1
|
Pereira RW, Ramabhadran RO. Accurate Computation of Aqueous p Kas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box p K-Yay Method. J Phys Chem A 2023; 127:9121-9138. [PMID: 37862610 DOI: 10.1021/acs.jpca.3c02977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.
Collapse
Affiliation(s)
- Roshni W Pereira
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
| |
Collapse
|
2
|
Twenty years of amino acid determination using capillary electrophoresis: A review. Anal Chim Acta 2021; 1174:338233. [DOI: 10.1016/j.aca.2021.338233] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/28/2022]
|
3
|
Kazarjan J, Vaher M, Mahlapuu R, Hansen M, Soomets U, Kaljurand M. Separation of glutathione and its novel analogues and determination of their dissociation constants by capillary electrophoresis. Electrophoresis 2013; 34:1820-7. [DOI: 10.1002/elps.201200611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 02/16/2013] [Accepted: 02/17/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Jana Kazarjan
- Department of Chemistry; Tallinn University of Technology; Tallinn; Estonia
| | - Merike Vaher
- Department of Chemistry; Tallinn University of Technology; Tallinn; Estonia
| | - Riina Mahlapuu
- The Centre of Excellence for Translational Medicine; Faculty of Medicine; Department of Biochemistry; University of Tartu; Tartu; Estonia
| | - Mats Hansen
- The Centre of Excellence for Translational Medicine; Faculty of Medicine; Department of Biochemistry; University of Tartu; Tartu; Estonia
| | - Ursel Soomets
- The Centre of Excellence for Translational Medicine; Faculty of Medicine; Department of Biochemistry; University of Tartu; Tartu; Estonia
| | - Mihkel Kaljurand
- Department of Chemistry; Tallinn University of Technology; Tallinn; Estonia
| |
Collapse
|
4
|
Henchoz Y, Schappler J, Geiser L, Prat J, Carrupt PA, Veuthey JL. Rapid determination of pK a values of 20 amino acids by CZE with UV and capacitively coupled contactless conductivity detections. Anal Bioanal Chem 2007; 389:1869-78. [PMID: 17874082 DOI: 10.1007/s00216-007-1568-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 07/23/2007] [Accepted: 08/20/2007] [Indexed: 10/22/2022]
Abstract
A rapid and universal capillary zone electrophoresis (CZE) method was developed to determine the dissociation constants (pK (a)) of the 20 standard proteogenic amino acids. Since some amino acids are poorly detected by UV, capacitively coupled contactless conductivity detection (C(4)D) was used as an additional detection mode. The C(4)D coupling proved to be very successful on a conventional CE-UV instrument, neither inducing supplementary analyses nor instrument modification. In order to reduce the analysis time for pK (a) determination, two strategies were applied: (i) a short-end injection to reduce the effective length, and (ii) a dynamic coating procedure to generate a large electroosmotic flow (EOF), even at pH values as low as 1.5. As a result, the analysis time per amino acid was less than 2 h, using 22 optimized buffers covering a pH range from 1.5 to 12.0 at a constant ionic strength of 50 mM. pK (a) values were calculated using an appropriate mathematical model describing the relationship between effective mobility and pH. The obtained pK (a) values were in accordance with the literature.
Collapse
Affiliation(s)
- Yveline Henchoz
- Laboratoire de Chimie Analytique Pharmaceutique, Section des sciences pharmaceutiques, Université de Genève, Université de Lausanne, Bd d'Yvoy 20, 1211 Geneva 4, Switzerland
| | | | | | | | | | | |
Collapse
|
5
|
Zusková I, Novotná A, Vceláková K, Gas B. Determination of limiting mobilities and dissociation constants of 21 amino acids by capillary zone electrophoresis at very low pH. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 841:129-34. [PMID: 16567135 DOI: 10.1016/j.jchromb.2006.03.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Revised: 03/06/2006] [Accepted: 03/07/2006] [Indexed: 10/24/2022]
Abstract
The dependence of the effective electrophoretic mobility on pH of the background electrolyte was experimentally determined by capillary zone electrophoresis (CZE) for cationic forms of amino acids. The pH of the background electrolytes was in the highly acidic range, 1.6-2.6 pH units, to ensure a high degree of protonation of the amino acids. Poly(vinyl alcohol) was added to the background electrolytes to avoid possible adsorption of the analytes at the inner capillary wall. Non-linear regression of the experimental data was applied to obtain the parameters of the relevant regression functions--the actual mobilities and mixed dissociation constants corresponding to the actual ionic strength. The extended Onsager and Debye-Hückel law was used to calculate the limiting mobilities and thermodynamic dissociation constants. The comparison of the experimental electropherogram with the computer prediction by PeakMaster using the determined data is presented for the selected sample of amino acids.
Collapse
Affiliation(s)
- Iva Zusková
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic.
| | | | | | | |
Collapse
|
6
|
Lisková A, Krivánková L. Determination of dissociation constants of compounds with potential cognition enhancing activity by capillary zone electrophoresis. Electrophoresis 2005; 26:4429-39. [PMID: 16273587 DOI: 10.1002/elps.200500433] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Accurate determination of pK(a) values is important for proper characterization of newly synthesized molecules. In this work we have used CZE for determination of pK(a) values of new compounds prepared from intermediates, 2, 3 and 4-(2-chloro-acetylamino)-phenoxyacetic acids, by substituting chloride for 2-oxo-pyrrolidine, 2-oxo-piperidine or 2-oxo-azepane. These substances are expected to have a cognition enhancing activity and free radicals scavenging effect. Measurements were performed in a polyacrylamide-coated fused-silica capillary of 0.075 mm ID using direct UV detection at 254 nm. Three electrolyte systems were used for measurements to eliminate effects of potential interactions between tested compounds and components of the BGE. In the pH range 2.7-5.4, chloride, formate, acetate and phosphate were used as BGE co-ions, and sodium, beta-alanine and epsilon-aminocaproate as counterions. Mobility standards were measured simultaneously with the tested compounds for calculations of correct electrophoretic mobilities. Several approaches for the calculation of the pK(a) values were used. The values of pK(a) were determined by standard point-to-point calculation using Henderson-Hasselbach equation. Mobility and pH data were also evaluated by using nonlinear regression. Three parameter sigmoidal function fitted the experimental data with correlation coefficients higher than 0.99. Results from CZE measurements were compared with spectrophotometric measurements performed in sodium formate buffer solutions and evaluated at wavelength where the highest absorbance difference for varying pH was recorded. The experimental pK(a) values were compared with corresponding values calculated by the SPARC online calculator. Results of all three used methods were in good correlation.
Collapse
Affiliation(s)
- Anna Lisková
- Institute of Chemical Drugs, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | | |
Collapse
|
7
|
Fu S, Zhang F, Zhang X, Xu Q, Xiao H, Liang X. Physicochemical Characterization of the Strychnos Alkaloids by Capillary Zone Electrophoresis. ANAL SCI 2005; 21:1303-8. [PMID: 16317898 DOI: 10.2116/analsci.21.1303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A capillary zone electrophoresis (CZE) method has been developed for investigating the physicochemical characteristics of five Strychnos alkaloids in Strychnos nux-vomica L. Firstly, the dissociation constants of the five Strychnos alkaloids were determined, based on the relation between the effective mobility of the solutes and the buffer pH. The mathematical relationship was strictly deduced from the fundamental electrophoretic theory and the dissociation equilibrium. Secondly, an equation describing the relation between the migration time of alkaloids of similar structure and their molecular weights was developed and used to predict the migration order and to calculate the electrosomotic velocity. The results predicted by the theory agreed with those from experiments.
Collapse
Affiliation(s)
- Shaoping Fu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, China
| | | | | | | | | | | |
Collapse
|
8
|
Matoga M, Laborde-Kummer E, Langlois MH, Dallet P, Bosc JJ, Jarry C, Dubost JP. Determination of pKa values of 2-amino-2-oxazolines by capillary electrophoresis. J Chromatogr A 2003; 984:253-60. [PMID: 12564697 DOI: 10.1016/s0021-9673(02)01848-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The dissociation constants of new 2-amino-2-oxazolines were determined by capillary electrophoresis (CE) as a new technique. A method based on a linear model has been used in the CE determination. A series of eight 2-amino-2-oxazolines are investigated to determine their ionization constant. Among them, three new oxazolines synthesized are presented. The Ka values were obtained from the plots of reciprocal effective mobility against inverse concentrations of protons. The potentiometric method (PM) was performed as a comparative method. No significant differences were observed between the determined dissociation constants using both methods. Thus, the pKa values have been found to vary between 8.55 and 8.68.
Collapse
Affiliation(s)
- M Matoga
- Chimie Analytique, EA 2962, UFR Sciences Pharmaceutiques, Université Bordeaux 2 Victor Segalen, 146 rue Léo Saignat, Case 110, 33076 Bordeaux Cedex, France
| | | | | | | | | | | | | |
Collapse
|
9
|
Miller JM, Blackburn AC, Shi Y, Melzak AJ, Ando HY. Semi-empirical relationships between effective mobility, charge, and molecular weight of pharmaceuticals by pressure-assisted capillary electrophoresis: applications in drug discovery. Electrophoresis 2002; 23:2833-41. [PMID: 12207289 DOI: 10.1002/1522-2683(200209)23:17<2833::aid-elps2833>3.0.co;2-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Relationships between effective mobility (m(eff)), calculated charge (Z(c)), and molecular weight (MW) are semi-empirically derived for pharmaceuticals using pressure-assisted capillary electrophoresis (PACE). We determined the m(eff) at 12 different pH points (2.0-11.4) of 66 pharmaceutical-like compounds ranging in MW from 79 to 825 g/mol. Plots of the observed m(eff) values versus Z(c)/MW(x ) (where x is a fractional coefficient) gave linear relationships. For anions, it was found that the best correlation (R(2) = 0.9666) exists when the fractional coefficient is equal to 0.4920, resulting in the equation m(eff) = 0.1853 (Z(c)/MW (0.4920)). For cations, the best linear relationship (R(2) = 0.9861) gave the equation m(eff) = 0.3888 (Z(c)/MW (0.6330)). The m(eff), Z(c)/MW(x) relationships were then applied to: (i) developing a technique for selecting an appropriate pH to achieve optimal separation of pharmaceuticals and (ii) determining the maximum charge of a molecule in the pH range of determination of negative log of the dissociation constants (pK(a)) by PACE, thus enabling the correct choice of model equation to be automated without structure analysis.
Collapse
Affiliation(s)
- Jonathan M Miller
- Pharmaceutical Research and Development, World Wide Pharmaceutical Sciences, Pfizer Global Research and Development - Ann Arbor Laboratories, Ann Arbor, MI, USA.
| | | | | | | | | |
Collapse
|
10
|
Jiménez-Lozano E, Marqués I, Barrón D, Beltrán J, Barbosa J. Determination of pKa values of quinolones from mobility and spectroscopic data obtained by capillary electrophoresis and a diode array detector. Anal Chim Acta 2002. [DOI: 10.1016/s0003-2670(02)00435-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
11
|
Koval D, Kasicka V, Jirácek J, Collinsová M, Garrow TA. Determination of dissociation constant of phosphinate group in phosphinic pseudopeptides by capillary zone electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 770:145-54. [PMID: 12013221 DOI: 10.1016/s1570-0232(01)00595-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Capillary zone electrophoresis (CZE) was used for determination of dissociation constant of phosphinate group in phosphinic pseudopeptides, i.e. peptides where one peptide bond is substituted by phosphinic acid moiety -PO2--CH2-. The dissociation constants were determined for a set of newly synthesized pseudopeptides derived from a structure N-Ac-Val-Ala(psi)(PO2--CH2)Leu-His-NH2 by nonlinear regression of experimentally measured pH dependence of their effective electrophoretic mobilities. CZE experiments were carried out in Tris-phosphate background electrolytes in the pH range 1.4-3.2. The pseudopeptides were synthesized as a mixture of four diastereomers, the separation of which was achieved in most cases. Moreover, differences of the effective mobilities of the pseudopeptide diastereomers enabled simultaneous determination of the dissociation constant of their phosphinate group without necessity of previous isolation of individual isomers.
Collapse
Affiliation(s)
- Dugan Koval
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague
| | | | | | | | | |
Collapse
|
12
|
Koval D, Kasicka V, Jirácek J, Collinsová M, Garrow TA. Analysis and characterization of phosphinic pseudopeptides by capillary zone electrophoresis. Electrophoresis 2002; 23:215-22. [PMID: 11840526 DOI: 10.1002/1522-2683(200202)23:2<215::aid-elps215>3.0.co;2-p] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Capillary zone electrophoresis (CZE) was applied to analysis and characterization of phosphinic pseudopeptides with the general structure N-Ac-Val-Ala(psi)(PO2(-)-CH(2)) Leu-Xaa-NH(2), where Xaa represents one of 20 proteinogenic amino acid residues. Pseudopeptides containing neutral or acidic amino acid residues in position Xaa were analyzed as anions in weakly alkaline (pH 8.1) Tris-Tricine background electrolyte (BGE), pseudopeptides with basic amino acid residues in position Xaa were analyzed as cations in acid BGEs (Tris-phosphate buffers). Acidity of phosphinic acid moiety in peptides with basic amino acid residues was determined from the dependence of effective mobility of these peptides on pH in the acid pH region (pH 1.4-2.8). Additionally, separation of diastereomers of some peptides was achieved.
Collapse
Affiliation(s)
- Dusan Koval
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | | | | | | |
Collapse
|
13
|
Prata C, Bonnafous P, Fraysse N, Treilhou M, Poinsot V, Couderc F. Recent advances in amino acid analysis by capillary electrophoresis. Electrophoresis 2001; 22:4129-38. [PMID: 11824633 DOI: 10.1002/1522-2683(200111)22:19<4129::aid-elps4129>3.0.co;2-i] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amino acids are studied extensively using capillary electrophoresis. In this review we will report the different researchs which have been done in the literature since 1998. We will describe the developments of, detection methods, separations of enantiomers, the new medical applications, and amino acids in food and plants.
Collapse
Affiliation(s)
- C Prata
- Université Paul Sabatier, IMRCP, UMR 5623, Toulouse, France
| | | | | | | | | | | |
Collapse
|
14
|
Jia Z, Ramstad T, Zhong M. Medium-throughput pKa screening of pharmaceuticals by pressure-assisted capillary electrophoresis. Electrophoresis 2001; 22:1112-8. [PMID: 11358135 DOI: 10.1002/1522-2683()22:6<1112::aid-elps1112>3.0.co;2-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A fast screening method for the determination of the dissociation constants (pKa) of acidic, basic, and multivalent compounds was developed by using pressure-assisted capillary electrophoresis (PACE). External air pressure was applied to shorten the analysis time. The separation efficiency decreases as air pressure increases. However, it was found that air pressure does not affect the measurement of electrophoretic mobility and pKa significantly when it is less than 2 psi. The method was evaluated in terms of accuracy, precision, and ruggedness by using a set of 48 compounds with literature pKa values ranging from 2 to 10. The difference between the measured pKa values and literature values is less than 0.2 units. The throughput is approximately 20 compounds per day with a 12-point measurement ranging from pH 2.5 to 11. It was demonstrated that this method is applicable for pKa screening of pharmaceuticals with diverse chemical structures.
Collapse
Affiliation(s)
- Z Jia
- Pharmacia Corporation, Pharmaceutics, Pharmaceutical Sciences, Kalamazoo, MI, USA
| | | | | |
Collapse
|
15
|
Barták P, Pěchová D, Tarkowski P, Bednář P, Kotouček M, Stránský Z, Vespalec R. Determination of the first dissociation constant of 6-benzylaminopurine. Anal Chim Acta 2000. [DOI: 10.1016/s0003-2670(00)01037-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|