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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.
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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
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Santana AG, Robinson K, Vickers C, Deen MC, Chen H, Zhou S, Dai B, Fuller M, Boraston AB, Vocadlo DJ, Clarke LA, Withers SG. Pharmacological Chaperones for GCase that Switch Conformation with pH Enhance Enzyme Levels in Gaucher Animal Models. Angew Chem Int Ed Engl 2022; 61:e202207974. [DOI: 10.1002/anie.202207974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Andrés G. Santana
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
| | - Kyle Robinson
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
| | - Chelsea Vickers
- Dept. of Biochemistry and Microbiology University of Victoria Victoria BC, V8W 3P6 Canada
| | - Matthew C. Deen
- Dept. of Chemistry and Dept. of Mol. Biology and Biochemistry Simon Fraser University Burnaby BC, V5A 1S6 Canada
| | - Hong‐Ming Chen
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
| | - Stephen Zhou
- Dept. of Medical Genetics University of British Columbia Women's Hospital & Health Centre Vancouver BC, V6H 3N1 Canada
| | - Ben Dai
- Dept. of Medical Genetics University of British Columbia Women's Hospital & Health Centre Vancouver BC, V6H 3N1 Canada
| | - Maria Fuller
- Genetics and Molecular Pathology SA Pathology at Women's and Children's Hospital N. Adelaide South Australia 5006 Australia
| | - Alisdair B. Boraston
- Dept. of Biochemistry and Microbiology University of Victoria Victoria BC, V8W 3P6 Canada
| | - David J. Vocadlo
- Dept. of Chemistry and Dept. of Mol. Biology and Biochemistry Simon Fraser University Burnaby BC, V5A 1S6 Canada
| | - Lorne A. Clarke
- Dept. of Medical Genetics University of British Columbia Women's Hospital & Health Centre Vancouver BC, V6H 3N1 Canada
| | - Stephen G. Withers
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
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3
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Santana A, Robinson K, Vickers C, Deen M, Chen HM, Zhou S, Dai B, Fuller M, Boraston A, Vocadlo D, Clarke L, Withers S. Pharmacological Chaperones for GCase That Switch Conformation with pH Enhance Enzyme Levels in Gaucher Animal Models. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Chelsea Vickers
- University of Victoria Faculty of Science Biochemistry and Microbiology CANADA
| | | | | | - Stephen Zhou
- The University of British Columbia Dept. of Medical Genetics, CANADA
| | - Ben Dai
- The University of British Columbia Dept of Medical genetics CANADA
| | - Maria Fuller
- Womens and Childrens Hospital, Adelaide Genetics and Molecular Pathology AUSTRALIA
| | | | | | - Lorne Clarke
- The University of British Columbia Dept. of Medical Genetics CANADA
| | - Stephen Withers
- University of British Columbia Chemistry 2036 Main Mall V6T 1Z1 Vancouver CANADA
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Steinmann C, Sauer SPA. The aug-cc-pVTZ-J basis set for the p-block fourth-row elements Ga, Ge, As, Se, and Br. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:1134-1145. [PMID: 33929770 DOI: 10.1002/mrc.5166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The aug-cc-pVTZ-J basis set family is extended to include the fourth-row p-block elements Ga, Ge, As, Se, and Br. We use the established approach outlined by Sauer and coworkers (J. Chem. Phys. 115, 1324 [2001], J. Chem. Phys. 133, 054308 [2010], J. Chem. Theory Comput. 7, 4070 [2011], and J. Chem. Theory Comput. 7, 4077 [2011]) where the completely uncontracted aug-cc-pVTZ basis set is saturated with tight s-, p-, d-, and f-functions to form the aug-cc-pVTZ-Juc basis set for the tested elements. The saturation is carried out on the simplest hydrides possible for the tested elements GaH, GeH4 , AsH3 , H2 Se, and HBr until an improvement is less than 0.01% for all s-, p-, and d-functions added. f-Functions are added to an improvement less than or equal to 1.0% due to the computational expense these functions add. The saturated aug-cc-pVTZ-Juc (26s16p12d5f) is then recontracted using the molecular orbital coefficients from self-consistent field calculations on the simple hydrides to improve computational efficiency. During contraction of the basis set, we observe that the linear hydrogen bromide molecule has a slower convergence than the other tested molecules which sets a limit on the accuracy obtained. All calculations with the contracted aug-cc-pVTZ-J [17s10p7d5f] gives results that are within 1.0% of the uncontracted results at considerable computational savings.
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Affiliation(s)
- Casper Steinmann
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Ruyonga MR, Mendoza O, Browne M, Samoshin VV. Exploration of
trans
‐2‐(azaarylsulfanyl)‐cyclohexanols as potential pH‐triggered conformational switches. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mulinde R. Ruyonga
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
| | - Oscar Mendoza
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
| | - Michael Browne
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
| | - Vyacheslav V. Samoshin
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
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Viayna A, Antermite SG, de Candia M, Altomare CD, Luque FJ. Interplay between Ionization and Tautomerism in Bioactive β-Enamino Ester-Containing Cyclic Compounds: Study of Annulated 1,2,3,6-Tetrahydroazocine Derivatives. J Phys Chem B 2019; 124:28-37. [PMID: 31841339 DOI: 10.1021/acs.jpcb.9b08904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Depending on the chemical scaffold, a bioactive species could reflect the interplay between ionization and tautomerism, which is often complicated by the possibility of populating different conformational states, in the case of flexible ligands. In this context, theoretical methods can be valuable to discern the role of these factors, as shown here for β-enamino esters of 1,2,3,6-tetrahydroazocino-fused ring systems, some of which had proven to be suitable scaffolds for designing novel acetylcholinesterase inhibitors. The compounds investigated herein form two clusters with distinctive experimental pKa values (i.e., α,β-diesters and β-esters ranging within 6.1-7.3 and 8.2-9.0 pKa intervals, respectively), which implies a drastic difference in the most populated species at physiological conditions. While chemoinformatic tools did not provide a consistent description of the actual pKa values, the theoretical analysis performed for the protonated and neutral species of these compounds revealed a marked change in the tautomeric preference of the tetrahydroazocine moiety upon (de)protonation. Excellent agreement between the calculated and experimental pKa values was found when the tautomeric preference of the protonated and neutral species was considered. Overall, this study highlights the potential use of high-level computational methods to disclose the mutual influence between ionization, tautomerism, and conformational preferences in multifunctional (bio)organic compounds.
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Affiliation(s)
- Antonio Viayna
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (ITQCUB) , University of Barcelona , Av. Prat de la Riba 171 , E-08921 Santa Coloma de Gramenet , Spain
| | - Salvatore G Antermite
- Department of Pharmacy-Drug Sciences , University of Bari Aldo Moro , Via E. Orabona 4 , I-70125 Bari , Italy
| | - Modesto de Candia
- Department of Pharmacy-Drug Sciences , University of Bari Aldo Moro , Via E. Orabona 4 , I-70125 Bari , Italy
| | - Cosimo D Altomare
- Department of Pharmacy-Drug Sciences , University of Bari Aldo Moro , Via E. Orabona 4 , I-70125 Bari , Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (ITQCUB) , University of Barcelona , Av. Prat de la Riba 171 , E-08921 Santa Coloma de Gramenet , Spain
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Zhang XX, Deng T, Jia GZ. Nuclear spin-spin coupling constants prediction based on XGBoost and LightGBM algorithms. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1696478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Xin-xin Zhang
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
| | - Tong Deng
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
| | - Guo-zhu Jia
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
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Schnack-Petersen AK, Haase PAB, Faber R, Provasi PF, Sauer SPA. RPA(D) and HRPA(D): Two new models for calculations of NMR indirect nuclear spin-spin coupling constants. J Comput Chem 2019; 39:2647-2666. [PMID: 30515901 DOI: 10.1002/jcc.25712] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/26/2018] [Accepted: 09/23/2018] [Indexed: 01/21/2023]
Abstract
In this article, the RPA(D) and HRPA(D) models for the calculation of linear response functions are presented. The performance of the new RPA(D) and HRPA(D) models is compared to the performance of the established RPA, HRPA, and SOPPA models in calculations of indirect nuclear spin-spin coupling constants using the CCSD model as a reference. The doubles correction offers a significant improvement on both the RPA and HRPA models; however, the improvement is more dramatic in the case of the RPA model. For all coupling types investigated in this study, the results obtained using the HRPA(D) model are comparable in accuracy to those given by the SOPPA model, while requiring between 30% and 90% of the calculation time needed for SOPPA. The RPA(D) model, while of slightly lower accuracy compared to the CCSD model than HRPA(D), offered calculation times of only approximately 25% of those required for SOPPA for all the investigated molecules. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Pi A B Haase
- Van Swinderen Institute, University of Groningen, Groningen, The Netherlands
| | - Rasmus Faber
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patricio F Provasi
- Department of Physics-IMIT, Northeastern University-CONICET, Corrientes, Argentina
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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van der Vorm S, Hansen T, van Rijssel ER, Dekkers R, Madern JM, Overkleeft HS, Filippov DV, van der Marel GA, Codée JDC. Furanosyl Oxocarbenium Ion Conformational Energy Landscape Maps as a Tool to Study the Glycosylation Stereoselectivity of 2-Azidofuranoses, 2-Fluorofuranoses and Methyl Furanosyl Uronates. Chemistry 2019; 25:7149-7157. [PMID: 30882938 PMCID: PMC6563709 DOI: 10.1002/chem.201900651] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/12/2019] [Indexed: 12/16/2022]
Abstract
The 3D shape of glycosyl oxocarbenium ions determines their stability and reactivity and the stereochemical course of SN 1 reactions taking place on these reactive intermediates is dictated by the conformation of these species. The nature and configuration of functional groups on the carbohydrate ring affect the stability of glycosyl oxocarbenium ions and control the overall shape of the cations. We herein map the stereoelectronic substituent effects of the C2-azide, C2-fluoride and C4-carboxylic acid ester on the stability and reactivity of the complete suite of diastereoisomeric furanoses by using a combined computational and experimental approach. Surprisingly, all furanosyl donors studied react in a highly stereoselective manner to provide the 1,2-cis products, except for the reactions in the xylose series. The 1,2-cis selectivity for the ribo-, arabino- and lyxo-configured furanosides can be traced back to the lowest-energy 3 E or E3 conformers of the intermediate oxocarbenium ions. The lack of selectivity for the xylosyl donors is related to the occurrence of oxocarbenium ions adopting other conformations.
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10
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Fujita H, Hayakawa N, Kunishima M. Cooperation of the Neutral and the Cationic Leaving Group Pathways in Acid-Catalyzed O-Benzylation of TriBOT. J Org Chem 2018; 83:10684-10687. [PMID: 30005572 DOI: 10.1021/acs.joc.8b01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction profile of acid-catalyzed O-benzylation with 2,4,6-tris(benzyloxy)-1,3,5-triazine (TriBOT) was analyzed to study the reaction kinetics. The first-order kinetic constant for the formation of benzyl cation species from N-protonated TriBOT (neutral leaving group pathway) was estimated and compared with that of the model compound for TriBOT. Since rapid consumption of TriBOT in the late stage could not be explained solely by this pathway, cooperation of another reaction mechanism, the cationic leaving group pathway, was proposed to rationalize the rate acceleration.
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Affiliation(s)
- Hikaru Fujita
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical, and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Naoko Hayakawa
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical, and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Munetaka Kunishima
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical, and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
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Pedersen CM, Bols M. On the nature of the electronic effect of multiple hydroxyl groups in the 6-membered ring - the effects are additive but steric hindrance plays a role too. Org Biomol Chem 2018; 15:1164-1173. [PMID: 28084490 DOI: 10.1039/c6ob02427k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Research during the last two decades has shown a remarkable directional component of the substituent effects of hydroxy groups, which has a profound effect on the properties of hydroxylated compounds such as carbohydrates. While the epimerisation of a single hydroxyl function is well studied the consequence of multiple epimerisations is more speculative. In this work the effect of three epimerisations was investigated. To this end epimeric 2-phenyl iminoxylitols that have a phenyl group as a conformational anchor and thus hydroxyl groups in the axial or equatorial position, respectively, were synthesized and their pKa and conformation were studied. The results show that the large difference in the electronic effect between the axial and equatorial hydroxyls is partially cancelled by counteracting steric hindrance from 1,3-diaxial interactions. Hydrogen bonding does not appear to play any role in the electronic influence of the hydroxyl groups.
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Affiliation(s)
- Christian Marcus Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.
| | - Mikael Bols
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.
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Samoshin VV, Zheng Y, Liu X. Trans
-2-Aminocyclohexanol derivatives as pH-triggered conformational switches. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3689] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vyacheslav V. Samoshin
- Department of Chemistry, College of the Pacific; University of the Pacific; Stockton CA 95211 USA
| | - Yu Zheng
- Department of Chemistry, College of the Pacific; University of the Pacific; Stockton CA 95211 USA
| | - Xin Liu
- Department of Chemistry, College of the Pacific; University of the Pacific; Stockton CA 95211 USA
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