1
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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; 45:1846-1869. [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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2
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Dong HC, Hsu PJ, Kuo JL. Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials. Phys Chem Chem Phys 2024; 26:11126-11139. [PMID: 38530660 DOI: 10.1039/d3cp05659g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.
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Affiliation(s)
- Hieu Cao Dong
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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3
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Thøgersen J, Chatterley AS, Weidner T, Jensen F. Peptide Bond of Aqueous Dipeptides Is Resilient to Deep Ultraviolet Irradiation. J Am Chem Soc 2023; 145:9777-9785. [PMID: 37075197 DOI: 10.1021/jacs.3c01469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
The susceptibility of aqueous dipeptides to photodissociation by deep ultraviolet irradiation is studied by femtosecond spectroscopy supported by density functional theory calculations. The primary photodynamics of the aqueous dipeptides of glycyl-glycine (gly-gly), alalyl-alanine (ala-ala), and glycyl-alanine (gly-ala) show that upon photoexcitation at a wavelength of 200 nm, about 10% of the excited dipeptides dissociate by decarboxylation within 100 ps, while the rest of the dipeptides return to their native ground state. Accordingly, the vast majority of the excited dipeptides withstand the deep ultraviolet excitation. In those relatively few cases, where excitation leads to dissociation, the measurements show that deep ultraviolet irradiation breaks the Cα-C bond rather than the peptide bond. The peptide bond is thereby left intact, and the decarboxylated dipeptide moiety is open to subsequent reactions. The experiments indicate that the low photodissociation yield and in particular the resilience of the peptide bond to dissociation are due to rapid internal conversion from the excited state to the ground state, followed by efficient vibrational relaxation facilitated by intramolecular coupling among the carbonate and amide modes. Thus, the entire process of internal conversion and vibrational relaxation to thermal equilibrium on the dipeptide ground state occurs on a time scale of less than 2 ps.
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Affiliation(s)
- Jan Thøgersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Adam S Chatterley
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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4
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Andersson Å, Yatsyna V, Linares M, Rijs A, Zhaunerchyk V. Indication of 3 10-Helix Structure in Gas-Phase Neutral Pentaalanine. J Phys Chem A 2023; 127:938-945. [PMID: 36669091 PMCID: PMC9900583 DOI: 10.1021/acs.jpca.2c07863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 310-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.
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Affiliation(s)
- Åke Andersson
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Vasyl Yatsyna
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden,FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Mathieu Linares
- Laboratory
of Organic Electronics and Group of Scientific Visualization Department
of Science and Technology (ITN), Linköping
University, 601 74 Norrköping, Sweden
| | - Anouk Rijs
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,Division
of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular
and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands,
| | - Vitali Zhaunerchyk
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden,
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5
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Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
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Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
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6
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Azougagh O, Essayeh S, Achalhi N, El Idrissi A, Amhamdi H, Loutou M, El Ouardi Y, Salhi A, Abou-Salama M, El Barkany S. New benzyltriethylammonium/urea deep eutectic solvent: Quantum calculation and application to hyrdoxylethylcellulose modification. Carbohydr Polym 2022; 276:118737. [PMID: 34823773 DOI: 10.1016/j.carbpol.2021.118737] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022]
Abstract
In this paper, a new deep eutectic solvent (DES) has been successfully synthesized that is based on benzyltriethylammonium bromide as a hydrogen bond acceptor (HBA) and urea as a hydrogen bond donor (HBD). However, its usability in modifying cellulose derivatives, especially acylating hydroxyethylcellulose (HEC) was investigated. The chemical modification (acetylation) of HEC was carried out in BTEAB/urea DES system without any additional conventional solvent or catalyst. However, the proposed structure of acetylated HEC (HECA) was confirmed according to the structural spectra analyses FTIR-ATR, 1H, 13C, and APT-NMR. The crystalline behavior of acetylated and unmodified HEC in the DES system has been evaluated using XRD patterns, where the thermal stability was evaluated basing on the TD-TGA thermograms. Hence, SEM images and EDX spectra were recorded to prove the changes that are expected at the morphological level and elemental profile. Yet, the nanometric sheets aspect was observed. The Functional Density Theory (DFT) was investigated as a useful computational tool to understand mechanism and donor-acceptor interactions. The topological parameters (electron density Laplacian, kinetic energy density, potential energy density, and energy density) at the bond critical points (BCP), between TBEAB and urea, are deducted according to Quantum Bader's theory, and Atoms-in-molecules (AIM). The non-covalent interactions and steric effect in the DES system were studied using the reduced density gradient isosurface (RDG). Theoretical and computational calculations revealed that the H-bonds and the electrostatic coexist, as predominant interactions in the BTEAB-based DES resulting chemical structure, and mechanism formation. The physical interactions between the component entities of DES lead to a new equilibrium that is more stable than that of HBA and HBD in their separate states.
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Affiliation(s)
- Omar Azougagh
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohamed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Soumya Essayeh
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohamed 1st University, P. B. 300, Nador 62700, Morocco
| | - Nafea Achalhi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohamed 1st University, 60000 Oujda, Morocco
| | - Abderrahmane El Idrissi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohamed 1st University, 60000 Oujda, Morocco
| | - Hassan Amhamdi
- Applied Chemistry Unit, Sciences and Technologies Faculty, Abdelmalek Essaadi University, 32 003 Al Hoceima, Morocco
| | - Mohamed Loutou
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohamed 1st University, P. B. 300, Nador 62700, Morocco
| | - Youssef El Ouardi
- LIMOME Laboratory, Dhar El Mehraz Faculty of Sciences, Sidi Mohamed Ben Abdellah University, B.P. 1796, Atlas, Fes 30000, Morocco; Laboratory of Separation Technology, Lappeenranta University of Technology, P.O. Box 20, FI-53851 Lappeenranta, Finland
| | - Amin Salhi
- Applied Chemistry Unit, Sciences and Technologies Faculty, Abdelmalek Essaadi University, 32 003 Al Hoceima, Morocco
| | - Mohamed Abou-Salama
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohamed 1st University, P. B. 300, Nador 62700, Morocco
| | - Soufian El Barkany
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohamed 1st University, P. B. 300, Nador 62700, Morocco.
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7
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Wang P, Shu C, Ye H, Biczysko M. Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data. J Phys Chem A 2021; 125:9826-9837. [PMID: 34752094 DOI: 10.1021/acs.jpca.1c06504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.
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Affiliation(s)
- Ping Wang
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chong Shu
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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8
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Zagorec-Marks W, Dodson LG, Weis P, Schneider EK, Kappes MM, Weber JM. Intrinsic Structure and Electronic Spectrum of Deprotonated Biliverdin: Cryogenic Ion Spectroscopy and Ion Mobility. J Am Chem Soc 2021; 143:17778-17785. [PMID: 34637616 DOI: 10.1021/jacs.1c08701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the structural and spectroscopic properties of singly deprotonated biliverdin anions in vacuo, using a combination of cryogenic ion spectroscopy, ion mobility spectrometry, and density functional theory. The ion mobility results show that at least two conformers are populated, with the dominant conformer at 75-90% relative abundance. The vibrational NH stretching signatures are sensitive to the tetrapyrrole structure, and they indicate that the tetrapyrrole system is in a helical conformation, consistent with simulated ion mobility collision cross sections. The vibrational spectrum in the fingerprint region of this singly deprotonated species shows that the two propionate groups share the remaining acidic proton. The S1 band of the electronic spectrum in vacuo is broad, despite ion trap temperatures of 20 K during ion preparation, with a congested Franck-Condon envelope showing partially resolved vibrational features. The vertical transition exhibits a small solvatochromic red shift (-320 cm-1) in aqueous solution.
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Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Leah G Dodson
- JILA and NIST, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Erik K Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
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9
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León I, Montero R, Longarte A, Fernández JA. Revisiting the Spectroscopy of Water Dimer in Jets. J Phys Chem Lett 2021; 12:1316-1320. [PMID: 33535759 PMCID: PMC9157493 DOI: 10.1021/acs.jpclett.0c03001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Laser spectroscopy in jets is one of the main sources of structural data from molecular aggregates. Consequently, numerous and sophisticated experimental systems have been developed to extract precise information, which is usually interpreted in the light of quantum mechanical calculations. However, even with the most sophisticated experiments, it is sometimes difficult to interpret the experimental results. We present here the example of water dimer and how after almost 70 years, the assignment of its mass-resolved IR spectrum still generates controversy that extends toward the mechanism of ionization of water aggregates.
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Affiliation(s)
- Iker León
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Unidad Asociada CSIC, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Raúl Montero
- SGIKER
Laser Facility, University of the Basque
Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Asier Longarte
- Department
of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - José A. Fernández
- Department
of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
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10
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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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11
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Kumar S, Mishra KK, Singh SK, Borish K, Dey S, Sarkar B, Das A. Observation of a weak intra-residue C5 hydrogen-bond in a dipeptide containing Gly-Pro sequence. J Chem Phys 2019; 151:104309. [DOI: 10.1063/1.5115040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kamal K. Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Santosh K. Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Biplab Sarkar
- Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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12
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Competition between folded and extended structures of alanylalanine (Ala-Ala) in a molecular beam. Phys Chem Chem Phys 2019; 21:14126-14132. [DOI: 10.1039/c9cp00140a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural analysis of the neutral dipeptide Ala-Ala by action spectroscopy using IRMPD-VUV spectroscopy reveals predominance of extended structure.
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Affiliation(s)
- Vasyl Yatsyna
- University of Gothenburg
- Department of Physics
- Sweden
- Radboud University
- Institute for Molecules and Materials
| | - Ranim Mallat
- University of Gothenburg
- Department of Physics
- Sweden
| | - Tim Gorn
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | - Michael Schmitt
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | | | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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