1
|
Decarboxylation of orotic acid analogues: Comparison of solution and gas-phase reactivity. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
2
|
Senger NA, Bliss CE, Keeffe JR, Gronert S, Wu W. Stabilities of Uracil and Pyridone-Based Carbanions: A Systematic Study in the Gas Phase and Solution and Implications for the Mechanism of Orotidine-5'-Monophosphate Decarboxylase. Tetrahedron 2013; 69:5287-5292. [PMID: 24072938 DOI: 10.1016/j.tet.2013.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The stabilities of the C6-centered carbanions derived from 1,3-dimethyluracil, N-methyl-2-pyridone, and N-methyl-4-pyridone were systematically investigated in the gas phase and in DMSO and water solutions. The stabilities of the carbanions in the gas phase and DMSO were directly measured through their reactions with carbon acids with known proton affinity or pKa values. The stabilities of the carbanions in DMSO were also probed through their kinetic isotope effects of protonation over deuteriation using acids with different acidity. The stabilities of the carbanions in water were determined through the rates of hydrogen-deuterium exchange reactions of the corresponding conjugate acids. The carbanions derived from the two pyridones were found to have the same stability, whereas the carbanion derived from 1,3-dimethyluracil was more stable. The order of the stability of the carbanions showed no correlation with the decarboxylation rates of their corresponding carboxylic acids. The implications of the results for the mechanism of orotidine-5'-monophosphate decarboxylase (ODCase) are discussed.
Collapse
Affiliation(s)
- Nicholas A Senger
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
| | | | | | | | | |
Collapse
|
3
|
Synthesis and application of proline based organocatalyst for highly enantioselective aldol reaction by hydrogen bonding. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.08.123] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
4
|
Huang S, Gronert S, Wu W. Polarization in the structures of uracil and thiouracils: Implication for binding with orotidine 5'-monophosphate decarboxylase. Bioorg Med Chem Lett 2011; 21:6341-2. [PMID: 21937230 DOI: 10.1016/j.bmcl.2011.08.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/20/2011] [Accepted: 08/25/2011] [Indexed: 11/18/2022]
Abstract
The structures of the uracil and thiouracils were examined using NMR spectroscopy and crystal structure data when available. The relationships between the extent of polarization and the C5-C6 bond length as well as the H5-H6 coupling constants were probed. It was found that the bond length and coupling constants correlate well with the proton affinities at the carbonyl or thiocarbonyl groups at C4 but not C2. The possible implication in the tighter binding of thiouracil based nucleotides to orotidine-5'-monophosphate decarboxylase was discussed.
Collapse
Affiliation(s)
- Sha Huang
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | | | | |
Collapse
|
5
|
Cheng X, Wang J, Tang K, Liu Y, Liu C. Decarboxylation of pyrrole-2-carboxylic acid: A DFT investigation. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.07.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
6
|
Koehn SK, Tran NL, Gronert S, Wu W. The stability of aryl carbanions derived from pyridine N-oxide: the role of resonance in stabilizing aryl anions. J Am Chem Soc 2010; 132:390-5. [PMID: 20000602 PMCID: PMC2802662 DOI: 10.1021/ja906473v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase stability of carbanions centered at various positions on pyridine N-oxide were investigated by computational and experimental methods. In addition, G3MP2 computations were completed on ring-deprotonated pyridine and N-methylpyridinium. With these species, the effect of a nitrogen-centered positive charge on carbanion stability was assessed. Introduction of the nitrogen-oxide group into the benzene ring decreases the DeltaH(acid) by approximately 20 kcal/mol, but surprisingly, the effect is nearly independent of the position of the group (ortho, meta, or para). The results indicate that the N-oxide offers a balance of field, resonance, and local effects that cancels out any positional preferences. G3MP2 calculations indicate that a similar lack of positional selectivity is seen in nitrobenzene and benzonitrile. Overall, the data suggest that pi-effects are limited in phenyl anions, and as a result, ylide-like, rather than carbene-like, resonance structures are most important in the anions derived from ring deprotonation of arenes and heterocycles of these general types.
Collapse
Affiliation(s)
- Scott K Koehn
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | | | | | | |
Collapse
|
7
|
Lewis CA, Wolfenden R. Orotic acid decarboxylation in water and nonpolar solvents: a potential role for desolvation in the action of OMP decarboxylase. Biochemistry 2009; 48:8738-45. [PMID: 19678695 DOI: 10.1021/bi901085m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OMP decarboxylase (ODCase) generates a very large rate enhancement without the assistance of metals or other cofactors. The uncatalyzed decarboxylation of 1-methylorotate in water is shown to involve the monoanion, although uncharged 1-methylorotic acid is decarboxylated at a similar rate. To measure the extent to which the rate of the nonenzymatic decarboxylation of orotate derivatives might be enhanced by their removal from solvent water, the 1-phosphoribosyl moiety of OMP was replaced with 1-substituents that would allow it to enter less polar solvents. When the tetrabutylammonium salt of 1-cyclohexylorotate was transferred from water to a series of dipolar aprotic solvents, its rate of decarboxylation increased markedly, varying with the relative ability of each solvent to release the substrate in the ground state from stabilization by solvent water acting as a proton donor. These findings are consistent with the view that separation of the substrate from solvent water may contribute, at least to a limited extent, to the rate enhancement produced by ODCase. This enzyme's active site, like that of another cofactorless enzyme recently shown to produce a rate enhancement similar in magnitude (uroporphyrinogen decarboxylase), is equipped with an ammonium group positioned in such a way as to balance the electrostatic charge of the carboxylate group of the substrate and later supply a proton to the incipient carbanion in a relatively waterless environment.
Collapse
Affiliation(s)
- Charles A Lewis
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | |
Collapse
|
8
|
Effect of water molecules on the decarboxylation of Orotidine 5′-monophosphate catalyzed by Orotidine 5′-monophosphate decarboxylase. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
9
|
Wong FM, Capule CC, Chen DX, Gronert S, Wu W. Surprisingly Low Aqueous Acidity at the α-Positions of Pyridiniums and Pyrimidinium: The Role of Solvation. Org Lett 2008; 10:2757-60. [DOI: 10.1021/ol800892d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Freeman M. Wong
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Christina C. Capule
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - David X. Chen
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Scott Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Weiming Wu
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| |
Collapse
|
10
|
Wong FM, Capule C, Wu W. Stability of the 6-carbanion of uracil analogues: mechanistic implications for model reactions of orotidine-5'-monophosphate decarboxylase. Org Lett 2007; 8:6019-22. [PMID: 17165919 PMCID: PMC2743169 DOI: 10.1021/ol0624981] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[Structure: see text] The pKa's of the 6-CH groups of N-methyl-2-pyridone and N-methyl-4-pyridone in aqueous solution were determined. No correlation between the stability of the carbanions and the rate of decarboxylation of the corresponding carboxylic acids was found.
Collapse
|
11
|
Yeoh FY, Cuasito RR, Capule CC, Wong FM, Wu W. Carbanions from decarboxylation of orotate analogs: stability and mechanistic implications. Bioorg Chem 2007; 35:338-43. [PMID: 17400276 PMCID: PMC2757000 DOI: 10.1016/j.bioorg.2007.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 02/09/2007] [Accepted: 02/10/2007] [Indexed: 11/15/2022]
Abstract
The pKa's of the 6-CH groups of 1,3-dimethyluracil, N-methyl-2-pyridone, and N-methyl-4-pyridone were determined through their reactions with bases derived from carbon acids with known pKa and the reactions of their corresponding carbanions with the carbon acids. No correlation between the stability of the carbanions and the rate of decarboxylation of corresponding carboxylic acids was found.
Collapse
Affiliation(s)
| | | | | | | | - Weiming Wu
- To whom correspondence should be addressed: Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132. Telephone: (415) 338-1436. Fax: (415) 338-2384.
| |
Collapse
|
12
|
Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG. Mechanisms and free energies of enzymatic reactions. Chem Rev 2006; 106:3188-209. [PMID: 16895324 PMCID: PMC4477011 DOI: 10.1021/cr050293k] [Citation(s) in RCA: 297] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Shuhua Ma
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Dan T. Major
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Kwangho Nam
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|
13
|
Wong FM, Wu W. Accelerated decarboxylation of 1,3-dimethylorotic acid in ionic liquid. Bioorg Chem 2006; 34:99-104. [PMID: 16499947 DOI: 10.1016/j.bioorg.2006.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 01/09/2006] [Accepted: 01/16/2006] [Indexed: 11/29/2022]
Abstract
The solvent effect of ionic liquids on the decarboxylation of 1,3-dimethylorotic acid and its analogue in ionic was investigated. The rate acceleration observed was proposed to be a result of the stabilization of the zwitterionic intermediates by the charged groups available in these special solvents.
Collapse
Affiliation(s)
- Freeman M Wong
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | | |
Collapse
|