1
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Borocci S, Grandinetti F, Sanna N, Zazza C. Noble Gas Anions: An Overview of Strategies and Bonding Motifs. Chem Asian J 2024:e202400191. [PMID: 38735841 DOI: 10.1002/asia.202400191] [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: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
This review article aims to provide an overview of the strategies employed to prepare noble gas anions under different environments and experimental conditions, and of the bonding motifs typically occurring in these species. Observed systems include anions fixed into synthesized salts, detected in the gas phase or in high-pressure devices. The major role of the theoretical calculations is also highlighted, not only in support of the experiments, but also as effective in predicting still unreported species. The chemistry of noble gas anions overall appears as a varied and rich paint, offering fascinating opportunities for both experimentalists and theoreticians.
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Affiliation(s)
- Stefano Borocci
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100, Viterbo, Italy
- Istituto per i Sistemi Biologici (ISB) del CNR, Sede di Roma -, Meccanismi di Reazione c/o Dipartimento di Chimica, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Felice Grandinetti
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100, Viterbo, Italy
- Istituto per i Sistemi Biologici (ISB) del CNR, Sede di Roma -, Meccanismi di Reazione c/o Dipartimento di Chimica, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Nico Sanna
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100, Viterbo, Italy
- Istituto per la Scienza e Tecnologia dei Plasmi (ISTP) del CNR, Via Amendola 122/D, 70126, Bari, Italy
| | - Costantino Zazza
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100, Viterbo, Italy
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2
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Adasme-Carreño F, Ochoa-Calle A, Galván M, Ireta J. Conformational preference of dipeptide zwitterions in aqueous solvents. Phys Chem Chem Phys 2024; 26:8210-8218. [PMID: 38384231 DOI: 10.1039/d3cp05742a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides (Leu-Leu, Leu-Phe, Phe-Leu, Ile-Leu, Phe-Phe, Ala-Val, Val-Ala, Ala-Ile, Ile-Ala, Ile-Val, Val-Ile and Val-Val) in the zwitterionic state. First, the accuracy of density functional theory (DFT), combined with different implicit solvent models, for describing zwitterions in aqueous solvent is assessed by comparing the predicted against the experimental glycine tautomerization energy, i.e., the energetic difference between canonical and zwitterionic glycine in aqueous solvents. It is found that among the tested solvation schemes, the charge-asymmetric nonlocally determined local-electric solvation model (CANDLE) predicts an energetic difference in excellent agreement with the experimental value. Next, DFT-CANDLE is used to determine the most favorable solvated conformation for each of the investigated dipeptide zwitterions. The CANDLE-solvated structures are obtained by exploring the conformational space of each dipeptide zwitterion concatenating DFT calculations, in vacuum, with classical molecular dynamics simulations, in explicit solvents, and DFT calculations including explicit water molecules. It is found that the energetically most favorable conformations are similar to those of the dipeptide zwitterions in their respective crystal structures. Such structural agreement is indicative of the DFT-CANDLE accomplishment of the description of solvated zwitterions, and suggests that these biomolecules self-assemble as quasi-rigid objects.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectorá de Investigación y Postgrado Universidad Católica del Maule, Talca 3480112, Chile.
- Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480112, Chile
| | - Alvaro Ochoa-Calle
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Marcelo Galván
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
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3
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Gómez S, Bottari C, Egidi F, Giovannini T, Rossi B, Cappelli C. Amide Spectral Fingerprints are Hydrogen Bonding-Mediated. J Phys Chem Lett 2022; 13:6200-6207. [PMID: 35770492 PMCID: PMC9272440 DOI: 10.1021/acs.jpclett.2c01277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.
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Affiliation(s)
- Sara Gómez
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Cettina Bottari
- Elettra
Sincrotrone Trieste S.C.p.A., S. S. 14 Km 163.5 in Area Science Park, I-34149, Trieste, Italy
| | - Franco Egidi
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Tommaso Giovannini
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Barbara Rossi
- Elettra
Sincrotrone Trieste S.C.p.A., S. S. 14 Km 163.5 in Area Science Park, I-34149, Trieste, Italy
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Chiara Cappelli
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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4
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Thomas DA, Taccone M, Ober K, Mucha E, Meijer G, von Helden G. Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects. J Phys Chem A 2021; 125:9279-9287. [PMID: 34652165 PMCID: PMC8558860 DOI: 10.1021/acs.jpca.1c05705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO4-···H+···-OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martín Taccone
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Katja Ober
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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5
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Laimer F, Zappa F, Scheier P, Gatchell M. Multiply Charged Helium Droplet Anions. Chemistry 2021; 27:7283-7287. [PMID: 33385183 PMCID: PMC8251920 DOI: 10.1002/chem.202005004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/19/2020] [Indexed: 01/20/2023]
Abstract
The detection of multiply charged helium droplet anions is reported for the first time. By ionizing droplets of superfluid helium with low energy electrons (up to 25 eV), it was possible to produce droplets containing up to five negative charges, which remain intact on the timescale of the experiment. The appearance sizes for different charge states are determined and are found to be orders of magnitude larger than for the equivalent cationic droplets, starting at 4 million He atoms for dianions. Droplets with He*− as charge carriers show signs of being metastable, but this effect is quenched by the pickup of water molecules.
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Affiliation(s)
- Felix Laimer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - Fabio Zappa
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria.,Departamento de Física-ICE, Universidade Federal de Juiz de Fora, Campus Universitário, 36036-900, Juiz de Fora, MG, Brazil
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - Michael Gatchell
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria.,Department of Physics, Stockholm University, 10691, Stockholm, Sweden
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6
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Phys Chem Chem Phys 2021; 22:20284-20294. [PMID: 32966425 DOI: 10.1039/d0cp03136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.
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Affiliation(s)
- Gildas Goldsztejn
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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7
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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8
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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9
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Thomas DA, Mucha E, Lettow M, Meijer G, Rossi M, von Helden G. Characterization of a trans-trans Carbonic Acid-Fluoride Complex by Infrared Action Spectroscopy in Helium Nanodroplets. J Am Chem Soc 2019; 141:5815-5823. [PMID: 30883095 PMCID: PMC6727381 DOI: 10.1021/jacs.8b13542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The high Lewis basicity
and small ionic radius of fluoride promote
the formation of strong ionic hydrogen bonds in the complexation of
fluoride with protic molecules. Herein, we report that carbonic acid,
a thermodynamically disfavored species that is challenging to investigate
experimentally, forms a complex with fluoride in the gas phase. Intriguingly,
this complex is highly stable and is observed in abundance upon nanoelectrospray
ionization of an aqueous sodium fluoride solution in the presence
of gas-phase carbon dioxide. We characterize the structure and properties
of the carbonic acid–fluoride complex, F–(H2CO3), and its deuterated isotopologue, F–(D2CO3), by helium nanodroplet
infrared action spectroscopy in the photon energy range of 390–2800
cm–1. The complex adopts a C2v symmetry structure with the carbonic acid
in a planar trans–trans conformation and both OH groups forming
ionic hydrogen bonds with the fluoride. Substantial vibrational anharmonic
effects are observed in the infrared spectra, most notably a strong
blue shift of the symmetric hydrogen stretching fundamental relative
to predictions from the harmonic approximation or vibrational second-order
perturbation theory. Ab initio thermostated ring-polymer molecular
dynamics simulations indicate that this blue shift originates from
strong coupling between the hydrogen stretching and bending vibrations,
resulting in an effective weakening of the OH···F– ionic hydrogen bonds.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
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10
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Habka S, Sohn WY, Vaquero-Vara V, Géléoc M, Tardivel B, Brenner V, Gloaguen E, Mons M. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins. Phys Chem Chem Phys 2018; 20:3411-3423. [DOI: 10.1039/c7cp07605c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.
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Affiliation(s)
- S. Habka
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - W. Y. Sohn
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | | | - M. Géléoc
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - B. Tardivel
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - V. Brenner
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - E. Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - M. Mons
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
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11
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Franke PR, Douberly GE. Rotamers of Isoprene: Infrared Spectroscopy in Helium Droplets and Ab Initio Thermochemistry. J Phys Chem A 2017; 122:148-158. [DOI: 10.1021/acs.jpca.7b10260] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter R. Franke
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, United States
| | - Gary E. Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, United States
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12
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Brice JT, Liang T, Raston PL, McCoy AB, Douberly GE. Infrared Stark and Zeeman spectroscopy of OH–CO: The entrance channel complex along the OH + CO → trans-HOCO reaction pathway. J Chem Phys 2016; 145:124310. [DOI: 10.1063/1.4963226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph T. Brice
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Tao Liang
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Paul L. Raston
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Anne B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Gary E. Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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13
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Fornaro T, Biczysko M, Bloino J, Barone V. Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases. Phys Chem Chem Phys 2016; 18:8479-90. [PMID: 26940362 PMCID: PMC5612391 DOI: 10.1039/c5cp07386c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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Gloaguen E, Tardivel B, Mons M. Gas phase double-resonance IR/UV spectroscopy of an alanine dipeptide analogue using a non-covalently bound UV-tag: observation of a folded peptide conformation in the Ac-Ala-NH2–toluene complex. Struct Chem 2015. [DOI: 10.1007/s11224-015-0690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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