1
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Tupikina EY, Sigalov MV, Alkhuder O, Tolstoy PM. Charge Relay Without Proton Transfer: Coupling of Two Short Hydrogen Bonds via Imidazole in Models of Catalytic Triad of Serine Protease Active Site. Chemphyschem 2024; 25:e202300970. [PMID: 38563616 DOI: 10.1002/cphc.202300970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
A homologous series of 20 substituted alcohol-imidazole-acetate model complexes imitating the charge relay system in Ser-His-Asp catalytic triad of serine proteases is considered quantum-chemically. We show qualitatively that the geometries of alcohol-imidazole and imidazole-acetate short hydrogen bonds are strongly coupled via the central imidazole and such complexes are capable of effectively relaying the charge from acetate to alcohol moiety upon relatively small concerted proton displacements. We hypothesize an alternative catalytic mechanism of serine proteases that does not require two complete proton transfers or hydrogen bond breakage between Ser and His residues.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Mark V Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Omar Alkhuder
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
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2
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Perrin CL. Symmetry of Hydrogen Bonds: Application of NMR Method of Isotopic Perturbation and Relevance of Solvatomers. Molecules 2023; 28:molecules28114462. [PMID: 37298938 DOI: 10.3390/molecules28114462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Short, strong, symmetric, low-barrier hydrogen bonds (H-bonds) are thought to be of special significance. We have been searching for symmetric H-bonds by using the NMR technique of isotopic perturbation. Various dicarboxylate monoanions, aldehyde enols, diamines, enamines, acid-base complexes, and two sterically encumbered enols have been investigated. Among all of these, we have found only one example of a symmetric H-bond, in nitromalonamide enol, and all of the others are equilibrating mixtures of tautomers. The nearly universal lack of symmetry is attributed to the presence of these H-bonded species as a mixture of solvatomers, meaning isomers (or stereoisomers or tautomers) that differ in their solvation environment. The disorder of solvation renders the two donor atoms instantaneously inequivalent, whereupon the hydrogen attaches to the less well solvated donor. We therefore conclude that there is no special significance to short, strong, symmetric, low-barrier H-bonds. Moreover, they have no heightened stability or else they would have been more prevalent.
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Affiliation(s)
- Charles L Perrin
- Department of Chemistry & Biochemistry University of California, La Jolla, San Diego, CA 92093, USA
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3
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Marceca E, Noble JA, Dedonder-Lardeux C, Jouvet C. Loss of CO 2 from Monodeprotonated Phthalic Acid upon Photodissociation and Dissociative Electron Detachment. J Phys Chem A 2021; 125:7406-7413. [PMID: 34415759 DOI: 10.1021/acs.jpca.1c04854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The decarboxylation (CO2 loss) mechanism of cold monodeprotonated phthalic acid was studied in a photodissociation action spectrometer by quantifying mass-selected product anions and neutral particles as a function of the excitation energy. The analysis proceeded by interpreting the translational energy distribution of the generated uncharged products, and with the help of quantum calculations. In particular, this study reveals different fragmentation pathways in the deprotonated anion and in the radical generated upon electron photodetachment. Unlike the behavior found in other deprotonated aryl carboxylic acids, which do not fragment in the anion excited state, a double loss of CO2 molecules takes place in the phthalic monoanion. Moreover, at higher excitation energies the phthalic monoanion experiences decarboxylative photodetachment with a statistical distribution of product translational energies, which contrasts with the impulsive dissociation reactions characteristic of other aryl carboxylic anions.
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Affiliation(s)
- Ernesto Marceca
- INQUIMAE (CONICET-Universidad de Buenos Aires), DQIAQF (Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria), 3er piso, Pab. II, 1428 Buenos Aires, Argentina
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4
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Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State. Symmetry (Basel) 2021. [DOI: 10.3390/sym13050756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide).
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5
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Jóźwiak K, Jezierska A, Panek JJ, Goremychkin EA, Tolstoy PM, Shenderovich IG, Filarowski A. Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates. Molecules 2020; 25:E4720. [PMID: 33066679 PMCID: PMC7587347 DOI: 10.3390/molecules25204720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 01/18/2023] Open
Abstract
Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car-Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.
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Affiliation(s)
- Kinga Jóźwiak
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
| | - Eugene A. Goremychkin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia;
| | - Ilya G. Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
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6
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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7
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Perrin CL, Shrinidhi A, Burke KD. Isotopic-Perturbation NMR Study of Hydrogen-Bond Symmetry in Solution: Temperature Dependence and Comparison of OHO and ODO Hydrogen Bonds. J Am Chem Soc 2019; 141:17278-17286. [PMID: 31590490 DOI: 10.1021/jacs.9b08492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Is a hydrogen bond symmetric, with the hydrogen centered between two donor atoms, or is it asymmetric, with the hydrogen closer to one but jumping to the other? The NMR method of isotopic perturbation has been used to distinguish these. Previous evidence from isotope shifts implies that a wide variety of dicarboxylate monanions are asymmetric, present as a rapidly equilibrating mixture of tautomers. However, calculations of hydrogen trajectories across an anharmonic potential-energy surface could reproduce the observed isotope shifts in a phthalate monoanion. Therefore, it was concluded that those isotope shifts are instead consistent with isotope-induced desymmetrization on a symmetric potential-energy surface. To distinguish between these two interpretations, the 18O-induced isotope effects on the 13C NMR chemical shifts of cyclohexene-1,2-dicarboxylate monoanion in chloroform-d and on the 19F NMR chemical shifts of difluoromaleate monoanion in D2O have been investigated. In both cases the isotope effects are larger at lower temperature and also with deuterium in the hydrogen bond. It is concluded that these behaviors are consistent with the perturbation of an equilibrium between asymmetric tautomers and inconsistent with isotope-induced desymmetrization on a symmetric potential-energy surface.
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Affiliation(s)
- Charles L Perrin
- Department of Chemistry and Biochemistry , University of California-San Diego , La Jolla , California 92093-0358 , United States
| | - Annadka Shrinidhi
- Department of Chemistry and Biochemistry , University of California-San Diego , La Jolla , California 92093-0358 , United States
| | - Kathryn D Burke
- Department of Chemistry and Biochemistry , University of California-San Diego , La Jolla , California 92093-0358 , United States
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8
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Milovanović B, Stanković IM, Petković M, Etinski M. Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution. Chemphyschem 2019; 20:2852-2859. [PMID: 31544323 DOI: 10.1002/cphc.201900704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/31/2019] [Indexed: 11/10/2022]
Abstract
The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O-H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.
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Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
| | | | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
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9
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Koeppe B, Pylaeva SA, Allolio C, Sebastiani D, Nibbering ETJ, Denisov GS, Limbach HH, Tolstoy PM. Polar solvent fluctuations drive proton transfer in hydrogen bonded complexes of carboxylic acid with pyridines: NMR, IR and ab initio MD study. Phys Chem Chem Phys 2018; 19:1010-1028. [PMID: 27942642 DOI: 10.1039/c6cp06677a] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We study a series of intermolecular hydrogen-bonded 1 : 1 complexes formed by chloroacetic acid with 19 substituted pyridines and one aliphatic amine dissolved in CD2Cl2 at low temperature by 1H and 13C NMR and FTIR spectroscopy. The hydrogen bond geometries in these complexes vary from molecular (O-HN) to zwitterionic (O-H-N+) ones, while NMR spectra show the formation of short strong hydrogen bonds in intermediate cases. Analysis of C[double bond, length as m-dash]O stretching and asymmetric CO2- stretching bands in FTIR spectra reveal the presence of proton tautomerism. On the basis of these data, we construct the overall proton transfer pathway. In addition to that, we also study by use of ab initio molecular dynamics the complex formed by chloroacetic acid with 2-methylpyridine, surrounded by 71 CD2Cl2 molecules, revealing a dual-maximum distribution of hydrogen bond geometries in solution. The analysis of the calculated trajectory shows that the proton jumps between molecular and zwitterionic forms are indeed driven by dipole-dipole solvent-solute interactions, but the primary cause of the jumps is the formation/breaking of weak CHO bonds from solvent molecules to oxygen atoms of the carboxylate group.
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Affiliation(s)
- B Koeppe
- Department of Chemistry, Humboldt-Universität zu Berlin, Germany
| | - S A Pylaeva
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg, Germany.
| | - C Allolio
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg, Germany.
| | - D Sebastiani
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg, Germany.
| | - E T J Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
| | - G S Denisov
- Department of Physics, St.Petersburg State University, Russia
| | - H-H Limbach
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - P M Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University, Russia.
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10
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Madurga S, Nedyalkova M, Mas F, Garcés JL. Ionization and Conformational Equilibria of Citric Acid: Delocalized Proton Binding in Solution. J Phys Chem A 2017; 121:5894-5906. [PMID: 28703587 DOI: 10.1021/acs.jpca.7b05089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microspeciation of citric acid is studied by analyzing NMR titration data. When the site binding (SB) model, which assumes fully localized proton binding to the carboxylic groups, is used to obtain microscopic energy parameters (dissociation constants, pair and triplet interaction energies between charged carboxylate groups), contradictory results are obtained. The resulting macroscopic constants are in very good agreement with the values reported in the literature using potentiometry. However, the found pair interaction energy between the terminal carboxylates and the triplet interaction energy are physically meaningless. To solve this apparent contradiction, we consider the possibility of delocalized proton binding, so that the proton can be exchanged at high velocity in the NMR time scale through short, strong, low-barrier (SSLB) hydrogen bonds. With this aim, ab initio MP2 calculations using the SMD polarizable continuum model for the solvent were performed and the fully roto-microspeciation elucidated. First, fully localized proton binding was assumed, and the resulting microstate probabilities are in reasonable agreement with those reported in previous works that use selective blocking of the carboxylic groups. They are, however, in clear disagreement with the microstate probabilities derived from the NMR titration data, which predict, within a very narrow confidence interval, a unique microspecies for the symmetric di-ionized form. Moreover, counterintuitively, the interaction between terminal charged groups is much larger than that between central and terminal groups. As a consequence, we have explored the possibility of delocalized proton binding by calculating the energy of intermediate proton positions between two carbolxylic groups. The results reveal that the exchange of the proton through the hydrogen bonds is in some cases produced without energetic barrier. This effect is specially relevant in the di-ionized form, with all the most stable conformations forming a SSLB, which together would constitute the only microstate detected by NMR. An alternative reaction scheme for the ionization process, based on proton delocalization, is proposed.
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Affiliation(s)
- Sergio Madurga
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB) , C/Martı́ i Franquès, 1, 08028 Barcelona, Catalonia, Spain
| | - Miroslava Nedyalkova
- Inorganic Chemistry Department, Faculty of Chemistry and Pharmacy "St Kliment Ohridski", University of Sofia , 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Francesc Mas
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB) , C/Martı́ i Franquès, 1, 08028 Barcelona, Catalonia, Spain
| | - Josep Lluís Garcés
- Chemistry Department and AGROTECNIO, University of Lleida (UdL) , Rovira Roure, 191, 25198 Lleida Catalonia, Spain
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11
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Lu J, Hung I, Brinkmann A, Gan Z, Kong X, Wu G. Solid-State 17 O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong. Angew Chem Int Ed Engl 2017; 56:6166-6170. [PMID: 28225158 DOI: 10.1002/anie.201700488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Indexed: 11/07/2022]
Abstract
While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state 17 O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state 17 O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol-1 , suggesting that not all LBHBs are particularly strong.
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Affiliation(s)
- Jiasheng Lu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Andreas Brinkmann
- Measurement Science and Standards, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario, K1A 0R6, Canada
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Xianqi Kong
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
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12
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Lu J, Hung I, Brinkmann A, Gan Z, Kong X, Wu G. Solid‐State
17
O NMR Reveals Hydrogen‐Bonding Energetics: Not All Low‐Barrier Hydrogen Bonds Are Strong. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700488] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiasheng Lu
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance National High Magnetic Field Laboratory 1800 East Paul Dirac Drive Tallahassee FL 32310 USA
| | - Andreas Brinkmann
- Measurement Science and Standards National Research Council Canada 1200 Montreal Road Ottawa Ontario K1A 0R6 Canada
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance National High Magnetic Field Laboratory 1800 East Paul Dirac Drive Tallahassee FL 32310 USA
| | - Xianqi Kong
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Gang Wu
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario K7L 3N6 Canada
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13
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Pylaeva SA, Elgabarty H, Sebastiani D, Tolstoy PM. Symmetry and dynamics of FHF− anion in vacuum, in CD2Cl2 and in CCl4. Ab initio MD study of fluctuating solvent–solute hydrogen and halogen bonds. Phys Chem Chem Phys 2017; 19:26107-26120. [DOI: 10.1039/c7cp04493c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asymmetric solvation of FHF− by halogen- and hydrogen-bonding solvents breaks the symmetry of the anion.
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Affiliation(s)
- S. A. Pylaeva
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - H. Elgabarty
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - D. Sebastiani
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - P. M. Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University
- Russia
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14
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Affiliation(s)
- Charles L. Perrin
- Department of Chemistry & Biochemistry University of California, San Diego, La Jolla, California 92093-0358, United States
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15
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Mori Y, Masuda Y. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Bedin M, Karim A, Reitti M, Carlsson ACC, Topić F, Cetina M, Pan F, Havel V, Al-Ameri F, Sindelar V, Rissanen K, Gräfenstein J, Erdélyi M. Counterion influence on the N-I-N halogen bond. Chem Sci 2015; 6:3746-3756. [PMID: 29218144 PMCID: PMC5707496 DOI: 10.1039/c5sc01053e] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/20/2015] [Indexed: 12/13/2022] Open
Abstract
A detailed investigation of the influence of counterions on the [N-I-N]+ halogen bond in solution, in the solid state and in silico is presented. Translational diffusion coefficients indicate close attachment of counterions to the cationic, three-center halogen bond in dichloromethane solution. Isotopic perturbation of equilibrium NMR studies performed on isotopologue mixtures of regioselectively deuterated and nondeuterated analogues of the model system showed that the counterion is incapable of altering the symmetry of the [N-I-N]+ halogen bond. This symmetry remains even in the presence of an unfavorable geometric restraint. A high preference for the symmetric geometry was found also in the solid state by single crystal X-ray crystallography. Molecular systems encompassing weakly coordinating counterions behave similarly to the corresponding silver(i) centered coordination complexes. In contrast, systems possessing moderately or strongly coordinating anions show a distinctly different behavior. Such silver(i) complexes are converted into multi-coordinate geometries with strong Ag-O bonds, whereas the iodine centered systems remain linear and lack direct charge transfer interaction with the counterion, as verified by 15N NMR and DFT computation. This suggests that the [N-I-N]+ halogen bond may not be satisfactorily described in terms of a pure coordination bond typical of transition metal complexes, but as a secondary bond with a substantial charge-transfer character.
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Affiliation(s)
- Michele Bedin
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
| | - Alavi Karim
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
| | - Marcus Reitti
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
| | - Anna-Carin C Carlsson
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
| | - Filip Topić
- University of Jyvaskyla , Department of Chemistry , Nanoscience Center , P.O. Box. 35, FI-40014 University of Jyvaskyla , Finland
| | - Mario Cetina
- University of Jyvaskyla , Department of Chemistry , Nanoscience Center , P.O. Box. 35, FI-40014 University of Jyvaskyla , Finland
- Department of Applied Chemistry , Faculty of Textile Technology , University of Zagreb , Prilaz baruna Filipovića 28a , HR-10000 Zagreb , Croatia
| | - Fangfang Pan
- University of Jyvaskyla , Department of Chemistry , Nanoscience Center , P.O. Box. 35, FI-40014 University of Jyvaskyla , Finland
| | - Vaclav Havel
- Department of Chemistry and RECETOX , Masaryk University , Kamenice 5 , 625 00 Brno , Czech Republic
| | - Fatima Al-Ameri
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
| | - Vladimir Sindelar
- Department of Chemistry and RECETOX , Masaryk University , Kamenice 5 , 625 00 Brno , Czech Republic
| | - Kari Rissanen
- University of Jyvaskyla , Department of Chemistry , Nanoscience Center , P.O. Box. 35, FI-40014 University of Jyvaskyla , Finland
| | - Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden . ; Tel: +46-31-786 9033
- The Swedish NMR Centre , Medicinaregatan 5 , SE-413 90 Gothenburg , Sweden
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17
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Pylaeva S, Allolio C, Koeppe B, Denisov GS, Limbach HH, Sebastiani D, Tolstoy PM. Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system. Phys Chem Chem Phys 2015; 17:4634-44. [PMID: 25586486 DOI: 10.1039/c4cp04727c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.
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Affiliation(s)
- Svetlana Pylaeva
- Department of Physics, St. Petersburg State University, Ulianovskaya st. 3, 198504 St. Petersburg, Russia.
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18
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Abstract
Complexes containing multiple arginines are common in proteins. The arginines are typically salt-bridged or hydrogen-bonded, so that their charges do not repel. Here we present a quantum calculation of a ring in which the components of a salt bridge composed of a guanidinium, the arginine side chain, and a carboxylic acid are separated by water molecules. When one water molecule is displaced from the ring, atomic charges of the other water molecule, as well as other properties, are significantly affected. The exchange and correlation energy differences between optimized and displaced rings are larger than thermal energy at room temperature, and larger than the sum of other energy differences. This suggests that calculations on proteins and other systems where such a ring may occur must take quantum effects into account; charges on certain atoms shift as substituents are added to the system: another water molecule, an -OH, or -CN bonded to either moiety. Also, charge shifts accompany proton shifts from the acid to guanidinium to ionize the salt bridge. The consequences of moving one water out of the ring give evidence for electron delocalization. Bond order and atomic charges are determined using natural bond orbital calculations. The geometry of the complex changes with ionization as well as the -OH and -CN additions but not in a simple manner. These results help in understanding the role of groups of arginines in salt-bridged clusters in proteins.
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Affiliation(s)
- Alisher M Kariev
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Michael E Green
- Department of Chemistry, City College of New York, New York, New York 10031, United States
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19
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20
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Perrin CL, Burke KD. Variable-temperature study of hydrogen-bond symmetry in cyclohexene-1,2-dicarboxylate monoanion in chloroform-d. J Am Chem Soc 2014; 136:4355-62. [PMID: 24527684 DOI: 10.1021/ja500174y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The symmetry of the hydrogen bond in hydrogen cyclohexene-1,2-dicarboxylate monoanion was determined in chloroform using the NMR method of isotopic perturbation. As the temperature decreases, the (18)O-induced (13)C chemical-shift separations increase not only at carboxyl carbons but also at ipso (alkene) carbons. The magnitude of the ipso increase is consistent with an (18)O isotope effect on carboxylic acid acidity. Therefore it is concluded that this monoanion is a mixture of tautomers in rapid equilibrium, rather than a single symmetric structure in which a chemical-shift separation arises from coupling between a desymmetrizing vibration and anharmonic isotope-dependent vibrations, which is expected to show the opposite temperature dependence.
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Affiliation(s)
- Charles L Perrin
- Department of Chemistry, University of California-San Diego , La Jolla, California 92093-0358, United States
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21
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Kawashima Y, Tachikawa M. Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion. J Chem Theory Comput 2013; 10:153-63. [DOI: 10.1021/ct4007986] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yukio Kawashima
- Quantum Chemistry Division, Graduate School of Science, Graduate
School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division, Graduate School of Science, Graduate
School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan
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22
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Kawashima Y, Tachikawa M. Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.03.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Guo J, Tolstoy PM, Koeppe B, Golubev NS, Denisov GS, Smirnov SN, Limbach HH. Hydrogen Bond Geometries and Proton Tautomerism of Homoconjugated Anions of Carboxylic Acids Studied via H/D Isotope Effects on 13C NMR Chemical Shifts. J Phys Chem A 2012; 116:11180-8. [DOI: 10.1021/jp304943h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Guo
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Peter M. Tolstoy
- Department of Chemistry, St. Petersburg State University, Universitetsky Pr.
26, 198504, St. Petersburg, Russia
| | - Benjamin Koeppe
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Nikolai S. Golubev
- Department of Physics, St. Petersburg State University, Uljanovskaja 1, 198504,
St. Petersburg, Russia
| | - Gleb S. Denisov
- Department of Physics, St. Petersburg State University, Uljanovskaja 1, 198504,
St. Petersburg, Russia
| | - Sergei N. Smirnov
- Department of Chemistry, St. Petersburg State University, Universitetsky Pr.
26, 198504, St. Petersburg, Russia
| | - Hans-Heinrich Limbach
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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24
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Mori Y, Takano K. Location of protons in N–H⋯N hydrogen-bonded systems: a theoretical study on intramolecular pyridine–dihydropyridine and pyridine–pyridinium pairs. Phys Chem Chem Phys 2012; 14:11090-8. [DOI: 10.1039/c2cp41425b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Dopieralski P, Perrin CL, Latajka Z. On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective. J Chem Theory Comput 2011; 7:3505-13. [PMID: 26598249 DOI: 10.1021/ct200580c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water.
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Affiliation(s)
| | - Charles L Perrin
- Department of Chemistry and Biochemistry, University of California at San Diego , La Jolla, California 92093-0358, United States
| | - Zdzislaw Latajka
- Faculty of Chemistry, University of Wroclaw , Joliot-Curie 14, 50-383 Wroclaw, Poland
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26
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Guo J, Tolstoy PM, Koeppe B, Denisov GS, Limbach HH. NMR study of conformational exchange and double-well proton potential in intramolecular hydrogen bonds in monoanions of succinic acid and derivatives. J Phys Chem A 2011; 115:9828-36. [PMID: 21809856 DOI: 10.1021/jp201073j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a (1)H, (2)H, and (13)C NMR study of the monoanions of succinic (1), meso- and rac-dimethylsuccinic (2, 3), and methylsuccinic (4) acids (with tetraalkylammonium as the counterion) dissolved in CDF(3)/CDF(2)Cl at 300-120 K. In all four monoanions, the carboxylic groups are linked by a short intramolecular OHO hydrogen bond revealed by the bridging-proton chemical shift of about 20 ppm. We show that the flexibility of the carbon skeleton allows for two gauche isomers in monoanions 1, 2, and 4, interconverting through experimental energy barriers of 10-15 kcal/mol (the process itself and the energy barrier are also reproduced in MP2/6-311++G** calculations). In 3, one of the gauche forms is absent because of the steric repulsion of the methyl groups. In all four monoanions, the bridging proton is located in a double-well potential and subject, at least to some extent, to proton tautomerism, for which we estimate the two proton positions to be separated by ca. 0.2 Å. In 1 and 3, the proton potential is symmetric. In 2, slowing the conformational interconversion introduces an asymmetry to the proton potential, an effect that might be strong enough even to synchronize the proton tautomerism with the interconversion of the two gauche forms. In 4, the asymmetry of the proton potential is due to the asymmetric substitution. The intramolecular H-bond is likely to remain intact during the interconversion of the gauche forms in 1, 3, and 4, whereas the situation in 2 is less clear.
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Affiliation(s)
- Jing Guo
- Institute of Chemistry and Biochemistry, Free University of Berlin , Takustrasse 3, D-14195 Berlin, Germany
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27
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Guo J, Koeppe B, Tolstoy PM. Trimethylglycine complexes with carboxylic acids and HF: solvation by a polar aprotic solvent. Phys Chem Chem Phys 2011; 13:2335-41. [DOI: 10.1039/c0cp01659d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Abstract
In a symmetric hydrogen bond (H-bond), the hydrogen atom is perfectly centered between the two donor atoms. The energy diagram for hydrogen motion is thus a single-well potential, rather than the double-well potential of a more typical H-bond, in which the hydrogen is covalently bonded to one atom and H-bonded to the other. Examples of symmetric H-bonds are often found in crystal structures, and they exhibit the distinctive feature of unusually short length: for example, the O-O distance in symmetric OHO H-bonds is found to be less than 2.5 Å. In comparison, the O-O distance in a typical asymmetric H-bond, such as ROH···OR(2), ranges from about 2.7 to 3.0 Å. In this Account, we briefly review and update our use of the method of isotopic perturbation to search for a symmetric, centered, or single-well-potential H-bond in solution. Such low-barrier H-bonds are thought to be unusually strong, owing perhaps to the resonance stabilization of two identical resonance forms [A-H···B ↔ A···H-B]. This presumptive bond strength has been invoked to explain some enzyme-catalyzed reactions. Yet in solution, a wide variety of OHO, OHN, and NHN H-bonds have all been found to be asymmetric, in double-well potentials. Examples include the monoanion of (±)-2,3-di-tert-butylsuccinic acid and a protonated tetramethylnaphthalenediamine, even though these two ions are often considered prototypes of species with strong H-bonds. In fact, all of the purported examples of strong, symmetric H-bonds have been found to exist in solution as pairs of asymmetric tautomers, in contrast to their symmetry in some crystals. The asymmetry can be attributed to the disorder of the local solvation environment, which leads to an equilibrium among solvatomers (that is, isomers that differ in solvation). If the disorder of the local environment is sufficient to break symmetry, then symmetry itself is not sufficient to stabilize the H-bond, and symmetric H-bonds do not have an enhanced stability or an unusual strength. Nor are short H-bonds unusually strong. We discuss previous evidence for "short, strong, low-barrier" H-bonds and show it to be based on ambiguous comparisons. The role of such H-bonds in enzyme-catalyzed reactions is then ascribed not to any unusual strength of the H-bond itself but to relief of "strain."
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Affiliation(s)
- Charles L. Perrin
- Department of Chemistry & Biochemistry, University of California—San Diego, La Jolla, California 92093-0358, United States
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29
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Pirc G, Stare J, Mavri J. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate. J Chem Phys 2010; 132:224506. [PMID: 20550407 DOI: 10.1063/1.3429251] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.
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Affiliation(s)
- Gordana Pirc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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30
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Sigalov M, Vainer R, Khodorkovsky V. Strong intramolecular hydrogen bonding within the dimedone–aldehyde adducts. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Molecular dynamics simulations and mechanism of organic reactions: non-TST behaviors. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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32
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DFT studies and AIM analysis of intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ5-[1,2]oxaphosphinin-4-one and its derivatives. Struct Chem 2009. [DOI: 10.1007/s11224-009-9556-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Perrin CL, Lau JS, Kim YJ, Karri P, Moore C, Rheingold AL. Asymmetry of the “Strongest” OHO Hydrogen Bond, in the Monoanion of (±)-α,α′-Di-tert-butylsuccinate. J Am Chem Soc 2009; 131:13548-54. [DOI: 10.1021/ja905806h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Charles L. Perrin
- Department of Chemistry, University of California—San Diego, La Jolla, California 92093-0358
| | - Jonathan S. Lau
- Department of Chemistry, University of California—San Diego, La Jolla, California 92093-0358
| | - Yeong-Joon Kim
- Department of Chemistry, University of California—San Diego, La Jolla, California 92093-0358
| | - Phaneendrasai Karri
- Department of Chemistry, University of California—San Diego, La Jolla, California 92093-0358
| | - Curtis Moore
- Department of Chemistry, University of California—San Diego, La Jolla, California 92093-0358
| | - Arnold L. Rheingold
- Department of Chemistry, University of California—San Diego, La Jolla, California 92093-0358
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34
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Abstract
A classic question regarding hydrogen bonds (H-bonds) concerns their symmetry. Is the hydrogen centered or is it closer to one donor and jumping between them? These possibilities correspond to single- and double-well potentials, respectively. The NMR method of isotopic perturbation can answer this question. It is illustrated with 3-hydroxy-2-phenylpropenal and then applied to dicarboxylate monoanions. The 18O-induced 13C NMR splittings signify that their intramolecular H-bonds are asymmetric and that each species is a pair of tautomers, not a single symmetric structure, even though maleate and phthalate are symmetric in crystals. The asymmetry is seen across a wide range of solvents and a wide variety of monoanions, including 2,3-di-tert-butylsuccinate and zwitterionic phthalates. Asymmetry is also seen in monoprotonated 1,8-bis(dimethylamino)naphthalenediamines, N,N'-diaryl-6-aminofulvene-2-aldimines, and 6-hydroxy-2-formylfulvene. The asymmetry is attributed to the disorder of the local environment, establishing an equilibrium between solvatomers. The broader implications of these results regarding the role of solvation in breaking symmetry are discussed. It was prudent to confirm a secondary deuterium isotope effect (IE) on amine basicity by NMR titration of a mixture of PhCH2NH2 and PhCHDNH2. The IE is of stereoelectronic origin. It is proposed that symmetric H-bonds can be observed in crystals but not in solution because a disordered environment induces asymmetry, whereas a crystal can guarantee a symmetric environment. The implications for the controversial role of low-barrier H-bonds in enzyme-catalyzed reactions are discussed.
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Affiliation(s)
- Charles L. Perrin
- 1Department of Chemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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35
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Perrin CL, Lau JS. Hydrogen-Bond Symmetry in Zwitterionic Phthalate Anions: Symmetry Breaking by Solvation. J Am Chem Soc 2006; 128:11820-4. [PMID: 16953621 DOI: 10.1021/ja063797o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cationic nitrogen of zwitterion 1 is located symmetrically with respect to its intramolecular OHO hydrogen bond. Incorporation of one (18)O allows investigation of the H-bond symmetry by the NMR method of isotopic perturbation. In both CD(3)OD and CD(2)Cl(2) equilibrium isotope shifts are detected at the carboxyl and ipso carbons. Therefore, 1 exists as a pair of interconverting tautomers, not as a single symmetric structure with its hydrogen centered between the two oxygens. The H-bond is instantaneously asymmetric, and there is an equilibrium between solvatomers (isomers or stereoisomers that differ in solvation). The broader implications of this result regarding the role of the local environment ("solvation") in breaking symmetry are discussed.
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Affiliation(s)
- Charles L Perrin
- Department of Chemistry, University of California-San Diego, La Jolla, California 92093-0506, USA.
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36
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Pakiari A, Eskandari K. The chemical nature of very strong hydrogen bonds in some categories of compounds. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.10.040] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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37
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Emmler T, Gieschler S, Limbach H, Buntkowsky G. A simple method for the characterization of OHO-hydrogen bonds by 1H-solid state NMR spectroscopy. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.01.045] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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39
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Balcells D, Drudis-Solé G, Besora M, Dölker N, Ujaque G, Maseras F, Lledós A. Some critical issues in the application of quantum mechanics/molecular mechanics methods to the study of transition metal complexes. Faraday Discuss 2003; 124:429-41; discussion 443-55. [PMID: 14527230 DOI: 10.1039/b211473a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of quantum mechanics/molecular mechanics (QM/MM) methods in transition metal chemistry is growing steadily. It becomes therefore appropriate to assess the importance of a number of technical issues associated to their implementation. This work presents the discussion of several of these issues, including the eventual need for conformational searches, the choice of the MM force field and the possibility of its tuning. The examples presented here prove that a proper handling of these technical aspects can lead to an improvement in the efficiency and quality of QM/MM calculations.
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Affiliation(s)
- David Balcells
- Unitat de Química Física, Edifici Cn, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
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40
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Yamataka H, Aida M. Ab Initio Direct Molecular Dynamics Simulations and QM/MM Computations in Search of Organic Reaction Mechanisms. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.2555] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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41
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Perrin CL, Ohta BK. Symmetry of O-H-O and N-H-N hydrogen bonds in 6-hydroxy-2-formylfulvene and 6-aminofulvene-2-aldimines. Bioorg Chem 2002; 30:3-15. [PMID: 11954999 DOI: 10.1006/bioo.2001.1222] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The symmetry of the hydrogen bonds in 6-hydroxy-2-formylfulvene and two N,N'-diaryl-6-aminofulvene-2-aldimines is probed by the NMR technique of isotopic perturbation. Observed deuterium-induced 13C NMR isotope shifts at several positions can be attributed to a combination of an intrinsic shift and the perturbation of a tautomeric equilibrium. The most dramatic are at the aldehydic or aldiminic carbon signals, where the observed isotope shift for the unlabeled carbon is +376 or +223 ppb. This large downfield shift is contrary to the small upfield shift expected for a four-bond intrinsic shift and can be attributed only to a perturbation shift. Therefore these intramolecular hydrogen bonds are asymmetric, the proton resides in a double-minimum potential surface, and each molecule exists as a pair of rapidly interconverting tautomers, regardless of solvent. The symmetry of the hydrogen bond is not governed only by the O-O or N-N distance. It is proposed that symmetric hydrogen bonds can be observed in crystalline phases but not as yet in solution because the disorder of the solvation environment induces an asymmetry of the hydrogen bond, whereas a crystal can guarantee a symmetric environment. These results provide no insight into the source of the stabilization attributed to low-barrier hydrogen bonds if they lack the special feature of symmetry.
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Affiliation(s)
- Charles L Perrin
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0358, USA.
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42
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Perrin CL, Ohta BK. Symmetry of N-H-N hydrogen bonds in 1,8-bis(dimethylamino)naphthalene.H+ and 2,7-dimethoxy-1,8-bis(dimethylamino)naphthalene.H+. J Am Chem Soc 2001; 123:6520-6. [PMID: 11439038 DOI: 10.1021/ja0036965] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In solution, are the hydrogen bonds in monoprotonated N,N,N',N'-tetramethyl-1,8-naphthalenediamines single- or double-well? To answer this question, isotopic perturbation of equilibrium is applied to a mixture of -d(0), -d(3), -d(6), -d(9), and -d(12) isotopologs. The N-methyls of the 2,7-dimethoxy analogue show intrinsic isotope shifts from the geminal CD(3) and from only one distant CD(3), an unusual stereochemical effect transmitted across the hydrogen bond. The (13)C NMR splittings and intensities at the various ring carbons of both ions are consistent with perturbation isotope shifts, intrinsic shifts, or a combination of both. The perturbation shifts mean that the protons reside in a double-minimum potential and that each ion is a pair of rapidly interconverting tautomers. The significance of this result for the role of low-barrier hydrogen bonds in enzyme-catalyzed reactions is discussed.
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Affiliation(s)
- C L Perrin
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093-0358, USA
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43
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Loring JS, Karlsson M, Fawcett WR, Casey WH. Infrared spectra of phthalic acid, the hydrogen phthalate ion, and the phthalate ion in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:1635-1642. [PMID: 11471716 DOI: 10.1016/s1386-1425(01)00391-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The infrared spectra of a series of aqueous solutions containing phthalic acid (1,2-benzenedicarboxylic acid) and varying pH were examined using attenuated total reflection Fourier transform infrared spectroscopy and potentiometry. The basis spectra of phthalic acid, the hydrogen phthalate ion, and the phthalate ion were isolated using a factor analysis in which the absorbance of these species varies with pH and total phthalate concentration according to equilibrium and mass balance relations. Assignments of these basis spectra were made by comparison with spectra calculated ab initio. The conditional formation constants of phthalic acid and the hydrogen phthalate ion were determined at 25.0+/-0.1 degrees C in 0.6 M NaCl ionic media using infrared spectroscopy and in 1.5 M NaCl ionic media using both infrared spectroscopy and potentiometry.
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Affiliation(s)
- J S Loring
- Department of Land, Air, and Water Resources, University of California, Davis 95616, USA
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Schah-Mohammedi P, Shenderovich IG, Detering C, Limbach HH, Tolstoy PM, Smirnov SN, Denisov GS, Golubev NS. Hydrogen/Deuterium-Isotope Effects on NMR Chemical Shifts and Symmetry of Homoconjugated Hydrogen-Bonded Ions in Polar Solution. J Am Chem Soc 2000. [DOI: 10.1021/ja0017615] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Parwin Schah-Mohammedi
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Ilja G. Shenderovich
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Carsten Detering
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Hans-Heinrich Limbach
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Peter M. Tolstoy
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Sergei N. Smirnov
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Gleb S. Denisov
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
| | - Nikolai S. Golubev
- Institut für Chemie der Freien Universität Berlin Takustrasse 3, D-14195, Berlin, Germany Institute of Physics, St. Petersburg State University 198904 St. Petersburg, Russia
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