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Zarycz MNC, Schiel MA, Angelina E, Enriz RD. Covalence and π-electron delocalization influence on hydrogen bonds in proton transfer process of o-hydroxy aryl Schiff bases: A combined NMR and QTAIM analysis. J Chem Phys 2021; 155:054307. [PMID: 34364326 DOI: 10.1063/5.0058422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Within the framework of the density functional theory approach, we studied the relationship between the chemical nature of intramolecular hydrogen bonds (HBs) and nuclear magnetic resonance (NMR) parameters, J-couplings and 1H-chemical shifts [δ(1H)], of the atoms involved in such bonds in o-hydroxyaryl Schiff bases during the proton transfer process. For the first time, the shape of the dependence of the degree of covalence in HBs on 1J(N-H), 1J(O-H), 2hJ(O-N), and δ(1H) during the proton transfer process in o-hydroxyaryl Schiff bases was analyzed. Parameters obtained from Bader's theory of atoms in molecules were used to assess the dependence of covalent character in HBs with both the NMR properties. The influence of π-electronic delocalization on 2hJ(N-O) under the proton transfer process was investigated. 2hJ(O-N) in a Mannich base was also studied in order to compare the results with an unsaturated system. In addition, substituent effects on the phenolic ring were investigated. Our results indicate that the covalent character of HBs on both sides of the transition state undergoes a smooth exponential increase as the δ(1H) moves downfield. The degree of covalence of the N⋯H (O⋯H) bond increases linearly as 1J(N-H) (1J(O-H)) becomes more negative, even after reaching the transition state. Non-vanishing values of spin dipolar (SD) and paramagnetic spin orbital terms of 2hJ(O-N) show that π-electronic delocalization has a non-negligible effect on tautomeric equilibrium and gives evidence of the presence of the resonance assisted HB.Variation of the SD term of 2hJ(O-N) follows a similar pattern as the change in the para-delocalization aromaticity index of the chelate ring.
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Affiliation(s)
- M Natalia C Zarycz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - M Ayelén Schiel
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste; Instituto de Química Básica y Aplicada (IQUIBA-NEA). CONICET, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
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Lomas JS. Relationships between NMR shifts and interaction energies in biphenyls, alkanes, aza-alkanes, and oxa-alkanes with X─H … H─Y and X─H … Z (X, Y = C or N; Z = N or O) hydrogen bonding. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:1121-1135. [PMID: 31218728 DOI: 10.1002/mrc.4900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Hydrogen-hydrogen C─H… H─C bonding between the bay-area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis-2-butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom-atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact ("in") and the other is not ("out"), show a rough correlation with the corresponding C─H… H─C exchange energies. The "in" and "in,in" isomers of selected aza- and diaza-cycloalkanes, respectively, are X─H… H─N hydrogen bonded, whereas the "out" and "in,out" isomers display X─H… N hydrogen bonds (X = C or N). Oxa-alkanes and the "in" isomers of aza-oxa-alkanes are X─H… O hydrogen bonded. There is a very good general correlation, including both N─H… H─Y (Y = C or N) and N─H… Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For "in" CH protons, the data for the different C─H… H─Y and C─H… Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory.
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Affiliation(s)
- John S Lomas
- Interfaces, Traitements, Organisation et Dynamique des Systèmes (CNRS UMR-7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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Albareda M, Palacios JM, Imperial J, Pacios LF. Computational study of the Fe(CN)2CO cofactor and its binding to HypC protein. J Phys Chem B 2013; 117:13523-33. [PMID: 24094065 DOI: 10.1021/jp407574n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the intricate maturation process of [NiFe]-hydrogenases, the Fe(CN)2CO cofactor is first assembled in a HypCD complex with iron coordinated by cysteines from both proteins and CO is added after ligation of cyanides. The small accessory protein HypC is known to play a role in delivering the cofactor needed for assembling the hydrogenase active site. However, the chemical nature of the Fe(CN)2CO moiety and the stability of the cofactor-HypC complex are open questions. In this work, we address geometries, properties, and the nature of bonding of all chemical species involved in formation and binding of the cofactor by means of quantum calculations. We also study the influence of environmental effects and binding to cysteines on vibrational frequencies of stretching modes of CO and CN used to detect the presence of Fe(CN)2CO. Carbon monoxide is found to be much more sensitive to sulfur binding and the polarity of the medium than cyanides. The stability of the HypC-cofactor complex is analyzed by means of molecular dynamics simulation of cofactor-free and cofactor-bound forms of HypC. The results show that HypC is stable enough to carry the cofactor, but since its binding cysteine is located at the N-terminal unstructured tail, it presents large motions in solution, which suggests the need for a guiding interaction to achieve delivery of the cofactor.
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Affiliation(s)
- Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo , 28223 Madrid, Spain
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Gómez-Casado C, Roth-Walter F, Jensen-Jarolim E, Díaz-Perales A, Pacios LF. Modeling iron-catecholates binding to NGAL protein. J Mol Graph Model 2013; 45:111-21. [DOI: 10.1016/j.jmgm.2013.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022]
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5
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Gálvez O, Gómez Martín JC, Gómez PC, Saiz-Lopez A, Pacios LF. A theoretical study on the formation of iodine oxide aggregates and monohydrates. Phys Chem Chem Phys 2013; 15:15572-83. [DOI: 10.1039/c3cp51219c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Sibrian-Vazquez M, Escobedo JO, Lowry M, Fronczek FR, Strongin RM. Field effects induce bathochromic shifts in xanthene dyes. J Am Chem Soc 2012; 134:10502-8. [PMID: 22642754 PMCID: PMC3384756 DOI: 10.1021/ja302445w] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is ongoing interest in near-infrared (NIR) absorbing and emitting dyes for a variety of biomedical and materials applications. Simple and efficient synthetic procedures enable the judicious tuning of through-space polar (field) effects as well as low barrier hydrogen bonding to modulate the HOMO-LUMO gap in xanthene dyes. This affords unique NIR-absorbing xanthene chromophores.
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Affiliation(s)
- Martha Sibrian-Vazquez
- Department of Chemistry, Portland State University, 1719 SW 10th Ave., Portland, Oregon 97201, United States
| | - Jorge O. Escobedo
- Department of Chemistry, Portland State University, 1719 SW 10th Ave., Portland, Oregon 97201, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University, 1719 SW 10th Ave., Portland, Oregon 97201, United States
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Robert M. Strongin
- Department of Chemistry, Portland State University, 1719 SW 10th Ave., Portland, Oregon 97201, United States
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7
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Martyniak A, Majerz I, Filarowski A. Peculiarities of quasi-aromatic hydrogen bonding. RSC Adv 2012. [DOI: 10.1039/c2ra20846f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Majerz I, Dziembowska T. Does the five-member hydrogen bond ring in quinoline carboxamides exist? J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Filarowski A, Majerz I. AIM Analysis of Intramolecular Hydrogen Bonding in O-Hydroxy Aryl Schiff Bases. J Phys Chem A 2008; 112:3119-26. [DOI: 10.1021/jp076253x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- A. Filarowski
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
| | - I. Majerz
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
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Cheng M, Pu X, Wong NB, Li M, Tian A. Substituent effects on the hydrogen-bonded complex of aniline–H2O: a computational study. NEW J CHEM 2008. [DOI: 10.1039/b717465a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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11
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Tafazzoli M, Amini S. A survey of hydrogen bonding in imidazole and its 4-nitro derivative by ab initio and DFT calculations of chemical shielding. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.09.089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLoS Biol 2006; 4:e99. [PMID: 16602823 PMCID: PMC1413570 DOI: 10.1371/journal.pbio.0040099] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 01/27/2006] [Indexed: 11/19/2022] Open
Abstract
A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p
Ka models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p
Ka unit, suggesting a bond shortening of ˜0.02 Å/p
Ka unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = −0.2 kcal/mol/p
Ka unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = −2.0 kcal/mol/p
Ka unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ˜300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
Enzymatic reactions require exquisitely detailed molecular interactions. Here the authors show that geometric complementarity is likely more important than electrostatic charge in contributing to the binding necessary for catalytic reactions.
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Affiliation(s)
- Daniel A Kraut
- 1Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Paul A Sigala
- 1Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Brandon Pybus
- 2Department of Biochemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Corey W Liu
- 3Stanford Magnetic Resonance Laboratory, Stanford University, Stanford, California, United States of America
| | - Dagmar Ringe
- 2Department of Biochemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gregory A Petsko
- 2Department of Biochemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Daniel Herschlag
- 1Department of Biochemistry, Stanford University, Stanford, California, United States of America
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Pacios LF, Gómez PC, Gálvez O. Variation of atomic charges on proton transfer in strong hydrogen bonds: The case of anionic and neutral imidazole–acetate complexes. J Comput Chem 2006; 27:1650-61. [PMID: 16900495 DOI: 10.1002/jcc.20476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.
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Affiliation(s)
- Luis F Pacios
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.T.S.I. Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain.
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14
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Pacios LF. Computational study of the process of hydrogen bond breaking: The case of the formamide–formic acid complex. J Comput Chem 2006; 27:1641-9. [PMID: 16900492 DOI: 10.1002/jcc.20475] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) quantum calculations are used to study the formamide-formic acid complex (FFAC), a system bound by two hydrogen bonds, N--H...O and O--H...O, that forms a bond ring at equilibrium. When the intermolecular separation between monomers R increases, this ring opens at a distance for which the weaker N--H...O bond breaks remaining the stronger O--H...O bond. The computational study characterizes that process addressing changes of interaction energy DeltaE, structure and properties of the electron density rho(r) as well as spatial distributions of rho(r), the electrostatic potential U(r), and the electron localization function eta(r). It is shown that the spatial derivatives of DeltaE, the topology of rho(r), and qualitative changes noticed in U(r) = 0 isocontours allow to identify a precise distance R for which one can say the N--H...O hydrogen bond has broken. Both levels of theory predict essentially the same changes of structure and electron properties associated to the process of breaking and virtually identical distances at which it takes place.
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Affiliation(s)
- Luis F Pacios
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.T.S.I. Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain.
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Pacios LF, Gálvez O, Gómez PC. Variation of geometries and electron properties along proton transfer in strong hydrogen-bond complexes. J Chem Phys 2005; 122:214307. [PMID: 15974738 DOI: 10.1063/1.1899103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proton transfer in hydrogen-bond systems formed by 4-methylimidazole in both neutral and protonated cationic forms and by acetate anion are studied by means of MP26-311++G(d,p) ab initio calculations. These two complexes model the histidine (neutral and protonated)-aspartate diad present in the active sites of enzymes the catalytic mechanism of which involves the formation of strong hydrogen bonds. We investigate the evolution of geometries, natural bond orbital populations of bonds and electron lone pairs, topological descriptors of the electron density, and spatial distributions of the electron localization function along the process N-H...O-->N...H...O-->N...H-O, which represents the stages of the H-transfer. Except for a sudden change in the population of electron lone pairs in N and O at the middle N...H...O stage, all the properties analyzed show a smooth continuous behavior along the covalent --> hydrogen bond transit inherent to the transfer, without any discontinuity that could identify a formation or breaking of the hydrogen bond. This way, the distinction between covalent or hydrogen-bonding features is associated to subtle electron rearrangement at the intermolecular space.
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Affiliation(s)
- L F Pacios
- Unidad de Química, Departamento de Biotecnología, E.T.S.I. Montes, Universidad Politécnica de Madrid, Madrid 28040, Spain.
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