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Prieto-Díaz R, Fojo-Carballo H, Majellaro M, Tandarić T, Azuaje J, Brea J, Loza MI, Barbazán J, Salort G, Chotalia M, Rodríguez-Pampín I, Mallo-Abreu A, Rita Paleo M, García-Mera X, Ciruela F, Gutiérrez-de-Terán H, Sotelo E. Exploring Biginelli-based scaffolds as A 2B adenosine receptor antagonists: Unveiling novel structure-activity relationship trends, lead compounds, and potent colorectal anticancer agents. Biomed Pharmacother 2024; 173:116345. [PMID: 38442670 DOI: 10.1016/j.biopha.2024.116345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Antagonists of the A2B adenosine receptor have recently emerged as targeted anticancer agents and immune checkpoint inhibitors within the realm of cancer immunotherapy. This study presents a comprehensive evaluation of novel Biginelli-assembled pyrimidine chemotypes, including mono-, bi-, and tricyclic derivatives, as A2BAR antagonists. We conducted a comprehensive examination of the adenosinergic profile (both binding and functional) of a large compound library consisting of 168 compounds. This approach unveiled original lead compounds and enabled the identification of novel structure-activity relationship (SAR) trends, which were supported by extensive computational studies, including quantum mechanical calculations and free energy perturbation (FEP) analysis. In total, 25 molecules showed attractive affinity (Ki < 100 nM) and outstanding selectivity for A2BAR. From these, five molecules corresponding to the new benzothiazole scaffold were below the Ki < 10 nM threshold, in addition to a novel dual A2A/A2B antagonist. The most potent compounds, and the dual antagonist, showed enantiospecific recognition in the A2BAR. Two A2BAR selective antagonists and the dual A2AAR/A2BAR antagonist reported in this study were assessed for their impact on colorectal cancer cell lines. The results revealed a significant and dose-dependent reduction in cell proliferation. Notably, the A2BAR antagonists exhibited remarkable specificity, as they did not impede the proliferation of non-tumoral cell lines. These findings support the efficacy and potential that A2BAR antagonists as valuable candidates for cancer therapy, but also that they can effectively complement strategies involving A2AAR antagonism in the context of immune checkpoint inhibition.
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Affiliation(s)
- Rubén Prieto-Díaz
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Hugo Fojo-Carballo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Maria Majellaro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Tana Tandarić
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Uppsala 75124, Sweden
| | - Jhonny Azuaje
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - José Brea
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - María I Loza
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jorge Barbazán
- Grupo de Oncología Médica Traslacional (ONCOMET), Instituto de Investigación Sanitaria, Santiago de Compostela (IDIS), Hospital Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela 15706, Spain.
| | - Glòria Salort
- Unidad de Farmacología, Departamento de Patología y Terapéutica Experimental, Facultad de Medicina y Ciencias de la Salud, Instituto de Neurociencia, Universitat de Barcelona, L'Hospitalet de Llobregat 08907, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, L'Hospitalet de Llobregat 08907, Spain; Laboratorio de Neurofarmacología, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'investigació Sanitària Illes Balears (IdISBa), University of the Balearic Islands, Palma de Mallorca 07122, Spain
| | - Meera Chotalia
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Iván Rodríguez-Pampín
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Ana Mallo-Abreu
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - M Rita Paleo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Xerardo García-Mera
- Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Francisco Ciruela
- Unidad de Farmacología, Departamento de Patología y Terapéutica Experimental, Facultad de Medicina y Ciencias de la Salud, Instituto de Neurociencia, Universitat de Barcelona, L'Hospitalet de Llobregat 08907, Spain; Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, L'Hospitalet de Llobregat 08907, Spain
| | - Hugo Gutiérrez-de-Terán
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Uppsala 75124, Sweden.
| | - Eddy Sotelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
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Šebesta F, Sovová Ž, Burda JV. Determination of Amino Acids' p Ka: Importance of Cavity Scaling within Implicit Solvation Models and Choice of DFT Functionals. J Phys Chem B 2024; 128:1627-1637. [PMID: 38345944 PMCID: PMC10895671 DOI: 10.1021/acs.jpcb.3c07007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Protonation states of molecules significantly influence the thermodynamics and kinetics of chemical reactions. This is especially important in biochemical processes, where appropriate protonation states of amino acids control the exo/endoergicity of practically all biochemical cycles. This paper is focused on appraisal of the impact of DFT functionals and PCM solvation models on the accuracy of pKa evaluations for all proteinogenic amino acids. Eight functionals (B3LYP, PBE0, revPBE0, M06-2X, M11, M11-L, TPSSh, and ωB97X-D) and four basis sets are considered, together with four kinds of implicit solvation models when additional attention is paid to a cavity construction. An influence of nonelectrostatic contributions and Wertz's corrections on Gibbs free energy is investigated together with accuracy of provided proton solvation energy. The best model is based on the M06-2X/6-311++G**/D-PCM/UAKS computational level. The fitting procedure is utilized to improve the accuracy of the evaluated models. All of these results are also compared with values obtained from the COSMOtherm program and CCSD(T) calculations. Results for cysteine and histidine are discussed individually, as they can be found in different protonation states at neutral pH.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Žofie Sovová
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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3
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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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4
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Hashemi A, Peljo P, Laasonen K. Understanding Electron Transfer Reactions Using Constrained Density Functional Theory: Complications Due to Surface Interactions. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:3398-3407. [PMID: 36865990 PMCID: PMC9969872 DOI: 10.1021/acs.jpcc.2c06537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The kinetic rates of electrochemical reactions depend on electrodes and molecules in question. In a flow battery, where the electrolyte molecules are charged and discharged on the electrodes, the efficiency of the electron transfer is of crucial importance for the performance of the device. The purpose of this work is to present a systematic atomic-level computational protocol for studying electron transfer between electrolyte and electrode. The computations are done by using constrained density functional theory (CDFT) to ensure that the electron is either on the electrode or in the electrolyte. The ab initio molecular dynamics (AIMD) is used to simulate the movement of the atoms. We use the Marcus theory to predict electron transfer rates and the combined CDFT-AIMD approach to compute the parameters for the Marcus theory where it is needed. We model the electrode with a single layer of graphene and methylviologen, 4,4'-dimethyldiquat, desalted basic red 5, 2-hydroxy-1,4-naphthaquinone, and 1,1-di(2-ethanol)-4,4-bipyridinium were selected for the electrolyte molecules. All of these molecules undergo consecutive electrochemical reactions with one electron being transferred at each stage. Because of significant electrode-molecule interactions, it is not possible to evaluate outer-sphere ET. This theoretical study contributes toward the development of a realistic-level prediction of electron transfer kinetics suitable for energy storage applications.
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Affiliation(s)
- Arsalan Hashemi
- Research
Group of Computational Chemistry, Department of Chemistry and Materials
Science, Aalto University, FI-00076 Aalto, Finland
| | - Pekka Peljo
- Research
Group of Battery Materials and Technologies, Department of Mechanical
and Materials Engineering, Faculty of Technology, University of Turku, 20014 Turun Yliopisto, Finland
| | - Kari Laasonen
- Research
Group of Computational Chemistry, Department of Chemistry and Materials
Science, Aalto University, FI-00076 Aalto, Finland
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5
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Busch M, Ahlberg E, Ahlberg E, Laasonen K. How to Predict the p K a of Any Compound in Any Solvent. ACS OMEGA 2022; 7:17369-17383. [PMID: 35647457 PMCID: PMC9134414 DOI: 10.1021/acsomega.2c01393] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Acid-base properties of molecules in nonaqueous solvents are of critical importance for almost all areas of chemistry. Despite this very high relevance, our knowledge is still mostly limited to the pK a of rather few compounds in the most common solvents, and a simple yet truly general computational procedure to predict pK a's of any compound in any solvent is still missing. In this contribution, we describe such a procedure. Our method requires only the experimental pK a of a reference compound in water and a few standard quantum-chemical calculations. This method is tested through computing the proton solvation energy in 39 solvents and by comparing the pK a of 142 simple compounds in 12 solvents. Our computations indicate that the method to compute the proton solvation energy is robust with respect to the detailed computational setup and the construction of the solvation model. The unscaled pK a's computed using an implicit solvation model on the other hand differ significantly from the experimental data. These differences are partly associated with the poor quality of the experimental data and the well-known shortcomings of implicit solvation models. General linear scaling relationships to correct this error are suggested for protic and aprotic media. Using these relationships, the deviations between experiment and computations drop to a level comparable to that observed in water, which highlights the efficiency of our method.
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Affiliation(s)
- Michael Busch
- Department
of Chemistry and Material Science, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Ernst Ahlberg
- Universal
Prediction AB, 42677 Gothenburg, Sweden
- Department
of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Elisabet Ahlberg
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemigården 4, 41296 Gothenburg, Sweden
| | - Kari Laasonen
- Department
of Chemistry and Material Science, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150 Espoo, Finland
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Zhao N, Zhao C, Liu K, Zhang W, Tsang DCW, Yang Z, Yang X, Yan B, Morel JL, Qiu R. Experimental and DFT investigation on N-functionalized biochars for enhanced removal of Cr(VI). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118244. [PMID: 34592327 DOI: 10.1016/j.envpol.2021.118244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/07/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
In this study, N-functionalized biochars with varied structural characteristics were designed by loading poplar leaf with different amounts of urea at 1:1 and 1:3 ratios through pyrolysis method. The addition of urea significantly increased the N content of biochar and facilitated the formation of amine (-NH-, -NH2), imine (-HCNH), benzimidazole (-C7H5N2), imidazole (-C3H3N2), and pyrimidine (-C4H3N2) groups due to substitution reaction and Maillard reaction. The effect of pH on Cr(VI) removal suggested that decrease in solution pH favored the formation of electrostatic attraction between the protonated functional groups and HCrO4-. And, experimental and density functional theory study were used to probe adsorption behaviors and adsorption mechanism which N-functionalized biochars interacted with Cr(VI). The protonation energy calculations indicated that N atoms in newly formed N-containing groups were better proton acceptors. Adsorption kinetics and isotherm experiments exhibited that N-functionalized biochars had greater removal rate and removal capacity for Cr(VI). The removal rate of Cr(VI) on N-functionalized biochar was 10.5-15.5 times that of untreated biochar. Meanwhile, N-functionalized biochar of NB3 with the largest number of adsorption sites for -C7H5N2, -NH2, -OH, -C3H3N2, and phthalic acid (-C8H5O4) exhibited the supreme adsorption capacity for Cr(VI) through H bonds and the highest adsorption energy was -5.01 kcal/mol. These mechanistic findings on the protonation and adsorption capacity are useful for better understanding the functions of N-functionalized biochars, thereby providing a guide for their use in various environmental applications.
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Affiliation(s)
- Nan Zhao
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Chuanfang Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China
| | - Kunyuan Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Weihua Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Zaikuan Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xixiang Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China; School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou Higher Education Mega Center, South China Normal University, Guangzhou, PR China
| | - Bofang Yan
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jean Louis Morel
- Université de Lorraine, INRA, Laboratoire Sols et Environnement, 2, avenue de la forêt de Haye - BP 20163, 54505, Vandœuvre-lès-Nancy, France
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China.
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7
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Anderson ME, Marks MB, Cundari TR. Bifunctional activation of methane by bioinspired transition metal complexes. A simple methane protease model. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Zhao N, Zhao C, Tsang DCW, Liu K, Zhu L, Zhang W, Zhang J, Tang Y, Qiu R. Microscopic mechanism about the selective adsorption of Cr(VI) from salt solution on O-rich and N-rich biochars. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124162. [PMID: 33065456 DOI: 10.1016/j.jhazmat.2020.124162] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/02/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
The adsorption of Cr(VI) on biochars can be suppressed by coexisting anions, but the roles of O-containing functional groups and in particular N-containing functional groups are unclear. In this study, we combined spectroscopic and molecular simulation approaches to investigate the selective adsorption of Cr(VI) on the O-rich (PB, UB1) and N-rich (UB3, UB5) biochars under strong competition of anions. The elemental analysis and pyrolysis-gas chromatography/mass spectrometry indicated that the structures of PB and UB1 were similar, and so were the UB3 and UB5. Quantification of functional groups showed that for UB1, 75.3% of Cr(VI) removal was attributed to O-containing groups, while 53.3-72.7% of that was mediated by N-containing groups in UB3 and UB5. X-ray photoelectron spectra and density functional theory calculations confirmed that for O-rich biochars, surface complexation and strong H-bonds between carboxyl/hydroxyl and HCrO4- improved Cr(VI) removal in the presence of anions, while for N-rich biochars, Cr(VI) adsorption was depressed by coexisting anions in the order of Cl->NO3- >SO42- because of the weaker H-bond between protonated amino groups and HCrO4-. This study presents a novel approach for quantitative, molecular-level evaluation of the roles of biochar functional groups in the Cr(VI) removal from complex environmental systems.
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Affiliation(s)
- Nan Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China; School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chuanfang Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, PR China
| | - Kunyuan Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ling Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Weihua Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jing Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yetao Tang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Rongliang Qiu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China; School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
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9
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Rachuru S, Vandanapu J, Skelton AA. Theoretical Determination of pKas of P(1)-H Phospholes and their Comparison with N(1)-H Azoles. Aust J Chem 2021. [DOI: 10.1071/ch21122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
pKas of P(1)-H deprotonation of all phosphole group compounds, phosphole (C4H4PH), 1,2 and 1,3-diphospholes (C3H3PPH), 1,2,3, and 1,2,4-triphospholes (C2H2P2PH), tetraphosphole (CHP3PH), and pentaphosphole (P4PH) are determined by DFT calculations. We have compared these to the pKas of the analogue azole group compounds and the factors that cause the differences of these values are discussed in terms of the stabilities of both the phosphole anions and azole anions.
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10
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Pereira RW, Ramabhadran RO. pK-Yay: A Black-Box Method Using Density Functional Theory and Implicit Solvation Models to Compute Aqueous p Ka Values of Weak and Strong Acids. J Phys Chem A 2020; 124:9061-9074. [PMID: 32970437 DOI: 10.1021/acs.jpca.0c06298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The concept of pKa is very important in chemistry and biology. Over the past two decades, electronic structure calculations have made huge strides toward becoming reliable counterparts to experiments in determining solution-phase pKa values. However, invariably, the computation of pKa values involves the use of methods whose error bars are intrinsically larger (definitely >2 kcal/mol with density functionals) than the accuracy desired for the estimation of pKa values (<1 or 1.5 pKa units). This scenario presents an ample scope for innovation in developing systematic error cancellation methods even today. In this work, we have developed the pK-Yay method. It is a user-friendly black-box method used to compute aqueous pKa values of strong and weak acids employing routinely used and computationally inexpensive density functionals and implicit solvation models. It does not require the use of any explicit solvent molecule or modifying any other parameter in an electronic structure program. As part of evaluating the method, a comprehensive test set of 26 weak and strong organic and mineral acids covering 35 pKa units (20 to -15) was assembled. The detailed description of the method, its performance with different functionals (ωB97X-D performed best for organic acids with a mean absolute error (MAE) of 0.8 pKa units, and B2-PLYP performed best for strong acids with an MAE of 1.6 pKa units), the strengths and limitations in the present version, and a future scope to improve the accuracy and reduce its empirical nature are presented herein.
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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, and 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, and Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
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11
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Guan AS, Liang IX, Zhou CX, Cundari TR. Metal and Ligand Effects on Coordinated Methane pKa: Direct Correlation with the Methane Activation Barrier. J Phys Chem A 2020; 124:7283-7289. [DOI: 10.1021/acs.jpca.0c04756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amy S. Guan
- Department of Chemistry Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5070, United States
| | - Ivy X. Liang
- Department of Chemistry Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5070, United States
| | - Christopher X. Zhou
- Department of Chemistry Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5070, United States
| | - Thomas R. Cundari
- Department of Chemistry Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5070, United States
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12
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Grumbles WM, Cundari TR. Computational Determination of p Ka(C–H) in 3d Transition Metal-Methyl Complexes. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William M. Grumbles
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle, #305070, Denton, Texas 76203-5017, United States
| | - Thomas R. Cundari
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle, #305070, Denton, Texas 76203-5017, United States
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13
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Baldasare CA, Seybold PG. Computational Estimation of the Gas-Phase and Aqueous Acidities of Carbon Acids. J Phys Chem A 2020; 124:2152-2159. [PMID: 32058710 DOI: 10.1021/acs.jpca.9b11964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbon acids are compounds which ionize by dissociating along carbon-hydrogen bonds. Although commonly noted for the extremely low acidities of some members of this class, these compounds in fact display a wide range of pKas and upon proper substitution can even form strong acids. This study employs density functional theory to estimate the gas-phase acidities (ΔG°s) of these compounds and applies a quantitative structure-activity relationship (QSAR) method at the B3LYP/6-31+G** level with the CPCM aqueous solvent model to estimate their aqueous pKas. For the latter study, the energy difference ΔE(H2O) in water between the parent compounds and their dissociation products was used as a single parameter. Good quality QSAR regression equations were obtained for both the gas-phase (R2 = 0.9905) and aqueous (R2 = 0.9647) dissociations. These equations should be useful for the estimation of missing pKas for compounds in this class. A general discussion of the features affecting the pKas of these compounds is also given.
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Affiliation(s)
- Corey A Baldasare
- Department of Chemistry, Wright State University, Dayton, Ohio 45435, United States
| | - Paul G Seybold
- Department of Chemistry, Wright State University, Dayton, Ohio 45435, United States
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14
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Sandoval-Lira J, Mondragón-Solórzano G, Lugo-Fuentes LI, Barroso-Flores J. Accurate Estimation of p Kb Values for Amino Groups from Surface Electrostatic Potential ( VS,min) Calculations: The Isoelectric Points of Amino Acids as a Case Study. J Chem Inf Model 2020; 60:1445-1452. [PMID: 32108480 DOI: 10.1021/acs.jcim.9b01173] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Theoretical calculation of equilibrium dissociation constants is a very computationally demanding and time-consuming process since it requires an extremely accurate computation of the solvation free energy changes for each of the species involved. By correlating the minimum surface electrostatic potential (VS,min) on the nitrogen atom of several aliphatic amino groups-calculated at the density functional theory (DFT) ωB97X-D/cc-pVDZ level of theory-we obtained regression models for each kind of substitution pattern from which we interpolate their corresponding pKb values with remarkable accuracy: primary R2 = 0.9519; secondary R2 = 0.9112; and tertiary R2 = 0.8172 (N = 20 for each family). These models were validated with tests sets (N = 5) with mean absolute error (MAE) values of 0.1213 (primary), 0.4407 (secondary), and 0.3057 (tertiary). Combining this ansatz with another previously reported by our group to estimate pKa values [Caballero-García, G.; et al. Molecules 2019, 24(1), 79] we are able to reproduce the isoelectric points of 13 amino acids with no titrable side chains with MAE = 0.4636 pI units.
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Affiliation(s)
- Jacinto Sandoval-Lira
- Centro Conjunto de Investigación en Quı́mica Sustentable UAEM-UNAM, Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano, Toluca de Lerdo 50200, México.,Instituto de Quı́mica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
| | - Gustavo Mondragón-Solórzano
- Centro Conjunto de Investigación en Quı́mica Sustentable UAEM-UNAM, Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano, Toluca de Lerdo 50200, México.,Instituto de Quı́mica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
| | - Leonardo I Lugo-Fuentes
- Departamento de Quı́mica, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, México
| | - Joaquín Barroso-Flores
- Centro Conjunto de Investigación en Quı́mica Sustentable UAEM-UNAM, Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano, Toluca de Lerdo 50200, México.,Instituto de Quı́mica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
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15
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Xu L, Coote ML. Methods To Improve the Calculations of Solvation Model Density Solvation Free Energies and Associated Aqueous pKa Values: Comparison between Choosing an Optimal Theoretical Level, Solute Cavity Scaling, and Using Explicit Solvent Molecules. J Phys Chem A 2019; 123:7430-7438. [DOI: 10.1021/acs.jpca.9b04920] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Longkun Xu
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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16
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Fan C, Song M. Mechanistic Insights into Protonated Diamines-catalyzed Decarboxylation of Oxaloacetate. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666181003133432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The chemical mechanisms of protonated diamines-catalyzed decarboxylation of oxaloacetic
acid anions in water solutions have been studied by using density functional theory. The calculated results
show that the activated Gibbs free energy of the decarboxylation step is the highest in the whole
diamine-catalytic processes for OA2-, and protonated ethylenediamine (ENH+) is the best catalyst of
the five diamines, which is consistent with the study of Thalji et al. However, for OA-, different with
OA2-, the dehydration step is the rate-determining one except 1,3-diaminopropane, and protonated 1,4-
diaminobutane is the best catalyst of the five catalysts. The results also indicate that the second amino
group participates in the reaction as the proton acceptor or proton donor, and it assists in decarboxylation
by hydrogen bonds, decreasing the active Gibbs free energy barrier of the whole catalytic process.
These results provide insight into the precise catalytic mechanism of several enzymes whose reactions
are known to proceed via an imine intermediate.
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Affiliation(s)
- Chuangang Fan
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou City, Shandong Province, 256600, China
| | - Mingzhi Song
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou City, Shandong Province, 256600, China
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17
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A computational study of electrocatalytic CO2 reduction by Mn(I) complexes: Role of bipyridine substituents. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2018.11.210] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Chylewska A, Biedulska M, Głębocka A, Raczyńska ED, Makowski M. Drug-like properties and complete physicochemical profile of pyrazine‑2‑amidoxime: A combined multi-experimental and computational studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Ristić MM, Petković M, Milovanović B, Belić J, Etinski M. New hybrid cluster-continuum model for pKa values calculations: Case study of neurotransmitters’ amino group acidity. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Zeng Q, Jones MR, Brooks BR. Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. J Comput Aided Mol Des 2018; 32:1179-1189. [PMID: 30128926 DOI: 10.1007/s10822-018-0150-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/25/2022]
Abstract
In this work, quantum mechanical methods were used to predict the microscopic and macroscopic pKa values for a set of 24 molecules as a part of the SAMPL6 blind challenge. The SMD solvation model was employed with M06-2X and different basis sets to evaluate three pKa calculation schemes (direct, vertical, and adiabatic). The adiabatic scheme is the most accurate approach (RMSE = 1.40 pKa units) and has high correlation (R2 = 0.93), with respect to experiment. This approach can be improved by applying a linear correction to yield an RMSE of 0.73 pKa units. Additionally, we consider including explicit solvent representation and multiple lower-energy conformations to improve the predictions for outliers. Adding three water molecules explicitly can reduce the error by 2-4 pKa units, with respect to experiment, whereas including multiple local minima conformations does not necessarily improve the pKa prediction.
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Affiliation(s)
- Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA.
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA
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21
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Wang Z, Zheng Y, Zheng Y, Xue XS, Ji P. A Systematic Theoretical Study on the Acidities for Cations of Ionic Liquids in Dimethyl Sulfoxide. J Phys Chem A 2018; 122:5750-5755. [DOI: 10.1021/acs.jpca.8b02265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhen Wang
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
- State Key Laboratory on Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yongjun Zheng
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Yong Zheng
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Xiao-Song Xue
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
- State Key Laboratory on Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pengju Ji
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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22
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Lian P, Johnston RC, Parks JM, Smith JC. Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution. J Phys Chem A 2018; 122:4366-4374. [DOI: 10.1021/acs.jpca.8b01751] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Peng Lian
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Ryne C. Johnston
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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23
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Banerjee S, Bhanja SK, Kanti Chattopadhyay P. Quantum chemical predictions of aqueous pK values for OH groups of some α-hydroxycarboxylic acids based on ab initio and DFT calculations. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Malloum A, Fifen JJ, Conradie J. Solvation energies of the proton in methanol revisited and temperature effects. Phys Chem Chem Phys 2018; 20:29184-29206. [DOI: 10.1039/c8cp05823g] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Various functionals assessing solvation free energies and enthalpies of the proton in methanol.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics, Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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25
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Pérez-González A, Castañeda-Arriaga R, Verastegui B, Carreón-González M, Alvarez-Idaboy JR, Galano A. Estimation of empirically fitted parameters for calculating pK
a values of thiols in a fast and reliable way. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2179-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017; 9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022] Open
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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Affiliation(s)
- Fernando Luís Barroso daSilva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903, Ribeirão Preto, SP, Brazil.
- UCD School of Physics, UCD Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Luis Gustavo Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900 - Universidade de São Paulo, BR-14040-901, Ribeirão Preto, SP, Brazil
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27
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Nazemi A, Cundari TR. Control of C-H Bond Activation by Mo-Oxo Complexes: pK a or Bond Dissociation Free Energy (BDFE)? Inorg Chem 2017; 56:12319-12327. [PMID: 28945088 DOI: 10.1021/acs.inorgchem.7b01738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A density functional theory (DFT) study (BMK/6-31+G(d)) was initiated to investigate the activation of benzylic carbon-hydrogen bonds by a molybdenum-oxo complex with a potentially redox noninnocent supporting ligand-a simple mimic of the active species of the enzyme ethylbenzene dehydrogenase (EBDH)-through deprotonation (C-H bond heterolysis) or hydrogen atom abstraction (C-H bond homolysis) routes. Activation free-energy barriers for neutral and anionic Mo-oxo complexes were high, but lower for anionic complexes than neutral complexes. Interesting trends as a function of substituents were observed that indicated significant Hδ+ character in the transition states (TS), which was further supported by the preference for [2 + 2] addition over HAA for most complexes. Hence, it was hypothesized that C-H activation by these EBDH mimics is controlled more by the pKa than by the bond dissociation free energy of the C-H bond being activated. Therefore, the results suggest promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active-site mimics.
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Affiliation(s)
- Azadeh Nazemi
- Department of Chemistry, Center of Advanced Scientific Computing and Modeling (CASCaM), University of North Texas , 1155 Union Circle, #305070, Denton, Texas 76203-5017, United States
| | - Thomas R Cundari
- Department of Chemistry, Center of Advanced Scientific Computing and Modeling (CASCaM), University of North Texas , 1155 Union Circle, #305070, Denton, Texas 76203-5017, United States
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28
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Matsui T, Shigeta Y, Morihashi K. Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical Groups. J Chem Theory Comput 2017; 13:4791-4803. [DOI: 10.1021/acs.jctc.7b00587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Toru Matsui
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kenji Morihashi
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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29
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Hellweg A, Eckert F. Brick by brick computation of the gibbs free energy of reaction in solution using quantum chemistry and COSMO‐RS. AIChE J 2017. [DOI: 10.1002/aic.15716] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Arnim Hellweg
- COSMOlogic GmbH & Co. KGImbacher Weg 46LeverkusenD‐51379 Germany
| | - Frank Eckert
- COSMOlogic GmbH & Co. KGImbacher Weg 46LeverkusenD‐51379 Germany
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30
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Jaidane NE. Structures and spectroscopy of medium size protonated ammonia clusters at different temperatures, H+(NH3)10–16. J Chem Phys 2017; 146:044305. [DOI: 10.1063/1.4974179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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32
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Abstract
C6H5COOH requires at least eight H2O molecules for its dissociation. A linear correlation is observed between pKa and nH2O; an unknown pKa can thus be predicted.
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Affiliation(s)
- Parvathi Krishnakumar
- Homi Bhabha National Institute
- Training School Complex
- Mumbai-400094
- India
- Bhabha Atomic Research Centre
| | - Dilip Kumar Maity
- Homi Bhabha National Institute
- Training School Complex
- Mumbai-400094
- India
- Bhabha Atomic Research Centre
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33
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De Meyer T, Ensing B, Rogge SMJ, De Clerck K, Meijer EJ, Van Speybroeck V. Acidity Constant (pK a ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods. Chemphyschem 2016; 17:3447-3459. [PMID: 27570194 PMCID: PMC5129556 DOI: 10.1002/cphc.201600734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/14/2022]
Abstract
pH‐Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH‐sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pKa value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.
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Affiliation(s)
- Thierry De Meyer
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052, Zwijnaarde, Belgium.,Department of Textiles, Ghent University, Technologiepark 907, 9052, Zwijnaarde, Belgium
| | - Bernd Ensing
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Sven M J Rogge
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052, Zwijnaarde, Belgium
| | - Karen De Clerck
- Department of Textiles, Ghent University, Technologiepark 907, 9052, Zwijnaarde, Belgium
| | - Evert Jan Meijer
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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34
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Galano A, Pérez-González A, Castañeda-Arriaga R, Muñoz-Rugeles L, Mendoza-Sarmiento G, Romero-Silva A, Ibarra-Escutia A, Rebollar-Zepeda AM, León-Carmona JR, Hernández-Olivares MA, Alvarez-Idaboy JR. Empirically Fitted Parameters for Calculating pKa Values with Small Deviations from Experiments Using a Simple Computational Strategy. J Chem Inf Model 2016; 56:1714-24. [PMID: 27585285 DOI: 10.1021/acs.jcim.6b00310] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two empirically fitted parameters have been derived for 74 levels of theory. They allow fast and reliable pKa calculations using only the Gibbs energy difference between an acid and its conjugated base in aqueous solution (ΔGs(BA)). The parameters were obtained by least-squares fits of ΔGs(BA) vs experimental pKa values for phenols, carboxylic acids, and amines using training sets of 20 molecules for each chemical family. Test sets of 10 molecules per family-completely independent from the training set-were used to verify the reliability of the fitting parameters method. It was found that, except for MP2, deviations from experiments are lower than 0.5 pKa units. Moreover, mean unsigned errors lower than 0.35 pKa units were found for the 98.6%, 98.6%, and 94.6% of the tested levels of theory for phenols, carboxylic acids and amines, respectively. The parameters estimated here are expected to facilitate computationally based estimations of pKa values of species for which this magnitude is still unknown, with uncertainties similar to the experimental ones. However, the present study deals only with molecules of modest complexity, thus the reliability of the FP method for more complex systems remains to be tested.
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Affiliation(s)
| | | | | | - Leonardo Muñoz-Rugeles
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México , México D.F.04510, México
| | | | - Antonio Romero-Silva
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México , México D.F.04510, México
| | | | | | - Jorge Rafael León-Carmona
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México , México D.F.04510, México
| | | | - Juan Raúl Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México , México D.F.04510, México
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35
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Kromann JC, Larsen F, Moustafa H, Jensen JH. Prediction of pKa values using the PM6 semiempirical method. PeerJ 2016; 4:e2335. [PMID: 27602298 PMCID: PMC4991863 DOI: 10.7717/peerj.2335] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/16/2016] [Indexed: 12/11/2022] Open
Abstract
The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6-0.7 pH units. For carboxylic acids, the accuracy (0.7-1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5-0.6), slightly worse (0.5-1.0), and worse (1.0-2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2-5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.
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Affiliation(s)
- Jimmy C Kromann
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | - Frej Larsen
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | - Hadeel Moustafa
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | - Jan H Jensen
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
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36
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Rossini E, Netz RR, Knapp EW. Computing pKa Values in Different Solvents by Electrostatic Transformation. J Chem Theory Comput 2016; 12:3360-9. [DOI: 10.1021/acs.jctc.6b00446] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emanuele Rossini
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse
36a, D-14195 Berlin, Germany
| | - Roland R. Netz
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ernst-Walter Knapp
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse
36a, D-14195 Berlin, Germany
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37
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Abstract
We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment.
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Affiliation(s)
- Junming Ho
- Agency for Science, Technology and Research, Institute of High Performance Computing , 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632.,Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mehmed Z Ertem
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973, United States
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38
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Rebollar-Zepeda AM, Galano A. Quantum mechanical based approaches for predicting pKa values of carboxylic acids: evaluating the performance of different strategies. RSC Adv 2016. [DOI: 10.1039/c6ra16221e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The FP method is recommended for estimating pKa values of carboxylic acids for which this information is still unknown, especially in combination with the PBE0 functional (MUE = 0.26) and the SMD solvent model.
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Affiliation(s)
- Aida Mariana Rebollar-Zepeda
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- México D.F
- Mexico
| | - Annia Galano
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- México D.F
- Mexico
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39
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Jaidane NE. Structures and spectroscopy of protonated ammonia clusters at different temperatures. Phys Chem Chem Phys 2016; 18:26827-26843. [DOI: 10.1039/c6cp03240k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Campus Universitaire
- Tunis
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Campus Universitaire
- Tunis
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40
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Nieto-Draghi C, Fayet G, Creton B, Rozanska X, Rotureau P, de Hemptinne JC, Ungerer P, Rousseau B, Adamo C. A General Guidebook for the Theoretical Prediction of Physicochemical Properties of Chemicals for Regulatory Purposes. Chem Rev 2015; 115:13093-164. [PMID: 26624238 DOI: 10.1021/acs.chemrev.5b00215] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Carlos Nieto-Draghi
- IFP Energies nouvelles , 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Guillaume Fayet
- INERIS, Parc Technologique Alata, BP2 , 60550 Verneuil-en-Halatte, France
| | - Benoit Creton
- IFP Energies nouvelles , 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Xavier Rozanska
- Materials Design S.A.R.L. , 18, rue de Saisset, 92120 Montrouge, France
| | - Patricia Rotureau
- INERIS, Parc Technologique Alata, BP2 , 60550 Verneuil-en-Halatte, France
| | | | - Philippe Ungerer
- Materials Design S.A.R.L. , 18, rue de Saisset, 92120 Montrouge, France
| | - Bernard Rousseau
- Laboratoire de Chimie-Physique, Université Paris Sud , UMR 8000 CNRS, Bât. 349, 91405 Orsay Cedex, France
| | - Carlo Adamo
- Institut de Recherche Chimie Paris, PSL Research University, CNRS, Chimie Paristech , 11 rue P. et M. Curie, F-75005 Paris, France.,Institut Universitaire de France , 103 Boulevard Saint Michel, F-75005 Paris, France
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41
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Aidas K, Lanevskij K, Kubilius R, Juška L, Petkevičius D, Japertas P. Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD. J Comput Chem 2015; 36:2158-67. [PMID: 26154878 DOI: 10.1002/jcc.23998] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/01/2015] [Accepted: 06/12/2015] [Indexed: 01/09/2023]
Abstract
Aqueous pK(a) of selected primary benzenesulfonamides are predicted in a systematic manner using density functional theory methods and the SMD solvent model together with direct and proton exchange thermodynamic cycles. Some test calculations were also performed using high-level composite CBS-QB3 approach. The direct scheme generally does not yield a satisfactory agreement between calculated and measured acidities due to a severe overestimation of the Gibbs free energy changes of the gas-phase deprotonation reaction by the used exchange-correlation functionals. The relative pK(a) values calculated using proton exchange method compare to experimental data very well in both qualitative and quantitative terms, with a mean absolute error of about 0.4 pK(a) units. To achieve this accuracy, we find it mandatory to perform geometry optimization of the neutral and anionic species in the gas and solution phases separately, because different conformations are stabilized in these two cases. We have attempted to evaluate the effect of the conformer-averaged free energies in the pK(a) predictions, and the general conclusion is that this procedure is highly too costly as compared with the very small improvement we have gained.
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Affiliation(s)
- Kęstutis Aidas
- VšĮ "Aukštieji algoritmai", A. Mickevičiaus g. 29, LT-08117, Vilnius, Lithuania
- Department of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saulėtekio al. 9, LT-10222, Vilnius, Lithuania
| | - Kiril Lanevskij
- VšĮ "Aukštieji algoritmai", A. Mickevičiaus g. 29, LT-08117, Vilnius, Lithuania
| | - Rytis Kubilius
- VšĮ "Aukštieji algoritmai", A. Mickevičiaus g. 29, LT-08117, Vilnius, Lithuania
| | - Liutauras Juška
- VšĮ "Aukštieji algoritmai", A. Mickevičiaus g. 29, LT-08117, Vilnius, Lithuania
| | - Daumantas Petkevičius
- Department of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saulėtekio al. 9, LT-10222, Vilnius, Lithuania
| | - Pranas Japertas
- VšĮ "Aukštieji algoritmai", A. Mickevičiaus g. 29, LT-08117, Vilnius, Lithuania
- ACD/Labs, Inc., 8 King Street East, Suite 107, Toronto, Ontario, Canada, M5C 1B5
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42
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Koo BJ, Huynh M, Halbach RL, Stubbe J, Nocera DG. Modulation of Phenol Oxidation in Cofacial Dyads. J Am Chem Soc 2015; 137:11860-3. [PMID: 26305909 DOI: 10.1021/jacs.5b05955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presentation of two phenols on a xanthene backbone is akin to the tyrosine dyad (Y730 and Y731) of ribonucleotide reductase. X-ray crystallography reveals that the two phenol moieties are cofacially disposed at 4.35 Å. Cyclic voltammetry reveals that phenol oxidation is modulated within the dyad, which exhibits a splitting of one-electron waves with the second oxidation of the phenol dyad occurring at larger positive potential than that of a typical phenol. In contrast, a single phenol appended to a xanthene exhibits a two-electron process, consistent with reported oxidation pathways of phenols in acetonitrile. The perturbation of the phenol potential by stacking is reminiscent of a similar effect for guanines stacked within DNA base pairs.
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Affiliation(s)
- Bon Jun Koo
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Michael Huynh
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Robert L Halbach
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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43
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Chen R, Chung SH. Molecular dynamics simulations of Na+ and leucine transport by LeuT. Biochem Biophys Res Commun 2015; 464:281-5. [DOI: 10.1016/j.bbrc.2015.06.143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022]
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44
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Kiani F, Abbaszadeh M, Pousti M, Koohyar F. Theoretically nanoscale study on ionization of muscimol nano drug in aqueous solution. BRAZ J PHARM SCI 2015. [DOI: 10.1590/s1984-82502015000100021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In the present work, acid dissociation constant (pKa) values of muscimol derivatives were calculated using the Density Functional Theory (DFT) method. In this regard, free energy values of neutral, protonated and deprotonated species of muscimol were calculated in water at the B3LYP/6-31G(d) basis sets. The hydrogen bond formation of all species had been analyzed using the Tomasi's method. It was revealed that the theoretically calculated pKa values were in a good agreement with the existing experimental pKa values, which were determined from capillary electrophoresis, potentiometric titration and UV-visible spectrophotometric measurements.
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45
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Mora-Diez N, Egorova Y, Plommer H, Tremaine PR. Theoretical study of deuterium isotope effects on acid–base equilibria under ambient and hydrothermal conditions. RSC Adv 2015. [DOI: 10.1039/c4ra14087g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The calculated difference between pKa values in H2O and D2O is in excellent agreement with experiment.
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Affiliation(s)
| | - Yulia Egorova
- Department of Chemistry
- Thompson Rivers University
- Kamloops
- Canada
| | - Hart Plommer
- Department of Chemistry
- Thompson Rivers University
- Kamloops
- Canada
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46
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Ho J. Are thermodynamic cycles necessary for continuum solvent calculation of pKas and reduction potentials? Phys Chem Chem Phys 2014; 17:2859-68. [PMID: 25503399 DOI: 10.1039/c4cp04538f] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Continuum solvent calculations of pKas and reduction potentials usually entail the use of a thermodynamic cycle to express the reaction free energy in terms of gas phase energies and free energies of solvation. In this work, we present a systematic study comparing the solution phase free energy changes obtained in this manner with those directly computed within the SMD solvation model against a large test set of 117 pKas and 42 reduction potentials in water and DMSO. The inclusion of vibrational contributions in the free energy of solvation has a negligible impact on the accuracy of thermodynamic cycle predictions of pKas and reduction potentials. Additionally, when gas phase energies in the thermodynamic cycle are computed at more accurate levels of theory, very similar results (mean unsigned difference of 0.5 kcal mol(-1)) can be achieved when the high-level computations (MP2/GTMP2Large and G3(MP2)-RAD(+)) are directly carried out within the continuum model. Increasing the accuracy of the electronic structure theory may or may not improve the agreement with experiment suggesting that the error is largely in the solvation model. For amino acids where their gas and solution phase species exist as different tautomers, the direct approach provided a significant improvement in calculated pKas. These results demonstrate that direct calculation of solution phase pKas and reduction potentials within the SMD model provides a general and reliable approximation to corresponding thermodynamic cycle based protocols, and is recommended for systems where solvation induced changes in geometry are significant. Further studies are necessary to ascertain whether the results are generalisable to other continuum solvation models.
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Affiliation(s)
- Junming Ho
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA.
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47
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Quantum chemical calculations of the pK a of C60H2 in DMSO, toluene—DMSO mixture, and water. Russ Chem Bull 2014. [DOI: 10.1007/s11172-014-0473-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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48
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Fifen JJ, Dhaouadi Z, Nsangou M. Revision of the Thermodynamics of the Proton in Gas Phase. J Phys Chem A 2014; 118:11090-7. [DOI: 10.1021/jp508968z] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean Jules Fifen
- Department
of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire
de Spectroscopie Atomique et Moléculaire, Faculté des
Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire 1060, Tunis, Tunisia
| | - Mama Nsangou
- University of Maroua, P.O. Box, 46, Maroua, Cameroon
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49
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Liu Y, Rowley CN, Kerton FM. Combined Experimental and Computational Studies on the Physical and Chemical Properties of the Renewable Amide, 3-Acetamido-5-acetylfuran. Chemphyschem 2014; 15:4087-94. [DOI: 10.1002/cphc.201402376] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/15/2014] [Indexed: 11/10/2022]
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50
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Chen R, Gryn’ova G, Wu Y, Coote ML, Chung SH. Mechanisms and Energetics of Potassium Channel Block by Local Anesthetics and Antifungal Agents. Biochemistry 2014; 53:6786-92. [DOI: 10.1021/bi5009408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Yingliang Wu
- College of Life Sciences, Wuhan University, Wuhan, China
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