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Oh YH, Lee SY, Kong X, Oh HB, Lee S. Thermodynamic Reversal and Structural Correlation of 24-Crown-8/Protonated Tryptophan and 24-Crown 8/Protonated Serine Noncovalent Complexes in the Gas Phase vs in Solution: Quantum Chemical Analysis. ACS OMEGA 2024; 9:23793-23801. [PMID: 38854571 PMCID: PMC11154897 DOI: 10.1021/acsomega.4c01782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
We investigate the structures of 24-crown-8/H+/l-tryptophan (CR/TrpH+) and 24-crown-8/H+/l-serine (CR/SerH+) noncovalent host-guest complex both in the gas phase and in an aqueous solution by quantum chemical methods. The Gibbs free energies of the complex in the two phases are calculated to determine the thermodynamically most favorable conformer in each phase. Our predictions indicate that both the carboxyl and the ammonium in CR/TrpH+ and the ammonium in the CR/SerH+ complexes in the lowest Gibbs free energy configurations form hydrogen bonds (H-bonds) with the CR host in the gas phase, while the conformer with the "naked" (devoid of H-bond with the CR host) -CO2H (and/or -OH) is much less favorable (Gibbs free energy higher by >3.6 kcal/mol). In the solution phase, however, a "thermodynamic reversal" occurs, making the higher Gibbs free energy gas-phase CR/TrpH+ and CR/SerH+ conformers thermodynamically more favorable under the influence of solvent molecules. Consequently, the global minimum Gibbs free energy structure in solution is structurally correlated with the thermodynamically much less gas-phase conformer. Discussions are provided concerning the possibility of elucidating host-guest-solvent interactions in solution from the gas-phase host-guest configurations in molecular detail.
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Affiliation(s)
- Young-Ho Oh
- Department
of Chemistry, Konkuk University, Seoul 05029, Republic of Korea
- Department
of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea
| | - So Yeon Lee
- Department
of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Xianglei Kong
- State
Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center
for New Organic Matter, and Tianjin Key Laboratory of Biosensing and
Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Han Bin Oh
- Department
of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Sungyul Lee
- Department
of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea
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2
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Foreman MM, Alessio M, Krylov AI, Weber JM. Influence of Transition Metal Electron Configuration on the Structure of Metal-EDTA Complexes. J Phys Chem A 2023; 127:2258-2264. [PMID: 36877889 DOI: 10.1021/acs.jpca.2c07996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The vibrational spectra of cold complexes of ethylenediaminetetraacetic acid (EDTA) with transition metal dications in vacuo show how the electronic structure of the metal provides a geometric template for interaction with the functional groups of the binding pocket. The OCO stretching modes of the carboxylate groups of EDTA serve as structural probes, informing on the spin state of the ion as well as the coordination number in the complex. The results highlight the flexibility of EDTA in accepting a large range of metal cations in its binding site.
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Affiliation(s)
- Madison M Foreman
- JILA and Department of Chemistry, University of Colorado at Boulder, UCB 440, Boulder, Colorado 80309, United States
| | - Maristella Alessio
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado at Boulder, UCB 440, Boulder, Colorado 80309, United States
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3
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Shen J, Cheng F, Chen Y, Li Z, Liu Y, Yuan Y, Zhou P, Liu W, Lai B, Zhang Y. Vanadium trioxide mediated peroxymonosulfate for fast metronidazole oxidation: Stepwise oxidation of vanadium for donating electrons. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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4
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Foreman MM, Weber JM. Ion Binding Site Structure and the Role of Water in Alkaline Earth EDTA Complexes. J Phys Chem Lett 2022; 13:8558-8563. [PMID: 36067512 DOI: 10.1021/acs.jpclett.2c02391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The interactions between molecular hosts and ionic guests and their dependence on the chemical environment are challenging to disentangle from solution data alone. The vibrational spectra of cold complexes of ethylenediaminetetraacetic acid (EDTA) chelating alkaline earth dications in vacuo encode structural characteristics of these complexes and their dependence on the size of the bound ion. The correlation between metal binding geometry and the relative intensities of vibrational bands of the carboxylate groups forming the binding pocket allows us to characterize water-induced changes in molecular geometry. The evolution of these structural markers from bare ions to water adducts to aqueous solution illustrates the role of water for the structure of ion binding sites in chelators. The binding pocket of EDTA opens up in aqueous solution, bringing the bound ion closer to the mouth of the binding site and leading to an increased exposure of the ion to the chemical environment.
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Affiliation(s)
- Madison M Foreman
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
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5
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Kantakevičius P, Mathiah C, Johannissen LO, Hay S. Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion-Protein Interactions. J Chem Theory Comput 2022; 18:2367-2374. [PMID: 35319190 PMCID: PMC9171819 DOI: 10.1021/acs.jctc.1c00898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Metal ions are associated with a
variety of proteins and play critical
roles in a wide range of biochemical processes. There are multiple
ways to study and quantify protein–metal ion interactions,
including molecular dynamics simulations. Recently, the AMBER molecular
mechanics forcefield was modified to include a 12-6-4 Lennard-Jones
potential, which allows for a better description of nonbonded terms
through the additional pairwise Cij coefficients.
Here, we demonstrate a method of generating Cij parameters that allows parametrization of specific metal
ion-ligating groups in order to tune binding energies computed by
thermodynamic integration. The new Cij coefficients were tested on a series of chelators: ethylenediaminetetraacetic
acid, nitrilotriacetic acid, egtazic acid, and the EF1 loop peptides
from the proteins lanmodulin and calmodulin. The new parameters show
significant improvements in computed binding energies relative to
existing force fields and produce coordination numbers and ion-oxygen
distances that are in good agreement with experimental values. This
parametrization method should be extensible to a range of other systems
and could be readily adapted to tune properties other than binding
energies.
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Affiliation(s)
- Paulius Kantakevičius
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
| | - Calvin Mathiah
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
| | - Linus O Johannissen
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
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6
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Cao Y, You W, Lei G, Zheng X, Shen L, Liu F, Jiang L. Enabling High Efficiency and Rapid Regeneration of α-FeOOH@Fe-EDTA for Slurry Desulfurization. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c03976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanning Cao
- National Engineering Research Center of Chemical Fertilizer Catalyst, School of Chemical Engineering, Fuzhou University, Gongye Road 523, Gulou District, Fuzhou, Fujian 350002, P. R. China
- Qingyuan Innovation Laboratory, Quanzhou 362801, China
| | - Weilong You
- National Engineering Research Center of Chemical Fertilizer Catalyst, School of Chemical Engineering, Fuzhou University, Gongye Road 523, Gulou District, Fuzhou, Fujian 350002, P. R. China
| | - Ganchang Lei
- National Engineering Research Center of Chemical Fertilizer Catalyst, School of Chemical Engineering, Fuzhou University, Gongye Road 523, Gulou District, Fuzhou, Fujian 350002, P. R. China
- Qingyuan Innovation Laboratory, Quanzhou 362801, China
| | - Xiaohai Zheng
- National Engineering Research Center of Chemical Fertilizer Catalyst, School of Chemical Engineering, Fuzhou University, Gongye Road 523, Gulou District, Fuzhou, Fujian 350002, P. R. China
- Qingyuan Innovation Laboratory, Quanzhou 362801, China
| | - Lijuan Shen
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Fujian Liu
- National Engineering Research Center of Chemical Fertilizer Catalyst, School of Chemical Engineering, Fuzhou University, Gongye Road 523, Gulou District, Fuzhou, Fujian 350002, P. R. China
- Qingyuan Innovation Laboratory, Quanzhou 362801, China
| | - Lilong Jiang
- National Engineering Research Center of Chemical Fertilizer Catalyst, School of Chemical Engineering, Fuzhou University, Gongye Road 523, Gulou District, Fuzhou, Fujian 350002, P. R. China
- Qingyuan Innovation Laboratory, Quanzhou 362801, China
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7
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Warneke J, Wang XB. Measuring Electronic Structure of Multiply Charged Anions to Understand Their Chemistry: A Case Study on Gaseous Polyhedral closo-Borate Dianions. J Phys Chem A 2021; 125:6653-6661. [PMID: 34323504 DOI: 10.1021/acs.jpca.1c04618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Research on multiply charged anions (MCAs) in the gas phase has been intensively performed during the past decades, mainly to understand fundamental molecular physics phenomena, for example, intramolecular Coulomb repulsion and existence of the repulsive Coulomb barrier. However, the relevance of these investigations with respect to understanding MCAs' chemistry appears often vague. Here, we discuss how insights into the electronic structure obtained from negative ion photoelectron spectroscopy (NIPES) combined with theoretical calculations and collision-induced dissociation can provide a fundamental understanding of the intrinsic chemical reactivity of MCAs and their fragments. This is exemplified in our studies on polyhedral closo-borate dianions [BnXn]2- (n = 6, 10, 11, 12; X = H, F-I, CN) and their fragment ions. For example, the rational design of closo-borate dianions with specific electronic properties is described, which leads to generating highly reactive fragments. Depending on the dianionic precursor, these fragments are tuned to either bind noble gases effectively or activate small molecules like CO and N2. The intrinsic electronic properties of closo-borate dianions are further compared to their electrochemistry in solutions, revealing solvent effects on the redox potentials. Neutral host molecules such as cyclodextrins are found to bind strongly to [BnXn]2-, and gas phase NIPES provides insights into the intrinsic host-guest interactions. Finally, outlooks including the direct NIPES of molecular fragment ions that cannot be generated in the condensed phase and their utilization in preparative mass spectrometry are discussed.
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Affiliation(s)
- Jonas Warneke
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, 04103 Leipzig, Germany.,Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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8
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Wang L, Yuan Q, Cao W, Han J, Zhou X, Liu S, Wang XB. Probing Orientation-Specific Charge-Dipole Interactions between Hexafluoroisopropanol and Halides: A Joint Photoelectron Spectroscopy and Theoretical Study. J Phys Chem A 2020; 124:2036-2045. [PMID: 32077296 DOI: 10.1021/acs.jpca.0c00024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The interactions between hexafluoroisopropanol (HFIP) and halogen anions X- (F-, Cl-, Br-, and I-) have been investigated using negative ion photoelectron (NIPE) spectroscopy and ab initio calculations. The measured NIPE spectrum of each [HFIP·X]- (X = Cl, Br, and I) complex shows a pattern identical to the corresponding X- by shifting to the high electron binding energy side, indicative of the formation of the [HFIP···X-] structure in which X- interacts with HFIP via charge-dipole interactions. However, the spectrum of [HFIP·F]- appears completely different from that of F- and is more similar to the spectrum of the deprotonated HFIP anion (HFIP-H-). The geometry and electron density calculations indicate that a neutral HF molecule is formed upon HFIP interacting with F- via proton transfer, rendering a stable structure of [HFIP-H···HF]-. Two conformers of [HFIP-H·HF]- with HFIP being in synperiplanar and antiperiplanar configurations, respectively, are observed, providing direct experimental evidences to show the distinctly different and orientation-specific interactions between HFIP and halide anions.
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Affiliation(s)
- Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jia Han
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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9
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Yuan Q, Cao W, Wang XB. Cryogenic and temperature-dependent photoelectron spectroscopy of metal complexes. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1719699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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10
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Zhang H, Cao W, Yuan Q, Wang L, Zhou X, Liu S, Wang XB. Spectroscopic evidence for intact carbonic acid stabilized by halide anions in the gas phase. Phys Chem Chem Phys 2020; 22:19459-19467. [DOI: 10.1039/d0cp02338h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The whole series of halide anions can stabilize elusive carbonic acid in the gas phase through dual hydrogen bonds.
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Affiliation(s)
- Hanhui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Wenjin Cao
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Qinqin Yuan
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Xue-Bin Wang
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
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