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A DFT study on the tautomerization of vitamin B3 (niacin). COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Pal R, Jelsch C, Momma K, Grabowsky S. π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:231-246. [PMID: 35411861 PMCID: PMC9004022 DOI: 10.1107/s2052520622001457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.
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Affiliation(s)
- Rumpa Pal
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | | | - Koichi Momma
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, Japan
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Pal R, Jelsch C, Malaspina LA, Edwards AJ, Murshed MM, Grabowsky S. syn and anti polymorphs of 2,6-dimethoxy benzoic acid and its molecular and ionic cocrystals: Structural analysis and energetic perspective. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Navasardyan MA, Grishanov DA, Prikhodchenko PV, Churakov AV. dl-Piperidinium-2-carboxyl-ate bis-(hydrogen peroxide): unusual hydrogen-bonded peroxide chains. Acta Crystallogr E Crystallogr Commun 2020; 76:1331-1335. [PMID: 32844024 PMCID: PMC7405570 DOI: 10.1107/s205698902000972x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/16/2020] [Indexed: 03/24/2023]
Abstract
The title compound, C6H11NO2·2H2O2, is the richest (by molar ratio) in hydrogen peroxide among the peroxosolvates of aliphatic α-amino acids. The asymmetric unit contains a zwitterionic pipecolinic acid mol-ecule and two hydrogen peroxide mol-ecules. The two crystallographically independent hydrogen peroxide mol-ecules form a different number of hydrogen bonds: one forms two as donor and two as acceptor ([2,2] mode) and the other forms two as donor and one as acceptor ([2,1] mode). The latter hydrogen peroxide mol-ecule forms infinite hydrogen-bonded hydro-peroxo chains running along the c-axis direction, which is unusual for aliphatic α-amino acid peroxosolvates.
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Affiliation(s)
- Mger A. Navasardyan
- Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russian Federation
| | - Dmitry A. Grishanov
- Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russian Federation
| | - Petr V. Prikhodchenko
- Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russian Federation
| | - Andrei V. Churakov
- Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russian Federation
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Giubertoni G, Sofronov OO, Bakker HJ. Effect of intramolecular hydrogen-bond formation on the molecular conformation of amino acids. Commun Chem 2020; 3:84. [PMID: 36703397 PMCID: PMC9814578 DOI: 10.1038/s42004-020-0329-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/21/2020] [Indexed: 01/29/2023] Open
Abstract
The molecular conformation of the carboxyl group can be crucial for its chemical properties and intermolecular interactions, especially in complex molecular environments such as polypeptides. Here, we study the conformational behaviour of the model amino acid N-acetylproline in solution at room temperature with two-dimensional infrared spectroscopy. We find that the carboxyl group of N-acetylproline adopts two distinct conformations, syn- and anti-. In the syn-conformer the O-H group is oriented at ~60∘ with respect to the C=O and in the anti-conformer the O-H is anti-parallel to the C=O. In hydrogen-bond accepting solvents such as dimethyl sulfoxide or water, we observe that, similar to simple carboxylic acids, around 20% of the -COOH groups adopt an anti-conformation. However, when N-acetylproline is dissolved in a weakly hydrogen-bond accepting solvent (acetonitrile), we observe the formation of a strong intramolecular hydrogen bond between the carboxyl group in the anti-conformation and the amide group, which stabilizes the anti-conformer, increasing its relative abundance to ~60%.
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Affiliation(s)
- Giulia Giubertoni
- grid.417889.b0000 0004 0646 2441AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Oleksandr O. Sofronov
- grid.417889.b0000 0004 0646 2441AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Huib J. Bakker
- grid.417889.b0000 0004 0646 2441AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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Sofronov O, Giubertoni G, Pérez de Alba Ortíz A, Ensing B, Bakker HJ. Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions. J Phys Chem Lett 2020; 11:3466-3472. [PMID: 32293901 PMCID: PMC7212517 DOI: 10.1021/acs.jpclett.0c00711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the carboxyl group strongly depends on the conformation of this group. Interestingly, up to now there has been no experimental investigation of the geometry and the stability of different COOH conformers under biorelevant conditions. Here, we investigate the conformational isomerism of the side chain COOH group of N-acetyl aspartic acid amide using polarization-resolved two-dimensional infrared spectroscopy. We find that the carboxyl group shows two distinct near-planar conformers (syn and anti) when dissolved in water at room temperature. Both conformers are significantly populated in aqueous solution (75 ± 10% and 25 ± 10% for syn and anti, respectively). Molecular dynamics simulations show that the anti conformer interacts more strongly with water molecules than the syn conformer, explaining why this conformer is significantly present in aqueous solution.
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Affiliation(s)
| | | | - Alberto Pérez de Alba Ortíz
- Amsterdam
Center for Multiscale Modeling and Van ’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bernd Ensing
- Amsterdam
Center for Multiscale Modeling and Van ’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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Soudani S, Hajji M, Mi JX, Jelsch C, Lefebvre F, Guerfel T, Ben Nasr C. Synthesis, structure and theoretical simulation of a zinc(II) coordination complex with 2,3-pyridinedicarboxylate. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lim VT, Bayly CI, Fusti-Molnar L, Mobley DL. Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. J Chem Inf Model 2019; 59:1957-1964. [PMID: 30742770 PMCID: PMC6538459 DOI: 10.1021/acs.jcim.8b00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the syn conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We focus on the carboxyl torsional potential and configurations of microhydrated acetic acid from molecular dynamics simulations, probing the effects of solvent, force field (GAFF vs GAFF2), and partial charge assignment of acetic acid. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.
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Affiliation(s)
- Victoria T. Lim
- Department of Chemistry, University of California, Irvine, California 92697
| | | | | | - David L. Mobley
- Department of Chemistry, University of California, Irvine, California 92697
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697
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