1
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Fox AC, Boettger JD, Berger EL, Burton AS. The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations. Life (Basel) 2023; 13:1796. [PMID: 37763200 PMCID: PMC10532638 DOI: 10.3390/life13091796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.
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Affiliation(s)
- Allison C. Fox
- NASA Postdoctoral Program, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Jason D. Boettger
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Eve L. Berger
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
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2
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Kabanda MM, Bahadur I, Singh P. Antioxidant and anticancer properties of plant‐based bioactive flavonoids cardamonin and alpinetin: A theoretical insight from
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OOH antiradical and Cu (II) chelation mechanisms. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mwadham M. Kabanda
- Department of Chemistry, School of Natural and Mathematical Sciences, Faculty of Science, Engineering and Agriculture University of Venda Thohoyandou South Africa
| | - Indra Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North‐West University South Africa
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi New Delhi India
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3
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Da-yang TE, Fifen JJ, Conradie J, Conradie MM. Structures, temperature effect, binding and clustering energies of Cu2+(MeOH)n=1-8 clusters and extrapolations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119439] [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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4
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Madala NE, Kabanda MM. LC-MS based validation and DFT investigation on the antioxidant properties of clovamide: •OH and •OOH scavenging and Cu(II) chelation mechanisms. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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5
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Kabanda MM, Gbashi S, Madala NE. Proportional coexistence of okanin chalcone glycoside and okanin flavanone glycoside in Bidens pilosa leaves and theoretical investigation on the antioxidant properties of their aglycones. Free Radic Res 2020; 55:53-70. [PMID: 33267705 DOI: 10.1080/10715762.2020.1859107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bidens pilosa plant has been shown to produce okanin flavanone glycoside and its chalcone derivative. In most other plants, due to chalcone isomerase enzyme, the flavanone tends to exist in higher proportions than their chalcone precursors. Herein we have utilized liquid chromatography-mass spectrometry approach and shown that within the leaves of Bidens pilosa plant the two okanin glycosides exist in unusual equal proportional distribution, which indicates that Bidens pilosa plant is an alternative rich source of these highly sought-after antioxidant molecules. The aglycone okanin chalcone (ONC) and okanin flavanone (ONF) have experimentally been shown to exhibit antioxidant activity. However, experimental findings have not conclusively determined which of the two compounds is a more potent antiradical than the other. Herein, the density functional theory (DFT) method is utilized to establish, from structural and thermodynamic energetic considerations, the preferred antioxidant molecule between the two aglycone okanins. A theoretical study on the antioxidant properties of ONC and ONF has been performed by considering their radical scavenging and metal cation (Mn+, where M = Cu(II) or Fe (III)) chelation ability. The study has been performed using B3LYP/6-31 + G(d,p) method. In the case of the metal chelation mechanism, the LANL2DZ pseudo-potential was selected to describe the selected Mn+ cations. The results of the study suggest that ONC is a better radical scavenger than ONF because of the extended electron delocalization on its neutral radical, which is due to the presence of conjugation within the ONC neutral radical after hydrogen atom abstraction. In the metal chelation mechanism, it is noted that the binding energies depend on the media, the nature of the ligand and the cation and the cation coordination site on the ligand. The charge and the spin density on Mn+ decrease on coordination to the ligand. The ability of the ligands to reduce Mn+ cations, coupled with the strong Mn+ binding properties, has significant implication on the antioxidant ability of both okanins. However, since ONC⋅⋅⋅M+n interaction results in higher binding energy than ONF⋅⋅⋅M+n interaction, the implication is that ONC is a preferred free metal ion chelator than ONF.
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Affiliation(s)
- Mwadham M Kabanda
- Department of Chemistry, University of Venda, Thohoyandou, South Africa
| | - Sefater Gbashi
- Department of Biotechnology and Food Technology, University of Johannesburg, Auckland Park, South Africa
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6
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Roglans A, Pla-Quintana A, Solà M. Mechanistic Studies of Transition-Metal-Catalyzed [2 + 2 + 2] Cycloaddition Reactions. Chem Rev 2020; 121:1894-1979. [DOI: 10.1021/acs.chemrev.0c00062] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna Roglans
- Institut de Quı́mica Computacional i Catàlisi (IQCC) and Departament de Quı́mica, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003, Girona, Catalonia, Spain
| | - Anna Pla-Quintana
- Institut de Quı́mica Computacional i Catàlisi (IQCC) and Departament de Quı́mica, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003, Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Quı́mica Computacional i Catàlisi (IQCC) and Departament de Quı́mica, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003, Girona, Catalonia, Spain
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7
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Stasyuk AJ, Stasyuk OA, Solà M, Voityuk AA. Cyclo[18]carbon: the smallest all-carbon electron acceptor. Chem Commun (Camb) 2020; 56:352-355. [DOI: 10.1039/c9cc08399e] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recently synthesized C18 molecule demonstrates strong electron acceptor properties similar to C60.
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Affiliation(s)
- Anton J. Stasyuk
- Institute of Computational Chemistry and Catalysis and Department of Chemistry University of Girona
- 17003 Girona
- Spain
| | - Olga A. Stasyuk
- Institute of Computational Chemistry and Catalysis and Department of Chemistry University of Girona
- 17003 Girona
- Spain
| | - Miquel Solà
- Institute of Computational Chemistry and Catalysis and Department of Chemistry University of Girona
- 17003 Girona
- Spain
| | - Alexander A. Voityuk
- Institute of Computational Chemistry and Catalysis and Department of Chemistry University of Girona
- 17003 Girona
- Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA)
- 08010 Barcelona
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8
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Ferullo RM, Zubieta CE, Belelli PG. Hydrogenated polycyclic aromatic hydrocarbons (HnPAHs) as catalysts for hydrogenation reactions in the interstellar medium: a quantum chemical model. Phys Chem Chem Phys 2019; 21:12012-12020. [DOI: 10.1039/c9cp02329a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional studies show that neutral HnPAHs are able to catalyze the formation of water with no activation barrier.
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Affiliation(s)
- Ricardo M. Ferullo
- Departamento de Química
- Universidad Nacional del Sur – INQUISUR (UNS, CONICET)
- 8000 Bahía Blanca
- Argentina
| | - Carolina E. Zubieta
- Departamento de Química
- Universidad Nacional del Sur – INQUISUR (UNS, CONICET)
- 8000 Bahía Blanca
- Argentina
| | - Patricia G. Belelli
- Grupo de Materiales y Sistemas Catalíticos – IFISUR (UNS, CONICET)
- 8000 Bahía Blanca
- Argentina
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9
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Mammino L. Complexes of arzanol with a Cu 2+ ion: a DFT study. J Mol Model 2017; 23:276. [PMID: 28900733 DOI: 10.1007/s00894-017-3443-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/15/2017] [Indexed: 11/29/2022]
Abstract
Arzanol (C22H26O7) is a naturally occurring acylphloroglucinol largely responsible for the anti-inflammatory, anti-oxidant, antibiotic and antiviral activities of Helichrysum italicum. Like all acylphloroglucinols, the molecule contains a carboxylic substituent (-COR group); for arzanol, this is a -COCH3 group. The molecule is further characterized by the presence of an α-pyrone ring bonded in meta to -COR through a methylene bridge, and of a prenyl chain bonded to the other meta position. The molecule can form up to three intramolecular hydrogen bonds (IHB) simultaneously, and their presence and patterns are the major stabilizing factors. This work considers complexes of representative conformers of arzanol with a Cu2+ ion, taking into account the different possibilities for the binding of the Cu2+ ion to the electron-density rich sites of the molecule and including simultaneous coordination to two geometrically suitable sites. Calculations were performed at the DFT/B3LYP level, using the 6-31+G(d,p) basis set for the C, O and H atoms and the LANL2DZ pseudopotential for the Cu2+ ion. Interaction energies show preference for simultaneous binding of Cu2+ to two sites. Simultaneous binding to the O of a phenol OH neighboring the prenyl chain and to the π bond of the prenyl chain appears to be the most favorable option, followed by simultaneous binding to the sp2 O of the α-pyrone ring and the O of the phenol OH ortho to -COR on the side of the α-pyrone ring. The charge of the Cu2+ ion is reduced to +1 or slightly less in the complexes, which is consistent with the molecules' antioxidant (reducing) ability. Graphical abstract The copper ion prefers to attach to two sites of the arzanol molecule simultaneously. The arzanol molecule reduces the charge of the copper ion from +2 to +1 by transferring an electron to it; it becomes a radical molecular cation. The distribution of the unpaired electron in the molecule (as highlighted by the spin density maps) depends on the site/s to which the Cu2+ ion binds and on the molecule's conformer.
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Affiliation(s)
- Liliana Mammino
- Department of Chemistry, University of Venda, Thohoyandou, South Africa.
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10
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Song X, Li S, Jiang Z, Zhang Y. Theoretical study on structures and infrared spectroscopy of Cu2+(H2O)Ar n (n = 1–4). RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s003602441709031x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Galván-García EA, Agacino-Valdés E, Franco-Pérez M, Gómez-Balderas R. [Cu(H2O) n ]2+ (n = 1–6) complexes in solution phase: a DFT hierarchical study. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2056-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Goings JJ, Ohlsen SM, Blaisdell KM, Schofield DP. Sorption of H2 to Open Metal Sites in a Metal–Organic Framework: A Symmetry-Adapted Perturbation Theory Analysis. J Phys Chem A 2014; 118:7411-7. [DOI: 10.1021/jp412779q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Joshua J. Goings
- Department of Chemistry and
Biochemistry, Seattle Pacific University, Seattle, Washington 98119, United States
| | - Suzanna M. Ohlsen
- Department of Chemistry and
Biochemistry, Seattle Pacific University, Seattle, Washington 98119, United States
| | - Kara M. Blaisdell
- Department of Chemistry and
Biochemistry, Seattle Pacific University, Seattle, Washington 98119, United States
| | - Daniel P. Schofield
- Department of Chemistry and
Biochemistry, Seattle Pacific University, Seattle, Washington 98119, United States
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13
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Georgieva I, Mihaylov T, Trendafilova N. Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies. J Inorg Biochem 2014; 135:100-12. [PMID: 24680836 DOI: 10.1016/j.jinorgbio.2014.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 11/15/2022]
Abstract
The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed.
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Affiliation(s)
- I Georgieva
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 11 Acad. G. Bonchev Str., Sofia, Bulgaria.
| | - Tz Mihaylov
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 11 Acad. G. Bonchev Str., Sofia, Bulgaria
| | - N Trendafilova
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 11 Acad. G. Bonchev Str., Sofia, Bulgaria
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14
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Rivada-Wheelaghan O, Ortuño MA, García-Garrido SE, Díez J, Alonso PJ, Lledós A, Conejero S. A stable, mononuclear, cationic Pt(iii) complex stabilised by bulky N-heterocyclic carbenes. Chem Commun (Camb) 2014; 50:1299-301. [DOI: 10.1039/c3cc48553f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The thermally stable, mononuclear, paramagnetic Pt(iii) complex [PtI2(IPr)2][BArF] exhibiting a square-planar structure has been isolated and fully characterised.
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Affiliation(s)
- Orestes Rivada-Wheelaghan
- Instituto de Investigaciones Químicas (IIQ)
- Departamento de Química Inorgánica
- CSIC and Universidad de Sevilla
- 41092 Sevilla, Spain
| | - Manuel A. Ortuño
- Departament de Química
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès, Spain
| | - Sergio E. García-Garrido
- Laboratorio de Compuestos Organometálicos y Catálisis (Unidad asociada al CSIC)
- Departamento de Química Orgánica e Inorgánica
- Universidad de Oviedo
- Oviedo, Spain
| | - Josefina Díez
- Laboratorio de Compuestos Organometálicos y Catálisis (Unidad asociada al CSIC)
- Departamento de Química Orgánica e Inorgánica
- Universidad de Oviedo
- Oviedo, Spain
| | - Pablo J. Alonso
- Instituto de Ciencia de Materiales de Aragón (ICMA)
- Universidad de Zaragoza and CSIC
- Zaragoza, Spain
| | - Agustí Lledós
- Departament de Química
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès, Spain
| | - Salvador Conejero
- Instituto de Investigaciones Químicas (IIQ)
- Departamento de Química Inorgánica
- CSIC and Universidad de Sevilla
- 41092 Sevilla, Spain
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15
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Conde A, Vilella L, Balcells D, Díaz-Requejo MM, Lledós A, Pérez PJ. Introducing Copper as Catalyst for Oxidative Alkane Dehydrogenation. J Am Chem Soc 2013; 135:3887-96. [DOI: 10.1021/ja310866k] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ana Conde
- Laboratorio de Catálisis
Homogénea, Departamento de Química y Ciencia de los
Materiales, Unidad Asociada al CSIC, CIQSO-Centro de Investigación
en Química Sostenible, Universidad de Huelva, Campus de El Carmen 21007 Huelva, Spain
| | - Laia Vilella
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra,
Spain
| | - David Balcells
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra,
Spain
- Centre for Theoretical
and Computational
Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern N-0315, Oslo, Norway
| | - M. Mar Díaz-Requejo
- Laboratorio de Catálisis
Homogénea, Departamento de Química y Ciencia de los
Materiales, Unidad Asociada al CSIC, CIQSO-Centro de Investigación
en Química Sostenible, Universidad de Huelva, Campus de El Carmen 21007 Huelva, Spain
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra,
Spain
| | - Pedro J. Pérez
- Laboratorio de Catálisis
Homogénea, Departamento de Química y Ciencia de los
Materiales, Unidad Asociada al CSIC, CIQSO-Centro de Investigación
en Química Sostenible, Universidad de Huelva, Campus de El Carmen 21007 Huelva, Spain
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16
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Kabanda MM, Ebenso EE. Structures, Stabilization Energies, and Binding Energies of Quinoxaline···(H2O)n, Quinoxaline Dimer, and Quinoxaline···Cu Complexes: A Theoretical Study. J Phys Chem A 2013; 117:1583-95. [PMID: 23343309 DOI: 10.1021/jp309356b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mwadham M. Kabanda
- Department of Chemistry, North-West University (Mafikeng Campus), Private Bag x2046, Mmabatho 2735,
South Africa
| | - Eno E. Ebenso
- Department of Chemistry, North-West University (Mafikeng Campus), Private Bag x2046, Mmabatho 2735,
South Africa
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17
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Dancing multiplicity states supported by a carboxylated group in dicopper structures bonded to O2. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1336-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Mammino L. Investigation of the antioxidant properties of hyperjovinol A through its Cu(II) coordination ability. J Mol Model 2012; 19:2127-42. [DOI: 10.1007/s00894-012-1684-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 11/06/2012] [Indexed: 11/28/2022]
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19
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Rivada-Wheelaghan O, Ortuño MA, Díez J, García-Garrido SE, Maya C, Lledós A, Conejero S. Characterization of a Paramagnetic, Mononuclear Pt(III)–Alkyl Complex Intermediate in Carbon–Halogen Bond Coupling Reactions. J Am Chem Soc 2012; 134:15261-4. [DOI: 10.1021/ja307139p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Orestes Rivada-Wheelaghan
- Instituto de Investigaciones
Químicas (IIQ), Departamento de Química Inorgánica, CSIC and Universidad de Sevilla, Avda. Américo
Vespucio 49, 41092, Sevilla, Spain
| | - Manuel A. Ortuño
- Departament de Química, Universitat Autònoma de Barcelona, Edifici Cn,
08193 Cerdanyola del Vallès, Spain
| | - Josefina Díez
- Laboratorio de Compuestos Organometálicos
y Catálisis (Unidad Asociada al CSIC), Departamento de Química
Orgánica e Inorgánica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - Sergio E. García-Garrido
- Laboratorio de Compuestos Organometálicos
y Catálisis (Unidad Asociada al CSIC), Departamento de Química
Orgánica e Inorgánica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - Celia Maya
- Instituto de Investigaciones
Químicas (IIQ), Departamento de Química Inorgánica, CSIC and Universidad de Sevilla, Avda. Américo
Vespucio 49, 41092, Sevilla, Spain
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, Edifici Cn,
08193 Cerdanyola del Vallès, Spain
| | - Salvador Conejero
- Instituto de Investigaciones
Químicas (IIQ), Departamento de Química Inorgánica, CSIC and Universidad de Sevilla, Avda. Américo
Vespucio 49, 41092, Sevilla, Spain
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20
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He Y, Bin Y, Liang Y, Xiang J. Density functional investigation of the molecular structures, vibrational and absorption spectra of metal thiolate complexes, M(SC6H5)3 (M=As, Sb or Bi). COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Sánchez-Sanz G, Alkorta I, Elguero J, Yáñez M, Mó O. Strong interactions between copper halides and unsaturated systems: new metallocycles? Or the importance of deformation. Phys Chem Chem Phys 2012; 14:11468-77. [PMID: 22801772 DOI: 10.1039/c2cp41230f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The complexes formed by CuF with CC double and triple bonds have been studied at the MP2 and CCSD(T) computational levels. The interaction of CuF with acetylene, ethylene and their fluoro derivatives is very strong, with interaction energies close to those of conventional covalent bonds. Hence, these complexes could be actually viewed as a new kind of metallocycles, with significantly strong Cu-C linkages. All electronic indexes analyzed by means of the AIM, ELF and NBO formalisms, indicate that the strength of the interaction should increase with the number of fluorine substituents in both series of compounds. Surprisingly, however, although both series of compounds exhibit the same bonding arrangements, they follow opposite stability trends and the expected increase of the interaction energies with the number of fluorine substituents is only observed in the acetylene series. The reason for this unexpected behavior is once more associated with the effects triggered by the distortion of the interacting subunits. Deformation not only has a direct energetic cost but dramatically affects the intrinsic properties of the interacting systems.
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Affiliation(s)
- Goar Sánchez-Sanz
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
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22
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Liu Z, Cheng R, He X, Wu X, Liu B. DFT Functional Benchmarking on the Energy Splitting of Chromium Spin States and Mechanistic Study of Acetylene Cyclotrimerization over the Phillips Cr(II)/Silica Catalyst. J Phys Chem A 2012; 116:7538-49. [DOI: 10.1021/jp302529q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zhen Liu
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130
Meilong Road, 200237 Shanghai, China
| | - Ruihua Cheng
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130
Meilong Road, 200237 Shanghai, China
| | - Xuelian He
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130
Meilong Road, 200237 Shanghai, China
| | - Xiaojun Wu
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130
Meilong Road, 200237 Shanghai, China
| | - Boping Liu
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130
Meilong Road, 200237 Shanghai, China
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23
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A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion. J Mol Model 2012; 18:1365-74. [PMID: 21761180 PMCID: PMC3313029 DOI: 10.1007/s00894-011-1162-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 06/24/2011] [Indexed: 11/30/2022]
Abstract
The present study analyzed binding of Cu2+ to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches including electron correlation effects. In order to shed light on the character of interactions between Cu2+ and peptides, which are expected to be mainly electrostatic in nature, decomposition of interaction energy into physically meaningful components was applied.
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24
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Dahl EW, Baddour FG, Fiedler SR, Hoffert WA, Shores MP, Yee GT, Djukic JP, Bacon JW, Rheingold AL, Doerrer LH. Antiferromagnetic coupling across a tetrametallic unit through noncovalent interactions. Chem Sci 2012. [DOI: 10.1039/c1sc00608h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Alí-Torres J, Maréchal JD, Rodríguez-Santiago L, Sodupe M. Three dimensional models of Cu(2+)-Aβ(1-16) complexes from computational approaches. J Am Chem Soc 2011; 133:15008-14. [PMID: 21846101 DOI: 10.1021/ja203407v] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Elucidation of the coordination of metal ions to Aβ is essential to understand their role in its aggregation and to rationally design new chelators with potential therapeutic applications in Alzheimer disease. Because of that, in the last 10 years several studies have focused their attention in determining the coordination properties of Cu(2+) interacting with Aβ. However, more important than characterizing the first coordination sphere of the metal is the determination of the whole Cu(2+)-Aβ structure. In this study, we combine homology modeling (HM) techniques with quantum mechanics based approaches (QM) to determine plausible three-dimensional models for Cu(2+)-Aβ(1-16) with three histidines in their coordination sphere. We considered both ε and δ coordination of histidines 6, 13, and 14 as well as the coordination of different possible candidates containing oxygen as fourth ligand (Asp1, Glu3, Asp7, Glu11, and CO(Ala2)). Among the 32 models that enclose COO(-), the lowest energy structures correspond to [O(E3),N(δ)(H6),N(ε)(H13),N(ε)(H14)] (1), [O(E3),N(δ)(H6),N(δ)(H13),N(δ)(H14)] (2), and [O(D7),N(ε)(H6),N(δ)(H13),N(δ)(H14)] (3). The most stable model containing CO(Ala2) as fourth ligand in the Cu(2+) coordination sphere is [O(c)(A2),N(ε)(H6),N(δ)(H13),N(ε)(H14)] (4). An estimation of the relative stability between Glu3 (1) and CO(Ala2) (4) coordinated complexes seems to indicate that the preference for the latter coordination may be due to solvent effects. The present results also show the relationship between the peptidic and metallic moieties in defining the overall geometry of the complex and illustrate that the final stability of the complexes results from a balance between the metal coordination site and amyloid folding upon complexation.
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Affiliation(s)
- Jorge Alí-Torres
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
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26
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Martín EI, Martínez JM, Sánchez Marcos E. Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine. J Chem Phys 2011; 134:024503. [PMID: 21241116 DOI: 10.1063/1.3528934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.
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Affiliation(s)
- Elisa I Martín
- Departamento de Química Física, Universidad de Sevilla, E-41012 Sevilla, Spain
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27
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Corral I, Palacios A, Yáñez M. Electronic structure and lifetimes of GaX2+ (X = N, O, F) in the gas phase. Unraveling stability trends. Phys Chem Chem Phys 2011; 13:18365-72. [DOI: 10.1039/c1cp21534e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Alí-Torres J, Rodríguez-Santiago L, Sodupe M. Computational calculations of pKa values of imidazole in Cu(ii) complexes of biological relevance. Phys Chem Chem Phys 2011; 13:7852-61. [DOI: 10.1039/c0cp02319a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Corral I, Yáñez M. [MLn]2+ doubly charged systems: modeling, bonding, life times and unimolecular reactivity. Phys Chem Chem Phys 2011; 13:14848-64. [DOI: 10.1039/c1cp20622b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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30
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Rios-Font R, Sodupe M, Rodríguez-Santiago L, Taylor PR. The Role of Exact Exchange in the Description of Cu2+−(H2O)n (n = 1−6) Complexes by Means of DFT Methods. J Phys Chem A 2010; 114:10857-63. [DOI: 10.1021/jp105376s] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Raquel Rios-Font
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Luis Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Peter R. Taylor
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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31
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van Duin ACT, Bryantsev VS, Diallo MS, Goddard WA, Rahaman O, Doren DJ, Raymand D, Hermansson K. Development and validation of a ReaxFF reactive force field for Cu cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases. J Phys Chem A 2010; 114:9507-14. [PMID: 20707333 PMCID: PMC4224311 DOI: 10.1021/jp102272z] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H(2)O)(n)](2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H(2)O)(n)](2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion, and inversion in [Cu(H(2)O)(6)](2+) clusters and first- and second-shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis.
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Affiliation(s)
- Adri C T van Duin
- Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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32
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Jeanvoine Y, Spezia R. Cu2+ binding chalcogen–chalcogen bridges: A problematic case for DFT. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of L-histidine and zwitterionic L-histidine. Amino Acids 2010; 39:1309-19. [PMID: 20364281 DOI: 10.1007/s00726-010-0573-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
Abstract
Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-histidine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water on structures of His·M(H2O)m, m=0.1 complexes have been determined theoretically employing density functional theories using extended basis sets. Of the five stable complexes investigated the relative stability of the gas-phase complexes computed with DFT methods (with one exception of K+ systems) suggest metallic complexes of the neutral L-histidine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of L-histidine in the presence of the metal cations Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+ were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to L-histidine is exhibited by the Cu2+ cation. The computed Gibbs energies ΔG are negative, span a rather broad energy interval (from -130 to -1,300 kJ/mol), and upon hydration are appreciably lowered.
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34
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Cramer CJ, Truhlar DG. Density functional theory for transition metals and transition metal chemistry. Phys Chem Chem Phys 2009; 11:10757-816. [PMID: 19924312 DOI: 10.1039/b907148b] [Citation(s) in RCA: 1079] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.
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Affiliation(s)
- Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA.
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35
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Alagona G, Ghio C. Antioxidant Properties of Pterocarpans through Their Copper(II) Coordination Ability. A DFT Study in Vacuo and in Aqueous Solution. J Phys Chem A 2009; 113:15206-16. [DOI: 10.1021/jp905521u] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Giuliano Alagona
- CNR-IPCF, Institute for Physico-Chemical Processes, MML, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Caterina Ghio
- CNR-IPCF, Institute for Physico-Chemical Processes, MML, Via Moruzzi 1, I-56124 Pisa, Italy
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36
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Xerri B, Flament JP, Petitjean H, Berthomieu C, Berthomieu D. Vibrational Modeling of Copper−Histamine Complexes: Metal−Ligand IR Modes Investigation. J Phys Chem B 2009; 113:15119-27. [DOI: 10.1021/jp905917z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bertrand Xerri
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Jean-Pierre Flament
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Hugo Petitjean
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Catherine Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Dorothee Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
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37
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Damin A, Vitillo JG, Ricchiardi G, Bordiga S, Lamberti C, Groppo E, Zecchina A. Modeling CO and N2 Adsorption at Cr Surface Species of Phillips Catalyst by Hybrid Density Functionals: Effect of Hartree−Fock Exchange Percentage. J Phys Chem A 2009; 113:14261-9. [DOI: 10.1021/jp902650m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alessandro Damin
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
| | - Jenny G. Vitillo
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
| | - Gabriele Ricchiardi
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
| | - Silvia Bordiga
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
| | - Carlo Lamberti
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
| | - Elena Groppo
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
| | - Adriano Zecchina
- Dipartimento di Chimica IFM, and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, University of Torino, Via P.Giuria 7, I-10125 Torino
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38
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Poater A. Oxidation of Copper(I) Hexaaza Macrocyclic Dinuclear Complexes. J Phys Chem A 2009; 113:9030-40. [DOI: 10.1021/jp9040716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Albert Poater
- Modeling Lab for Nanostructures and Catalysis (MoLNaC), Dipartimento di Chimica, Università degli Studi di Salerno, via Ponte don Melillo, Fisciano (SA) 84084, Italy
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39
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Constantino E, Rimola A, Sodupe M, Rodríguez-Santiago L. Coordination of (Glycyl)nglycine (n = 1−3) to Co+ and Co2+. J Phys Chem A 2009; 113:8883-92. [DOI: 10.1021/jp901179t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Erika Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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40
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Su P, Li H. Energy decomposition analysis of covalent bonds and intermolecular interactions. J Chem Phys 2009; 131:014102. [DOI: 10.1063/1.3159673] [Citation(s) in RCA: 749] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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Jeanvoine Y, Spezia R. Mn2+-, Fe2+-, Co2+-, Ni2+-, Cu2+-, and Zn2+-Binding Chalcogen−Chalcogen Bridges: A Compared MP2 and B3LYP Study. J Phys Chem A 2009; 113:7878-87. [DOI: 10.1021/jp811460f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yannick Jeanvoine
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587 CNRS, Université d’Evry Val d’Essonne, Bd F. Mitterrand, 91025 Evry Cedex, France
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587 CNRS, Université d’Evry Val d’Essonne, Bd F. Mitterrand, 91025 Evry Cedex, France
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42
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Güell M, Luis JM, Rodríguez-Santiago L, Sodupe M, Solà M. Structure, Bonding, and Relative Stability of the Ground and Low-Lying Electronic States of CuO2. The Role of Exact Exchange. J Phys Chem A 2009; 113:1308-17. [DOI: 10.1021/jp8031379] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mireia Güell
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi E-17071, Girona, Catalonia, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - Josep M. Luis
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi E-17071, Girona, Catalonia, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - Luís Rodríguez-Santiago
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi E-17071, Girona, Catalonia, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - Mariona Sodupe
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi E-17071, Girona, Catalonia, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - Miquel Solà
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi E-17071, Girona, Catalonia, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
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43
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Alagona G, Ghio C. Plicatin B conformational landscape and affinity to copper (I and II) metal cations. A DFT study. Phys Chem Chem Phys 2009; 11:776-90. [DOI: 10.1039/b813464b] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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44
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Estephane J, Groppo E, Vitillo JG, Damin A, Lamberti C, Bordiga S, Zecchina A. Chromocene in porous polystyrene: an example of organometallic chemistry in confined spaces. Phys Chem Chem Phys 2009; 11:2218-27. [DOI: 10.1039/b814109f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Constantino E, Tortajada J, Sodupe M, Rodríguez-Santiago L. Coordination Properties of Lysine Interacting with Co(I) and Co(II). A Theoretical and Mass Spectrometry Study. J Phys Chem A 2008; 112:12385-92. [DOI: 10.1021/jp805764y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - J. Tortajada
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - M. Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - L. Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
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Bryantsev VS, Diallo MS, van Duin ACT, Goddard III WA. Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model. J Phys Chem A 2008; 112:9104-12. [DOI: 10.1021/jp804373p] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vyacheslav S. Bryantsev
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
| | - Mamadou S. Diallo
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
| | - Adri C. T. van Duin
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
| | - William A. Goddard III
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
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Remko M, Fitz D, Rode BM. Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of L-arginine and zwitterionic L-arginine. J Phys Chem A 2008; 112:7652-61. [PMID: 18652440 DOI: 10.1021/jp801418h] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-arginine is examined. The effects of metal ions (Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+)) and water on structures of Arg x M(H2O)m , m = 0, 1 complexes have been determined theoretically by employing the density functional theories (DFT) and using extended basis sets. Of the three stable complexes investigated, the relative stability of the gas-phase complexes computed with DFT methods (with the exception of K(+) systems) suggests metallic complexes of the neutral L-arginine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of arginine in the presence of the metal cations Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+) were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to arginine is exhibited by the Cu(2+) cation. The computed Gibbs energies DeltaG(o) are negative, span a rather broad energy interval (from -150 to -1500 kJ/mol), and are appreciably lowered upon hydration.
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Affiliation(s)
- Milan Remko
- Department of Pharmaceutical Chemistry, Comenius University, Odbojarov 10, SK-832 32 Bratislava, Slovakia.
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Noguera M, Bertran J, Sodupe M. Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes. J Phys Chem B 2008; 112:4817-25. [PMID: 18358032 DOI: 10.1021/jp711982g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system. However, when Cu+ interacts with thymine, through the O2 carbonyl atom, the single proton transfer from thymine to adenine becomes thermodynamically spontaneous, and thus rare forms of the DNA bases may spontaneously appear. For Cu2+ cation, important effects on proton-transfer processes appear due to oxidation of the base pair, which stabilizes the different single proton-transfer products. Results for hydrated systems show that the presence of the water molecules interacting with the metal cation (and their mode of coordination) can strongly influence the ability of Cu2+ to induce oxidation on the base pair.
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Affiliation(s)
- Marc Noguera
- Departament de Química, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
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Ferrari AM, Pisani C. Reactivity of the non stoichiometric Ni3O4 phase supported at the Pd(100) surface: interaction with Au and other transition metal atoms. Phys Chem Chem Phys 2008; 10:1463-70. [PMID: 18309404 DOI: 10.1039/b717842e] [Citation(s) in RCA: 12] [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 have studied, employing ab initio periodic calculations, the interaction between the non-stoichiometric Ni(3)O(4) monolayer (a rhombic distribution of vacancies hereafter referred to as RH-Ni(3)O(4)) supported on the Pd(100) surface and several transition metal atoms (Ni, Cu, Pd, Pt, Ag, Au). The interaction produces a regular array of metal centers uniformly distributed in size and shape. According to the size of the atom and the ionization potential, the nature of the interaction ranges from an essentially electrostatic one to a polar-covalent one. The chemical reactivity versus the CO molecule of the overlayer resulting from the saturation with Au atoms of the Ni vacancies has been investigated.
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Affiliation(s)
- Anna Maria Ferrari
- Dipartimento di Chimica IFM and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, 10125 Torino, Italy
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50
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Rimola A, Constantino E, Rodríguez-Santiago L, Sodupe M. Binding Properties of Cu+/2+-(glycyl)nglycine Complexes (n = 1−3). J Phys Chem A 2008; 112:3444-53. [DOI: 10.1021/jp711189s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Erika Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | | | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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