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Sagiv L, Hirshberg B, Gerber RB. Hydrogenic Stretch Spectroscopy of Glycine–Water Complexes: Anharmonic Ab Initio Classical Separable Potential Calculations. J Phys Chem A 2019; 123:8377-8384. [DOI: 10.1021/acs.jpca.9b05378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lior Sagiv
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - Barak Hirshberg
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - R. Benny Gerber
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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2
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An ab iniio study on the micro-solvation of amino acids: On the number of water molecules necessary to stabilize the zwitter ion. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Smith ZM, Steinmetz V, Martens J, Oomens J, Poutsma JC. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation †. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 429:158-173. [PMID: 29962900 PMCID: PMC6020040 DOI: 10.1016/j.ijms.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH+, CavLi+, and CavNa+; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK+ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs+ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa+ and ArgK+. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na+, K+, and Cs+. A major difference between the zwitterionic forms of ArgM+ and CavM+ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay France
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences University of Amsterdam, Amsterdam, The Netherlands
| | - John C Poutsma
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
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4
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Theoretical study on electronic and vibrational properties of hydrogen bonds in glycine-water clusters. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.06.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gabas F, Conte R, Ceotto M. On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum. J Chem Theory Comput 2017; 13:2378-2388. [PMID: 28489368 PMCID: PMC5472367 DOI: 10.1021/acs.jctc.6b01018] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
present an on-the-fly ab initio semiclassical study of vibrational
energy levels of glycine, calculated by Fourier transform of the wavepacket
correlation function. It is based on a multiple coherent states approach
integrated with monodromy matrix regularization for chaotic dynamics.
All four lowest-energy glycine conformers are investigated by means
of single-trajectory semiclassical spectra obtained upon classical
evolution of on-the-fly trajectories with harmonic zero-point energy.
For the most stable conformer I, direct dynamics trajectories are
also run for each vibrational mode with energy equal to the first
harmonic excitation. An analysis of trajectories evolved up to 50 000
atomic time units demonstrates that, in this time span, conformers
II and III can be considered as isolated species, while conformers
I and IV show a pretty facile interconversion. Therefore, previous
perturbative studies based on the assumption of isolated conformers
are often reliable but might be not completely appropriate in the
case of conformer IV and conformer I for which interconversion occurs
promptly.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy
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Pérez de Tudela R, Marx D. Water-Induced Zwitterionization of Glycine: Stabilization Mechanism and Spectral Signatures. J Phys Chem Lett 2016; 7:5137-5142. [PMID: 27973910 DOI: 10.1021/acs.jpclett.6b02247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Not only the question of how many water molecules are required to stabilize the physiologically relevant charge-separated zwitterionic form of amino acids upon solvation but also the stabilization mechanism is still under debate. It is well known that a water bridge connecting the carboxyl with the amino group must be established. Here, we show that this is not yet a sufficient condition to stabilize the zwitterion. Instead, the formation of a bifurcated H-bonded water wire that connects the two charged groups turns out to be the key, which explains why an unexpectedly large number of water molecules of about nine is required to enable zwitterionization of microsolvated glycine. Moreover, this bifurcated wire allows one to pinpoint a frequency window that enables the detection of zwitterionization by spectroscopy. These findings will be relevant to probe and rationalize microsolvation-induced zwitterionization of not only amino acids but of other acid/base reactions that involve somewhat distant such functional groups within the same molecule.
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Affiliation(s)
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
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Kaufmann M, Leicht D, Schwan R, Mani D, Schwaab G, Havenith M. Helium droplet infrared spectroscopy of glycine and glycine–water aggregates. Phys Chem Chem Phys 2016; 18:28082-28090. [DOI: 10.1039/c6cp05042e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infrared absorption spectra of glycine and glycine–water aggregates embedded in superfluid helium nanodroplets were recorded in the frequency range 1000–1450 cm−1.
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Affiliation(s)
- Matin Kaufmann
- Physical Chemistry II
- Department of Chemistry and Biochemistry
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Daniel Leicht
- Physical Chemistry II
- Department of Chemistry and Biochemistry
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Raffael Schwan
- Physical Chemistry II
- Department of Chemistry and Biochemistry
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Devendra Mani
- Physical Chemistry II
- Department of Chemistry and Biochemistry
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Gerhard Schwaab
- Physical Chemistry II
- Department of Chemistry and Biochemistry
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Martina Havenith
- Physical Chemistry II
- Department of Chemistry and Biochemistry
- Ruhr-Universität Bochum
- Bochum
- Germany
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Kim SK, Lee HM, Kim KS. Disulfuric acid dissociated by two water molecules: ab initio and density functional theory calculations. Phys Chem Chem Phys 2015; 17:28556-64. [PMID: 26400266 DOI: 10.1039/c5cp05201g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied geometries, energies and vibrational spectra of disulfuric acid (H2S2O7) and its anion (HS2O7(-)) hydrated by a few water molecules, using density functional theory (M062X) and ab initio theory (SCS-MP2 and CCSD(T)). The most noteworthy result is found in H2S2O7(H2O)2 in which the lowest energy conformer shows deprotonated H2S2O7. Thus, H2S2O7 requires only two water molecules, the fewest number of water molecules for deprotonation among various hydrated monomeric acids reported so far. Even the second deprotonation of the first deprotonated species HS2O7(-) needs only four water molecules. The deprotonation is supported by vibration spectra, in which acid O-H stretching peaks disappear and specific three O-H stretching peaks for H3O(+) (eigen structure) appear. We have also kept track of variations in several geometrical parameters, atomic charges, and hybrid orbital characters upon addition of water. As the number of water molecules added increases, the S-O bond weakens in the case of H2S2O7, but strengthens in the case of HS2O7(-). It implies that the decomposition leading to H2SO4 and SO3 hardly occurs prior to the 2nd deprotonation at low temperatures.
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Affiliation(s)
- Seong Kyu Kim
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea.
| | - Han Myoung Lee
- Center for Superfunctional Materials, Department of Chemistry, Ulsan Institute of Science and Technology (UNIST), Ulsan 689-798, Korea.
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan Institute of Science and Technology (UNIST), Ulsan 689-798, Korea.
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9
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Guggemos N, Slavíček P, Kresin VV. Electric dipole moments of nanosolvated acid molecules in water clusters. PHYSICAL REVIEW LETTERS 2015; 114:043401. [PMID: 25679889 DOI: 10.1103/physrevlett.114.043401] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 06/04/2023]
Abstract
The electric dipole moments of (H2O)nDCl (n=3-9) clusters have been measured by the beam-deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at n≈5-6. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular-dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero-point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters and generally to the essential role played by motional effects in determining the response of fluxional nanoscale systems under realistic conditions.
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Affiliation(s)
- Nicholas Guggemos
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Vitaly V Kresin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
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Pathak AK. Stabilizing the zwitter-ionic form of amino acids in the gas phase: An ab initio study on the minimum number of solvents and ions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Rijs AM, Oomens J. IR Spectroscopic Techniques to Study Isolated Biomolecules. Top Curr Chem (Cham) 2014; 364:1-42. [DOI: 10.1007/128_2014_621] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Walker M, Sen A, Harvey AJ, Dessent CE. Complexation of anions to gas-phase amino acids: Conformation is critical in determining if the global minimum is canonical or zwitterionic. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Affiliation(s)
- Kenneth R. Leopold
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455;
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Tian SX, Li HB, Yang J. Monoanion BH4−Can Stabilize Zwitterionic Glycine with Dihydrogen Bonds. Chemphyschem 2009; 10:1435-7. [DOI: 10.1002/cphc.200900158] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Haranczyk M, Gutowski M. Effect of excess electron and one water molecule on relative stability of the canonical and zwitterionic tautomers of glycine. J Chem Phys 2008; 128:125101. [DOI: 10.1063/1.2838910] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Bush MF, Prell JS, Saykally RJ, Williams ER. One Water Molecule Stabilizes the Cationized Arginine Zwitterion. J Am Chem Soc 2007; 129:13544-53. [DOI: 10.1021/ja073796b] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Matthew F. Bush
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - James S. Prell
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Richard J. Saykally
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Evan R. Williams
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720-1460
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Blom MN, Compagnon I, Polfer NC, Helden GV, Meijer G, Suhai S, Paizs B, Oomens J. Stepwise Solvation of an Amino Acid: The Appearance of Zwitterionic Structures. J Phys Chem A 2007; 111:7309-16. [PMID: 17628045 DOI: 10.1021/jp070211r] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
How many solvent molecules are required to solvate an amino acid? This apparently simple question, which relates to the number of solvent molecules necessary to change the amino acid from its gas-phase neutral structure to the zwitterionic solvated structure, remains unanswered to date. Here we present experimental and theoretical (density functional theory: B3LYP/6-31+G**) infrared spectra for tryptophan-watern complexes where n = 1-6, which suggest that the zwitterionic structure becomes competitive in energy at the high end of the series. Compelling evidence for a gradual transition to zwitterionic structures comes from tryptophan-methanol complexes up to n = 9. Starting from n = 5, the infrared spectra show increasing intensity in the diagnostic asymmetric COO- stretch and in the weaker NH3+ bending modes as the cluster size increases. Moreover, convergence toward the Fourier transform infrared spectrum of a solution of tryptophan in methanol is clearly observed. For small solvent complexes (n = 1-4), the microsolvation by methanol and water is shown to behave very similarly. A detailed comparison of the experimental and the theoretical spectra allows us to determine both the preferred solvent binding sites on the amino acid and the evolution of conformational structures of tryptophan as the number of attached solvent molecules increases.
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Affiliation(s)
- Martine N Blom
- FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
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Abstract
The remarkable stabilities of the dipole-bound anions of the canonical and zwitterionic conformers of beta-alanine are predicted at the high level of theories, in which the former is the global minimum and the latter, the anti zwitterionic anion, is the local minimum. In contrast to the dipole-bound anions of glycine, the gauche zwitterionic anion of beta-alanine is an unstable conformer. The vertical electron detachment energies for the canonical and anti zwitterionic anions are 58 and 1145 meV, respectively. The photodetachment electron spectrum of the canonical anion is theoretically simulated on the basis of the Franck-Condon factor calculations.
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Affiliation(s)
- Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Bond Selective Chemistry, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.
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