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Salmahaminati, Roca-Sanjuán D. The Photophysics and Photochemistry of Phenylalanine, Tyrosine, and Tryptophan: A CASSCF/CASPT2 Study. ACS OMEGA 2024; 9:35356-35363. [PMID: 39184496 PMCID: PMC11339992 DOI: 10.1021/acsomega.4c00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/27/2024]
Abstract
Among all amino acids, the three aromatic systems including phenylalanine, tyrosine, and tryptophan are known to manifest UV light absorption at the higher wavelengths. Their fluorescent properties are important for protein detection and determination of the spatial structure. Based on ab initio quantum chemical calculations, the absorption spectra in the 0-12 eV UV range of these aromatic amino acids were interpreted, and the photochemistry of the lowest-lying excited states was studied. For that, molecular ground-state geometries were determined using both the coupled-cluster single and double (CCSD) and complete active space self-consistent field (CASSCF) methods. The vertical electronic transition energies, associated oscillator strengths, and electric dipole moments of the lowest excited states were computed at the CASPT2//CASSCF level. The decay mechanisms of the lowest-energy excited states were investigated by performing minimum energy path (MEPs) computations. The results showed that the CCSD and CASSCF computations yielded similar structures. The lowest-energy S1 state in phenylalanine and tyrosine, and S1 and S2 in tryptophan are mainly described by the π → π* excitation localized in the aromatic ring. Upon light absorption, the main photoresponse of the molecules is driven by the benzene, phenol, and indole chromophoric units.
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Affiliation(s)
- Salmahaminati
- Chemistry
Department, Faculty of Mathematics and Natural Science, Islamic University of Indonesia, Yogyakarta, 55581, Indonesia
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 Valencia, Spain
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2
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Fedorov DG. Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level. J Phys Chem A 2023; 127:9357-9364. [PMID: 37782030 DOI: 10.1021/acs.jpca.3c04847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
A many-body expansion of ionization potentials and electron affinities is developed based on a combination of the fragment molecular orbital method and equation-of-motion coupled-cluster (EOM-CC). In addition to site-specific values, obtained as one-body properties, pair and triple corrections are added to account for nonlocal EOM-CC contributions of the molecular environment of a chromophore. The developed method is applied to carboxylic acids, alkyl cations, a protein ubiquitin (Protein Data Bank ID 1UBQ), and a nano ribbon of white graphene elucidating the effect of environment on ionization potential and electron affinity.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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3
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Moore B, Mahoney K, Zeng MF, Djuricanin P, Momose T. Ultraviolet Photodissociation of Proteinogenic Amino Acids. J Am Chem Soc 2023; 145:11045-11055. [PMID: 37167534 DOI: 10.1021/jacs.3c00124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The ultraviolet photochemistry of the amino acids glycine, leucine, proline, and serine in their neutral forms was investigated using parahydrogen matrix-isolation spectroscopy. Irradiation by 213 nm light destroys the chirality of all three chiral amino acids as a result of the α-carbonyl C-C bond cleavage and hydrocarboxyl (HOCO) radical production. The temporal behavior of the Fourier-transform infrared spectra revealed that HOCO radicals rapidly reach a steady state, which occurs predominantly due to photodissociation of HOCO into CO + OH or CO2 + H. In glycine and leucine, the amine radicals generated by the α-carbonyl C-C bond cleavage rapidly undergo hydrogen elimination to yield methanimine and 3-methylbutane-1-imine, respectively. Breaking of the α-carbonyl C-C bond in proline appeared to yield 1-pyrroline, although due to its weak absorption it remains unconfirmed. In serine, additional products were formaldehyde and E/Z ethanimine. The present study shows that the direct production of HOCO previously observed in α-alanine generalizes to other amino acids of varying structure. It also revealed a tendency for amino acid photolysis to form imines rather than amine radicals. HOCO should be useful in the search for amino acids in interstellar space, particularly in combination with simple imine molecules.
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Affiliation(s)
- Brendan Moore
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kyle Mahoney
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Mei Fei Zeng
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Pavle Djuricanin
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Takamasa Momose
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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4
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Motalov VB, Korobov MA, Dunaev AM, Dunaeva VV, Kudin LS. Vapor Pressure and Thermodynamics of L-Tryptophan Sublimation. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221100030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Hadidi R, Božanić DK, Ganjitabar H, Garcia GA, Powis I, Nahon L. Conformer-dependent vacuum ultraviolet photodynamics and chiral asymmetries in pure enantiomers of gas phase proline. Commun Chem 2021; 4:72. [PMID: 36697576 PMCID: PMC9814706 DOI: 10.1038/s42004-021-00508-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Proline is a unique amino-acid, with a secondary amine fixed within a pyrrolidine ring providing specific structural properties to proline-rich biopolymers. Gas-phase proline possesses four main H-bond stabilized conformers differing by the ring puckering and carboxylic acid orientation. The latter defines two classes of conformation, whose large ionization energy difference allows a unique conformer-class tagging via electron spectroscopy. Photoelectron circular dichroism (PECD) is an intense chiroptical effect sensitive to molecular structures, hence theorized to be highly conformation-dependent. Here, we present experimental evidence of an intense and striking conformer-specific PECD, measured in the vacuum ultraviolet (VUV) photoionization of proline, as well as a conformer-dependent cation fragmentation behavior. This finding, combined with theoretical modeling, allows a refinement of the conformational landscape and energetic ordering, that proves inaccessible to current molecular electronic structure calculations. Additionally, astrochemical implications regarding a possible link of PECD to the origin of life's homochirality are considered in terms of plausible temperature constraints.
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Affiliation(s)
- Rim Hadidi
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France
| | - Dušan K Božanić
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France
- Department of Radiation Chemistry and Physics, "VINČA" Institute of Nuclear Sciences-National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Hassan Ganjitabar
- School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Gustavo A Garcia
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France
| | - Ivan Powis
- School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Laurent Nahon
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France.
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6
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Hartweg S, Garcia GA, Božanić DK, Nahon L. Condensation Effects on Electron Chiral Asymmetries in the Photoionization of Serine: From Free Molecules to Nanoparticles. J Phys Chem Lett 2021; 12:2385-2393. [PMID: 33660503 DOI: 10.1021/acs.jpclett.1c00258] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Structural changes at the molecular level, occurring at the onset of condensation, can be probed by angle-resolved valence photoelectron spectroscopy, which is inherently sensitive to the electronic structure. For larger condensed systems like aerosol particles, the observation of intrinsic angular anisotropies in photoemission (β parameters) is challenging due to the strong reduction of their magnitude by electron transport effects. Here, we use a less common, more sensitive observable in the form of the chiral asymmetry parameter to perform a comparative study of the VUV photoelectron spectroscopy and photoelectron circular dichroism (PECD) between pure gas phase enantiomers of the amino acid serine and their corresponding homochiral nanoparticles. We observe a relatively large (1%) and strongly kinetic energy-dependent asymmetry, discussed in terms of the emergence of local order and conformational changes potentially counterbalancing the loss of angular information due to electron transport scattering. This demonstrates the potential of PECD as a sensitive probe of the condensation effects from the gas phase to bulk-like chiral aerosol particles surpassing the potential of conventional photoemission observables such as β parameters.
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Affiliation(s)
- Sebastian Hartweg
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Cedex, Gif sur Yvette, France
| | - Gustavo A Garcia
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Cedex, Gif sur Yvette, France
| | - Dušan K Božanić
- Department of Radiation Chemistry and Physics, "VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, 11001 Belgrade, Serbia
| | - Laurent Nahon
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Cedex, Gif sur Yvette, France
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7
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Jinfeng Lu, Meng D, Li F, Guo M, Li Y. Theoretical Study of the Structure and Ionization Potentials of Proline. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420070201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Roy A, Seidel R, Kumar G, Bradforth SE. Exploring Redox Properties of Aromatic Amino Acids in Water: Contrasting Single Photon vs Resonant Multiphoton Ionization in Aqueous Solutions. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.7b11762] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anirban Roy
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Robert Seidel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Gaurav Kumar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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9
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Krauklis IV, Tulub AV, Shtyrov AA. Comparative characteristics of a tryptophan molecule in the gas phase and water. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617070010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Mu X, Song T, Siu CK, Chu IK. Tautomerization and Dissociation of Molecular Peptide Radical Cations. CHEM REC 2017. [DOI: 10.1002/tcr.201700013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyan Mu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Tao Song
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Chi-Kit Siu
- Department of Biology and Chemistry; City University of Hong Kong; 83 Tat Chee Avenue Kowloon Tong, Hong Kong SAR P. R. China
| | - Ivan K. Chu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
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11
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Sarkar S, Kronik L. Ionisation and (de-)protonation energies of gas-phase amino acids from an optimally tuned range-separated hybrid functional. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1150531] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Soumyajit Sarkar
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth, Israel
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth, Israel
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12
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Gil A, Simon S, Rodríguez-Santiago L, Bertrán J, Sodupe M. Influence of the Side Chain in the Structure and Fragmentation of Amino Acids Radical Cations. J Chem Theory Comput 2015; 3:2210-20. [PMID: 26636213 DOI: 10.1021/ct700055p] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational properties of ionized amino acids (Gly, Ala, Ser, Cys, Asp, Gln, Phe, Tyr, and His) have been theoretically analyzed using the hybrid B3LYP and the hybrid-meta MPWB1K functionals as well as with the post-Hartree Fock CCSD(T) level of theory. As a general trend, ionization is mainly localized at the -NH2 group, which becomes more planar and acidic, the intramolecular hydrogen bond in which -NH2 acts as proton donor being strengthened upon ionization. For this reason, the so-called conformer IV(+) becomes the most stable for nonaromatic amino acid radical cations. Aromatic amino acids do not follow this trend because ionization takes place mainly at the side chain. For these amino acids for which ionization of the side chain prevails over the -NH2 group, structures III(+) and II(+) become competitive. The Cα-X fragmentations of the ionized systems have also been studied. Among the different decompositions considered, the one that leads to the loss of COOH(•) is the most favorable one. Nevertheless, for aromatic amino acids fragmentations leading to R(•) or R(+) start being competitive. In fact, for His and Tyr, results indicate that the fragmentation leading to R(+) is the most favorable process.
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Affiliation(s)
- Adrià Gil
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain, and Institut de Química Computacional, Departament de Química, Universitat de Girona, Girona 17071, Spain
| | - Sílvia Simon
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain, and Institut de Química Computacional, Departament de Química, Universitat de Girona, Girona 17071, Spain
| | - Luis Rodríguez-Santiago
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain, and Institut de Química Computacional, Departament de Química, Universitat de Girona, Girona 17071, Spain
| | - Juan Bertrán
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain, and Institut de Química Computacional, Departament de Química, Universitat de Girona, Girona 17071, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain, and Institut de Química Computacional, Departament de Química, Universitat de Girona, Girona 17071, Spain
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13
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Determination of the molecular structure of gaseous proline by electron diffraction, supported by microwave and quantum chemical data. Struct Chem 2015. [DOI: 10.1007/s11224-015-0589-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Esquivel RO, Molina-Espíritu M, López-Rosa S, Soriano-Correa C, Barrientos-Salcedo C, Kohout M, Dehesa JS. Predominant information quality scheme for the essential amino acids: an information-theoretical analysis. Chemphyschem 2015; 16:2571-81. [PMID: 26175003 DOI: 10.1002/cphc.201500282] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/11/2015] [Indexed: 11/05/2022]
Abstract
In this work we undertake a pioneer information-theoretical analysis of 18 selected amino acids extracted from a natural protein, bacteriorhodopsin (1C3W). The conformational structures of each amino acid are analyzed by use of various quantum chemistry methodologies at high levels of theory: HF, M062X and CISD(Full). The Shannon entropy, Fisher information and disequilibrium are determined to grasp the spatial spreading features of delocalizability, order and uniformity of the optimized structures. These three entropic measures uniquely characterize all amino acids through a predominant information-theoretic quality scheme (PIQS), which gathers all chemical families by means of three major spreading features: delocalization, narrowness and uniformity. This scheme recognizes four major chemical families: aliphatic (delocalized), aromatic (delocalized), electro-attractive (narrowed) and tiny (uniform). All chemical families recognized by the existing energy-based classifications are embraced by this entropic scheme. Finally, novel chemical patterns are shown in the information planes associated with the PIQS entropic measures.
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Affiliation(s)
- Rodolfo O Esquivel
- Departamento de Química, Universidad Autónoma Metropolitana, 09340-México, D.F. (México). .,Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, 18071-Granada (Spain).
| | | | - Sheila López-Rosa
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, 18071-Granada (Spain).,Departamento de Física Aplicada II, Universidad de Sevilla, 41012-Sevilla (Spain)
| | - Catalina Soriano-Correa
- Laboratorio de Química Computacional, FES-Zaragoza, Universidad Nacional Autónoma de México, 09230-Iztapalapa, México, D.F. (México)
| | - Carolina Barrientos-Salcedo
- Facultad de Bioanálisis-Veracruz, Universidad Veracruzana, Laboratorio de Química Médica y Quimiogenómica, 91700-Veracruz (México)
| | - Miroslav Kohout
- Max Planck Institute for Chemical Physics of Solids, Noethnitzer Str. 40, 01187-Dresden (Germany)
| | - Jesús S Dehesa
- Departamento de Física Atómica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain)
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15
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Nettles WL, Song H, Farquhar ER, Fitzkee NC, Emerson JP. Characterization of the Copper(II) Binding Sites in Human Carbonic Anhydrase II. Inorg Chem 2015; 54:5671-80. [PMID: 26010488 PMCID: PMC4482258 DOI: 10.1021/acs.inorgchem.5b00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human carbonic anhydrase (CA) is a well-studied, robust, mononuclear Zn-containing metalloprotein that serves as an excellent biological ligand system to study the thermodynamics associated with metal ion coordination chemistry in aqueous solution. The apo form of human carbonic anhydrase II (CA) binds 2 equiv of copper(II) with high affinity. The Cu(2+) ions bind independently forming two noncoupled type II copper centers in CA (CuA and CuB). However, the location and coordination mode of the CuA site in solution is unclear, compared to the CuB site that has been well-characterized. Using paramagnetic NMR techniques and X-ray absorption spectroscopy we identified an N-terminal Cu(2+) binding location and collected information on the coordination mode of the CuA site in CA, which is consistent with a four- to five-coordinate N-terminal Cu(2+) binding site reminiscent to a number of N-terminal copper(II) binding sites including the copper(II)-amino terminal Cu(2+) and Ni(2+) and copper(II)-β-amyloid complexes. Additionally, we report a more detailed analysis of the thermodynamics associated with copper(II) binding to CA. Although we are still unable to fully deconvolute Cu(2+) binding data to the high-affinity CuA site, we derived pH- and buffer-independent values for the thermodynamics parameters K and ΔH associated with Cu(2+) binding to the CuB site of CA to be 2 × 10(9) and -17.4 kcal/mol, respectively.
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Affiliation(s)
- Whitnee L. Nettles
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
| | - He Song
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
| | - Erik R. Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas C. Fitzkee
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
| | - Joseph P. Emerson
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
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16
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Su CC, Yu Y, Chang PC, Chen YW, Chen IY, Lee YY, Wang CC. VUV Photoelectron Spectroscopy of Cysteine Aqueous Aerosols: A Microscopic View of Its Nucleophilicity at Varying pH Conditions. J Phys Chem Lett 2015; 6:817-23. [PMID: 26262658 DOI: 10.1021/acs.jpclett.5b00002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cysteine (Cys) is unique due to its highly reactive thiol group. It often regulates the biological function of proteins by acting as the redox site. Despite its biological significance, however, the valence electronic structure of Cys under the aqueous environments remains unavailable. Here, we report the VUV photoelectron spectroscopy of Cys aqueous aerosols via a newly built aerosol VUV photoelectron spectroscopy apparatus. The photoelectron spectra of Cys show distinct band shapes at varying pH conditions, reflecting the altered molecular orbital characters when its dominating form changes. The ionization energy of Cys is determined to be 8.98 ± 0.05 eV at low pH. A new feature at a binding energy of 6.97 ± 0.05 eV is observed at high pH, suggesting that the negative charge on the thiolate group becomes the first electron to be removed upon ionization. This work implies that when Cys is involved in redox processes, the charge transfer mechanism may be entirely altered under different pH conditions.
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Affiliation(s)
- Chien-Cheng Su
- †Department of Chemistry, National Sun Yat-sen University, 80424 Kaohsiung, Taiwan, Republic of China
| | - Youqing Yu
- †Department of Chemistry, National Sun Yat-sen University, 80424 Kaohsiung, Taiwan, Republic of China
| | - Po-Chiao Chang
- †Department of Chemistry, National Sun Yat-sen University, 80424 Kaohsiung, Taiwan, Republic of China
| | - Yu-Wei Chen
- †Department of Chemistry, National Sun Yat-sen University, 80424 Kaohsiung, Taiwan, Republic of China
| | - I-Ying Chen
- †Department of Chemistry, National Sun Yat-sen University, 80424 Kaohsiung, Taiwan, Republic of China
| | - Yin-Yu Lee
- ‡National Synchrotron Radiation Research Center, 30076 Hsinchu, Taiwan, Republic of China
| | - Chia C Wang
- †Department of Chemistry, National Sun Yat-sen University, 80424 Kaohsiung, Taiwan, Republic of China
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17
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Laksman J, Kooser K, Levola H, Itälä E, Ha DT, Rachlew E, Kukk E. Dissociation pathways in the cysteine dication after site-selective core ionization. J Phys Chem B 2014; 118:11688-95. [PMID: 25233490 DOI: 10.1021/jp508161s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A photoelectron-ion-ion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.
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Affiliation(s)
- J Laksman
- Department of Physics, University of Oulu , P.O. Box 3000, FIN-90014 Oulu, Finland
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18
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Tia M, Cunha de Miranda B, Daly S, Gaie-Levrel F, Garcia GA, Nahon L, Powis I. VUV photodynamics and chiral asymmetry in the photoionization of gas phase alanine enantiomers. J Phys Chem A 2014; 118:2765-79. [PMID: 24654892 DOI: 10.1021/jp5016142] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The valence shell photoionization of the simplest proteinaceous chiral amino acid, alanine, is investigated over the vacuum ultraviolet region from its ionization threshold up to 18 eV. Tunable and variable polarization synchrotron radiation was coupled to a double imaging photoelectron/photoion coincidence (i(2)PEPICO) spectrometer to produce mass-selected threshold photoelectron spectra and derive the state-selected fragmentation channels. The photoelectron circular dichroism (PECD), an orbital-sensitive, conformer-dependent chiroptical effect, was also recorded at various photon energies and compared to continuum multiple scattering calculations. Two complementary vaporization methods-aerosol thermodesorption and a resistively heated sample oven coupled to an adiabatic expansion-were applied to promote pure enantiomers of alanine into the gas phase, yielding neutral alanine with different internal energy distributions. A comparison of the photoelectron spectroscopy, fragmentation, and dichroism measured for each of the vaporization methods was rationalized in terms of internal energy and conformer populations and supported by theoretical calculations. The analytical potential of the so-called PECD-PICO detection technique-where the electron spectroscopy and circular dichroism can be obtained as a function of mass and ion translational energy-is underlined and applied to characterize the origin of the various species found in the experimental mass spectra. Finally, the PECD findings are discussed within an astrochemical context, and possible implications regarding the origin of biomolecular asymmetry are identified.
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Affiliation(s)
- Maurice Tia
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
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19
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Ganesan A, Mohammadi N, Wang F. From building blocks of proteins to drugs: a quantum chemical study on structure–property relationships of phenylalanine, tyrosine and dopa. RSC Adv 2014. [DOI: 10.1039/c3ra47364c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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20
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Ramaniah LM, Kamal C, Kshirsagar RJ, Chakrabarti A, Banerjee A. How universal are hydrogen bond correlations? A density functional study of intramolecular hydrogen bonding in low-energy conformers of α-amino acids. Mol Phys 2013. [DOI: 10.1080/00268976.2013.770174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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22
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Shaw JB, Ledvina AR, Zhang X, Julian RR, Brodbelt JS. Tyrosine deprotonation yields abundant and selective backbone cleavage in peptide anions upon negative electron transfer dissociation and ultraviolet photodissociation. J Am Chem Soc 2012; 134:15624-7. [PMID: 22970927 DOI: 10.1021/ja3032086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tyrosine deprotonation in peptides yields preferential electron detachment upon NETD or UVPD, resulting in prominent N-Cα bond cleavage N-terminal to the tyrosine residue. UVPD of iodo-tyrosine-modified peptides was used to generate localized radicals on neutral tyrosine side chains by homolytic cleavage of the C-I bond. Subsequent collisional activation of the radical species yielded the same preferential cleavage of the adjacent N-terminal N-Cα bond. LC-MS/MS analysis of a tryptic digest of BSA demonstrated that these cleavages are regularly observed for peptides when using high-pH mobile phases.
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Affiliation(s)
- Jared B Shaw
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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23
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Papp P, Shchukin P, Kočíšek J, Matejčík Š. Electron ionization and dissociation of aliphatic amino acids. J Chem Phys 2012; 137:105101. [DOI: 10.1063/1.4749244] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Wickrama Arachchilage AP, Wang F, Feyer V, Plekan O, Prince KC. Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly. J Chem Phys 2012; 136:124301. [PMID: 22462851 DOI: 10.1063/1.3693763] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We have investigated the electronic structure of three cyclic dipeptides: cyclo(Histidyl-Glycyl) (cHisGly), cyclo(Tyrosyl-Prolyl) (cTyrPro), and cyclo(Phenylalanyl-Phenylalanyl) (cPhePhe) in the vapor phase, by means of photoemission spectroscopy and theoretical modeling. The last compound was evaporated from the solid linear dipeptide, but cyclised, losing water to form cPhePhe in the gas phase. The results are compared with our previous studies of three other cyclopeptides. Experimental valence and core level spectra have been interpreted in the light of calculations to identify the basic chemical properties associated with the central diketopiperazine ring, and with the additional functional groups. The valence spectra are generally characterized by a restricted set of outer valence orbitals separated by a gap from most other valence orbitals. The theoretically simulated core and valence spectra of all three cyclic dipeptides agree reasonably well with the experimental spectra. The central ring and the side chains act as independent chromophores whose spectra do not influence one another, except for prolyl dipeptides, where the pyrrole ring is fused with the central ring. In this case, significant changes in the valence and core level spectra were observed, and explained by stronger hybridization of the valence orbitals.
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Affiliation(s)
- Anoja P Wickrama Arachchilage
- eChemistry Laboratory, Faculty of Life and Social Sciences, Swinburne University of Technology, Hawthorn, Melbourne, Victoria 3122, Australia
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Kopyra J, Szamrej I, Abdoul-Carime H, Farizon B, Farizon M. Decomposition of methionine by low energy electrons. Phys Chem Chem Phys 2012; 14:8000-4. [PMID: 22555818 DOI: 10.1039/c2cp40461c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we present the results from low energy (<12 eV) electron impact on isolated methionine, Met. We show that dissociative electron attachment is the operative mechanism for the sulfur content amino-acid fragmentation. The two most dominant fragments are attributed to the (Met-H)(-) and (C(4)NOH(5))(-) ions that are formed at energy below 2 eV. The formation of the latter anion is accompanied by the loss of neutral counterparts, which are most likely a water molecule and highly toxic methanethiol, CH(3)SH. Further fragments are associated with the damage at the sulfur end of the amino acid, producing the methyl sulfide anion CH(3)S(-) or sulfur containing neutrals. In the context of radiation induced damage to biological material at the nano-scale level, the present interest of methionine arises from the implication of the molecule in biological processes (e.g., S-adenosyl methionine for the stimulation of DNA methyltransferase reactions or protein synthesis).
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Affiliation(s)
- Janina Kopyra
- Department of Chemistry, Siedlce University, 3-Maja 54, 08-110 Siedlce, Poland.
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26
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Heck A, Woiczikowski PB, Kubař T, Giese B, Elstner M, Steinbrecher TB. Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation. J Phys Chem B 2012; 116:2284-93. [PMID: 22260641 DOI: 10.1021/jp2086297] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist.
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Affiliation(s)
- Alexander Heck
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
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27
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Kalcic CL, Reid GE, Lozovoy VV, Dantus M. Mechanism elucidation for nonstochastic femtosecond laser-induced ionization/dissociation: from amino acids to peptides. J Phys Chem A 2012; 116:2764-74. [PMID: 22141398 DOI: 10.1021/jp208421d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Femtosecond laser-induced ionization/dissociation (fs-LID) has been demonstrated as a novel ion activation method for use in tandem mass spectrometry. The technique opens the door to unique structural information about biomolecular samples that is not easily accessed by traditional means. fs-LID is able to cleave strong bonds while keeping weaker bonds intact. This feature has been found to be particularly useful for the mapping of post-translational modifications such as phosphorylation, which is difficult to achieve by conventional proteomic studies. Here we investigate the laser-ion interaction on a fundamental level through the characterization of fs-LID spectra for the protonated amino acids and two series of derivatized samples. The findings are used to better understand the fs-LID spectra of synthetic peptides. This is accomplished by exploring the effects of several single-residue substitutions.
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Affiliation(s)
- Christine L Kalcic
- Departments of Chemistry, Michigan State University East Lansing, Michigan 48824, USA
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28
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Ganesan A, Wang F, Brunger M, Prince K. Effects of alkyl side chains on properties of aliphatic amino acids probed using quantum chemical calculations. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:733-742. [PMID: 21862853 DOI: 10.1107/s0909049511029499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/21/2011] [Indexed: 05/31/2023]
Abstract
Effects of alkyl side chains (R-) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP < 290 eV (where IP is the ionization potential). The two glycyl parent spectral peaks of the amide 291.0 eV [C((2))] and carboxylic 293.5 eV [C((1))] C atoms are shifted in the aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12-16 eV, and hence this energy region of 12-16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO-LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.
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Affiliation(s)
- Aravindhan Ganesan
- Faculty of Life and Social Sciences, Swinburne University of Technology, Melbourne, Victoria, Australia
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29
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Ganisl B, Valovka T, Hartl M, Taucher M, Bister K, Breuker K. Electron detachment dissociation for top-down mass spectrometry of acidic proteins. Chemistry 2011; 17:4460-9. [PMID: 21433149 PMCID: PMC3120980 DOI: 10.1002/chem.201003709] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 02/01/2023]
Abstract
Electron detachment dissociation (EDD) is an emerging mass spectrometry (MS) technique for the primary structure analysis of peptides, carbohydrates, and oligonucleotides. Herein, we explore the potential of EDD for sequencing of proteins of up to 147 amino acid residues by using top-down MS. Sequence coverage ranged from 72% for Melittin, which lacks carboxylic acid functionalities, to 19% for an acidic 147-residue protein, to 12% for Ferredoxin, which showed unusual backbone fragmentation next to cysteine residues. A limiting factor for protein sequencing by EDD is the facile loss of small molecules from amino acid side chains, in particular CO(2). Based on the types of fragments observed and fragmentation patterns found, we propose detailed mechanisms for protein backbone cleavage and side chain dissociation in EDD. The insights from this study should further the development of EDD for top-down MS of acidic proteins.
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Affiliation(s)
- Barbara Ganisl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnrain 52a, 6020 Innsbruck (Austria), Fax: (+43) 512-507-2892 E-mail:
| | - Taras Valovka
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckPeter-Mayr-Strasse 1a, 6020 Innsbruck (Austria)
| | - Markus Hartl
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckPeter-Mayr-Strasse 1a, 6020 Innsbruck (Austria)
| | - Monika Taucher
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnrain 52a, 6020 Innsbruck (Austria), Fax: (+43) 512-507-2892 E-mail:
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckPeter-Mayr-Strasse 1a, 6020 Innsbruck (Austria)
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnrain 52a, 6020 Innsbruck (Austria), Fax: (+43) 512-507-2892 E-mail:
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30
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Ramaniah LM, Chakrabarti A, Kshirsagar R, Kamal C, Banerjee A. Density functional study of α-amino acids: structural, energetic and vibrational properties. Mol Phys 2011. [DOI: 10.1080/00268976.2011.558027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Close DM. Calculated vertical ionization energies of the common α-amino acids in the gas phase and in solution. J Phys Chem A 2011; 115:2900-12. [PMID: 21410277 DOI: 10.1021/jp200503z] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vertical ionization energies of the low-lying conformers of the α-amino acids found in proteins have been calculated. Geometry optimizations were first performed at the B3LYP/6-311G(d,p) level of theory, and then reoptimized at the MP2/6-311G(d,p) level of theory. Vertical ionization energies were then computed by three methods, electron propagator in the partial third-order (P3) approximation, Outer-Valence-Green's Functions, and by evaluating the difference in the total energy between the cation radical and the neutral amino acid in the geometry of the neutral species. When available, the results are compared to the experimental vertical ionization energies. The vertical ionization energies calculated using the MP2/P3 method gave the best overall agreement with the experimental results. Next, the ionization energies in solution are calculated for the zwitterionic forms of the α-amino acids by using IEFPCM methods. To obtain the vertical ionization energy in solution, it is necessary to use the nonequilibrium polarizable continuum model (NEPCM), the results of which are reported here for the α-amino acids.
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Affiliation(s)
- David M Close
- Department of Physics, Box 70652, East Tennessee State University, Johnson City, Tennessee 37614, United States.
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Gaie-Levrel F, Garcia GA, Schwell M, Nahon L. VUV state-selected photoionization of thermally-desorbed biomolecules by coupling an aerosol source to an imaging photoelectron/photoion coincidence spectrometer: case of the amino acids tryptophan and phenylalanine. Phys Chem Chem Phys 2011; 13:7024-36. [DOI: 10.1039/c0cp02798g] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Ke Y, El Aribi H, Siu CK, Siu KWM, Hopkinson AC. A comparison of the fragmentation pathways of [Cu(II)(Ma)(Mb)]•2+ complexes where Ma and Mb are peptides containing either a tryptophan or a tyrosine residue. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3485-3492. [PMID: 21072806 DOI: 10.1002/rcm.4783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
[Cu(II)(M(a))(M(b))](•2+) complexes, where M(a) and M(b) are dipeptides or tripeptides each containing either a tryptophan (W) or tyrosine (Y) residue, have been examined by means of electrospray tandem mass spectrometry. Collision-induced dissociations (CIDs) of complexes containing identical peptides having a tryptophan residue generated abundant radical cations of the peptides; by contrast, for complexes containing peptides having a tyrosine residue, the main fragmentation channel is dissociative proton transfer to give [M(a) + H](+) and [Cu(II)(M(b)-H)](•+). When there are two different peptides in the complex, each containing a tryptophan residue, radical cations are again the major products, with their relative abundances depending on the locations of the tryptophan residue in the peptides. In the CIDs of mixed complexes, where one peptide contains a tryptophan residue and the other a tyrosine residue, the main fragmentation channel is formation of the radical cation of the tryptophan-containing peptide and not proton transfer from the tyrosine-containing peptide to give a protonated peptide.
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Affiliation(s)
- Yuyong Ke
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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34
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Rai AK, Song C, Lin Z. An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 73:865-870. [PMID: 19482510 DOI: 10.1016/j.saa.2009.04.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 04/13/2009] [Indexed: 05/27/2023]
Abstract
An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.
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Affiliation(s)
- Amareshwar Kumar Rai
- Hefei National Laboratory for Physical Sciences, Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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Marksteiner M, Haslinger P, Sclafani M, Ulbricht H, Arndt M. UV and VUV Ionization of Organic Molecules, Clusters, and Complexes. J Phys Chem A 2009; 113:9952-7. [DOI: 10.1021/jp905039f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markus Marksteiner
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Haslinger
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michele Sclafani
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Hendrik Ulbricht
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Markus Arndt
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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36
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Kishor S, Dhayal S, Mathur M, Ramaniah LM. Structural and energetic properties ofα-amino acids: a first principles density functional study. Mol Phys 2008. [DOI: 10.1080/00268970802422577] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Plekan O, Feyer V, Richter R, Coreno M, Prince KC. Valence photoionization and photofragmentation of aromatic amino acids. Mol Phys 2008. [DOI: 10.1080/00268970801974875] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Electronic and vibrational polarizabilities of the twenty naturally occurring amino acids. Biophys Chem 2008; 132:139-47. [DOI: 10.1016/j.bpc.2007.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 10/31/2007] [Accepted: 11/01/2007] [Indexed: 11/21/2022]
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39
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Plekan O, Feyer V, Richter R, Coreno M, de Simone M, Prince KC, Carravetta V. Investigation of the Amino Acids Glycine, Proline, and Methionine by Photoemission Spectroscopy. J Phys Chem A 2007; 111:10998-1005. [DOI: 10.1021/jp075384v] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oksana Plekan
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Vitaliy Feyer
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Robert Richter
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Marcello Coreno
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Monica de Simone
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Kevin C. Prince
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Vincenzo Carravetta
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
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40
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Plekan O, Feyer V, Richter R, Coreno M, de Simone M, Prince K, Carravetta V. Photoemission and the shape of amino acids. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.05.110] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Huang Z, Lin Z, Song C. Protonation Processes and Electronic Spectra of Histidine and Related Ions. J Phys Chem A 2007; 111:4340-52. [PMID: 17474721 DOI: 10.1021/jp067280a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A full structural assignment of the neutral, protonated, and deprotonated histidine conformers in the gas phase is presented. A total of 3024 unique trial structures were generated by all combinations of internal single-bond rotamers of these species and optimized at the B3LYP/6-311G* level and further optimized at the B3LYP/6-311++G** level. A set of unique conformers is found, and their relative energies, free energies, dipole moments, rotational constants, electron affinities, ionization energies, and harmonic frequencies are determined. The population ratio of histidine and its tautomer is 1:0.16 at 298 K. Massive conformational changes are observed due to protonation and deprotonation, and the intramolecular H-bonds are characterized with the atoms in molecules theory. The calculated proton dissociation energy, gas-phase acidity, proton affinity, and gas-phase basicity are in excellent agreement with the experiments. The deprotonation and protonation of gaseous histidine both occur on the imidazole ring, explaining the versatile biofunctions of histidine in large biomolecules. The UV spectra of neutral and singly and doubly protonated histidine are investigated with the TDDFT/B3LYP/6-311+G(2df,p) calculations. The S0-S1, S0-S2, and S0-S3 excitations of histidine are mixed pipi*/npi* transitions at 5.37, 5.44, and 5.69 eV, respectively. The three excitation energies for histidine tautomer are 4.85, 5.47, and 5.52 eV, respectively. The three excitations for protonated histidine are mainly npi* transitions at 5.45, 5.67, and 5.82 eV, respectively. The S0-S1 excitation of protonated histidine produces ImH-CbetaH2-CalphaH(COOH)-NH2+, while the S0-S2 and S0-S3 transitions produce ImH-CbetaH2-CalphaH(NH2)-(COOH)+. These data may help to understand the mechanisms of the UV fragmentation of biomolecules.
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Affiliation(s)
- Zhijian Huang
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, China 230026
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42
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Maul R, Preuss M, Ortmann F, Hannewald K, Bechstedt F. Electronic excitations of glycine, alanine, and cysteine conformers from first-principles calculations. J Phys Chem A 2007; 111:4370-7. [PMID: 17461555 DOI: 10.1021/jp068294j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The electronic and optical properties are studied for three conformers of amino acid molecules using gradient-corrected (spin-) density functional theory within a projector-augmented wave scheme and the supercell method. We investigate single-particle excitations such as ionization energies and electron affinities as well as pair excitations. By comparing eigenvalues resulting from several local and nonlocal energy functionals, the influence of treatment of exchange and correlation is demonstrated. The excitations are described within the Delta-self-consistent field method with an occupation number constraint to obtain excitation energies and Stokes shifts. The results are used to also discuss the optical absorption properties. In contrast to the lowest single- and two-particle excitation energies, remarkable changes are found in absorption spectra in dependence on the conformation of the molecule geometry.
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Affiliation(s)
- R Maul
- Institut für Festkörpertheorie und-optik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena, Germany
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Dehareng D, Dive G. Charge Transfer Study through the Determination of the Ionization Energies of Tetrapeptides X3-Tyr, X = Gly, Ala, or Leu. Influence of the Inclusion of One Glycine in Alanine and Leucine Containing Peptides. J Phys Chem A 2006; 110:11975-87. [PMID: 17064186 DOI: 10.1021/jp064255w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH(2) terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH(2)=CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH(2) terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide.
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Affiliation(s)
- Dominique Dehareng
- Centre d'Ingéniérie des Protéines, Institut de Chimie B6a, Sart Tilman, B4000, Liège, Belgium.
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Zhang M, Lin Z. Ab initio studies of the conformers and conformational distribution of the gaseous hydroxyamino acid threonine. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Structure–activity analysis on ecdysteroids: A structural and quantum chemical approach based on two biological systems. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.10.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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