1
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Zou M, Hassan Y, Roy TK, McCoy AB, Lester MI. Infrared spectroscopy of the syn-methyl-substituted Criegee intermediate: A combined experimental and theoretical study. J Chem Phys 2024; 160:204309. [PMID: 38818894 DOI: 10.1063/5.0210122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
An IR-vacuum ultraviolet (VUV) ion-dip spectroscopy method is utilized to examine the IR spectrum of acetaldehyde oxide (CH3CHOO) in the overtone CH stretch (2νCH) spectral region. IR activation creates a depletion of the ground state population that reduces the VUV photoionization signal on the parent mass channel. IR activation of the more stable and populated syn-CH3CHOO conformer results in rapid unimolecular decay to OH + vinoxy products and makes the most significant contribution to the observed spectrum. The resultant IR-VUV ion-dip spectrum of CH3CHOO is similar to that obtained previously for syn-CH3CHOO using IR action spectroscopy with UV laser-induced fluorescence detection of OH products. The prominent IR features at 5984 and 6081 cm-1 are also observed using UV + VUV photoionization of OH products. Complementary theoretical calculations utilizing a general implementation of second-order vibrational perturbation theory provide new insights on the vibrational transitions that give rise to the experimental spectrum in the overtone CH stretch region. The introduction of physically motivated small shifts of the harmonic frequencies yields remarkably improved agreement between experiment and theory in the overtone CH stretch region. The prominent features are assigned as highly mixed states with contributions from two quanta of CH stretch and/or a combination of CH stretch with an overtone in mode 4. The generality of this approach is demonstrated by applying it to three different levels of electronic structure theory/basis sets, all of which provide spectra that are virtually indistinguishable despite showing large deviations prior to introducing the shifts to the harmonic frequencies.
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Affiliation(s)
- Meijun Zou
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Yarra Hassan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Tarun Kumar Roy
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Marsha I Lester
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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2
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Rahimi R, Saban N, Bar I. Conformational Mapping, Interactions, and Fluorine Impact by Combined Spectroscopic Approaches and Quantum Chemical Calculations. J Phys Chem Lett 2024; 15:3658-3667. [PMID: 38534060 DOI: 10.1021/acs.jpclett.4c00301] [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
Noncovalent interactions and their careful variation can be crucial in understanding molecular structures, conformational topographies, and properties. Here, we examine the fluorination impact on the structure and conformational behavior of 2-(2-fluorophenyl)ethyl alcohol (2-FPEAL) by monitoring the first individual ionization-loss-stimulated Raman spectra of the jet-cooled molecule. The comparison of two different broad-range spectra and predicted equivalents discloses two distinct structures. One possesses a folded side chain (gauche) and the other an extended chain (anti) with the terminal hydrogen atom pointing opposite or toward the fluorine side, indicating the improper previous tentative assignment of the latter. These conformers resemble and differ from the nonfluorinated analogue structures. Theoretical analyses reveal interconversion pathways of 2-FPEAL conformers during expansion and the delicate balance between attractive (C-H···F and O-H···π) and repulsive interactions. These findings show the achievements of our integrated approach, suggesting its potential for overcoming future structural challenges.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Noga Saban
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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3
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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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4
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Otaki H, Ishiuchi SI, Fujii M, Sugita Y, Yagi K. Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Phys Chem Chem Phys 2024; 26:9906-9914. [PMID: 38477212 DOI: 10.1039/d4cp00064a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Vibrational spectroscopy combined with theoretical calculations is a powerful tool for analyzing the interaction and conformation of peptides at the atomistic level. Nonetheless, identifying the structure becomes increasingly difficult as the peptide size grows large. One example is acetyl-SIVSF-N-methylamide, a capped pentapeptide, whose atomistic structure has remained unknown since its first observation [T. Sekiguchi, M. Tamura, H. Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, S. Ishiuchi and M. Fujii, Angew. Chem., Int. Ed., 2018, 57, 5626-5629]. Here, we propose a novel conformational search method, which exploits the structure-spectrum correlation using a similarity score that measures the agreement of theoretical and experimental spectra. Surprisingly, the two conformers have distinctly different energy and geometry. The second conformer is 25 kJ mol-1 higher in energy than the other, lowest-energy conformer. The result implies that there are multiple pathways in the early stage of the folding process: one to the global minimum and the other to a different basin. Once such a structure is established, the second conformer is unlikely to overcome the barrier to produce the most stable structure due to a vastly different hydrogen bond network of the backbone. Our proposed method can characterize the lowest-energy conformer and kinetically trapped, high-energy conformers of complex biomolecules.
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Affiliation(s)
- Hiroki Otaki
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo, Nagasaki, Nagasaki 852-8521, Japan
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Fujii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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5
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Sedmidubská B, Kočišek J. Interaction of low-energy electrons with radiosensitizers. Phys Chem Chem Phys 2024; 26:9112-9136. [PMID: 38376461 DOI: 10.1039/d3cp06003a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.
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Affiliation(s)
- Barbora Sedmidubská
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 182223 Prague, Czech Republic.
- Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Břehová 7, 11519 Prague, Czech Republic
- Institut de Chimie Physique, UMR 8000 CNRS and Faculté des sciences d'Orsay, Université Paris Saclay, F-91405 Orsay Cedex, France
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 182223 Prague, Czech Republic.
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6
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Liu D, Robin S, Gloaguen E, Brenner V, Mons M, Aitken DJ. Effects of sulfoxide and sulfone sidechain-backbone hydrogen bonding on local conformations in peptide models. Chem Commun (Camb) 2024; 60:2074-2077. [PMID: 38293794 DOI: 10.1039/d3cc05933b] [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: 02/01/2024]
Abstract
We examine peptide model systems designed to probe short-range N-H⋯OS sidechain-backbone hydrogen bonding involving amino acid residues with sidechain sulfoxide or sulfone functional groups and its effects on local conformations. A strong 7-membered ring hydrogen bond of this type accompanies an intra-residue N-H⋯OC interaction and stabilizes an extended backbone conformation in preference to classical folded structures.
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Affiliation(s)
- Dayi Liu
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.
| | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.
- Université Paris Cité, Faculté de Pharmacie, Paris 75006, France
| | - Eric Gloaguen
- Université Paris-Saclay, CNRS, ISMO, Orsay 91400, France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, DRF, Gif-sur-Yvette 91191, France
| | - Michel Mons
- Université Paris-Saclay, CEA, LIDYL, Gif-sur-Yvette 91191, France.
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.
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7
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Chen D, Gao J, Zheng D, Guo Z, Zhao Z. Gas Phase Conformation of Trisaccharides and Core Pentasaccharide: A Three-Step Tree-Based Sampling and Quantum Mechanical Computational Approach. Molecules 2023; 28:8093. [PMID: 38138582 PMCID: PMC10745714 DOI: 10.3390/molecules28248093] [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: 11/03/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
As an important component of N-linked glycoproteins, the core pentasaccharide is highly crucial to the potential application prospect of glycoprotein. However, the gas phase conformation study is a challenging one due to the size and complexity of the molecule, together with the necessity to rely on quantum chemistry modeling for relevant energetics and structures. In this paper, the structures of the trisaccharides and core pentasaccharides in N-linked glycans in the gas phase were constructed by a three-step tree-based (TSTB) sampling. Since single point energies of all the conformers are calculated at the temperature of zero, it is necessary to evaluate the stability at a high temperature. We calculate the Gibbs free energies using the standard thermochemistry model (T = 298.15 K). For trimannose, the energetic ordering at 298.15 K can be strongly changed compared to 0 K. Moreover, two structures of trimannose with high energies at 0 K are considered to provide a much better match of IR vibration signatures with the low Gibbs free energies. On this basis, the core pentasaccharide was constructed in three ways. The building configurations of core pentasaccharide were optimized to obtain reasonable low-energy stable conformers. Fortunately, the lowest-energy structure of core pentasaccharide is eventually the minimum at 0 K and 298.15 K. Furthermore, spectrum analysis of core pentasaccharide was carried out. Although poorly resolved, its contour from the experiment was in qualitative correspondence with the computed IR spectrum associated with its minimum free energy structure. A large number of strongly and weakly hydrogen-bonded hydroxyl and acetylamino groups contribute to a highly congested set of overlapping bands. Compared with traditional conformation generators, the TSTB sampling is employed to efficiently and comprehensively obtain preferred conformers of larger saccharides with lower energy.
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Affiliation(s)
- Dong Chen
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Jianming Gao
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Danting Zheng
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Zhiheng Guo
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Zuncheng Zhao
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
- Henan Province Engineering Research Center of Metal Matrix in situ Composites Based on Aluminum, Magnesium or Copper, Henan University, Kaifeng 475004, China
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8
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Lascu A, Vlascici D, Birdeanu M, Epuran C, Fratilescu I, Fagadar-Cosma E. The Influence of the Nature of the Polymer Incorporating the Same A 3B Multifunctional Porphyrin on the Optical or Electrical Capacity to Recognize Procaine. Int J Mol Sci 2023; 24:17265. [PMID: 38139093 PMCID: PMC10743720 DOI: 10.3390/ijms242417265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The multifunctionality of an A3B mixed-substituted porphyrin, namely 5-(4-carboxyphenyl)-10,15,20-tris(4-methylphenyl)porphyrin (5-COOH-3MPP), was proven due to its capacity to detect procaine by different methods, depending on the polymer matrix in which it is incorporated. The hybrid nanomaterial containing k-carrageenan and AuNPs (5-COOH-3MPP-k-carrageenan-AuNPs) was able to optically detect procaine in the concentration range from 5.76 × 10-6 M to 2.75 × 10-7 M, with a limit of detection (LOD) of 1.33 × 10-7 M. This method for the detection of procaine gave complementary results to the potentiometric one, which uses 5-COOH-3MPP as an electroactive material incorporated in a polyvinylchloride (PVC) membrane plasticized with o-NPOE. The detected concentration range by this ion-selective membrane electrode is wider (enlarged in the field of higher concentrations from 10-2 to 10-6 M), linearly dependent with a 53.88 mV/decade slope, possesses a detection limit of 7 × 10-7 M, a response time of 60 s, and has a certified stability for a working period of six weeks.
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Affiliation(s)
- Anca Lascu
- Institute of Chemistry “Coriolan Dragulescu”, Mihai Viteazu Ave. 24, 300223 Timisoara, Romania; (A.L.); (C.E.); (I.F.)
| | - Dana Vlascici
- Faculty of Chemistry, Biology, Geography, West University of Timisoara, 4 Vasile Parvan Ave., 300223 Timisoara, Romania;
| | - Mihaela Birdeanu
- National Institute for Research and Development in Electrochemistry and Condensed Matter, Plautius Andronescu Street 1, 300224 Timisoara, Romania;
| | - Camelia Epuran
- Institute of Chemistry “Coriolan Dragulescu”, Mihai Viteazu Ave. 24, 300223 Timisoara, Romania; (A.L.); (C.E.); (I.F.)
| | - Ion Fratilescu
- Institute of Chemistry “Coriolan Dragulescu”, Mihai Viteazu Ave. 24, 300223 Timisoara, Romania; (A.L.); (C.E.); (I.F.)
| | - Eugenia Fagadar-Cosma
- Institute of Chemistry “Coriolan Dragulescu”, Mihai Viteazu Ave. 24, 300223 Timisoara, Romania; (A.L.); (C.E.); (I.F.)
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9
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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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10
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Hua Y, Strauss M, Fisher S, Mauser MFX, Manchet P, Smacchia M, Geyer P, Shayeghi A, Pfeffer M, Eggenweiler TH, Daly S, Commandeur J, Mayor M, Arndt M, Šolomek T, Köhler V. Giving the Green Light to Photochemical Uncaging of Large Biomolecules in High Vacuum. JACS AU 2023; 3:2790-2799. [PMID: 37885583 PMCID: PMC10598566 DOI: 10.1021/jacsau.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
The isolation of biomolecules in a high vacuum enables experiments on fragile species in the absence of a perturbing environment. Since many molecular properties are influenced by local electric fields, here we seek to gain control over the number of charges on a biopolymer by photochemical uncaging. We present the design, modeling, and synthesis of photoactive molecular tags, their labeling to peptides and proteins as well as their photochemical validation in solution and in the gas phase. The tailored tags can be selectively cleaved off at a well-defined time and without the need for any external charge-transferring agents. The energy of a single or two green photons can already trigger the process, and it is soft enough to ensure the integrity of the released biomolecular cargo. We exploit differences in the cleavage pathways in solution and in vacuum and observe a surprising robustness in upscaling the approach from a model system to genuine proteins. The interaction wavelength of 532 nm is compatible with various biomolecular entities, such as oligonucleotides or oligosaccharides.
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Affiliation(s)
- Yong Hua
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Marcel Strauss
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Sergey Fisher
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Martin F. X. Mauser
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Pierre Manchet
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Martina Smacchia
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Geyer
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Tim Henri Eggenweiler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Steven Daly
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Jan Commandeur
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Marcel Mayor
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
- Institute
for Nanotechnology (INT), Karlsruhe Institute
of Technology (KIT), P.O. Box 3640, DE-76021 Karlsruhe Eggenstein-Leopoldshafen, Germany
- Lehn Institute
of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510274, P. R. China
| | - Markus Arndt
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Tomáš Šolomek
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Valentin Köhler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
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11
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Chahkandi B, Chahkandi M. An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide. BMC Chem 2023; 17:138. [PMID: 37828563 PMCID: PMC10571400 DOI: 10.1186/s13065-023-01051-9] [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: 06/26/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD-γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD-γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.
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Affiliation(s)
- Behzad Chahkandi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
| | - Mohammad Chahkandi
- Department of Chemistry, Hakim Sabzevari University, Sabzevar, 96179-76487, Iran
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12
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Roy TK, Liu T, Qian Y, Sojdak CA, Kozlowski MC, Lester MI. A five-carbon unsaturated Criegee intermediate: synthesis, spectroscopic identification, and theoretical study of 3-penten-2-one oxide. Chem Sci 2023; 14:10471-10477. [PMID: 37800006 PMCID: PMC10548502 DOI: 10.1039/d3sc03993e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/03/2023] [Indexed: 10/07/2023] Open
Abstract
Biogenic alkenes, such as isoprene and α-pinene, are the predominant source of volatile organic compounds (VOCs) emitted into the atmosphere. Atmospheric processing of alkenes via reaction with ozone leads to formation of zwitterionic reactive intermediates with a carbonyl oxide functional group, known as Criegee intermediates (CIs). CIs are known to exhibit a strong absorption (π* ← π) in the near ultraviolet and visible (UV-vis) region due to the carbonyl oxide moiety. This study focuses on the laboratory identification of a five-carbon CI with an unsaturated substituent, 3-penten-2-one oxide, which can be produced upon atmospheric ozonolysis of substituted isoprenes. 3-Penten-2-one oxide is generated in the laboratory by photolysis of a newly synthesized precursor, (Z)-2,4-diiodopent-2-ene, in the presence of oxygen. The electronic spectrum of 3-penten-2-one oxide was recorded by UV-vis induced depletion of the VUV photoionization signal on the parent m/z 100 mass channel using a time-of-flight mass spectrometer. The resultant electronic spectrum is broad and unstructured with peak absorption at ca. 375 nm. To complement the experimental findings, electronic structure calculations are performed at the CASPT2(12,10)/aug-cc-pVDZ level of theory. The experimental spectrum shows good agreement with the calculated electronic spectrum and vertical excitation energy obtained for the lowest energy conformer of 3-penten-2-one oxide. In addition, OH radical products resulting from unimolecular decay of energized 3-penten-2-oxide CIs are detected by UV laser-induced fluorescence. Finally, the experimental electronic spectrum is compared with that of a four-carbon, isoprene-derived CI, methyl vinyl ketone oxide, to understand the effects of an additional methyl group on the associated electronic properties.
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Affiliation(s)
- Tarun Kumar Roy
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Tianlin Liu
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Yujie Qian
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Christopher A Sojdak
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Marisa C Kozlowski
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Marsha I Lester
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
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13
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Takayanagi H, Bardaud JX, Hirata K, Brenner V, Gloaguen E, Ishiuchi SI, Fujii M. Stepwise hydration of [CH 3COOMg] + studied by cold ion trap infrared spectroscopy: insights into interactions in the magnesium channel selection filters. Phys Chem Chem Phys 2023; 25:23923-23928. [PMID: 37642502 DOI: 10.1039/d3cp00992k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The magnesium channel controls Mg2+ concentration in the cell and plays an indispensable role in biological functions. The crystal structure of the Magnesium Transport E channel suggested that Mg2+ hydrated by 6 water molecules is transported through a selection filter consisting of COO- groups on two Asp residues. This Mg2+ motion implies successive pairing with -OOC-R and dissociation mediated by water molecules. For another divalent ion, however, it is known that RCOO-⋯Ca2+ cannot be separated even with 12 water molecules. From this discrepancy, we probe the structure of Mg2+(CH3COO-)(H2O)4-17 clusters by measuring the infrared spectra and monitoring the vibrational frequencies of COO- with the help of quantum chemistry calculations. The hydration by (H2O)6 is not enough to induce ion separation, and partially-separated or separated pairs are formed from 10 water molecules at least. These results suggest that the ion separation between Mg2+ and carboxylate ions in the selection-filter of the MgtE channel not only results from water molecules in their first hydration shell, but also from additional factors including water molecules and protein groups in the second solvation shell of Mg2+.
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Affiliation(s)
- Hikaru Takayanagi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Jean-Xavier Bardaud
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, Gif-sur-Yvette 91191, France.
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, Gif-sur-Yvette 91191, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, Gif-sur-Yvette 91191, France.
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
- IRFI/IPWR, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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14
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Rahimi R, Saban N, Bar I. Synergistic Spectroscopic and Computational Characterization Evidencing the Preservation or Flipping of the Hydroxyl Group of 2-Phenylethyl Alcohol upon Single and Double Hydration. J Am Chem Soc 2023; 145:18455-18467. [PMID: 37561882 DOI: 10.1021/jacs.3c04762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Even apparently simple, obtaining and analyzing observations on molecules and clusters and unambiguously assigning their structures is challenging. We report here the first ionization-loss Raman spectra compared to quantum chemical predictions for establishing the structural preferences of hydrates of the neurotransmitters hydroxy analogue, 2-phenylethyl alcohol (PEAL). The spectra encode two monohydrates and two previously unnoticed dihydrates, consequences of water insertion and sidewise attachment to the O-H group of gauche PEALs, in PEAL-H2O and PEAL-(H2O)2, or the higher-energy gauche-trans PEAL in the latter. The electronic structures retain the stable PEAL or flip its O-H to convert the gauche-trans PEAL conformer to the global minimum-energy dihydrate. We disclose conventional and bifurcated hydrogen bonds and electron steric repulsions by noncovalent interaction analysis and correlations between the experimental O-H stretching vibrational frequencies and the O-H and H···X bond lengths and electron densities, pointing to implications on hydrate forms and our approach virtue.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Noga Saban
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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15
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Sahu N, Khire SS, Gadre SR. Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins. J Chem Phys 2023; 159:044309. [PMID: 37522406 DOI: 10.1063/5.0149572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.
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Affiliation(s)
- Nityananda Sahu
- Theoretische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Subodh S Khire
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Shridhar R Gadre
- Departments of Scientific Computing, Modelling & Simulation and Chemistry, Savitribai Phule Pune University, Pune 411007, India
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16
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Banaś K, Lenartowicz P, Staś M, Dziuk B, Siodłak D. Insight into the Structure of Victorin, the Host-Selective Toxin from the Oat Pathogen Cochliobolus victoriae. Studies of the Unique Dehydroamino Acid β-Chlorodehydroalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37486973 PMCID: PMC10401702 DOI: 10.1021/acs.jafc.3c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Victorins, a family of peptide toxins, produced by the fungal pathogen Cochliobolus victoriae and responsible for disease of some oat varieties, contain a β-chlorodehydroalanine residue, ΔAla(βCl). To determine the conformational properties of this unique dehydroamino acid, a series of model compounds was studied using X-ray, NMR, and FT-IR methods, supported by theoretical calculations. The ΔAla(βCl) geometrical isomers differ in conformational profile. The isomer Z prefers the helical conformation α (φ, ψ = -61°, -24°), PPII type conformation β (φ, ψ = -47°, 136°), and semiextended conformation β2 (φ, ψ = -116°, 9°) in weakly and more polar solutions. The isomer E prefers mainly the extended conformation C5 (φ, ψ = -177°, 160°), but with an increase of the environment polarity also conformations β (φ, ψ = -44°, 132°) and α (φ, ψ = -53°, -39°). In the most stable conformations the N-H···Cl hydrogen bond (5γ) occurs, created between the chlorine atom of the side chain and the N-H donor of the flanking amide group. The method of synthesis of the β-chlorodehydroalanine residue is proposed, by chlorination of dehydroalanine and then the photoisomerization from the isomer Z to E. The presented results indicate that the assignment of the geometrical isomer of the ΔAla(βCl) residue in naturally occurring victorins still remains an open question, despite being crucial for biological activity.
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Affiliation(s)
- Karolina Banaś
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Paweł Lenartowicz
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Monika Staś
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Błażej Dziuk
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
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17
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Liu D, Bardaud JX, Imani Z, Robin S, Gloaguen E, Brenner V, Aitken DJ, Mons M. Length-Dependent Transition from Extended to Folded Shapes in Short Oligomers of an Azetidine-Based α-Amino Acid: The Critical Role of NH···N H-Bonds. Molecules 2023; 28:5048. [PMID: 37446709 DOI: 10.3390/molecules28135048] [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: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.05-helix, formed by successive C5 H-bonds, is an elusive secondary structure. Using a combination of theoretical chemistry and spectroscopic studies in both the gas phase and solution phase, we have demonstrated that derivatives of 3-amino-1-methylazetidine-3-carboxylic acid, Aatc(Me) can form sidechain-backbone N-H···N C6γ H-bonds that accompany-and thereby stabilize-C5 H-bonds. In the capped trimer of Aatc(Me), extended C5/C6γ motifs are sufficiently robust to challenge classical 310-helix formation in solution and the fully-extended 2.05-helix conformer has been characterized in the gas phase. Concurrent H-bonding support for successive C5 motifs is a new axiom for stabilizing the extended backbone secondary structure in short peptides.
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Affiliation(s)
- Dayi Liu
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | | | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
- Université Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
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18
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Tanabe S, Hirata K, Tsukiyama K, Lisy JM, Ishiuchi SI, Fujii M. Can Ag + Permeate through a Potassium Ion Channel? A Bottom-Up Approach by Infrared Spectroscopy of the Ag + Complex with the Partial Peptide of a Selectivity Filter. J Phys Chem Lett 2023; 14:2886-2890. [PMID: 36924459 PMCID: PMC10041629 DOI: 10.1021/acs.jpclett.2c03366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Silver and silver ions have a long history of antimicrobial activity and medical applications. Nevertheless, the activity of Ag+ against bacteria, how it enters a cell, has not yet been established. The K+ channel, a membrane protein, is a possible route. The addition of a channel inhibitor (4-aminopyridine) to modulate the Ag+ uptake could support this view. However, the inhibitor enhances the uptake of Ag+, the opposite result. We have applied cold ion trap infrared laser spectroscopy to complexes of Ag+ and Ac-Tyr-NHMe (a model for GYG) which is a portion of the selectivity filter in the K+ channel to consider the question of permeation. With support from quantum chemical calculations, we have determined the stable conformations of the complex. The conformations strongly suggest that Ag+ would not readily permeate the K+ channel. The mechanism of the unexpected enhancement by the inhibitor is discussed.
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Affiliation(s)
- Satoru Tanabe
- Department
of Chemistry, School of Science, Tokyo University
of Science, 1-3 Kagurazaka,
Shinjuku-ku, Tokyo 162-8601, Japan
- Laboratory
for Chemistry and Life Science, Institute of innovative research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Keisuke Hirata
- Laboratory
for Chemistry and Life Science, Institute of innovative research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Department
of Chemistry, School of Science, Tokyo Institute
of Technology, 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- International
Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Koichi Tsukiyama
- Department
of Chemistry, School of Science, Tokyo University
of Science, 1-3 Kagurazaka,
Shinjuku-ku, Tokyo 162-8601, Japan
| | - James M. Lisy
- International
Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Shun-ichi Ishiuchi
- Laboratory
for Chemistry and Life Science, Institute of innovative research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Department
of Chemistry, School of Science, Tokyo Institute
of Technology, 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- International
Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Institute of innovative research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- International
Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- School of
Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho,
Midori-ku, Yokohama 226-8503, Japan
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19
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Imani Z, Mundlapati VR, Brenner V, Gloaguen E, Le Barbu-Debus K, Zehnacker-Rentien A, Robin S, Aitken DJ, Mons M. Non-covalent interactions reveal the protein chain δ conformation in a flexible single-residue model. Chem Commun (Camb) 2023; 59:1161-1164. [PMID: 36625351 DOI: 10.1039/d2cc06658k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The δ conformation is a local secondary structure in proteins that implicates a πamide N-H⋯N interaction between a backbone N atom and the NH of the following residue. Small-molecule models thereof have been limited so far to rigid proline-type compounds. We show here that in derivatives of a cyclic amino acid with a sulphur atom in the γ-position, specific side-chain/backbone N-H⋯S interactions stabilize the δ conformation sufficiently to allow it to compete with classical C5 and C7 H-bonded conformers.
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Affiliation(s)
- Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France
| | | | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette 91191, France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette 91191, France
| | | | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France.,Université de Paris, Faculté de Pharmacie, Paris 75006, France
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, Orsay 91400, France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette 91191, France
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20
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Villard J, Kılıç M, Rothlisberger U. Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures. J Chem Theory Comput 2023; 19:1080-1097. [PMID: 36692853 PMCID: PMC9933449 DOI: 10.1021/acs.jctc.2c01078] [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: 01/25/2023]
Abstract
Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide (Masson, A.; J. Am. Soc. Mass Spectrom.2015, 26, 1444-1454) and (ii) the doubly protonated cyclic decapeptide gramicidin S (Nagornova, N. S.; J. Am. Chem. Soc.2010, 132, 4040-4041). We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤10 kcal/mol (i), ≤5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra.
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21
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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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22
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Liu Y, Liu CP, Mang CY, Wu KC. Upon DFT-D3 dispersion correction and ECD spectral confirmation, only several conformers can stably coexist for three fungal cycloaspeptides (A, D, G). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121710. [PMID: 35952587 DOI: 10.1016/j.saa.2022.121710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Dispersion correction in theoretical determination of cyclopeptide conformations is emphasized. Whether in gas approximation or in solvation simulation, the density functional theory with London dispersion correction (DFT-D3) demonstrates that only 2-3 conformers can stably coexist for cycloaspeptides (A, D, G) at B3LYP-D3 and CAM-B3LYP-D3. Conformational rationality is confirmed by electronic circular dichroism (ECD). Whether for Cotton effect or for excitation energy, TD-B3LYP-D3 has better performances than TD-CAM-B3LYP-D3 because the former can better reproduce the experiment. A molecular orbital analysis is used to interpret ECD, where two energy bands observed in experiment originates from the ππ* transitions other than the σπ* transitions. Long-range correction and solvent effect make H-bonds shorten, and dispersion correction makes them further shorten.
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Affiliation(s)
- Yong Liu
- College of Pharmacy, Dali University, Dali 671000, China
| | - Cai-Ping Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Chao-Yong Mang
- College of Pharmacy, Dali University, Dali 671000, China.
| | - Ke-Chen Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
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23
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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
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Kalvoda T, Culka M, Rulíšek L, Andris E. Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method. J Phys Chem B 2022; 126:5949-5958. [PMID: 35930560 DOI: 10.1021/acs.jpcb.2c02861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in trans configuration and the corresponding 484 (222) dipeptides. To mimic the environment in a protein chain, the N- and C-termini of the studied systems were capped with acetyl and N-methylamide groups, respectively. We systematically varied the main chain dihedral angles (ϕ, ψ) by 40° steps and all side chain angles by 90° or 120° steps. We optimized the molecular geometries with the GFN2-xTB semiempirical (SQM) method and performed single point density functional theory calculations at the BP86-D3/DGauss-DZVP//COSMO-RS level in water, 1-octanol, N,N-dimethylformamide, and n-hexane. For each restrained (nonequilibrium) structure, we also calculated energy gradients (in water) and natural atomic charges. The exhaustive and unprecedented QM-based sampling enabled us to construct Ramachandran plots of quantum mechanical (QM(BP86-D3)//COSMO-RS) energies calculated on SQM structures, for all 506 (484 dipeptides and 22 amino acids) studied systems. We showed how the character of an amino acid side chain influences the conformational space of single amino acids and dipeptides. With clustering techniques, we were able to identify unique minima of amino acids and dipeptides (i.e., minima on the GFN2-xTB potential energy surfaces) and analyze the distribution of their BP86-D3//COSMO-RS conformational energies in all four solvents. We also derived an empirical formula for the number of unique minima based on the overall number of rotatable bonds within each peptide. The final peptide conformer data set (PeptideCs) comprises over 400 million structures, all of them annotated with QM(BP86-D3)//COSMO-RS energies. Thanks to its completeness and unbiased nature, the PeptideCs can serve, inter alia, as a data set for the validation of new methods for predicting the energy landscapes of protein structures. This data set may also prove to be useful in the development and reparameterization of biomolecular force fields. The data set is deposited at Figshare (10.25452/figshare.plus.19607172) and can be accessed using a simple web interface at http://peptidecs.uochb.cas.cz.
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Affiliation(s)
- Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
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25
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Dupont J, Guillot R, Lepère V, Zehnacker A. Jet-cooled laser spectroscopy and solid-state vibrational circular dichroism of the cyclo-(Tyr-Phe) diketopiperazine dipeptide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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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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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M. Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry. Molecules 2022; 27:molecules27103163. [PMID: 35630640 PMCID: PMC9144663 DOI: 10.3390/molecules27103163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm−1 spectral shift of the NH stretch engaged in a 7δ NH⋯S/Se bond.
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28
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D'mello VC, Goldsztejn G, Rao Mundlapati V, Brenner V, Gloaguen E, Charnay‐Pouget F, Aitken DJ, Mons M. Characterization of Asx Turn Types and Their Connate Relationship with β‐Turns. Chemistry 2022; 28:e202104328. [DOI: 10.1002/chem.202104328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Viola C. D'mello
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Graphene Research Labs KIADB IT Park Near Airport Bengaluru 562149 India
| | - Gildas Goldsztejn
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Université Paris-Saclay, CNRS Institut des Sciences Moléculaires d'Orsay (ISMO) 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Institut de Recherche en Astrophysique et Planétologie (IRAP) Université de Toulouse (UPS), CNRS, CNES 9 Avenue du Colonel Roche 31028 Toulouse France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Florence Charnay‐Pouget
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
- Present address: Université Clermont Auvergne, CNRS SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | - David J. Aitken
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
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29
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Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy. Molecules 2022; 27:molecules27072367. [PMID: 35408770 PMCID: PMC9000879 DOI: 10.3390/molecules27072367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.
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30
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Buschmann P, Lengsfeld KG, Djahandideh J, Grabow JU. From rotational resolved spectra to an extended increment system of planar moments allowing ad-hoc conformational identification – Exemplification by the broadband microwave spectrum of α-hydroxyisobutyric acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Fischer TLL, Bödecker MADI, Zehnacker A, Mata RA, Suhm MA. Setting up the HyDRA blind challenge for the microhydration of organic molecules. Phys Chem Chem Phys 2022; 24:11442-11454. [DOI: 10.1039/d2cp01119k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...
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32
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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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33
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Mundlapati VR, Imani Z, D'mello VC, Brenner V, Gloaguen E, Baltaze JP, Robin S, Mons M, Aitken DJ. N-H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives. Chem Sci 2021; 12:14826-14832. [PMID: 34820098 PMCID: PMC8597926 DOI: 10.1039/d1sc05014a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O
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C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom. In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.![]()
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Affiliation(s)
| | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France
| | - Viola C D'mello
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France .,Université de Paris, Faculté de Pharmacie 75006 Paris France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
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Niedner‐Schatteburg G, Kappes MM. Advancing Inorganic Coordination Chemistry by Spectroscopy of Isolated Molecules: Methods and Applications. Chemistry 2021; 27:15027-15042. [PMID: 34636096 PMCID: PMC8596414 DOI: 10.1002/chem.202102815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 12/14/2022]
Abstract
A unique feature of the work carried out in the Collaborative Research Center 3MET continues to be its emphasis on innovative, advanced experimental methods which hyphenate mass-selection with further analytical tools such as laser spectroscopy for the study of isolated molecular ions. This allows to probe the intrinsic properties of the species of interest free of perturbing solvent or matrix effects. This review explains these methods and uses examples from past and ongoing 3MET studies of specific classes of multicenter metal complexes to illustrate how coordination chemistry can be advanced by applying them. As a corollary, we will show how the challenges involved in providing well-defined, for example monoisomeric, samples of the molecular ions have helped to further improve the methods themselves thus also making them applicable to many other areas of chemistry.
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Affiliation(s)
| | - Manfred M. Kappes
- Institute of Physical Chemistry and Institute of NanotechnologyKarlsruhe Institute of Technology (KIT)76128KarlsruheGermany
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35
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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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36
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Wang H, Chen J, Duan C, Xu X, Zheng Y, Grabow JU, Gou Q, Caminati W. Switching Aromatic Character by Complexation: π to π* Change Seen in Molecular Rotation Spectra. J Phys Chem Lett 2021; 12:5150-5155. [PMID: 34032447 DOI: 10.1021/acs.jpclett.1c01318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A dominating F···π*aromatic interaction is found to govern the benzaldehyde···tetrafluoromethane complex, as revealed by this rotational spectroscopic investigation. Secondary F···π*-C=O- and C σ*CF4···πaromatic interactions also contribute to the stability of the observed isomer. Narrow splittings have been observed in the rotational spectrum originating from a 3-fold internal rotation of CF4 above the aromatic moiety, and a corresponding V3 barrier was determined to be 1.572(14) kJ mol-1. This is the first rotational spectroscopic evidence in the literature implying that the aromatic π* antibonding orbital can be activated not only by electron-withdrawing substituents but also by complexation partners containing atoms with high electronegativity, like CF4. The results emphasize the partner molecules' role to modulate the π electron structure and show a change in the orbital character (π or π*) when participating in the formation of noncovalent interactions.
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Affiliation(s)
- Hao Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Junhua Chen
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Chunguo Duan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Xuefang Xu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie Leibniz, Universität Hannover, 30167 Hannover, Germany
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Walther Caminati
- Dipartimento di Chimica "G. Ciamician", Università; di Bologna, I-40126 Bologna, Italy
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Mundlapati VR, Imani Z, Goldsztejn G, Gloaguen E, Brenner V, Le Barbu-Debus K, Zehnacker-Rentien A, Baltaze JP, Robin S, Mons M, Aitken DJ. A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine. Amino Acids 2021; 53:621-633. [PMID: 33743071 DOI: 10.1007/s00726-021-02967-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).
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Affiliation(s)
- Venkateswara Rao Mundlapati
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
- Institut de Recherche en Astrophysique Et Planétologie (IRAP), Université de Toulouse (UPS), CNRS, CNES, 9 Avenue du Colonel Roche, 31028, Toulouse, France
| | - Zeynab Imani
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Gildas Goldsztejn
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Eric Gloaguen
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Katia Le Barbu-Debus
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Anne Zehnacker-Rentien
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Jean-Pierre Baltaze
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Sylvie Robin
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
- Faculté de Pharmacie, Université de Paris, 75006, Paris, France
| | - Michel Mons
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France.
| | - David J Aitken
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France.
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Donon J, Habka S, Mons M, Brenner V, Gloaguen E. Conformational analysis by UV spectroscopy: the decisive contribution of environment-induced electronic Stark effects. Chem Sci 2021; 12:2803-2815. [PMID: 34164044 PMCID: PMC8179363 DOI: 10.1039/d0sc06074g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
UV chromophores are frequently used as probes of the molecular structure. In particular, they are sensitive to the electric field generated by the molecular environment, resulting in the observation of Stark effects on UV spectra. While these environment-induced electronic Stark effects (EI-ESE) are already used for conformational analysis in the condensed phase, this work explores the potential of such an approach when performed at much higher conformational resolution in the gas phase. By investigating model alkali benzylacetate and 4-phenylbutyrate ion pairs, where the electric field applied to the phenyl ring is chemically tuned by changing the nature of the alkali cation, this work demonstrates that precise conformational assignments can be proposed based on the correlation between the conformation-dependent calculated electric fields and the frequency of the electronic transitions observed in the experimental UV spectra. Remarkably, the sole analysis of Stark effects and fragmentation patterns in mass-selected UV spectra provided an accurate and complete conformational analysis, where spectral differences as small as a few cm-1 between electronic transitions were rationalized. This case study illustrates that the identification of EI-ESE together with their interpretation at the modest cost of a ground state electric field calculation qualify UV spectroscopy as a powerful tool for conformational analysis.
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Affiliation(s)
- Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay Bât 522 91191 Gif-sur-Yvette France
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