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Dudek WM, Ostrowski S, Dobrowolski JC. On Aromaticity of the Aromatic α-Amino Acids and Tuning of the NICS Indices to Find the Aromaticity Order. J Phys Chem A 2022; 126:3433-3444. [PMID: 35617165 PMCID: PMC9189847 DOI: 10.1021/acs.jpca.2c00346] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NICS aromaticity indices of the rings in flexible phenylalanine (Phe), tryptophan (Trp), tyrosine (Tyr), and histidine (His) chiral molecules were analyzed. These molecules have several dozens of conformers, and their rings are slightly non-planar. Therefore, the population-averaged NICSpav index was defined, and the NICS scans had to be performed with respect to planes found by the least-squares routine. A rule differentiating an obverse and a reverse ring face in aromatic amino acids was formulated. The NICS scan minima corresponding to the obverse and reverse face were unequal, which prompted us to use the term ring face aromaticity/ring face tropicity. It appeared that for Phe, Trp, Tyr, and His, the reverse face has always had higher ring face aromaticity/ring face tropicity than the obverse one. Despite the NICS modifications, uncertainty about the amino acid aromaticity order remained. This motivated us to use the integral INICS index newly proposed by Stanger as well. Then, the following sequence was obtained: Trp(phenyl) > Phe > Trp(pyrrole) > His > Tyr. The juxtaposition of the INICS indices of amino acids with that of some model rings revealed a fair transferability of the values. Finally, analysis of the substituent effect on INICS demonstrated that the aromaticity of Tyr is the lowest due to the strength of the OH group π-electron-donating effect able to perturb enough the ring charge distribution and its magnetic aromaticity. The NICS calculations were executed using the ARONICS program written within the project.
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Affiliation(s)
- Wojciech M Dudek
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Sławomir Ostrowski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
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Unveiling host-guest-solvent interactions in solution by identifying highly unstable host-guest configurations in thermal non-equilibrium gas phase. Sci Rep 2022; 12:8169. [PMID: 35581255 PMCID: PMC9114120 DOI: 10.1038/s41598-022-12226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
We propose a novel scheme of examining the host-guest-solvent interactions in solution from their gas phase structures. By adopting the permethylated β-cyclodextrin (perm β-CD)-protonated L-Lysine non-covalent complex as a prototypical system, we present the infrared multiple photon dissociation (IRMPD) spectrum of the gas phase complex produced by electrospray ionization technique. In order to elucidate the structure of perm β-CD)/LysH+ complex in the gas phase, we carry out quantum chemical calculations to assign the two strong peaks at 3,340 and 3,560 cm-1 in the IRMPD spectrum, finding that the carboxyl forms loose hydrogen bonding with the perm β-CD, whereas the ammonium group of L-Lysine is away from the perm β-CD unit. By simulating the structures of perm β-CD/H+/L-Lysine complex in solution using the supramolecule/continuum model, we find that the extremely unstable gas phase structure corresponds to the most stable conformer in solution.
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Lee ZR, Quinn LJ, Jones CW, Hayes SE, Dixon DA. Predicting the Mechanism and Products of CO 2 Capture by Amines in the Presence of H 2O. J Phys Chem A 2021; 125:9802-9818. [PMID: 34748350 DOI: 10.1021/acs.jpca.1c05950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An extensive correlated molecular orbital theory study of the reactions of CO2 with a range of substituted amines and H2O in the gas phase and aqueous solution was performed at the G3(MP2) level with a self-consistent reaction field approach. The G3(MP2) calculations were benchmarked at the CCSD(T)/CBS level for NH3 reactions. A catalytic NH3 reduces the energy barrier more than a catalytic H2O for the formation of H2NCOOH and H2CO3. In aqueous solution, the barriers to form both H2NCOOH and H2CO3 are reduced, with HCO3- formation possible with one amine present and H2NCOO- formation possible only with two amines. Further reactions of H2NCOOH to form HNCO and urea via the Bazarov reaction have high barriers and are unlikely in both the gas phase and aqueous solution. Reaction coordinates for CH3NH2, CH3CH2NH2, (CH3)2NH, CH3CH2CH2NH2, (CH3)3N, and DMAP were also calculated. The barrier for proton transfer correlates with amine basicity for alkylammonium carbamate (ΔG‡aq < 15 kcal/mol) and alkylammonium bicarbonate (ΔG‡aq < 30 kcal/mol) formation. In aqueous solution, carbamic acids, carbamates, and bicarbonates can all form in small amounts with ammonium carbamates dominating for primary and secondary alkylamines. These results have implications for CO2 capture by amines in both the gas phase and aqueous solution as well as in the solid state, if enough water is present.
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Affiliation(s)
- Zachary R Lee
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States.,Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky 40351, United States
| | - La'Darious J Quinn
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Christopher W Jones
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30332, United States
| | - Sophia E Hayes
- Department of Chemistry, Washington University, 1 Brookings Drive, Saint Louis, Missouri 63130, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
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Sun B, Liu C, Che D, Liu H, Guo S. Density functional theory-based investigation of HCN and NH 3 formation mechanisms during phenylalanine pyrolysis. RSC Adv 2020; 10:28431-28436. [PMID: 35519141 PMCID: PMC9055650 DOI: 10.1039/d0ra05482h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/21/2020] [Indexed: 01/26/2023] Open
Abstract
As sludge pyrolysis produces large amounts of toxic NH3 and HCN, many works have studied nitrogen transfer during this process, commonly employing amino acids as models of sludge protein. Herein, density functional theory is used to probe the production of HCN and NH3 during the pyrolysis of phenylalanine as a model, revealing the existence of two formation paths for each gas. In the first (lower-energy-barrier) NH3 formation path, the hydrogen bonding-assisted transfer of carboxyl group hydrogen to the amino group is followed by direct NH3 generation via decarboxylation, and the second (higher-energy-barrier) path features decarboxylation followed by the transfer of carboxyl group hydrogen to the adjacent carbon atom to form phenethylamine, the deamination of which affords NH3 and styrene. For HCN, the first (lower-energy-barrier) path features C2-C3 bond cleavage to afford dehydroglycine, which further decomposes to produce HCN, while in the second path, the decomposition of phenylalanine into phenethylamine, CO, and H2O is followed by internal hydrogen transfer in phenethylamine to generate HCN. The overall energy barrier of the two HCN formation paths exceeds that of NH3 formation paths, i.e., phenylalanine is more prone to afford NH3 than HCN upon pyrolysis.
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Affiliation(s)
- Baizhong Sun
- School of Energy and Power Engineering, Northeast Electric Power University Jilin 132000 China
| | - Chuanqun Liu
- School of Energy and Power Engineering, Northeast Electric Power University Jilin 132000 China
| | - Deyong Che
- School of Energy and Power Engineering, Northeast Electric Power University Jilin 132000 China
| | - Hongpeng Liu
- School of Energy and Power Engineering, Northeast Electric Power University Jilin 132000 China
| | - Shuai Guo
- School of Energy and Power Engineering, Northeast Electric Power University Jilin 132000 China
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Chandran J, Zheng Z, Thomas VI, Rajalakshmi C, Attygalle AB. LC-MS analysis of p-aminosalicylic acid under electrospray ionization conditions manifests a profound solvent effect. Analyst 2020; 145:5333-5344. [DOI: 10.1039/d0an00680g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Under identical mass spectrometric conditions, chromatographic peak intensities of p-aminosalicylic acid recorded by LC-MS, using methanol as the mobile phase are drastically different from those acquired using is it acetonitrile as the eluent.
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Affiliation(s)
- Jisha Chandran
- Inter University Instrumentation Centre (IUIC)
- School of Environmental Sciences
- Mahatma Gandhi University
- Kottayam
- 686560 India
| | - Zhaoyu Zheng
- Center for Mass Spectrometry
- Department of Chemistry and Chemical Biology
- Stevens Institute of Technology
- Hoboken
- USA
| | | | | | - Athula B. Attygalle
- Center for Mass Spectrometry
- Department of Chemistry and Chemical Biology
- Stevens Institute of Technology
- Hoboken
- USA
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Cui C, McNeill AS, Jackson WC, Raddatz MA, Stover ML, Dixon DA, Cassady CJ. Experimental and Computational Study of the Gas-Phase Acidities of Acidic Di- and Tripeptides. J Phys Chem B 2019; 123:606-613. [DOI: 10.1021/acs.jpcb.8b10924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Can Cui
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ashley S. McNeill
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Will C. Jackson
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michael A. Raddatz
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michele L. Stover
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A. Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J. Cassady
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Patrick AL, Cismesia AP, Tesler LF, Polfer NC. Effects of ESI conditions on kinetic trapping of the solution-phase protonation isomer of p-aminobenzoic acid in the gas phase. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 418:148-155. [PMID: 28781574 PMCID: PMC5542407 DOI: 10.1016/j.ijms.2016.09.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The effects of electrospray ionization (ESI) solvent and source temperature on the relative abundance of the preferred solution-phase (N-protonated; i.e. amine) versus preferred gas-phase (O-protonated; i.e., acid) isomers of p-aminobenzoic acid (PABA) were investigated. When PABA was electrosprayed from protic solvents (i.e., methanol/water), the infrared multiple photon dissociation (IRMPD) spectrum recorded was consistent with that for O-protonation, according to both calculations and previous studies. When aprotic solvent (i.e., acetonitrile) was used, a different spectrum was recorded and was assigned to the N-protonated isomer. As the amine is the preferred protonation site in solution, this suggests that an isomerization takes place under certain conditions. Photodissociation at the diagnostic band for the O-protonated isomer (NH2 stretching mode) was used to quantify the relative contributions of each isomer to ion signal as a function of ESI conditions. For mixtures of methanol and acetonitrile, the relative contribution of the O-protonated gas-phase structure increased as a function of methanol content. Yet, substituting methanol for water resulted in a marked decrease of isomerization to the O-protonated structure. The source temperature (i.e., temperature of a heated desolvation capillary) was found to play a key role in determining the extent of isomerization, with higher temperatures yielding increased presence of gas-phase structures. These results are consistent with a protic bridge mechanism, in which the ESI droplet temperatures, dependent on endothermic desolvation and radiative heating from the capillary, may determine the isomerization yield.
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Vytla Y, Angel LA. Applying Ion Mobility-Mass Spectrometry Techniques for Explicitly Identifying the Products of Cu(II) Reactions of 2His-2Cys Motif Peptides. Anal Chem 2016; 88:10925-10932. [PMID: 27740744 DOI: 10.1021/acs.analchem.6b02313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Cu(II) and pH titrations of four structurally similar 2His-2Cys motif peptides were investigated by electrospray ionization-ion mobility-mass spectrometry. The results provided insight into the pH dependent redox processes that took place in solution and identified the number of inter- or intramolecular disulfide bridges, the number of Cu(I) or Cu(II) ions, the deprotonation sites, and likely Cu(I/II) coordination of the various products. Competitive Cu(II) titrations of binary peptide mixtures at pH 5 indicated which species would preferably bind Cu(I) ions over forming the intramolecular disulfide bridge. Moreover, these reactions were pH dependent and included the formation of various multimers and multiple Cu(I/II) binding. For example, for the mildly acidic solution (pH ∼ 3-6) each monomer (whether it was free or in a multimer) primarily bound up to 3 Cu(I) ions, whereas at pH ∼ 8-11 the fully oxidized monomer or multimer (where all Cys formed a disulfide bond) primarily bound up to 2 Cu(II) ions. This behavior was indicative of linear bridging of Cu(I) by Cys thiolate and His imidazole groups, whereas the coordination of Cu(II) involved His and the nitrogens of deprotonated backbone amide groups, resulting in either distorted T-shaped or square planar geometries.
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Affiliation(s)
- Yashodharani Vytla
- Department of Chemistry, Texas A&M University-Commerce , Commerce, Texas 75428, United States
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce , Commerce, Texas 75428, United States
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9
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Stover ML, Plummer CE, Miller SR, Cassady CJ, Dixon DA. Gas-Phase Acidities of Phosphorylated Amino Acids. J Phys Chem B 2015; 119:14604-21. [DOI: 10.1021/acs.jpcb.5b08616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Chelsea E. Plummer
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Sean R. Miller
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
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10
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Plummer CE, Stover ML, Bokatzian SS, Davis JTM, Dixon DA, Cassady CJ. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides. J Phys Chem B 2015. [PMID: 26196065 DOI: 10.1021/acs.jpcb.5b04486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.
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Affiliation(s)
- Chelsea E Plummer
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michele L Stover
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Samantha S Bokatzian
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - John T M Davis
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A Dixon
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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