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Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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2
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Zhao Y, Liang L, Li Y, Hien KTT, Mizutani G, Rutt HN. Sum frequency generation spectroscopy of the attachment disc of a spider. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 263:120161. [PMID: 34293667 DOI: 10.1016/j.saa.2021.120161] [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: 03/12/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
The pyriform silk of the attachment disc of a spider was studied using infrared-visible vibrational sum frequency generation (SFG) spectroscopy. The spider can attach dragline and radial lines to many kinds of substrates in nature (concrete, alloy, metal, glass, plant branches, leaves, etc.) with the attachment disc. The adhesion can bear the spider's own weight, and resist the wind on its orb web. From our SFG spectroscopy study, the NH group of arginine side chain and/or NH2 group of arginine and glutamine side chain in the amino acid sequence of the attachment silk proteins are suggested to be oriented in the disc. It was inferred from the observed doublet SFG peaks at around 3300 cm-1 that the oriented peptide contains two kinds of structures.
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Affiliation(s)
- Yue Zhao
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Lin Liang
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Yanrong Li
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Khuat Thi Thu Hien
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Goro Mizutani
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | - Harvey N Rutt
- School of Electronic and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
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3
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Bahraminegad S, Pardakhty A, Sharifi I, Ranjbar M. The assessment of apoptosis, toxicity effects and anti-leishmanial study of Chitosan/CdO core-shell nanoparticles, eco-friendly synthesis and evaluation. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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4
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Sáenz-Tavera IDC, Rosas-García VM. Role of hydrogen bonding in the conformations of lidocaine, mepivacaine and bupivacaine under aqueous solvation. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Sugiura Y, Suzuki K, Takayanagi T, Kita Y, Tachikawa M. Reduction of OH vibrational frequencies in amino acids by positron attachment. J Comput Chem 2018; 39:2060-2066. [DOI: 10.1002/jcc.25387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/03/2018] [Accepted: 06/08/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Yutaro Sugiura
- Department of Chemistry; Saitama University; Shimo-Okubo 255, Sakura-ku Saitama 338-8570 Saitama Japan
| | - Kento Suzuki
- Department of Chemistry; Saitama University; Shimo-Okubo 255, Sakura-ku Saitama 338-8570 Saitama Japan
| | - Toshiyuki Takayanagi
- Department of Chemistry; Saitama University; Shimo-Okubo 255, Sakura-ku Saitama 338-8570 Saitama Japan
| | - Yukiumi Kita
- Graduate School of Nanobioscience, Yokohama City University; 22-2 Seto, Kanazawa-ku, Yokohama 236-0027 Kanagawa Japan
| | - Masanori Tachikawa
- Graduate School of Nanobioscience, Yokohama City University; 22-2 Seto, Kanazawa-ku, Yokohama 236-0027 Kanagawa Japan
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6
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A density functional theory investigation of the fragmentation mechanism of deprotonated asparagine. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Najbauer EE, Bazsó G, Apóstolo R, Fausto R, Biczysko M, Barone V, Tarczay G. Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations. J Phys Chem B 2015. [PMID: 26201050 DOI: 10.1021/acs.jpcb.5b05768] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10(3) s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations.
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Affiliation(s)
- Eszter E Najbauer
- †Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Bazsó
- †Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| | - Rui Apóstolo
- ‡Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui Fausto
- ‡Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Malgorzata Biczysko
- §Physics Department and International Centre for Quantum and Molecular Structure, Shanghai University, Shanghai, 200444 China
| | - Vincenzo Barone
- ∥Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - György Tarczay
- †Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
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Sengupta A, Ramabhadran RO, Raghavachari K. Accurate and Computationally Efficient Prediction of Thermochemical Properties of Biomolecules Using the Generalized Connectivity-Based Hierarchy. J Phys Chem B 2014; 118:9631-43. [DOI: 10.1021/jp505544y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Arkajyoti Sengupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | | | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Zanatta G, Gottfried C, Silva AM, Caetano EWS, Sales FAM, Freire VN. L-Asparagine crystals with wide gap semiconductor features: optical absorption measurements and density functional theory computations. J Chem Phys 2014; 140:124511. [PMID: 24697463 DOI: 10.1063/1.4869179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the absorption and complex dielectric function, with more structured curves for incident light polarized along the 100 and 101 directions.
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Affiliation(s)
- G Zanatta
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, 90035-003 Porto Alegre-RS, Brazil
| | - C Gottfried
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, 90035-003 Porto Alegre-RS, Brazil
| | - A M Silva
- Universidade Estadual do Piauí, 64260-000 Piripiri-Pi, Brazil
| | - E W S Caetano
- Instituto de Educação, Ciência e Tecnologia do Ceará, 60040-531 Fortaleza-CE, Brazil
| | - F A M Sales
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60455-760 Fortaleza-CE, Brazil
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60455-760 Fortaleza-CE, Brazil
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10
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Najbauer EE, Bazsó G, Góbi S, Magyarfalvi G, Tarczay G. Exploring the Conformational Space of Cysteine by Matrix Isolation Spectroscopy Combined with Near-Infrared Laser Induced Conformational Change. J Phys Chem B 2014; 118:2093-103. [DOI: 10.1021/jp412550q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eszter E. Najbauer
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - Gábor Bazsó
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - Sándor Góbi
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
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11
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Rode JE, Dobrowolski JC, Sadlej J. Prediction of l-Methionine VCD Spectra in the Gas Phase and Water Solution. J Phys Chem B 2013; 117:14202-14. [DOI: 10.1021/jp405462a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Joanna E. Rode
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
| | - Joanna Sadlej
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
- Faculty
of Chemistry, Warsaw University, 1 Pasteura Street, 02-093 Warsaw, Poland
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12
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Stepanian SG, Ivanov AY, Adamowicz L. Conformational composition of neutral leucine. Matrix isolation infrared and ab initio study. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Foldamers of β-peptides: conformational preference of peptides formed by rigid building blocks. The first MI-IR spectra of a triamide nanosystem. Amino Acids 2013; 45:957-73. [DOI: 10.1007/s00726-013-1552-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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14
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Bazsó G, Najbauer EE, Magyarfalvi G, Tarczay G. Near-Infrared Laser Induced Conformational Change of Alanine in Low-Temperature Matrixes and the Tunneling Lifetime of Its Conformer VI. J Phys Chem A 2013; 117:1952-62. [DOI: 10.1021/jp400196b] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Eszter E. Najbauer
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
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15
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Selvaraj ARK, Murugan NA, Ågren H. Solvent Polarity-Induced Conformational Unlocking of Asparagine. J Phys Chem A 2012; 116:11702-8. [DOI: 10.1021/jp307715n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ananda Rama Krishnan Selvaraj
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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Merten C, Xu Y. Matrix Isolation-Vibrational Circular Dichroism Spectroscopy of 3-Butyn-2-ol and its Binary Aggregates. Chemphyschem 2012; 14:213-9. [DOI: 10.1002/cphc.201200758] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Indexed: 11/10/2022]
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17
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Boeckx B, Maes G. Experimental and Theoretical Observation of Different Intramolecular H-bonds in Lysine Conformations. J Phys Chem B 2012; 116:12441-9. [DOI: 10.1021/jp306916e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bram Boeckx
- University of Leuven, Celestijnenlaan
200F, 3001 Heverlee, Belgium
| | - Guido Maes
- University of Leuven, Celestijnenlaan
200F, 3001 Heverlee, Belgium
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Boeckx B, Maes G. Simulating the Interaction between Amino Acids and DNA: A Combined Matrix-Isolation FT-IR and Theoretical Study of the 1-Methyluracil·Glycine H-Bond Complexes Using a Dual Sublimation Furnace. J Phys Chem B 2012; 116:11890-8. [DOI: 10.1021/jp307388e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bram Boeckx
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
| | - Guido Maes
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
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