscopy to distinguish various sources of chirality: The case of quinophaneoxazoline based ruthenium(II) complexes. Chirality 2024; 36:e23649. [PMID: 38409881 DOI: 10.1002/chir.23649] [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: 12/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
Five diastereomers of ruthenium(II) complexes based on quinolinophaneoxazoline ligands were investigated by vibrational circular dichroism (VCD) in the mid-IR and CH stretching regions. Diastereomers differ in three sources of chirality: the planar chirality of the quinolinophane moiety, the central chirality of an asymmetric carbon atom of the oxazoline ring, and the chirality of the ruthenium atom. VCD, allied to DFT calculations, has been found to be effective in disentangling the various forms of chirality. In particular, a VCD band is identified in the CH stretching region directly connected to the chirality of the metal. The analysis of the calculated VCD spectra is carried out by partitioning the complexes into fragments. The anharmonic analysis is also performed with a recently proposed reduced-dimensionality approach: such treatment is particularly important when examining spectroscopic regions highly perturbed by resonances, like the CH stretching region.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
| | - Renzo Ruzziconi
- Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
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8
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Groß J, Kühlborn J, Pusch S, Weber C, Andernach L, Renzer G, Eckhardt P, Brauer J, Opatz T. Comparison of different density functional theory methods for the calculation of vibrational circular dichroism spectra. Chirality 2023; 35:753-765. [PMID: 37227055 DOI: 10.1002/chir.23580] [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: 01/30/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum-mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC.
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Affiliation(s)
- Jonathan Groß
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jonas Kühlborn
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Pusch
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Carina Weber
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Lars Andernach
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Galit Renzer
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Paul Eckhardt
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jan Brauer
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
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9
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Kreienborg NM, Yang Q, Pollok CH, Bloino J, Merten C. Matrix-isolation and cryosolution-VCD spectra of α-pinene as benchmark for anharmonic vibrational spectra calculations. Phys Chem Chem Phys 2023; 25:3343-3353. [PMID: 36633064 DOI: 10.1039/d2cp04782a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The inclusion of anharmonicity in vibrational spectral analyis remains associated to small molecular systems with up to a dozen of atoms, with half a dozen of non-hydrogen atoms, typically thesize of propylene oxide. One may see two reasons for this: first of all, larger systems are often thought to be computationally too demanding (high computational costs) for a full anharmonic vibrational analysis. Second, the identification of resonances and their correction is often considered something only expert theoreticians could address because of the lack of unequivocal criteria. In this contribution, we illustrate that resonances can indeed become a complex problem, which can be handled almost transparently thanks to recent advances in vibrational perturbation theory (VPT2). The study also emphasizes the importance and the central role played by experiment in benchmarking novel theoretical approaches. In fact, we herein provide the currently highest resolution VCD spectra available for α- and β-pinene obtained under matrix-isolation conditions and in liquid Xenon as solvent. They are interpreted by VPT2 with novel tests for the identification of resonances. Hence, the study demonstrates the mutual stimulation of advances in both experimental techniques and computational models.
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Affiliation(s)
- Nora M Kreienborg
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Qin Yang
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Corina H Pollok
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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10
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Jähnigen S, Le Barbu-Debus K, Guillot R, Vuilleumier R, Zehnacker A. How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202215599. [PMID: 36441537 PMCID: PMC10107176 DOI: 10.1002/anie.202215599] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 11/29/2022]
Abstract
Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P21 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
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11
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Yang Q, Bloino J. An Effective and Automated Processing of Resonances in Vibrational Perturbation Theory Applied to Spectroscopy. J Phys Chem A 2022; 126:9276-9302. [DOI: 10.1021/acs.jpca.2c06460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Qin Yang
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610Prague, Czech Republic
| | - Julien Bloino
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
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12
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Dall’Osto G, Corni S. Time Resolved Raman Scattering of Molecules: A Quantum Mechanics Approach with Stochastic Schroedinger Equation. J Phys Chem A 2022; 126:8088-8100. [PMID: 36278928 PMCID: PMC9639147 DOI: 10.1021/acs.jpca.2c05245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Raman scattering is a very powerful tool employed to
characterize
molecular systems. Here we propose a novel theoretical strategy to
calculate the Raman cross-section in time domain, by computing the
cumulative Raman signal emitted during the molecular evolution in
time. Our model is based on a numerical propagation of the vibronic
wave function under the effect of a light pulse of arbitrary shape.
This approach can therefore tackle a variety of experimental setups.
Both resonance and nonresonance Raman scattering can be retrieved,
and also the time-dependent fluorescence emission is computed. The
model has been applied to porphyrin considering both resonance and
nonresonance conditions and varying the incident field duration. Moreover
the effect of the vibrational relaxation, which should be taken into
account when its time scale is similar to that of the Raman emission,
has been included through the stochastic Schroedinger equation approach.
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Affiliation(s)
- Giulia Dall’Osto
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
- CNR Institute of Nanoscience, via Campi 213/A, Modena, 41125, Italy
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13
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Yang Q, Kapitán J, Bouř P, Bloino J. Anharmonic Vibrational Raman Optical Activity of Methyloxirane: Theory and Experiment Pushed to the Limits. J Phys Chem Lett 2022; 13:8888-8892. [PMID: 36125432 PMCID: PMC9531246 DOI: 10.1021/acs.jpclett.2c02320] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Combining Raman scattering and Raman optical activity (ROA) with computer simulations reveals fine structural and physicochemical properties of chiral molecules. Traditionally, the region of interest comprised fundamental transitions within 200-1800 cm-1. Only recently, nonfundamental bands could be observed as well. However, theoretical tools able to match the observed spectral features and thus assist their assignment are rather scarce. In this work, we present an accurate and simple protocol based on a three-quanta anharmonic perturbative approach that is fully fit to interpret the observed signals of methyloxirane within 150-4500 cm-1. An unprecedented agreement even for the low-intensity combination and overtone transitions has been achieved, showing that anharmonic Raman and ROA spectroscopies can be valuable tools to understand vibrations of chiral molecules or to calibrate computational models.
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Affiliation(s)
- Qin Yang
- Scuola Normale
Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Josef Kapitán
- Department
of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí
2, 16610 Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale
Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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14
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Galimberti DR. Vibrational Circular Dichroism from DFT Molecular Dynamics: The AWV Method. J Chem Theory Comput 2022; 18:6217-6230. [PMID: 36112978 PMCID: PMC9558311 DOI: 10.1021/acs.jctc.2c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The paper illustrates the Activity Weighted Velocities
(AWV) methodology
to compute Vibrational Circular Dichroism (VCD) anharmonic spectra
from Density Functional Theory (DFT) molecular dynamics. AWV calculates
the spectra by the Fourier Transform of the time correlation functions
of velocities, weighted by specific observables: the Atomic Polar
Tensors (APTs) and the Atomic Axial Tensors (AATs). Indeed, AWV shows
to correctly reproduce the experimental spectra for systems in the
gas and liquid phases, both in the case of weakly and strongly interacting
systems. The comparison with the experimental spectra is striking
especially in the fingerprint region, as demonstrated by the three
benchmark systems discussed: (1S)-Fenchone in the
gas phase, (S)-(−)-Propylene oxide in the
liquid phase, and (R)-(−)-2-butanol in the
liquid phase. The time evolution of APTs and AATs can be adequately
described by a linear combination of the tensors of a small set of
appropriate reference structures, strongly reducing the computational
cost without compromising accuracy. Additionally, AWV allows the partition
of the spectral signal in its molecular components without any expensive
postprocessing and any localization of the charge density or the wave
function.
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Affiliation(s)
- Daria Ruth Galimberti
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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15
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Eikås KDR, Beerepoot MTP, Ruud K. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides. J Phys Chem A 2022; 126:5458-5471. [PMID: 35930395 PMCID: PMC9393892 DOI: 10.1021/acs.jpca.2c02953] [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: 11/30/2022]
Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
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Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.,Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
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16
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Carvalho JR, Vidal LN. Calculation of absolute Raman scattering cross-sections using vibrational self-consistent field/vibrational configuration interaction wave functions. J Comput Chem 2022; 43:1484-1494. [PMID: 35731622 DOI: 10.1002/jcc.26951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/21/2022] [Accepted: 06/02/2022] [Indexed: 11/12/2022]
Abstract
In the present study, the differential scattering cross-sections, depolarization ratios and Raman shifts of small molecular systems are obtained from configuration iteration wave functions of vibrational self-consistent field (VSCF) states. The transition polarizabilities were modeled using the Placzek approximation, neglecting those contributions not arising from the electric dipole mechanism. This theoretical approach is considered a good approximation for samples that absorb in the UV range if the excitation radiation falls in the visible region, as is the case of the molecules selected for the present study, namely: water, methane, and acetylene. Potential energy and electronic polarizability surfaces are calculated by the CCSD(T) and CC3 methods with aug-cc-p(C)V(T,Q,5)Z basis sets. The vibrational Hamiltonian includes the vibrational angular momentum contribution of the Watson kinetic energy operator. As expected, due to the variational nature of the VSCF and vibrational configuration interaction (VCI) methods, the Raman transition wavenumbers are substantially improved over the harmonic predictions. Surprisingly, the scattering cross-sections obtained using the harmonic approximation or the VSCF method better agrees with the experimental values than those cross-sections predicted using VCI wave functions. The more significant deviations of the VCI results from the experimental reference may be related to the significant uncertainties of the measured cross-sections. Still, it may also indicate that the VCI Raman transition moments may require a more accurate description of the electronic polarizability surface. Finally, the depolarization ratios calculated for H2 O and C2 D2 using harmonic and VCI wave functions have similar accuracy, whereas, for C2 H2 and C2 HD, the VCI results are more accurate.
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Affiliation(s)
- Jhonatas R Carvalho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Luciano N Vidal
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Curitiba, Paraná, Brazil
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17
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Carlini L, Chiarinelli J, Mattioli G, Castrovilli MC, Valentini V, De Stefanis A, Bauer EM, Bolognesi P, Avaldi L. Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide. J Phys Chem B 2022; 126:2968-2978. [PMID: 35438499 PMCID: PMC9059117 DOI: 10.1021/acs.jpcb.1c10736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Dipeptides, the prototype
peptides, exist in both linear (l-) and cyclo (c-) structures. Since the
first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a
temperature-induced process. In this work, combining several different
experimental techniques (mass spectrometry, infrared and Raman spectroscopy,
and thermogravimetric analysis) with tight-binding and ab initio simulations,
we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed
by water and driven by temperature, occurs in the condensed phase.
This process can be considered as a very efficient strategy to improve
dipeptide stability by turning the comparatively fragile linear structure
into the robust and more stable cyclic one. This mechanism may have
played a role in prebiotic chemistry and can be further exploited
in the preparation of nanomaterials and drugs.
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Affiliation(s)
- Laura Carlini
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Giuseppe Mattioli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Mattea Carmen Castrovilli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Veronica Valentini
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Adriana De Stefanis
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Elvira Maria Bauer
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
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18
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Zheng RH, Wei WM. Sum-frequency vibrational spectroscopy of methanol at interfaces due to Fermi resonance. Phys Chem Chem Phys 2022; 24:27204-27211. [DOI: 10.1039/d2cp01808j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We present a theoretical method of studying sum-frequency vibrational spectroscopy for the CH3 group of methanol at interfaces due to Fermi resonance, which provides a novel and untraditional point of view with respect to traditional approaches.
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Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, P. R. China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, Anhui, 230032, P. R. China
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19
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Górecki M, Frelek J. A Holistic Approach to Determining Stereochemistry of Potential Pharmaceuticals by Circular Dichroism with β-Lactams as Test Cases. Int J Mol Sci 2021; 23:273. [PMID: 35008698 PMCID: PMC8745598 DOI: 10.3390/ijms23010273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022] Open
Abstract
This paper's main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods is crucial, especially when other techniques, including X-ray crystallography, fail, are not applicable, or give inconclusive results. Based on various β-lactam derivatives as models, we show how to reliably determine their absolute configuration (AC) and preferred conformation from circular dichroism (CD) spectra. Comprehensive CD analysis, employing both approaches, i.e., traditional with their sector and helicity rules, and state-of-the-art supported by quantum chemistry (QC) calculations along with solvation models for both electronic (ECD) and vibrational (VCD) circular dichroism ranges, allows confident defining stereochemistry of the β-lactams studied. Based on an in-depth analysis of the results, we have shown that choosing a proper chiroptical method/s strictly depends on the specific case and certain structural features.
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Affiliation(s)
- Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland;
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20
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Ceselin G, Barone V, Tasinato N. Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry. J Chem Theory Comput 2021; 17:7290-7311. [PMID: 34666488 PMCID: PMC8582257 DOI: 10.1021/acs.jctc.1c00788] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The determination
of accurate equilibrium molecular structures
plays a fundamental role for understanding many physical–chemical
properties of molecules, ranging from the precise evaluation of the
electronic structure to the analysis of the role played by dynamical
and environmental effects in tuning their overall behavior. For small
semi-rigid systems in the gas phase, state-of-the-art quantum chemical
computations rival the most sophisticated experimental (from, for
example, high-resolution spectroscopy) results. For larger molecules,
more effective computational approaches must be devised. To this end,
we have further enlarged the compilation of available semi-experimental
(SE) equilibrium structures, now covering the most important fragments
containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new
SE100 database. Next, comparison with geometries optimized by methods
rooted in the density functional theory showed that the already remarkable
results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals
can be further improved by a linear regression (LR) approach. Use
of template fragments (taken from the SE100 library) together with
LR estimates for the missing interfragment parameters paves the route
toward accurate structures of large molecules, as witnessed by the
very small deviations between computed and experimental rotational
constants. The whole approach has been implemented in a user-friendly
tool, termed nano-LEGO, and applied to a number of demanding case
studies.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
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21
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Rotamerism and intramolecular interactions of n-propyl halides and their partially and fully fluorinated derivatives. Electronic structure, topology and vibrational spectroscopy. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
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Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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23
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Benassi E, Vaganova T, Malykhin E, Fan H. Impact of fluorination and chlorination on the electronic structure, topology and in-plane ring normal modes of pyridines. Phys Chem Chem Phys 2021; 23:18958-18974. [PMID: 34612435 DOI: 10.1039/d1cp02342j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seven partially and fully fluorinated/chlorinated pyridines were investigated by means of FT-IR and Raman spectroscopy combined with quantum chemical calculations, mainly aiming to detect how the nature and position of F and Cl substituents affect the in-plane ring normal modes (RNMs) of pyridines in terms of vibrational wavenumbers, force constants, IR intensities and Raman activities. Taking pyridine as the reference, the RNMs and some derived RNMs through coupling with related C-X (X = F, Cl) stretching vibrations were identified on the basis of their composition in terms of internal coordinates. The impact of fluorination and chlorination on these RNMs was also discussed from the perspective of frontier molecular orbitals (MOs), maps of the molecular electrostatic potential (MEP) and the molecular topology. Natural bond orbital (NBO) analysis revealed the consequences of substitutions on the intramolecular charge delocalisation and consequently the ring bond strength. Moreover, the effects of anharmonicity of the potential on vibrational frequencies were presented and discussed.
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Affiliation(s)
- Enrico Benassi
- Novosibirsk State University, Novosibirsk, 630090, Russia.
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24
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Vibrational intensities and anharmonicity in MIR, NIR and Raman spectra of liquid CHCl3, CDCl3, CHBr3 and CDBr3: Spectroscopic and theoretical study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Gawrilow M, Suhm MA. Quantifying Conformational Isomerism in Chain Molecules by Linear Raman Spectroscopy: The Case of Methyl Esters. Molecules 2021; 26:molecules26154523. [PMID: 34361676 PMCID: PMC8348275 DOI: 10.3390/molecules26154523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 02/01/2023] Open
Abstract
The conformational preferences of the ester group have the potential to facilitate the large amplitude folding of long alkyl chains in the gas phase. They are monitored by Raman spectroscopy in supersonic jet expansions for the model system methyl butanoate, after establishing a quantitative relationship with quantum-chemical predictions for methyl methanoate. This requires a careful analysis of experimental details, and a simulation of the rovibrational contours for near-symmetric top molecules. The technique is shown to be complementary to microwave spectroscopy in quantifying coexisting conformations. It confirms that a C-O-C(=O)-C-C chain segment can be collapsed into a single all-trans conformation by collisional cooling, whereas alkyl chain isomerism beyond this five-membered chain largely survives the jet expansion. This sets the stage for the investigation of linear alkyl alkanoates in terms of dispersion-induced stretched-chain to hairpin transitions by Raman spectroscopy.
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26
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Barone V, Alessandrini S, Biczysko M, Cheeseman JR, Clary DC, McCoy AB, DiRisio RJ, Neese F, Melosso M, Puzzarini C. Computational molecular spectroscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00034-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Richter WE, Duarte LJ, Vidal LN, Bruns RE. AC/DC Analysis: Broad and Comprehensive Approach to Analyze Infrared Intensities at the Atomic Level. J Phys Chem A 2021; 125:3219-3229. [PMID: 33847496 DOI: 10.1021/acs.jpca.1c01314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present a complete theoretical protocol to partition infrared intensities into terms owing to individual atoms by two different but related approaches: the atomic contributions (ACs) show how the entire molecular vibrational motion affects the electronic structure of a single atom and the total infrared intensity. On the other hand, the dynamic contributions (DCs) show how the displacement of a single atom alters the electronic structure of the entire molecule and the total intensity. The two analyses are complementary ways of partitioning the same total intensity and conserve most of the features of the total intensity itself. Combined, they are called the AC/DC analysis. These can be further partitioned following the CCTDP (or CCT) models according to the population analysis chosen by the researcher. The main conceptual features of the equations are highlighted, and representative numerical results are shown to support the interpretation of the equations. The results are invariant to rotation and translation and can readily be extended to molecules of any size, shape, or symmetry. Although the AC/DC analysis requires the choice of a charge model, all charge models that correctly reproduce the total molecular dipole moment can be used. A fully automated protocol managed by the Placzek program is made available, free of charge and with input examples.
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Affiliation(s)
- Wagner E Richter
- Department of Chemical Engineering, Federal University of Technology-Paraná, Ponta Grossa, Paraná 81280-340, Brazil
| | - Leonardo J Duarte
- Institute of Chemistry, State University of Campinas, Campinas, São Paulo 13081-970, Brazil
| | - Luciano N Vidal
- Department of Chemistry and Biology, Federal University of Technology-Paraná, Ponta Grossa, Paraná 81280-340, Brazil
| | - Roy E Bruns
- Institute of Chemistry, State University of Campinas, Campinas, São Paulo 13081-970, Brazil
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28
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Singh S, Czarnecki MA. How much anharmonicity is in vibrational spectra of CH 3I and CD 3I? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119176. [PMID: 33257247 DOI: 10.1016/j.saa.2020.119176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
This work presents new experimental and theoretical insights on vibrational spectra of CH3I and CD3I in the liquid phase. For the first time, we provided the contributions from different vibrational modes to mid-infrared (MIR) and near-infrared (NIR) spectra and estimated the extent of anharmonicity in the MIR region. Direct comparison of the intensities from ATR-IR and NIR transmission spectra was possible due to normalization of ATR-IR spectra. As a reference for normalization, we applied the area of the νs(CH3)/νs(CD3) band recorded in transmission mode. Our results show that the corresponding vibrational modes of CH3I and CD3I have similar contributions to the total intensity (MIR + NIR), however, these contributions are distributed in a different way between MIR and NIR regions. As expected, most of intensity in MIR spectra originates from the fundamental transitions (>90%). The fundamental bands together with the first overtones and the binary combinations contribute to more than 99% of MIR intensity for both compounds. Therefore, reliable reconstruction of MIR spectra can be achieved by considering only these vibrational modes. On the other hand, accurate simulation of NIR spectra requires including the higher-order transitions. In the case of CD3I, the fourth-order transitions contribute to 12.7% of NIR intensity. The contributions from NIR region are significantly smaller than those from MIR range and were estimated to be 6.7% for CH3I and 2.3% for CD3I. The theoretical calculations provide a reasonable estimation of the total contribution from the fundamental bands. Yet, the calculated contributions from the anharmonic transitions are different from those obtained from the experimental data. MIR spectra of CH3I and CD3I reveal an unexpected increase in the intensity of some overtones and combination bands indicating the presence of Fermi resonances. These resonances are responsible for differences in contributions from the first overtones and binary combinations between CH3I and CD3I.
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Affiliation(s)
- Swapnil Singh
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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29
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Franke PR, Stanton JF, Douberly GE. How to VPT2: Accurate and Intuitive Simulations of CH Stretching Infrared Spectra Using VPT2+K with Large Effective Hamiltonian Resonance Treatments. J Phys Chem A 2021; 125:1301-1324. [PMID: 33506678 DOI: 10.1021/acs.jpca.0c09526] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This article primarily discusses the utility of vibrational perturbation theory for the prediction of X-H stretching vibrations with particular focus on the specific variant, second-order vibrational perturbation theory with resonances (VPT2+K). It is written as a tutorial, reprinting most important formulas and providing numerous simple examples. It discusses the philosophy and practical considerations behind vibrational simulations with VPT2+K, including but not limited to computational method selection, cost-saving approximations, approaches to evaluating intensity, resonance identification, and effective Hamiltonian structure. Particular attention is given to resonance treatments, beginning with simple Fermi dyads and gradually progressing to arbitrarily large polyads that describe both Fermi and Darling-Dennison resonances. VPT2+K combined with large effective Hamiltonians is shown to be a reliable framework for modeling the complicated CH stretching spectra of alkenes. An error is also corrected in the published analytic formula for the VPT2 transition moment between the vibrational ground state and triply excited states.
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Affiliation(s)
- Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Gary E Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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30
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Frandsen BN, Deal AM, Lane JR, Vaida V. Lactic Acid Spectroscopy: Intra- and Intermolecular Interactions. J Phys Chem A 2020; 125:218-229. [PMID: 33377780 DOI: 10.1021/acs.jpca.0c09341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lactic acid, a relevant molecule in biology and the environment, is an α-hydroxy acid with a high propensity to form hydrogen bonds, both internally and to other hydrogen-bond-accepting molecules. This work includes the novel recording of infrared spectra of gas-phase lactic acid using Fourier transform infrared spectroscopy, and the vibrational absorption features of lactic acid are assigned with the aid of computationally simulated vibrational spectra with anharmonic corrections. Theoretical chemistry methods are used to relate intramolecular hydrogen-bond strengths to the relative stability of lactic acid conformers. The formation of hydrogen-bonded lactic acid dimers and 1:1 water complexes is investigated by simulated vibrational spectra and calculated thermodynamic parameters for the lactic acid monomer and dimer and its water complex in the gas phase. The results of this study are discussed in the context of environmental chemistry with an emphasis on indoor environments.
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Affiliation(s)
- Benjamin N Frandsen
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
| | - Alexandra M Deal
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
| | - Joseph R Lane
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Veronica Vaida
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
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31
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Scholten K, Engelage E, Merten C. Basis set dependence of S[double bond, length as m-dash]O stretching frequencies and its consequences for IR and VCD spectra predictions. Phys Chem Chem Phys 2020; 22:27979-27986. [PMID: 33290469 DOI: 10.1039/d0cp05420h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Benchmarking functionals and basis sets for the computational prediction of molecular properties is usually done on very small model systems. Larger organic molecules containing heavier second row atoms are not the typical model structures. We herein present the first survey of basis sets and functionals for the prediction of the IR and VCD spectra of chiral tosylates and sulfinates as we noted drastic deviations between computed harmonic frequencies obtained at B3LYP/6-311++G(2d,p) level of theory and those observed in experimental solution phase IR and VCD spectra. We show that the harmonic frequencies of the asymmetric and symmetric S[double bond, length as m-dash]O stretching modes of tosylates are predicted at significantly too low vibrational frequencies if the employed basis set does not provide higher order polarization functions. The results of our benchmarks show that at least the 6-311G(3df,2dp) basis (or equivalent Dunning and Ahlrichs variants) should be used.
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Affiliation(s)
- Kevin Scholten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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32
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Barone V, Puzzarini C. Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202024600021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.
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33
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Barone V, Ceselin G, Fusè M, Tasinato N. Accuracy Meets Interpretability for Computational Spectroscopy by Means of Hybrid and Double-Hybrid Functionals. Front Chem 2020; 8:584203. [PMID: 33195078 PMCID: PMC7645164 DOI: 10.3389/fchem.2020.584203] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Accuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double- and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules.
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Affiliation(s)
- Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Giorgia Ceselin
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Nicola Tasinato
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
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34
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Sheka EF, Golubev YA, Popova NA. Graphene Domain Signature of Raman Spectra of sp2 Amorphous Carbons. NANOMATERIALS 2020; 10:nano10102021. [PMID: 33066381 PMCID: PMC7602257 DOI: 10.3390/nano10102021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022]
Abstract
The standard D-G-2D pattern of Raman spectra of sp2 amorphous carbons is considered from the viewpoint of graphene domains presenting their basic structure units (BSUs) in terms of molecular spectroscopy. The molecular approximation allows connecting the characteristic D-G doublet spectra image of one-phonon spectra with a considerable dispersion of the C=C bond lengths within graphene domains, governed by size, heteroatom necklace of BSUs as well as BSUs packing. The interpretation of 2D two-phonon spectra reveals a particular role of electrical anharmonicity in the spectra formation and attributes this effect to a high degree of the electron density delocalization in graphene domains. A size-stimulated transition from molecular to quasi-particle phonon consideration of Raman spectra was experimentally traced, which allowed evaluation of a free path of optical phonons in graphene crystal.
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Affiliation(s)
- Elena F. Sheka
- Institute of Physical Researches and Technologies, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198 Moscow, Russia;
- Correspondence:
| | - Yevgeny A. Golubev
- Yushkin’s Institute of Geology, Komi Science Center, Ural Branch of RAS, Pervomayskaya 54, 167982 Syktyvkar, Russia;
| | - Nadezhda A. Popova
- Institute of Physical Researches and Technologies, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198 Moscow, Russia;
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35
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Petrovic AG, Polavarapu PL, Łopusiński A, Krasowska D, Wieczorek W, Szyrej M, Błaszczyk J, Drabowicz J. Absolute Configuration and Conformation of (-)- R- t-Butylphenylphosphinoamidate: Chiroptical Spectroscopy and X-ray Analysis. J Org Chem 2020; 85:14456-14466. [PMID: 32786637 PMCID: PMC7684576 DOI: 10.1021/acs.joc.0c00756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
The
absolute configuration and conformations of (−)-tert-butylphenylphosphinoamidate were determined using three
different chiroptical spectroscopic methods, namely vibrational circular
dichroism (VCD), electronic circular dichroism (ECD), and optical
rotatory dispersion (ORD). In each of the spectroscopic methods used,
experimental data for the (−)-enantiomer of tert-butylphenylphosphinoamidate were measured in the solution phase.
Using the concentration-dependent experimental infrared spectra, the
existence of dimers in the solution was investigated, and the monomer–dimer
equilibrium constant was determined. Concomitant quantum mechanical
predictions of the VCD, ECD, and ORD for monomeric tert-butylphenylphosphinoamidate were carried out using density functional
theory (DFT) calculations using the B3LYP functional and the 6-31G(d),
6-311G(2d,2p) and aug-cc-pVDZ basis sets. Similar predictions for
dimeric tert-butylphenylphosphinoamidate were also
obtained using the B3LYP/6-31G(d) method. A comparison of theoretically
predicted data with the corresponding experimental data led to the
elucidation of the absolute configuration as (−)-(R)-tert-butylphenylphosphinoamidate with one predominant
conformation in the solution. This conclusion was independently supported
by X-ray analysis of the complex with (+)-R-2,2′-dihydroxy-1,1′-binaphthol
((+)-R- BINOL).
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Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prasad L Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Andrzej Łopusiński
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dorota Krasowska
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Wanda Wieczorek
- Institute of General and Ecological Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924 Łódź, Poland
| | - Małgorzata Szyrej
- Institute of Chemistry, Jan Długosz University in Częstochowa, Armii Krajowej 13/15, 42-200 Częstochowa, Poland
| | - Jarosław Błaszczyk
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Józef Drabowicz
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland.,Institute of Chemistry, Jan Długosz University in Częstochowa, Armii Krajowej 13/15, 42-200 Częstochowa, Poland
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36
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Merten C. Recent Advances in the Application of Vibrational Circular Dichroism Spectroscopy for the Characterization of Asymmetric Catalysts. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000876] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christian Merten
- Fakultät für Chemie und Biochemie Organische Chemie II Ruhr Universität Bochum Universitätsstraße 150 44801 Bochum Germany
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37
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Beć KB, Grabska J, Huck CW, Czarnecki MA. Effect of conformational isomerism on NIR spectra of ethanol isotopologues. Spectroscopic and anharmonic DFT study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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38
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Palivec V, Michal P, Kapitán J, Martinez‐Seara H, Bouř P. Raman Optical Activity of Glucose and Sorbose in Extended Wavenumber Range. Chemphyschem 2020; 21:1272-1279. [DOI: 10.1002/cphc.202000261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Pavel Michal
- Department of OpticsPalacký University Olomouc 17. listopadu 12, 77146 Olomouc Czech Republic
| | - Josef Kapitán
- Department of OpticsPalacký University Olomouc 17. listopadu 12, 77146 Olomouc Czech Republic
| | - Hector Martinez‐Seara
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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39
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Green JA, Improta R. Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study. Phys Chem Chem Phys 2020; 22:5509-5522. [PMID: 32104818 DOI: 10.1039/c9cp06373k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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40
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A never-ending story in the sky: The secrets of chemical evolution. Phys Life Rev 2020; 32:59-94. [DOI: 10.1016/j.plrev.2019.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 01/13/2023]
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41
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Nafie LA. Vibrational optical activity: From discovery and development to future challenges. Chirality 2020; 32:667-692. [DOI: 10.1002/chir.23191] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
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42
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Pižl M, Picchiotti A, Rebarz M, Lenngren N, Yingliang L, Záliš S, Kloz M, Vlček A. Time-Resolved Femtosecond Stimulated Raman Spectra and DFT Anharmonic Vibrational Analysis of an Electronically Excited Rhenium Photosensitizer. J Phys Chem A 2020; 124:1253-1265. [PMID: 31971382 DOI: 10.1021/acs.jpca.9b10840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved femtosecond stimulated Raman spectra (FSRS) of a prototypical organometallic photosensitizer/photocatalyst ReCl(CO)3(2,2'-bipyridine) were measured in a broad spectral range ∼40-2000 (4000) cm-1 at time delays from 40 fs to 4 ns after 400 nm excitation of the lowest allowed electronic transition. Theoretical ground- and excited-state Raman spectra were obtained by anharmonic vibrational analysis using second-order vibrational perturbation theory on vibrations calculated by harmonic approximation at density functional theory-optimized structures. A good match with anharmonically calculated vibrational frequencies allowed for assigning experimental Raman features to particular vibrations. Observed frequency shifts upon excitation (ν(ReCl) and ν(CC inter-ring) vibrations upward; ν(CC, CN) and ν(Re-C) downward) are consistent with the bonding/antibonding characters of the highest occupied molecular orbital and the lowest unoccupied molecular orbital involved in excitation and support the delocalized formulation of the lowest triplet state as ReCl(CO)3 → bpy charge transfer. FSRS spectra show a mode-specific temporal evolution, providing insights into the intersystem crossing (ISC) mechanism and subsequent relaxation. Most of the Raman features are present at ∼40 fs and exhibit small shifts and intensity changes with time. The 1450-1600 cm-1 group of bands due to CC, CN, and CC(inter-ring) stretching vibrations undergoes extensive restructuring between 40 and ∼150 fs, followed by frequency upshifts and a biexponential (0.38, 21 ps) area growth, indicating progressing charge separation in the course of the formation and relaxation of the lowest triplet state. Early (40-150 fs) restructuring was also observed in the low-frequency range for ν(Re-Cl) and δ(Re-C-O) vibrations that are presumably activated by ISC. FSRS experimental innovations employed to measure low- and high-energy Raman features simultaneously are described and discussed in detail.
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Affiliation(s)
- Martin Pižl
- J. Heyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejškova 3 , 182 23 Prague , Czech Republic.,Department of Inorganic Chemistry , University of Chemistry and Technology, Prague , Technická 5 , CZ-166 28 Prague , Czech Republic
| | - Alessandra Picchiotti
- ELI Beamlines, Institute of Physics , Czech Academy of Sciences , Na Slovance 1999/2 , 182 00 Prague , Czech Republic
| | - Mateusz Rebarz
- ELI Beamlines, Institute of Physics , Czech Academy of Sciences , Na Slovance 1999/2 , 182 00 Prague , Czech Republic
| | - Nils Lenngren
- ELI Beamlines, Institute of Physics , Czech Academy of Sciences , Na Slovance 1999/2 , 182 00 Prague , Czech Republic
| | - Liu Yingliang
- Institute of Biotechnology , Czech Academy of Sciences , Průmyslová 595 , 252 50 Vestec , Czech Republic
| | - Stanislav Záliš
- J. Heyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejškova 3 , 182 23 Prague , Czech Republic
| | - Miroslav Kloz
- ELI Beamlines, Institute of Physics , Czech Academy of Sciences , Na Slovance 1999/2 , 182 00 Prague , Czech Republic
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejškova 3 , 182 23 Prague , Czech Republic.,School of Biological and Chemical Sciences , Queen Mary University of London , Mile End Road , London E1 4NS , U.K
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43
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Paoloni L, Mazzeo G, Longhi G, Abbate S, Fusè M, Bloino J, Barone V. Toward Fully Unsupervised Anharmonic Computations Complementing Experiment for Robust and Reliable Assignment and Interpretation of IR and VCD Spectra from Mid-IR to NIR: The Case of 2,3-Butanediol and trans-1,2-Cyclohexanediol. J Phys Chem A 2020; 124:1011-1024. [PMID: 31922423 PMCID: PMC7993639 DOI: 10.1021/acs.jpca.9b11025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
The infrared (IR)
and vibrational circular dichroism (VCD) spectra
of 2,3-butanediol and trans-1,2-cyclohexanediol from
900 to 7500 cm–1 (including mid-IR, fundamental
CH and OH stretchings, and near-infrared regions) have been investigated
by a combined experimental and computational strategy. The computational
approach is rooted in density functional theory (DFT) computations
of harmonic and leading anharmonic mechanical, electrical, and magnetic
contributions, followed by a generalized second-order perturbative
(GVPT2) evaluation of frequencies and intensities for all the above
regions without introducing any ad hoc scaling factor. After proper
characterization of large-amplitude motions, all resonances plaguing
frequencies and intensities are taken into proper account. Comparison
of experimental and simulated spectra allows unbiased assignment and
interpretation of the most interesting features. The reliability of
the GVPT2 approach for OH stretching fundamentals and overtones is
confirmed by the remarkable agreement with a local mode model purposely
tailored for the latter two regions. Together with the specific interest
of the studied molecules, our results confirm that an unbiased assignment
and interpretation of vibrational spectra for flexible medium-size
molecules can be achieved by means of a nearly unsupervised reliable,
robust, and user-friendly DFT/GVPT2 model.
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Affiliation(s)
- Lorenzo Paoloni
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Viale Europa 11 , 25123 Brescia , Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Viale Europa 11 , 25123 Brescia , Italy.,Consiglio Nazionale delle Ricerche-I.N.O. , c/o CSMT via Branze, 45 , 25123 Brescia , Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Viale Europa 11 , 25123 Brescia , Italy.,Consiglio Nazionale delle Ricerche-I.N.O. , c/o CSMT via Branze, 45 , 25123 Brescia , Italy
| | - Marco Fusè
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Julien Bloino
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Vincenzo Barone
- Scuola Normale Superiore , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
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44
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Hope M, Šebestík J, Kapitán J, Bouř P. Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides. J Phys Chem A 2020; 124:674-683. [DOI: 10.1021/acs.jpca.9b10557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Hope
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Norwegian University of Science and Technology NO-7491 Trondheim, Norway
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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45
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Polavarapu PL, Santoro E. Vibrational optical activity for structural characterization of natural products. Nat Prod Rep 2020; 37:1661-1699. [DOI: 10.1039/d0np00025f] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.
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46
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Puzzarini C, Barone V. The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy. Phys Chem Chem Phys 2020; 22:6507-6523. [PMID: 32163090 DOI: 10.1039/d0cp00561d] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, I-56126, Italy
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Yao F, Gong N, Fang W, Men Z. Spectroscopic evidence of a particular intermolecular interaction in iodomethane–ethanol mixtures: the cooperative effect of halogen bonding, hydrogen bonding, and the solvent effect. Phys Chem Chem Phys 2020; 22:5702-5710. [DOI: 10.1039/c9cp05886a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The particular intermolecular interaction of an iodomethane–ethanol mixture is revealed by NIR, Raman, DFT calculation, and 2D correlation analysis.
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Affiliation(s)
- Fei Yao
- School of Science, Changchun University of Science and Technology
- Changchun
- China
| | - Nan Gong
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory
- College of Physics
- Jilin University
- Changchun 130012
- China
| | - Wenhui Fang
- School of Science, Changchun University of Science and Technology
- Changchun
- China
| | - Zhiwei Men
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory
- College of Physics
- Jilin University
- Changchun 130012
- China
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Mattiat J, Luber S. Vibrational (resonance) Raman optical activity with real time time dependent density functional theory. J Chem Phys 2019; 151:234110. [DOI: 10.1063/1.5132294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Johann Mattiat
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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Walter M, Moseler M. Ab Initio Wavelength-Dependent Raman Spectra: Placzek Approximation and Beyond. J Chem Theory Comput 2019; 16:576-586. [DOI: 10.1021/acs.jctc.9b00584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Michael Walter
- Fraunhofer IWM, MikroTribologie Centrum μTC, Wöhlerstrasse 11, D-79108 Freiburg, Germany
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Michael Moseler
- Fraunhofer IWM, MikroTribologie Centrum μTC, Wöhlerstrasse 11, D-79108 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
- Physikalisches Institut, Universität Freiburg, Herrmann-Herder-Straße 3, D-79104 Freiburg, Germany
- Freiburger Materialforschungszentrum, Universität Freiburg, Stefan-Meier-Straße 21, D-79104 Freiburg, Germany
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50
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Evaluation of Molecular Polarizability and of Intensity Carrying Modes Contributions in Circular Dichroism Spectroscopies. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9214691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We re-examine the theory of electronic and vibrational circular dichroism spectroscopy in terms of the formalism of frequency-dependent molecular polarizabilities. We show the link between Fermi’s gold rule in circular dichroism and the trace of the complex electric dipole–magnetic dipole polarizability. We introduce the C++ code polar to compute the molecular polarizability complex tensors from quantum chemistry outputs, thus simulating straightforwardly UV-visible absorption (UV-Vis)/electronic circular dichroism (ECD) spectra, and infrared (IR)/vibrational circular dichroism (VCD) spectra. We validate the theory and the code by referring to literature data of a large group of chiral molecules, showing the remarkable accuracy of density functional theory (DFT) methods. We anticipate the application of this methodology to the interpretation of vibrational spectra in various measurement conditions, even in presence of metal surfaces with plasmonic properties. Our theoretical developments aim, in the long run, at embedding the quantum-mechanical details of the chiroptical spectroscopic response of a molecule into the simulation of the electromagnetic field distribution at the surface of plasmonic devices. Such simulations are also instrumental to the interpretation of the experimental spectra measured from devices designed to enhance chiroptical interactions by the surface plasmon resonance of metal nanostructures.
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