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Helbing T, Kirchner M, Becker J, Göttlich R. Separation of the Thorpe‐Ingold and Reactive Rotamer Effect by Using the Formation of Bicyclic Aziridinium Ions. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tim Helbing
- Justus Liebig Universitat Giessen Biology and Chemistry Heinrich-Buff-Ring 17 35392 Giessen GERMANY
| | | | - Jonathan Becker
- Justus Liebig Universitat Giessen Biology and Chemistry GERMANY
| | - Richard Göttlich
- University of Giessen: Justus Liebig Universitat Giessen Biology and Chemistry Heinrich-Buff-Ring 17 35392 Gießen GERMANY
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Pereira MS, Murta B, Oliveira TCF, Manfredi AM, Nome F, Hengge AC, Brandão TAS. Mechanistic Aspects of Phosphate Diester Cleavage Assisted by Imidazole. A Template Reaction for Obtaining Aryl Phosphoimidazoles. J Org Chem 2016; 81:8663-8672. [PMID: 27392322 DOI: 10.1021/acs.joc.6b01358] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Phosphoimidazole-containing compounds are versatile players in biological and chemical processes. We explore catalytic and mechanistic criteria for the efficient formation of cyclic aryl phosphoimidazoles in aqueous solution, viewed as a template reaction for the in situ synthesis of related compounds. To provide a detailed analysis for this reaction a series of o-(2'-imidazolyl)naphthyl (4-nitrophenyl) phosphate isomers were examined to provide a basis for analysis of both mechanism and the influence of structural factors affecting the nucleophilic attack of the imidazolyl group on the phosphorus center of the substrate. Formation of the cyclic aryl phosphoimidazoles was probed by NMR and ESI-MS techniques. Kinetic experiments show that cyclization is faster under alkaline conditions, with an effective molarity up to 2900 M for the imidazolyl group, ruling out competition from external nucleophiles. Heavy atom isotope effect and computational studies show that the reaction occurs through a SN2(P)-type mechanism involving a pentacoordinated phosphorus TS, with apical positions occupied by the incoming imidazolyl nucleophile and the p-nitrophenolate leaving group. The P-O bond to the leaving group is about 50-60% broken in the transition state.
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Affiliation(s)
- Mozart S Pereira
- Department of Chemistry, ICEX, Federal University of Minas Gerais , Belo Horizonte, MG 31270-901, Brazil
| | - Bárbara Murta
- Department of Chemistry, ICEX, Federal University of Minas Gerais , Belo Horizonte, MG 31270-901, Brazil
| | - Thaís C F Oliveira
- Department of Chemistry, ICEX, Federal University of Minas Gerais , Belo Horizonte, MG 31270-901, Brazil
| | - Alex M Manfredi
- Department of Chemistry, Federal University of Santa Catarina , Florianópolis, SC 88040-900, Brazil
| | - Faruk Nome
- Department of Chemistry, Federal University of Santa Catarina , Florianópolis, SC 88040-900, Brazil
| | - Alvan C Hengge
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
| | - Tiago A S Brandão
- Department of Chemistry, ICEX, Federal University of Minas Gerais , Belo Horizonte, MG 31270-901, Brazil
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4
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Gilmore K, Mohamed RK, Alabugin IV. The Baldwin rules: revised and extended. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1261] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kerry Gilmore
- Department of Biomolecular Systems; Max Planck Institute of Colloids and Interfaces; Potsdam Germany
| | - Rana K. Mohamed
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL USA
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL USA
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5
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Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Oliveira TCF, Carmo LFV, Murta B, Duarte LG, Nome RA, Rocha WR, Brandão TAS. Effective targeting of proton transfer at ground and excited states of ortho-(2′-imidazolyl)naphthol constitutional isomers. Phys Chem Chem Phys 2015; 17:2404-15. [DOI: 10.1039/c4cp04337e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Besides electronic effects at the excited state, ground and excited state acidities are largely affected by proximity and structural alignment.
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Affiliation(s)
- Thaís C. F. Oliveira
- Department of Chemistry
- ICEX
- Federal University of Minas Gerais
- Belo Horizonte
- Brazil
| | - Luiz F. V. Carmo
- Department of Chemistry
- ICEX
- Federal University of Minas Gerais
- Belo Horizonte
- Brazil
| | - Bárbara Murta
- Department of Chemistry
- ICEX
- Federal University of Minas Gerais
- Belo Horizonte
- Brazil
| | | | - Rene A. Nome
- Institute of Chemistry
- State University of Campinas
- Campinas
- Brazil
| | - Willian R. Rocha
- Department of Chemistry
- ICEX
- Federal University of Minas Gerais
- Belo Horizonte
- Brazil
| | - Tiago A. S. Brandão
- Department of Chemistry
- ICEX
- Federal University of Minas Gerais
- Belo Horizonte
- Brazil
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7
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Chokotho NCJ, Johnson CD. Constant Selectivity in Proton Exchange Reactions Between Aqueous Sulphuric Acid and Acetylenes. Isr J Chem 2013. [DOI: 10.1002/ijch.198500129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Karaman R, Fattash B, Qtait A. The future of prodrugs – design by quantum mechanics methods. Expert Opin Drug Deliv 2013; 10:713-29. [DOI: 10.1517/17425247.2013.786699] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Karaman R, Dajani KK, Qtait A, Khamis M. Prodrugs of acyclovir--a computational approach. Chem Biol Drug Des 2012; 79:819-34. [PMID: 22260647 DOI: 10.1111/j.1747-0285.2012.01335.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory calculation results demonstrated that the efficiency of the acid-catalyzed hydrolysis of Kirby's acid amides 1-15 is strongly dependent on the substitution on the C-C double bond and the nature of the amide N-alkyl group. Further, the results established that while in the gas phase the hydrolysis rate-limiting step is the tetrahedral intermediate formation in polar solvents such as water, the rate-limiting step could be either the formation or the collapse of the tetrahedral intermediate depending on the substitution on the C-C double bond and on the amide nitrogen substituent. Based on a linear correlation between the calculated and experimental effective molarities, the study on the systems reported herein could provide a good basis for designing prodrug systems that are less hydrophilic than their parental drugs and can be used, in different dosage forms, to release the parent drug in a controlled manner. For example, based on the calculated log effective molarities values, the predicted t(1/2) (a time needed for 50% of the reactant to be hydrolyzed to products) for acyclovir prodrugs, ProD 1-4, was 29.2 h, 6097 days, 4.6 min, and 8.34 h, respectively. Hence, the rate by which acyclovir prodrug releases acyclovir can be determined according to the structural features of the linker (Kirby's acid amide moiety).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestine.
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11
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Karaman R. Analyzing the efficiency in intramolecular amide hydrolysis of Kirby’s N-alkylmaleamic acids – A computational approach. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.07.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Karaman R. Computational-aided design for dopamine prodrugs based on novel chemical approach. Chem Biol Drug Des 2011; 78:853-63. [PMID: 21824329 DOI: 10.1111/j.1747-0285.2011.01208.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The goal of this project was to design novel dopamine prodrugs for the treatment of Parkinson's disease that can improve the overall biopharmaceutical profile of the current medications to enhance effectiveness and to ease the use of the medications. Based on Menger's study and other's kinetic studies on the cleavage reactions of some Kemp's acid amides to the corresponding amines and anhydrides, DFT calculations were made to find a candidate to be used as an efficient dopamine prodrug. The proposed dopamine prodrugs have a carboxylic group as a hydrophilic moiety and a hydrocarbon skeleton as a lipophilic moiety, where the combination of both groups ensures a moderate hydrophilic lipophilc balance value. The potential prodrugs are expected to give better bioavailability than the parental drug owing to improved absorption. Furthermore, the proposed prodrugs are believed to be more effective than l-dopa because the latter undergoes decarboxylation in the periphery before reaching the blood-brain barrier. Additionally, the predicted prodrugs can be used in different dosage forms (I.V., S.C., tablets, and others) because of their potential solubility in organic and aqueous media. It is expected that the proposed prodrugs will undergo cleavage reactions to release the parental dopamine drug with half-life time (t(½) ) of 12-20 h.
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, P.O. Box 20002, Jerusalem, Palestine.
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Gilmore K, Alabugin IV. Cyclizations of Alkynes: Revisiting Baldwin’s Rules for Ring Closure. Chem Rev 2011; 111:6513-56. [DOI: 10.1021/cr200164y] [Citation(s) in RCA: 387] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Kerry Gilmore
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, 32306-4390
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, 32306-4390
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Karaman R, Dajani K, Hallak H. Computer-assisted design for atenolol prodrugs for the use in aqueous formulations. J Mol Model 2011; 18:1523-40. [PMID: 21785934 DOI: 10.1007/s00894-011-1180-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/04/2011] [Indexed: 11/24/2022]
Abstract
Based on stability studies on the drugs atenolol and propranolol and some of their derivatives it is believed that increasing the lipophilicity of the drug will lead to an increase in the stability of its aqueous solutions and will provide a prodrug system with the potential for releasing atenolol in a controlled manner. Using DFT theoretical calculations we have calculated an intramolecular acid catalyzed hydrolysis in nine maleamic (4-amino-4-oxo-2butenoic) acids (Kirby's N-alkylmaleamic acids), 1-9. The DFT calculations confirmed that the acid-catalyzed hydrolysis mechanism in these systems involves: (1) a proton transfer from the hydroxyl of the carboxyl group to the adjacent amide carbonyl carbon, (2) an approach of the carboxylate anion toward the protonated amide carbonyl carbon to form a tetrahedral intermediate; and (3) a collapse of the tetrahedral intermediate into products. Furthermore, DFT calculations in different media revealed that the reaction rate-limiting step depends on the reaction medium. In aqueous medium the rate-limiting step is the collapse of the tetrahedral intermediate whereas in the gas phase the formation of the tetrahedral intermediate is the rate-limiting step. Furthermore, the calculations establish that the acid-catalyzed hydrolysis efficiency is largely sensitive to the pattern of substitution on the carbon-carbon double bond. Based on the experimental t(1/2) (the time needed for the conversion of 50% of the reactants to products) and EM (effective molarity) values for processes 1-9 we have calculated the t(1/2) values for the conversion of the two prodrugs to the parental drug, atenolol. The calculated t(1/2) values for ProD 1-2 are predicted to be 65.3 hours and 11.8 minutes, respectively. Thus, the rate by which atenolol prodrug undergoes cleavage to release atenolol can be determined according to the nature of the linker of the prodrug (Kirby's N-alkylmaleamic acids 1-9).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Box 20002, Jerusalem, Palestine.
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15
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2011. [DOI: 10.1016/s0040-4020(11)00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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17
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Computer-assisted design for paracetamol masking bitter taste prodrugs. J Mol Model 2011; 18:103-14. [PMID: 21491187 DOI: 10.1007/s00894-011-1040-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 03/14/2011] [Indexed: 10/18/2022]
Abstract
It is believed that the bitter taste of paracetamol, a pain killer drug, is due to its hydroxyl group. Hence, it is expected that blocking the hydroxy group with a suitable linker could inhibit the interaction of paracetamol with its bitter taste receptor/s and hence masking its bitterness. Using DFT theoretical calculations we calculated proton transfers in ten different Kirby's enzyme models, 1-10. The calculation results revealed that the reaction rate is linearly correlated with the distance between the two reactive centers (r(GM)) and the angle of the hydrogen bonding (α) formed along the reaction pathway. Based on these results three novel tasteless paracetamol prodrugs were designed and the thermodynamic and kinetic parameters for their proton transfers were calculated. Based on the experimental t(1/2) (the time needed for the conversion of 50% of the reactants to products) and EM (effective molarity) values for processes 1-10 we have calculated the t(1/2) values for the conversion of the three prodrugs to the parental drug, paracetamol. The calculated t(1/2) values for ProD 1-3 were found to be 21.3 hours, 4.7 hours and 8 minutes, respectively. Thus, the rate by which the paracetamol prodrug undergoes cleavage to release paracetamol can be determined according to the nature of the linker of the prodrug (Kirby's enzyme model 1-10). Further, blocking the phenolic hydroxyl group by a linker moiety is believed to hinder the paracetamol bitterness.
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18
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19
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Karaman R. Analyzing the efficiency of proton transfer to carbon in Kirby’s enzyme model—a computational approach. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2010. [DOI: 10.1016/s0040-4020(10)01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Karaman R. Prodrugs of aza nucleosides based on proton transfer reaction. J Comput Aided Mol Des 2010; 24:961-70. [PMID: 20941527 DOI: 10.1007/s10822-010-9389-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/01/2010] [Indexed: 10/19/2022]
Abstract
DFT calculation results for intramolecular proton transfer reactions in Kirby's enzyme models 1-7 reveal that the reaction rate is quite responsive to geometric disposition, especially to distance between the two reactive centers, r (GM), and the angle of attack, α (the hydrogen bonding angle). Hence, the study on the systems reported herein could provide a good basis for designing aza nucleoside prodrug systems that are less hydrophilic than their parental drugs and can be used, in different dosage forms, to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for prodrug 1ProD is predicted to be about 10¹⁰ times faster than that for prodrug 7ProD and about 10⁴ times faster than prodrug 3ProD: rate( 1ProD ) > rate( 3ProD ) > rate( 7ProD ). Hence, the rate by which the prodrug releases the aza nucleoside drug can be determined according to the structural features of the linker (Kirby's enzyme model).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestine.
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23
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Karaman R. A general equation correlating intramolecular rates with ‘attack’ parameters: distance and angle. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.07.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Abstract
Density Functional Theory (DFT) and ab initio calculation results for the proton transfer reaction in Kirby's enzyme models 1-6 reveal that the reaction rate is largely dependent on the existence of a hydrogen bonding net in the reactants and the corresponding transition states. Further, the distance between the two reacting centers and the angle of the hydrogen bonding formed along the reaction path has profound effects on the rate. Hence, the study on the systems reported herein could provide a good basis for designing antimalarial (atovaquone) pro-drug systems that can be used to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for pro-drug 1Pro may be predicted to be about 10¹¹ times faster than that for a pro-drug 4Pro and about 10⁴ times faster than pro-drug 2Pro: rate (1Pro) > rate (2Pro > rate (4Pro). Thus, the rate by which the pro-drug releases the antimalarial drug can be determined according to the nature of the linker (Kirby's enzyme model 1-6).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, P. O. Box 20002, Jerusalem, Palestine.
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25
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Karaman R. The effective molarity (EM)--a computational approach. Bioorg Chem 2010; 38:165-72. [PMID: 20451948 DOI: 10.1016/j.bioorg.2010.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/05/2010] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
Abstract
The effective molarity (EM) for 12 intramolecular S(N)2 processes involving the formation of substituted aziridines and substituted epoxides were computed using ab initio and DFT calculation methods. Strong correlation was found between the calculated effective molarity and the experimentally determined values. This result could open a door for obtaining EM values for intramolecular processes that are difficult to be experimentally provided. Furthermore, the calculation results reveal that the driving forces for ring-closing reactions in the two different systems are proximity orientation of the nucleophile to the electrophile and the ground strain energies of the products and the reactants.
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, P.O. Box 20002, Jerusalem, Palestine.
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26
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Karaman R. The efficiency of proton transfer in Kirby’s enzyme model, a computational approach. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.02.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Fressigné C, Maddaluno J. Are sp Lithiated Carbons More Nucleophilic than sp2or sp3Ones? A Comparative DFT Study of the Condensation of Propynyllithium Aggregates on Formaldehyde. J Org Chem 2010; 75:1427-36. [DOI: 10.1021/jo902315t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Catherine Fressigné
- Laboratoire de Chimie Théorique, CNRS UMR 7616, Université Pierre et Marie Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
- Institut de Recherche en Chimie Organique Fine, CNRS UMR 6014 & FR 3038, Université de Rouen, 76821-Mont St Aignan Cedex, France
| | - Jacques Maddaluno
- Institut de Recherche en Chimie Organique Fine, CNRS UMR 6014 & FR 3038, Université de Rouen, 76821-Mont St Aignan Cedex, France
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Karaman R. Effects of substitution on the effective molarity (EM) for five membered ring-closure reactions – A computational approach. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.09.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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The gem-disubstituent effect—a computational study that exposes the relevance of existing theoretical models. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.08.072] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Karaman R. Cleavage of Menger’s aliphatic amide: A model for peptidase enzyme solely explained by proximity orientation in intramolecular proton transfer. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Karaman R. The effective molarity (EM) puzzle in proton transfer reactions. Bioorg Chem 2009; 37:106-10. [PMID: 19487010 DOI: 10.1016/j.bioorg.2009.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/24/2009] [Accepted: 04/24/2009] [Indexed: 11/24/2022]
Abstract
The DFT and HF calculation results for the proton transfer reactions of three different systems reveal that the reaction mechanism (transfer of a proton to a nucleophile) is largely determined by the distance between the two reactive centers (r). Systems with relatively large r values tend to abstract a proton from a molecule of water, whereas, these with a relatively small r values prefer to be engaged intramolecularly and their interaction with water is only via hydrogen bonding. Further, the results indicate that the effective molarity (logEM) for an intramolecular process is strongly correlated with the distance between the two reacting centers (r) in accordance with Menger's "spatiotemporal hypothesis".
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestinian Territories.
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Accelerations in the Lactonization of Trimethyl Lock Systems Are due to Proximity Orientation and not to Strain Effects. ACTA ACUST UNITED AC 2009. [DOI: 10.1155/2009/240253] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DFT at B3LYP/6-31G(d,p) and HF at 6-31G and AM1 semiempirical calculations of thermodynamc
and kinetic parameters for the trimethyl lock system (an important enzyme model) indicate that the
remarkable enhancement in the lactonizations is largely the result of a proximity orientation as opposed
to the currently advanced strain effect.
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Karaman R. A new mathematical equation relating activation energy to bond angle and distance: A key for understanding the role of acceleration in lactonization of the trimethyl lock system. Bioorg Chem 2008; 37:11-25. [PMID: 18952252 DOI: 10.1016/j.bioorg.2008.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 08/19/2008] [Accepted: 08/31/2008] [Indexed: 11/17/2022]
Abstract
AM1 semi-empirical molecular orbital and ab initio HF at the 6-31G level calculations for the lactonization processes of 12 different hydroxy acids (1a-1l) which differ in their structural features have been conducted. The calculations obtained reveal the following: (1) The rate-limiting step in the lactonization process is formation of a tetrahedral intermediate and not its collapse as was previously reported. (2) The rate-limiting step in both the acid-catalyzed and uncatalyzed lactonization is composed of two successive steps: approach of the hydroxyl toward the carbonyl carbon until it reaches a distance of 1.4 -1.5A, followed by proton transfer from the ether-type oxygen to one of the hydroxyls in the tetrahedral intermediate. Calculations of the activation energies for formation of the tetrahedral intermediate in the 12 hydroxy acids studied indicate: (1) A linear relationship exists between the change in enthalpic energy (E) and the ratio of the attack angle (nucleophilic-oxygen/carbonyl-carbon/alphalambdapietaalpha-carbon) to the distance (nucleophilic-oxygen/carbonyl-carbon) termed alpha/r; (2) The slope (S) of E vs. alpha/r plots depend on the nature of the hydroxy acids. Furthermore, plots of S values against the experimental rate values (log k(exp)) show a linear correlation with a high correlation coefficient. The combined results suggest that hydroxy acids with low S values have high k(exp) values due to enthalpic proximity effects.
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Affiliation(s)
- Rafik Karaman
- College of Pharmacy, Al-Quds University, Abu-Dies, Jerusalem, Palestinian Territory.
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39
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Tetrahedron reports on organic chemistry. Tetrahedron 2008. [DOI: 10.1016/s0040-4020(08)00897-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)01371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00205-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Lectka T, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2006. [DOI: 10.1016/s0040-4020(06)01801-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Lectka T, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2006. [DOI: 10.1016/s0040-4020(06)00771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Titov IY, Chernysheva NB, Chudinov YB, Bogolyubov AA, Semenov VV. 4-Methylenedioxolan-2-ones as convenient synthons for the preparation of natural products of the berbine and calycotomine series. Russ Chem Bull 2006. [DOI: 10.1007/s11172-006-0293-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Chudinov YB, Gashev SB, Chernysheva NB, Semenov VV. Synthesis of annulated oxazolidinones as potential precursors of cyclic cis-β-amino alcohols. Russ Chem Bull 2006. [DOI: 10.1007/s11172-006-0225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Aza-2-dienes-1,3. Partie 5. Préparation deN-aminoimidazoles, 3H-pyrroles, triazolo[1,2,4][1,5-a]pyrazines et imidazo[1,2-a]pyrazines. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19870700123] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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48
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Posner PG, Motherwell PW. Tetrahedron reports on organic chemistry. Tetrahedron 2004. [DOI: 10.1016/s0040-4020(04)01396-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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49
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Tetrahedron reports on organic chemistry. Tetrahedron 2004. [DOI: 10.1016/s0040-4020(04)00315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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50
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Posner PG, Motherwell PW. Tetrahedron reports on organic chemistry. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01884-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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