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Ozawa H, Miyazawa T, Burdeos GC, Miyazawa T. Biological Functions of Antioxidant Dipeptides. J Nutr Sci Vitaminol (Tokyo) 2022; 68:162-171. [PMID: 35768247 DOI: 10.3177/jnsv.68.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the history of modern nutritional science, understanding antioxidants is one of the major topics. In many cases, food-derived antioxidants have π conjugate or thiol group in their molecular structures because π conjugate stabilizes radical by its delocalization and two thiol groups form a disulfide bond in its antioxidative process. In recent years, antioxidant peptides have received much attention because for their ability to scavenge free radicals, inhibition of lipid peroxidation, chelation of transition metal ions, as well as their additional nutritional value. Among them, dipeptides are attracting much interest as post-amino acids, which have residues in common with amino acids, but also have different physiological properties and functions from those of amino acids. Especially, dipeptides containing moieties of several amino acid (tryptophan, tyrosine, histidine, cysteine, and methionine) possess potent antioxidant activity. This review summarizes previous details of structural property, radical scavenging activity, and biological activity of antioxidant dipeptide. Hopefully, this review will help provide a new insight into the study of the biological functions of antioxidant dipeptides.
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Affiliation(s)
- Hitoshi Ozawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | - Taiki Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | | | - Teruo Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
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2
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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3
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A computational study of TyrGly hydration. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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León I, Alonso ER, Mata S, Alonso JL. A rotational study of the AlaAla dipeptide. Phys Chem Chem Phys 2020; 22:13867-13871. [PMID: 32368774 DOI: 10.1039/d0cp01043j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present the first rotational study of the AlaAla dipeptide, brought into the gas phase by laser ablation. Two different structures have been unveiled in the isolated environment of a supersonic expansion by Fourier transform microwave spectroscopy. These structures have been identified through their rotational and 14N quadrupole coupling constants. The flexibility of the -NH2 and -COOH ends allows the formation of strong intramolecular interactions giving rise to five- and seven-membered ring configurations.
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Affiliation(s)
- I León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - E R Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain. and Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain and Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, E-48940, Spain
| | - S Mata
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - J L Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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5
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El Guerdaoui A, Tijar R, Bourjila M, El Merbouh B, El Bouzaidi RD, El Gridani A. Conformational Space Analysis of Protected N-Formyl-L-Phenylalanine-N-Amide Amino Acid: Effects of the Intramolecular Basis Set Superposition Error. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Li J, Xu T, Ping Y, van Mourik T, Früchtl H, Kirk SR, Jenkins S. Consequences of theory level choice evaluated with new tools from QTAIM and the stress tensor for a dipeptide conformer. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Hameed R, Khan A, van Mourik T. Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1418029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rabia Hameed
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Afsar Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Tanja van Mourik
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
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9
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Camiruaga A, Usabiaga I, Insausti A, León I, Fernández JA. Sugar-peptidic bond interactions: spectroscopic characterization of a model system. Phys Chem Chem Phys 2017; 19:12013-12021. [PMID: 28443888 DOI: 10.1039/c7cp00615b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sugars are small carbohydrates which play numerous roles in living organisms such as storage of energy or as structural components. Modifications of specific sites within the glycan chain can modulate a carbohydrate's overall biological function as it happens with nucleic acids and proteins. Hence, identifying discrete carbohydrate modifications and understanding their biological effects is essential. A study of such processes requires of a deep knowledge of the interaction mechanism at the molecular level. Here, we use a combination of laser spectroscopy in jets and quantum mechanical calculations to characterize the interaction between phenyl-β-d-glucopyranoside and N-methylacetamide as a model to understand the interaction between a sugar and a peptide bond. The most stable structure of the molecular aggregate shows that the main interaction between the peptide fragment and the sugar proceeds via a C[double bond, length as m-dash]OH-O2 hydrogen bond. A second conformer was also found, in which the peptide establishes a C[double bond, length as m-dash]OH-O6 hydrogen bond with the hydroxymethyl substituent of the sugar unit. All the conformers present an additional interaction point with the aromatic ring. This particular preference of the peptide for the hydroxyl close to the aromatic ring could explain why glycogenin uses tyrosine in order to convert glucose into glycogen by exposing the O4H hydroxyl group for the other glucoses for the polymerization to take place.
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Affiliation(s)
- Ander Camiruaga
- Dpto. de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Bo Sarriena s/n, Leioa 48940, Spain.
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10
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Kaminský J, Jensen F. Conformational Interconversions of Amino Acid Derivatives. J Chem Theory Comput 2016; 12:694-705. [PMID: 26691979 DOI: 10.1021/acs.jctc.5b00911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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11
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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12
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RETRACTED ARTICLE: Functionalized benzyls as selective κ-OR agonists. Med Chem Res 2015. [DOI: 10.1007/s00044-014-1023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Toroz D, Rosbottom I, Turner TD, Corzo DMC, Hammond RB, Lai X, Roberts KJ. Towards an understanding of the nucleation of alpha-para amino benzoic acid from ethanolic solutions: a multi-scale approach. Faraday Discuss 2015; 179:79-114. [PMID: 25920721 DOI: 10.1039/c4fd00275j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The molecular assembly and subsequent nucleation of para-amino benzoic acid (PABA) from ethanolic solutions is probed using a multi-scale and multi-technique approach. This is applied by examining and interrelating information regarding the molecular, solution-state, cluster, solid-state and surface structures to understand why the alpha form of PABA is crystallised in preference to its low temperature beta form. Calculations suggest that conformational changes within the solute molecule play little or no role in directing the nucleation of either the alpha or beta crystal forms. Combined ab initio and molecular dynamics calculations of the stability of small clusters in solution suggests that the hydrogen-bonded carboxylic acid dimers, present in the alpha structure, are the most stable in solution and play a major role in the self-assembly and polymorphic expression of the alpha form in ethanol in preference to the beta form. These calculations are in good agreement with X-ray small-angle scattering analysis which reveals the presence of PABA clusters in ethanol which are consistent with the size and shape of a carboxylic acid dimer. SAXS studies also reveal the presence of larger cluster structures in a size range 10-40 nm which appear to grow, perhaps reflecting a change in the balance between monomers and dimers within the solution during the nucleation process. The results of crystallisation-kinetics experiments indicate an instantaneous nucleation mechanism where the number of instantaneously nucleated crystallites is calculated to be 1360-660 nuclei per ml and the subsequent growth is found to be only rate limited by diffusion of the growth unit to the crystallite surface. A linear dependence of growth rate with respect to supersaturation is observed for the (0 1 -1) capping face, which is associated with strong π-π stacking interactions. This is consistent with a solid-on-solid mechanism associated with surface roughened growth and concomitant poor lattice-perfection. Conversely, the side (1 0 -1) surface has a growth mechanism consistent with a 2D nucleation birth and spread mechanism. Hence, these mechanisms result in very fast growth along the b-axis and the needle-like morphology that is observed for alpha-PABA.
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Affiliation(s)
- D Toroz
- Institute of Particle Science and Engineering and Institute of Process, Research and Development, School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
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14
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Holroyd LF, van Mourik T. Tyrosine-glycine revisited: Resolving the discrepancy between theory and experiment. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Goerigk L, Collyer CA, Reimers JR. Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures. J Phys Chem B 2014; 118:14612-26. [DOI: 10.1021/jp510148h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lars Goerigk
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Charles A. Collyer
- School
of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- Centre
for Quantum and Molecular Structure, College of Sciences, Shanghai University, Shanghai 200444, China
- School
of Physics and Advanced Materials, The University of Technology, Sydney, New South Wales 2007, Australia
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16
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Yuan Y, Mills MJL, Popelier PLA, Jensen F. Comprehensive analysis of energy minima of the 20 natural amino acids. J Phys Chem A 2014; 118:7876-91. [PMID: 25084473 DOI: 10.1021/jp503460m] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(═O)-N(H)-(H)Cα(R)-C(═O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of βL, γL, δL, and αL of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-Cα-C(═O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-Cα(HαCβ)-C'(═O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.
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Affiliation(s)
- Yongna Yuan
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester M1 7DN, Great Britain and
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17
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A fragment based step-by-step strategy for determining the most stable conformers of biomolecules. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Aguado E, León I, Millán J, Cocinero EJ, Jaeqx S, Rijs AM, Lesarri A, Fernández JA. Unraveling the Benzocaine–Receptor Interaction at Molecular Level Using Mass-Resolved Spectroscopy. J Phys Chem B 2013; 117:13472-80. [DOI: 10.1021/jp4068944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Edurne Aguado
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Iker León
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Judith Millán
- Departamento
de Química, Facultad de
Ciencias, Estudios Agroalimentarios
e Informática, Universidad de La Rioja, Madre de Dios,
51, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Sander Jaeqx
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Anouk M. Rijs
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Alberto Lesarri
- Departamento de Química Física y Química
Inorgánica, Facultad de
Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
| | - José A. Fernández
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
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19
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Goerigk L, Reimers JR. Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries. J Chem Theory Comput 2013; 9:3240-51. [DOI: 10.1021/ct400321m] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lars Goerigk
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
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20
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Wang C, Lin Z, Zhang R. Zwitterions are the most stable form for neutral arginylglycine in gas phase: Clear theoretical evidence. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Ivanova B, Spiteller M. Organosilver(i/ii) catalyzed C–N coupling reactions – phenazines. Catal Sci Technol 2013. [DOI: 10.1039/c3cy20798f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Ivanova BB, Spiteller M. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure–activity relationships. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.04.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Ivanova B, Spiteller M. Coordination ability of bradykinin with ZnII- and AgI-metal ions – Experimental and theoretical study. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.06.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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24
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Ivanova B, Spiteller M. Coordination ability of silver(I) with antimycins and actinomycins – Properties of the T-shaped chromophores. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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León I, Millán J, Cocinero EJ, Lesarri A, Castaño F, Fernández JA. Mimicking anaesthetic-receptor interaction: a combined spectroscopic and computational study of propofol···phenol. Phys Chem Chem Phys 2012; 14:8956-63. [PMID: 22516915 DOI: 10.1039/c2cp40656j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Propofol is a general anaesthetic that exerts its action by interaction with the GABA(A) receptor. Crystallographic studies suggest that there is a direct interaction between propofol and the phenolic residue of a tyrosine in the channel. In this study we create propofol···phenol clusters by their co-expansion in jets. The complex is probed using a set of mass-resolved spectroscopic strategies: 2-color REMPI, UV/UV hole-burning, IR/UV double resonance and the novel technique IR/IR/UV triple resonance. The existence of at least six different isomers in the expansion is demonstrated. All the isomers are stabilized by interactions between their aromatic rings. Additionally, in some conformers the OH moieties form hydrogen bonds in some of the isomers, with propofol and phenol alternating their donor-acceptor roles, while in others the -OH···OH angle points to a dipole-dipole interaction. Interpretation of the data in the light of dispersion-corrected DFT calculations shows that shallow barriers separate all the isomers, both in the ground and excited electronic states. Comparison of the structures of the complex with the X-ray diffraction data is also offered.
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Affiliation(s)
- Iker León
- Dpto. Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Bo Sarriena s/n, Leioa 48940, Spain
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26
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Yu W, Wu Z, Chen H, Liu X, MacKerell AD, Lin Z. Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures. J Phys Chem B 2012; 116:2269-83. [PMID: 22260814 DOI: 10.1021/jp207807a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides.
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Affiliation(s)
- Wenbo Yu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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27
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Atwood RE, Urban JJ. Conformations of the Glycine Tripeptide Analog Ac-Gly-Gly-NHMe: A Computational Study Including Aqueous Solvation Effects. J Phys Chem A 2012; 116:1396-408. [DOI: 10.1021/jp206152d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rex E. Atwood
- Chemistry Department, United States Naval Academy, 572 Holloway Road, Annapolis,
Maryland 21402, United States
| | - Joseph J. Urban
- Chemistry Department, United States Naval Academy, 572 Holloway Road, Annapolis,
Maryland 21402, United States
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Ivanova B, Spiteller M. Structure and properties of camptothecin derivatives, their protonated forms, and model interaction with the topoisomerase I-DNA complex. Biopolymers 2011; 97:134-44. [DOI: 10.1002/bip.21714] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/22/2011] [Accepted: 08/24/2011] [Indexed: 11/05/2022]
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Lamshöft M, Ivanova B. Protonation and coordination ability of small peptides – theoretical and experimental approaches for elucidation. J COORD CHEM 2011. [DOI: 10.1080/00958972.2011.598926] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Marc Lamshöft
- a Institute of Environmental Research of the Faculty of Chemistry, Dortmund University of Technology , Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Bojidarka Ivanova
- a Institute of Environmental Research of the Faculty of Chemistry, Dortmund University of Technology , Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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Abo-Riziq A, Grace L, Crews B, Callahan MP, van Mourik T, Vries MSD. Conformational Structure of Tyrosine, Tyrosyl-glycine, and Tyrosyl-glycyl-glycine by Double Resonance Spectroscopy. J Phys Chem A 2011; 115:6077-87. [DOI: 10.1021/jp110601w] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ali Abo-Riziq
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Louis Grace
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bridgit Crews
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael P. Callahan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St. Andrews North Haugh, St. Andrews, Fife KY16 9ST, Scotland, U.K
| | - Mattanjah S. de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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Toroz D, van Mourik T. Structure of the gas-phase glycine tripeptide. Phys Chem Chem Phys 2010; 12:3463-73. [DOI: 10.1039/b921897a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Cao J, van Mourik T. Performance of the M06-L density functional for a folded Tyr–Gly conformer. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Yu W, Xu X, Li H, Pang R, Fang K, Lin Z. Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers. J Comput Chem 2009; 30:2105-21. [PMID: 19242963 DOI: 10.1002/jcc.21211] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Conformations of peptides are the basis for their property studies and the predictions of peptide structures are highly important in life science but very complex in practice. Here, thorough searches on the potential energy surfaces of 13 representative dipeptides by considering all possible combinations of the bond rotational degrees of freedom are performed using the density functional theory based methods. Careful analyses of the conformers of the 13 dipeptides and the corresponding amino acids reveal the connections between the structures of dipeptide and amino acids. A method for finding all important dipeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid conformations is thus proposed. Applying the method to another eight dipeptides carefully examined by others shows that the new approach is both highly efficient and reliable by providing the most complete ensembles of dipeptide conformers and much improved agreements between the theoretical and experimental IR spectra. The method opens the door for the determination of the stable structures of all dipeptides with a manageable amount of effort. Preliminary result on the applicability of the method to the tripeptide structure determination is also presented. The results are the first step towards proving Anfinsen's hypothesis by revealing the relationships between the structures of the simplest peptide and its constituting amino acids. It implies that the structures of peptides are not only determined by their amino acid sequences, but also closely linked with the amino acid conformations.
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Affiliation(s)
- Wenbo Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
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Burke RM, Dessent CEH. Effect of cation complexation on the structure of a conformationally flexible multiply charged anion: stabilization of excess charge in the Na+ x adenosine 5'-triphosphate dianion ion-pair complex. J Phys Chem A 2009; 113:2683-92. [PMID: 19249856 DOI: 10.1021/jp805868u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report a computational study of the conformationally and tautomerically flexible cation-dianion complex of Na(+) with doubly deprotonated adenosine 5'-triphosphate (ATP) using a hierarchical selection method. The method uses molecular dynamics to generate initial conformeric structures, followed by a classification process that groups conformers into five "families" to ensure that a representative sample of structures is retained for further analysis, while very similar conformational structures are eliminated. Hierarchical ab initio calculations (DFT and MP2) of typical conformers of the families are then performed to identify the lowest-energy conformeric structures. The procedure described should provide a useful methodology for conducting higher-level ab initio calculations of medium-sized gas-phase biological molecules for interpreting contemporary laser spectroscopy measurements. For Na(+) x [ATP-2H](2) (considering tautomers where the phosphate chain of ATP is doubly deprotonated), the calculations reveal that the sodium cation interacts directly with the negatively charged phosphates (maximum distance = 2.54 A) in all of the low-energy conformers, while a number of the structures also display close cation-adenine interactions producing compact ball-like structures. These compact structures generally correspond to the lowest-energy conformers. The structural variation between the bare [ATP-2H](2-) molecular ion (Burke et al. J. Phys. Chem. A 2005 , 109 , 9775-9785) and the Na(+) x [ATP-2H](2-) cluster is discussed in detail, including the effect of sodiation on the intramolecular hydrogen-bonding network within ATP in a gas-phase environment.
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Affiliation(s)
- Ruth M Burke
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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Pluháčková K, Grimme S, Hobza P. On the Importance of Electron Correlation Effects for the Intramolecular Stacking Geometry of a Bis-Thiophene Derivative. J Phys Chem A 2008; 112:12469-74. [DOI: 10.1021/jp8051664] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kristýna Pluháčková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague, Czech Republic, Organisch-Chemisches Institut, Corrensstrasse 40, 48149 Münster, Germany, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
| | - Stefan Grimme
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague, Czech Republic, Organisch-Chemisches Institut, Corrensstrasse 40, 48149 Münster, Germany, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague, Czech Republic, Organisch-Chemisches Institut, Corrensstrasse 40, 48149 Münster, Germany, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
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Koleva BB, Zareva S, Kolev T, Spiteller M. New Au(III), Pt(II) and Pd(II) complexes with glycyl-containing homopeptides. J COORD CHEM 2008. [DOI: 10.1080/00958970802108817] [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]
Affiliation(s)
- Bojidarka B. Koleva
- a Lehrstuhl für Analytische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150 , 44780 Bochum, Germany
| | - Sonya Zareva
- b Sofia University , St. Kl. Ohridski”, 1, J. Bourchier blvd., 1164 Sofia, Bulgaria
| | - Tsonko Kolev
- c Institut für Umweltforschung, Universität Dortmund , Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Michael Spiteller
- c Institut für Umweltforschung, Universität Dortmund , Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
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van Mourik T. Basis Set Superposition Error Effects Cause the Apparent Nonexistence of the Ethene/Benzenium Ion Complex on the MP2 Potential Energy Surface. J Phys Chem A 2008; 112:11017-20. [DOI: 10.1021/jp806986t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tanja van Mourik
- School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife KY16 9ST, Scotland, U.K
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Mourik TV. Assessment of Density Functionals for Intramolecular Dispersion-Rich Interactions. J Chem Theory Comput 2008; 4:1610-9. [DOI: 10.1021/ct800231f] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tanja van Mourik
- School of Chemistry, University of St. Andrews, North Haugh Fife KY16 9ST, Scotland, U.K
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Koleva BB, Kolev T, Lamshöft M, Spiteller M. Synthesis, spectroscopic analysis and structure deduction of gold(III), palladium(II) and platinum(II) complexes with the tripeptide glycyl-l-phenylalanyl-glycine. TRANSIT METAL CHEM 2008. [DOI: 10.1007/s11243-008-9132-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Valdes H, Spiwok V, Rezac J, Reha D, Abo-Riziq A, de Vries M, Hobza P. Potential-Energy and Free-Energy Surfaces of Glycyl-Phenylalanyl-Alanine (GFA) Tripeptide: Experiment and Theory. Chemistry 2008; 14:4886-98. [DOI: 10.1002/chem.200800085] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Grimme S, Mück-Lichtenfeld C, Antony J. Analysis of non-covalent interactions in (bio)organic molecules using orbital-partitioned localized MP2. Phys Chem Chem Phys 2008; 10:3327-34. [DOI: 10.1039/b803508c] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Echenique P, Alonso JL. Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets. J Comput Chem 2008; 29:1408-22. [DOI: 10.1002/jcc.20900] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Shields AE, van Mourik T. Comparison of ab Initio and DFT Electronic Structure Methods for Peptides Containing an Aromatic Ring: Effect of Dispersion and BSSE. J Phys Chem A 2007; 111:13272-7. [DOI: 10.1021/jp076496p] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashley E. Shields
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Tanja van Mourik
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
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Kaminský J, Jensen F. Force Field Modeling of Amino Acid Conformational Energies. J Chem Theory Comput 2007; 3:1774-88. [DOI: 10.1021/ct700082f] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakub Kaminský
- Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark, and Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark, and Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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Holroyd LF, van Mourik T. Insufficient description of dispersion in B3LYP and large basis set superposition errors in MP2 calculations can hide peptide conformers. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.05.072] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Adesokan AA, Chaban GM, Dopfer O, Gerber RB. Vibrational Spectroscopy of Protonated Imidazole and its Complexes with Water Molecules: Ab Initio Anharmonic Calculations and Experiments. J Phys Chem A 2007; 111:7374-81. [PMID: 17500546 DOI: 10.1021/jp070785w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH+), and its complexes with water (ImH+)(H2O)n, are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH+)(H2O)N2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH+)H2O and (ImH+)(H2O)2 show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH+ shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH+ have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.
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Affiliation(s)
- Adeyemi A Adesokan
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, USA
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