1
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Thammanatpong K, Surawatanawong P. Mechanisms of hydrogen evolution by six-coordinate cobalt complexes: a density functional study on the role of a redox-active pyridinyl-substituted diaminotriazine benzamidine ligand as a proton relay. Dalton Trans 2024; 53:6006-6019. [PMID: 38469898 DOI: 10.1039/d3dt03960a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The hydrogen evolution reaction is an important process for energy storage. The six-coordinate cobalt complex [CoIII(L1-)(LH)]2+ (LH = N-(4-amino-6-(pyridin-2-yl)-1,3,5-triazin-2-yl)benzamidine) was found to catalyze photocatalytic hydrogen evolution. In this work, we performed density functional calculations to obtain the reduction potentials and the proton-transfer free energy of possible intermediates to determine the preferred pathways for proton reduction. The mechanism involves the metal-based reduction of Co(III) to Co(II) before the protonation at the amidinate N on the pyridinyl-substituted diaminotriazine benzamidinate ligand L1- to form [CoII(LH)(LH)]2+. Essentially, the subsequent electron transfer is not metal-based reduction, but rather ligand-based reduction to form [CoII(LH)(LH˙1-)]1+. Through a proton-coupled electron transfer process, the cobalt hydride [CoIIH(LH)(LH2˙)]1+ is formed as the key intermediate for hydrogen evolution. As the cobalt hydride complex is coordinatively saturated, a structural change is required when the hydride on Co is coupled with the proton on pyridine. Notably, the redox-active nature of the ligand results in the low acidity of the protonated pyridine moiety of LH2˙, which impedes its function as a proton relay. Our findings suggest that separating the proton relay fragment from the electron reservoir fragment of the redox-active ligand is preferred for fully utilizing both features in catalytic H2 evolution.
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Affiliation(s)
- Kittimeth Thammanatpong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
- Center of Sustainable Energy and Green Materials, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
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2
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Guo J, Albesa A, Wexler C. Advantages of Multidimensional Biasing in Accelerated Dynamics: Application to the Calculation of the Acid p Ka for Acetic Acid. J Phys Chem B 2023; 127:8446-8455. [PMID: 37738501 DOI: 10.1021/acs.jpcb.3c03795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The use of accelerated sampling methods such as metadynamics has shown a significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine the difference in free energies between two or more chemically distinct states such as in the calculation of acid dissociation constants Ka. In this case, the most common method is to bias the system via a single collective variable (CV) representing the coordination number of the proton donor group, which yields results in reasonable agreement with experiments. Here we study the deprotonation of acetic acid using the reactive force field ReaxFF and observe a significant dependence of Ka on the simulation box size when biasing only the coordination number CV, which is due to incomplete sampling of the deprotonated state for small simulation systems and inefficient sampling for larger ones. Incorporating a second CV representing the distance between the H3O+ cation and the acetate anion results in substantially more efficient sampling, both accelerating the dynamics and virtually eliminating the computational box size dependence.
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Affiliation(s)
- Jiasen Guo
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Alberto Albesa
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
- INIFTA, Universidad Nacional de La Plata, B1900 La Plata, Argentina
| | - Carlos Wexler
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
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3
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Biela M, Kleinová A, Uhliar M, Klein E. Investigation of substituent effect on O–C bond dissociation enthalpy of methoxy group in meta- and para-substituted anisoles. J Mol Graph Model 2023; 122:108465. [PMID: 37062128 DOI: 10.1016/j.jmgm.2023.108465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/08/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023]
Abstract
This paper is focused on the theoretical investigation of O-C Bond Dissociation Enthalpy (BDE) of methoxy OCH3 group in 15 meta- and 15 para-substituted anisoles in gas phase, non-polar environment, and water. Density Functional Theory (DFT) calculations were carried out using M06-2X functional and 6-311++G(d,p) basis set. Obtained BDEs were correlated with Brown and Okamoto σp+ and Hammett σm constants representing commonly used descriptors of electron-donating or electron-withdrawing substituent effect. Obtained linear dependences allow the prediction of substituent effect on BDE using σp+ and σm constants. Calculated reaction enthalpies were also compared with available experimental and theoretical ab initio G4 values. Found results suggest that employed method may provide reliable thermochemistry data for demethylation of naturally occurring (poly)phenolic compounds, as well. In all studied environments, substituent induced changes in O-C BDE can be considered equal to those observed for the dissociation of phenolic O-H bond of substituted phenols.
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4
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Xu W, Sun TY, Di Y, Hao X, Wu YD. Inverse Electron-Demanding Diels-Alder Reactions in the Chemical Synthesis of Prenylated Indole Alkaloids Containing a Bicycle[2.2.2]diazaoctane Moiety: A Theoretical Study. Chem Asian J 2023; 18:e202300063. [PMID: 36806582 DOI: 10.1002/asia.202300063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 02/22/2023]
Abstract
The Diels-Alder reaction is believed to be a key step in the biosynthesis of prenylated indole alkaloids containing a bicycle[2.2.2]diazaoctane moiety. Many chemical syntheses of bicyclic structures by Diels-Alder reactions have been reported, but the reaction mechanism remains underexplored. We have carried out DFT calculations on both acid- and base-promoted Diels-Alder reactions in these syntheses and reveal that the reactions occur through an inverse-electron demand mechanism. We hope that the new mechanism is helpful for the mechanistic understanding of the biosynthesis of this class of important natural products.
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Affiliation(s)
- Wenqiang Xu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China
| | - Tian-Yu Sun
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China
| | - Yingtong Di
- State Key Laboratory of Phytochemistry and, Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
| | - Xiaojiang Hao
- State Key Laboratory of Phytochemistry and, Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China.,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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5
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Simulation and experimental study on mechanism and kinetics of 1,1,2-trichloroethane dehydrochlorination reaction. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Barlow JM, Clarke LE, Zhang Z, Bím D, Ripley KM, Zito A, Brushett FR, Alexandrova AN, Yang JY. Molecular design of redox carriers for electrochemical CO 2 capture and concentration. Chem Soc Rev 2022; 51:8415-8433. [PMID: 36128984 DOI: 10.1039/d2cs00367h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Developing improved methods for CO2 capture and concentration (CCC) is essential to mitigating the impact of our current emissions and can lead to carbon net negative technologies. Electrochemical approaches for CCC can achieve much higher theoretical efficiencies compared to the thermal methods that have been more commonly pursued. The use of redox carriers, or molecular species that can bind and release CO2 depending on their oxidation state, is an increasingly popular approach as carrier properties can be tailored for different applications. The key requirements for stable and efficient redox carriers are discussed in the context of chemical scaling relationships and operational conditions. Computational and experimental approaches towards developing redox carriers with optimal properties are also described.
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Affiliation(s)
- Jeffrey M Barlow
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Lauren E Clarke
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Zisheng Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
| | - Katelyn M Ripley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Alessandra Zito
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Fikile R Brushett
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
| | - Jenny Y Yang
- Department of Chemistry, University of California, Irvine, California 92697, USA.
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7
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Lan X, Dai Y, Jing W, Meng X, Liu F, Wang S, He A, Li N. DFT investigation on the carbonate radical formation in the system containing carbon dioxide and hydroxyl free radical. J Mol Graph Model 2022; 114:108182. [DOI: 10.1016/j.jmgm.2022.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
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8
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Shen X, Wang W, Wang Q, Liu J, Huang F, Sun C, Yang C, Chen D. Mechanism of iron complexes catalyzed in the N-formylation of amines with CO 2 and H 2: the superior performance of N-H ligand methylated complexes. Phys Chem Chem Phys 2021; 23:16675-16689. [PMID: 34337631 DOI: 10.1039/d1cp00608h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
CO2 hydrogenation into value-added chemicals not only offer an economically beneficial outlet but also help reduce the emission of greenhouse gases. Herein, the density functional theory (DFT) studies have been carried out on CO2 hydrogenation reaction for formamide production catalyzed by two different N-H ligand types of PNP iron catalysts. The results suggest that the whole mechanistic pathway has three parts: (i) precatalyst activation, (ii) hydrogenation of CO2 to generate formic acid (HCOOH), and (iii) amine thermal condensation to formamide with HCOOH. The lower turnover number (TON) of a bifunctional catalyst system in hydrogenating CO2 may attribute to the facile side-reaction between CO2 and bifunctional catalyst, which inhibits the generation of active species. Regarding the bifunctional catalyst system addressed in this work, we proposed a ligand participated mechanism due to the low pKa of the ligand N-H functional in the associated stage in the catalytic cycle. Remarkably, catalysts without the N-H ligand exhibit the significant transfer hydrogenation through the metal centered mechanism. Due to the excellent catalytic nature of the N-H ligand methylated catalyst, the N-H bond was not necessary for stabilizing the intermediate. Therefore, we confirmed that N-H ligand methylated catalysts allow for an efficient CO2 hydrogenation reaction compared to the bifunctional catalysts. Furthermore, the influence of Lewis acid and strong base on catalytic N-formylation were considered. Both significantly impact the catalytic performance. Moreover, the catalytic activity of PNMeP-based Mn, Fe and Ru complexes for CO2 hydrogenation to formamides was explored as well. The energetic span of Fe and Mn catalysts are much closer to the precious metal Ru, which indicates that such non-precious metal catalysts have potentially valuable applications.
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Affiliation(s)
- Xinyu Shen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
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9
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Distinct roles of Ag(I) and Cu(II) as cocatalysts in the intramolecular cyclization of N-methyl-N-phenylanthranilic acid: A theoretical investigation. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Ni/Cu-catalyzed silylation of allylic alcohol: Theoretical studies on the mechanisms, regioselectivity, and role of ligand. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Thomsen B, Shiga M. Nuclear quantum effects on autoionization of water isotopologs studied by ab initio path integral molecular dynamics. J Chem Phys 2021; 154:084117. [PMID: 33639728 DOI: 10.1063/5.0040791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this study, we investigate the nuclear quantum effects (NQEs) on the acidity constant (pKA) of liquid water isotopologs under the ambient condition by path integral molecular dynamics (PIMD) simulations. We compared simulations using a fully explicit solvent model with a classical polarizable force field, density functional tight binding, and ab initio density functional theory, which correspond to empirical, semiempirical, and ab initio PIMD simulations, respectively. The centroid variable with respect to the proton coordination number of a water molecule was restrained to compute the gradient of the free energy, which measures the reversible work of the proton abstraction for the quantum mechanical system. The free energy curve obtained by thermodynamic integration was used to compute the pKA value based on probabilistic determination. This technique not only reproduces the pKA value of liquid D2O experimentally measured (14.86) but also allows for a theoretical prediction of the pKA values of liquid T2O and aqueous HDO and HTO, which are unknown due to their scarcity. It is also shown that the NQEs on the free energy curve can result in a downshift of 4.5 ± 0.9 pKA units in the case of liquid water, which indicates that the NQEs plays an indispensable role in the absolute determination of pKA. The results of this study can help inform further extensions into the calculation of the acidity constants of isotope substituted species with high accuracy.
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Affiliation(s)
- Bo Thomsen
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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12
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Study on the mechanisms of the lubricating oil antioxidants: Experimental and molecular simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115099] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Dutra FR, Silva CDS, Custodio R. On the Accuracy of the Direct Method to Calculate p Ka from Electronic Structure Calculations. J Phys Chem A 2020; 125:65-73. [PMID: 33356255 PMCID: PMC7872415 DOI: 10.1021/acs.jpca.0c08283] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
The
direct method (HA(soln) ⇌ A(soln)– + H(soln)+) for calculating
pKa of monoprotic acids is as efficient
as thermodynamic cycles. A selective adjustment of proton free energy
in solution was used with experimental pKa data. The procedure was analyzed at different levels of theory.
The solvent was described by the solvation model density (SMD) model,
including or not explicit water molecules, and three training sets
were tested. The best performance under any condition was obtained
by the G4CEP method with a mean absolute error close to 0.5 units
of pKa and an uncertainty around ±1
unit of pKa for any training set including
or excluding explicit solvent molecules. PM6 and AM1 performed very
well with average absolute errors below 0.75 units of pKa but with uncertainties up to ±2 units of pKa, using only the SMD solvent model. Density
functional theory (DFT) results were highly dependent on the basis
functions and explicit water molecules. The best performance was observed
for the local spin density approximation (LSDA) functional in almost
all calculations and under certain conditions, as high as those obtained
by G4CEP. Basis set complexity and explicit solvent molecules were
important factors to control DFT calculations. The training set molecules
should consider the diversity of compounds.
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Affiliation(s)
- Felipe Ribeiro Dutra
- Instituto de Química, Universidade Estadual de Campinas, P.O. Box 6154, Barão Geraldo, 13083-970 Campinas, São Paulo, Brazil
| | - Cleuton de Souza Silva
- Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Campus de Itacoatiara, 69100-021 Itacoatiara, Amazonas, Brazil
| | - Rogério Custodio
- Instituto de Química, Universidade Estadual de Campinas, P.O. Box 6154, Barão Geraldo, 13083-970 Campinas, São Paulo, Brazil
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14
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Computational studies of acidities of some hydroxycoumarins. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Yeh JY, Matsagar BM, S. Chen S, Sung HL, Tsang DC, Li YP, Wu KCW. Synergistic effects of Pt-embedded, MIL-53-derived catalysts (Pt@Al2O3) and NaBH4 for water-mediated hydrogenolysis of biomass-derived furfural to 1,5-pentanediol at near-ambient temperature. J Catal 2020. [DOI: 10.1016/j.jcat.2020.07.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Ahmed M, Hussein IA, Onawole AT, Saad MA. Development of a New Borax-Based Formulation for the Removal of Pyrite Scales. ACS OMEGA 2020; 5:14308-14315. [PMID: 32596568 PMCID: PMC7315426 DOI: 10.1021/acsomega.0c00556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
In the oil and gas industry, pyrite forms one of the most hardened scales in reservoirs, which hinders the flow of fluids. Consequently, this leads to blockage of the downhole tubular, formation damage, and complete shutdown of production and operational processes. Herein, a new green formulation based on borax (K2B4O7) is proposed for pyrite scale removal. The temperature effect, disk rotational speed, and borax concentration have been investigated using a rotating disk apparatus. Also, XPS and SEM-EDX analyses were conducted on the pyrite disk surface before and after the treatment with the green formulation. The new formulation showed the potential ability to dissolve pyrite without generating the toxic hydrogen sulfide (H2S). The dissolution rate of the scale in the new formulation is increased by 16% compared to that in a previous green formulation composed of 20 wt %DTPA+9 wt % K2CO3. Molecular modeling technique using DFT was used to study the solvation energies of Fe2+ and Fe3+. The latter had a higher solvation energy than the former, which confirmed that upon using the borax-based formulation to oxidize Fe2+ to Fe3+. It will aid the dissolution of pyrite scales. The new formulation achieved a corrosion rate that is 25 times lower than that of 15 wt % HCl, which is commercially used in treating scales. Finally, the proposed new formulation does not require the use of corrosion inhibitors; hence, it is expected to result in a more economical scale treatment method.
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Affiliation(s)
- Musa Ahmed
- Gas
Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Ibnelwaleed A. Hussein
- Gas
Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Abdulmujeeb T. Onawole
- Gas
Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammed A. Saad
- Chemical
Engineering Department, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
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17
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Reyna-Luna J, Flores R, Gómez-Balderas R, Franco-Pérez M. Chemical Equilibrium of Zinc Acetate Complexes in Ethanol Solution. A Theoretical Description through Thermodynamic Cycles. J Phys Chem B 2020; 124:3355-3370. [PMID: 32216349 DOI: 10.1021/acs.jpcb.9b10687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Gibbs free energy of complexation between the Zn(II) species and acetate ligands, forming the [Zn(OAc)n]2-n complexes with n = 1, 2 in an ethanol solution, was assessed by two different theoretical protocols based on thermodynamic cycles. In both approaches, the solution phase Gibbs free energy of each reaction is computed by summing up contributions from gas phase thermochemistry calculations to solvation Gibbs free energies obtained in a hybrid fashion, i.e., each (neutral or electrically charged) solute was first solvated by explicit solvent molecules in order to capture relevant (micro) solute-solvent and/or solvent-solvent interactions and then, a continuum model calculation is performed in order to get the corresponding bulky solute-solvent contributions. For our first thermodynamic protocol, here denominated as variant 1, a set of x independent solvent molecules are used to screen each of the involved solutes, while the variant 2 strategy uses the fact that a set of solvent molecules may exist as aggregates (or molecular clusters) in the solvent macroscopic media, before the solvation process of solutes. Our selected quantum theoretical protocol was the M05-2X/6-31+G(d)/SMD level. We made a systematic exploration about the influence of several sources of errors, such as the solvent conformation, the number of solvent molecules used to screen each of the involved solutes, the coordination geometry of the metallic center before and after the complexation process, and the pertinence of using molecular geometries optimized in gas phase and in ethanol solution, for the computation of the Gibbs free energy variation regarding the two chemical reactions under study. We set an accuracy threshold equal or less than 4.0 kcal·mol-1, with respect to the corresponding experimental records. The robustness of our thermodynamic strategies was then tested by computing the gas phase free energy contributions to the (solution phase) reaction free energies here assessed, using different density functional approximations, namely the M05-2X, BH&HLYP, PBE0, ωb97X-D and M06-2X functionals in conjunction with the larger 6-311+G(d,p) basis set.
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Affiliation(s)
- Julieta Reyna-Luna
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510 Ciudad de México, México.,Laboratorio de Fisicoquímica Analítica, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores-Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, 54700, Estado de México, México
| | - Raúl Flores
- Laboratorio de Fisicoquímica Analítica, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores-Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, 54700, Estado de México, México
| | - Rodolfo Gómez-Balderas
- Laboratorio de Fisicoquímica Analítica, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores-Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, 54700, Estado de México, México
| | - Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510 Ciudad de México, México
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18
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Khalilinia E, Ebrahimi A. π-Stacking effects on acid capacity of p-aminobenzoic acid. Struct Chem 2020. [DOI: 10.1007/s11224-020-01530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Alburquerque PR, Ramachandran BR, Junk T, Karsili TNV. Hydrogen-Deuterium Exchange in Basic Near-Critical and Supercritical Media: An Experimental and Theoretical Study. J Phys Chem A 2020; 124:2530-2536. [PMID: 32149509 DOI: 10.1021/acs.jpca.9b10892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Treatment of homo- and heterocyclic aromatic substrates with basic deuterium oxide under near- or supercritical conditions results in rapid base-catalyzed hydrogen-deuterium exchange (HDE) in aromatic and benzylic positions. It has been postulated that HDE follows a simple deprotonation-reprotonation mechanism, but little evidence has been provided to date. This study correlates experimentally observed proton exchanges in n-butylbenzene with ab initio calculations of the acidities and potential energy (PE) profiles. In addition to providing further support for carbanion intermediacy in HDE, these results offer new insights into substrate acidities in near- and supercritical aqueous media and the optimal conditions required for their isotope exchange.
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Affiliation(s)
- Pia R Alburquerque
- Department of Chemistry, Grambling State University, Grambling, Louisiana 71245, United States
| | - B Ramu Ramachandran
- Institute for Micromanufacturing, Louisiana Tech University, Ruston, Louisiana 71272, United States
| | - Thomas Junk
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Tolga N V Karsili
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
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20
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Baetzold RC. Density Functional Calculations for Aqueous Silver Clusters Containing Water and Nitrate Ligands. J Phys Chem B 2019; 123:8300-8312. [PMID: 31478667 DOI: 10.1021/acs.jpcb.9b06634] [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 incorporation of a nitrate ion into silver-water aqueous clusters has been examined using PBE0 density functional theory with the solvent model density (SMD) solvation model. The Gibbs free energy of solvation and other thermodynamic variables are calculated using the harmonic/rigid rotor/ideal gas model at 298.15 K for aqueous solutes including the effects of solute relaxation in water and with London dispersive forces at the D3 level. Free energies of solvation for Ag+ and NO3- were found to agree well with experimental values of -118.2 and -60.1 kcal/mol, respectively, calculated using cluster-continuum models with six to eight water molecules and including solute relaxation and London D3 dispersive interactions. An analysis of data of varying cluster size upon calculated free energy is presented. A direct procedure is applied to aqueous clusters such as Agnz(NO3-)(H2O)5, Agnz(H2O)5, and (NO3-)(H2O)6 n = 1-4; z = 0, +1 in the SMD solvent representation to calculate equilibrium constants for nitrate association with silver clusters in solution that includes fully relaxed solutes. The equilibrium structures of the nitrate-containing clusters involve one or more bonds from nitrate oxygen to positive silver clusters. Water molecules interact with nitrate through H atoms, and overall, the structure represents a silver nitrate cluster with water ligands having similarity to a close ion pair in many aspects. The neutral silver atom is attached to nitrate through H-bonded water molecules. The ratio of nitrate-containing silver clusters to nitrate-free clusters using a calculated equilibrium constant of 0.51 L/mol for Ag+ is small in the range of many experiments. Similar values are found for positive silver clusters up to four atoms in size. The resulting procedures were applied to aqueous clusters of Agn(NO3)m+(n-m) that have been previously experimentally studied for silver reduction in aqueous solution. A chain-like structure with collinear and bidentate oxygen bonds to silver was found, and the equilibrium constants for clustering were determined. A simplified model calculation for the reduction of Ag(H2O)6+ clusters in the presence of silver clusters in aqueous media was studied to understand catalytic effects observed in these systems. The reduction potentials vary with silver cluster size indicating a more favorable reduction caused by the presence of larger silver clusters.
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21
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Cai F, You G, Zhao X, Hu H, Wu S. The Relationship between Specific Structure and Gas Permeability of Bromobutyl Rubber: A Combination of Experiments and Molecular Simulations. MACROMOL THEOR SIMUL 2019. [DOI: 10.1002/mats.201900025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Fei Cai
- State Key Laboratory of Organic‐Inorganic CompositesBeijing University of Chemical Technology Beijing 100029 P. R. China
| | - Guohua You
- College of Information Science and TechnologyBeijing University of Chemical Technology Beijing 100029 China
| | - Xiuying Zhao
- State Key Laboratory of Organic‐Inorganic CompositesBeijing University of Chemical Technology Beijing 100029 P. R. China
| | - Haihua Hu
- Petrochemical Research Institute PetroChina, Gan Su Lanzhou 730060 P. R. China
| | - Sizhu Wu
- State Key Laboratory of Organic‐Inorganic CompositesBeijing University of Chemical Technology Beijing 100029 P. R. China
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22
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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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23
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Mirzaei S, Ivanov MV, Timerghazin QK. Improving Performance of the SMD Solvation Model: Bondi Radii Improve Predicted Aqueous Solvation Free Energies of Ions and pKa Values of Thiols. J Phys Chem A 2019; 123:9498-9504. [DOI: 10.1021/acs.jpca.9b02340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Saber Mirzaei
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1414, United States
| | - Maxim V. Ivanov
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1414, United States
| | - Qadir K. Timerghazin
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1414, United States
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24
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Ahn S, Hong M, Sundararajan M, Ess DH, Baik MH. Design and Optimization of Catalysts Based on Mechanistic Insights Derived from Quantum Chemical Reaction Modeling. Chem Rev 2019; 119:6509-6560. [DOI: 10.1021/acs.chemrev.9b00073] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Seihwan Ahn
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Mannkyu Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Mahesh Sundararajan
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
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25
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26
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Onizhuk MO, Panteleimonov AV, Kholin YV, Ivanov VV. Dissociation Constants of Silanol Groups of Silic Acids: Quantum Chemical Estimations. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618020026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Caine BA, Dardonville C, Popelier PLA. Prediction of Aqueous p K a Values for Guanidine-Containing Compounds Using Ab Initio Gas-Phase Equilibrium Bond Lengths. ACS OMEGA 2018; 3:3835-3850. [PMID: 31458625 PMCID: PMC6641350 DOI: 10.1021/acsomega.8b00142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/21/2018] [Indexed: 05/06/2023]
Abstract
In this work, we demonstrate the existence of linear relationships between gas-phase equilibrium bond lengths of the guanidine skeleton of 2-(arylamino)imidazolines and their aqueous pK a value. For a training set of 22 compounds, in the most stable conformation of their lowest energy tautomeric form, three bonds were found to exhibit r 2 and q 2 values >0.95 and root-mean-squared-error of estimation values ≤0.25 when regressed individually against pK a. The equations describing these one-bond-length linear relationships, in addition to a multiple linear regression model using all three bond lengths, were then used to predict the experimental pK a values of an external test set of further 27 derivatives. The optimal protocol we derive here shows an overall mean absolute error (MAE) of 0.20 and standard deviation of errors of 0.18 for the test set. Predictions for a second test set of diphenyl-based bis(2-iminoimidazolidines) yielded an MAE of 0.27 and a standard deviation of 0.10. The predictive power of the optimal model is further demonstrated by its ability to correct erroneously reported experimental values. Finally, a previously established guanidine model is recalibrated at a new level of theory, and predictions are made for novel phenylguanidine derivatives, showing an MAE of just 0.29. The protocols established and tested here pass both of Roy's modern and stringent MAE-based criteria for a "good" quantitative structure-activity relationship/quantitative structure-property relationship model predictivity. Notably, the ab initio bond length high correlation subset protocol developed in this work demonstrates lower MAE values than the Marvin program by ChemAxon for all test sets.
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Affiliation(s)
- Beth A. Caine
- Manchester
Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
| | | | - Paul L. A. Popelier
- Manchester
Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
- E-mail: . Phone: +44 161
3064511 (P.L.A.P.)
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28
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Harned AM. Concerning the mechanism of iodine(iii)-mediated oxidative dearomatization of phenols. Org Biomol Chem 2018. [PMID: 29542797 DOI: 10.1039/c8ob00463c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The iodine(iii)-mediated oxidative dearomatization of phenols has proven to be a general method for the preparation of cyclohexadienones. While this is a widely used reaction, there is still a great deal of uncertainty regarding the mechanistic pathway followed by these reactions. In part, this is due to the highly unstable nature of many of the key intermediates, which makes their direct detection extremely difficult. In order to gain some insight into these mechanistic questions, DFT calculations [M06-2X/6-31+G(d) for C, H, and O and LANL2DZdp for iodine] were used to evaluate the two most commonly proposed reaction mechanisms. These results show that unimolecular fragmentation of an oxygen-bound intermediate to give a phenoxenium ion (TS1) is preferred over direct addition of the nucleophile to the aromatic ring of the activated phenol (TS3). In addition, results are presented that suggest protonation and/or hydrogen bonding may play a key role in lowering the energy of the unimolecular fragmentation pathway.
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Affiliation(s)
- Andrew M Harned
- Texas Tech University, Department of Chemistry & Biochemistry, 1204 Boston Ave., Lubbock, TX 79409-1061, USA.
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29
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Grauffel C, Chu B, Lim C. An efficient protocol for computing the pKa of Zn-bound water. Phys Chem Chem Phys 2018; 20:29637-29647. [DOI: 10.1039/c8cp05029e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present an efficient and accurate method for computing absolute pKw values in Zn2+ complexes.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 115
- Taiwan
| | - Benjamin Chu
- Department of Biomathematics
- David Geffen School of Medicine at UCLA
- USA
| | - Carmay Lim
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 115
- Taiwan
- Department of Chemistry
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30
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Yu CP, Gerlei KZ, Rágyanszki A, Jensen SJK, Viskolcz B, Csizmadia IG. Reactivity of Ala-Gly dipeptide with β-turn secondary structure. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.12.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Min CG, Ferreira PJ, Pinto da Silva L. Theoretically obtained insight into the mechanism and dioxetanone species responsible for the singlet chemiexcitation of Coelenterazine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:18-26. [DOI: 10.1016/j.jphotobiol.2017.07.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/01/2017] [Accepted: 07/14/2017] [Indexed: 12/13/2022]
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32
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Zahn D. A molecular simulation study of the auto-protolysis of ammonia as a function of temperature. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Haworth NL, Wang Q, Coote ML. Modeling Flexible Molecules in Solution: A pKa Case Study. J Phys Chem A 2017; 121:5217-5225. [DOI: 10.1021/acs.jpca.7b04133] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Naomi L. Haworth
- ARC Centre of Excellence
for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Qinrui Wang
- ARC Centre of Excellence
for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence
for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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34
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Zheng W, Wu Y, Yang W, Zhang Z, Zhang L, Wu S. A Combined Experimental and Molecular Simulation Study of Factors Influencing the Selection of Antioxidants in Butadiene Rubber. J Phys Chem B 2017; 121:1413-1425. [DOI: 10.1021/acs.jpcb.6b12339] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Zheng
- State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Youping Wu
- State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Wei Yang
- Global Energy Interconnection Research Institute, State Key Laboratory of Advanced Transmission Technology, Beijing 102211, P. R. China
| | - Zhuo Zhang
- Global Energy Interconnection Research Institute, State Key Laboratory of Advanced Transmission Technology, Beijing 102211, P. R. China
| | - Liqun Zhang
- State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Sizhu Wu
- State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
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35
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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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36
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Langmaier J, Pižl M, Samec Z, Záliš S. Extreme Basicity of Biguanide Drugs in Aqueous Solutions: Ion Transfer Voltammetry and DFT Calculations. J Phys Chem A 2016; 120:7344-50. [DOI: 10.1021/acs.jpca.6b04786] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jan Langmaier
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Martin Pižl
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
- Department
of Inorganic Chemistry, University of Chemistry and Technology, Prague 6, Technická 5, 166 28, Czech Republic
| | - Zdeněk Samec
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Stanislav Záliš
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
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37
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Chen CS, Lin ST. Prediction of pH Effect on the Octanol–Water Partition Coefficient of Ionizable Pharmaceuticals. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b02040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Chao-Shou Chen
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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38
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Close DM, Wardman P. Calculations of the Energetics of Oxidation of Aqueous Nucleosides and the Effects of Prototropic Equilibria. J Phys Chem A 2016; 120:4043-8. [PMID: 27219530 DOI: 10.1021/acs.jpca.6b02653] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently the calculated standard reduction potentials of the radical-cations of N-methyl substituted DNA bases have been reported that agree fairly well with the experimental results. However, there are issues reflecting the fact that the experimental results usually relate to the couple E(o)(Nuc(•),H(+)/NucH(+)), whereas the calculated results are for the E(o)(Nuc(•+)/Nuc) couple. To calculate the midpoint reduction potential at pH 7 (Em7), it is important to have accurate acid dissociation constants (pKs) for both ground-state bases and their radicals, and the effects of uncertainty in some of these values (e.g., that of the adenosine radical) must be considered. Calculations of the pKs of the radicals of the nucleic acid bases (as nucleosides) have been performed to explore the effects the various pKs have on calculating the values of Em7 and to see what improvements can be made with the accuracy of the calculations.
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Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University , Johnson City, Tennessee 37614, United States
| | - Peter Wardman
- Gray Cancer Institute, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Oxford OX3 7DQ, United Kingdom
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39
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Competition reaction-based prediction of polyamines’ stepwise protonation constants: a case study involving 1,4,7,10-tetraazadecane (2,2,2-tet). Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Yang C, Pei S, Chen B, Ye L, Yu H, Hu S. Density functional theory investigations on the binding modes of amidoximes with uranyl ions. Dalton Trans 2016; 45:3120-9. [DOI: 10.1039/c5dt04645a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
η1-O of tautomerized amidoximes and η1-O/η2-N–O of anionic amidoximes are all plausible coordination modes for amidoximes in ligating uranyl ions.
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Affiliation(s)
- Chuting Yang
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials
- Anhui University
- Hefei
- China
- Institute of Nuclear Physics and Chemistry
| | - Shuqi Pei
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials
- Anhui University
- Hefei
- China
- Department of Polymer Science and Engineering
| | - Baihua Chen
- Institute of Nuclear Physics and Chemistry
- CAEP
- Mianyang 621900
- China
| | - Lina Ye
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials
- Anhui University
- Hefei
- China
| | - Haizhu Yu
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials
- Anhui University
- Hefei
- China
| | - Sheng Hu
- Institute of Nuclear Physics and Chemistry
- CAEP
- Mianyang 621900
- China
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41
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Sutton CCR, da Silva G, Franks GV. Modeling the IR Spectra of Aqueous Metal Carboxylate Complexes: Correlation between Bonding Geometry and Stretching Mode Wavenumber Shifts. Chemistry 2015; 21:6801-5. [DOI: 10.1002/chem.201406516] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 11/09/2022]
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42
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Calculation of acidity/basicity values of some fluorinated compounds in gas phase and aqueous solution: A computational approach. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Sutton CCR, Franks GV, da Silva G. Modeling the antisymmetric and symmetric stretching vibrational modes of aqueous carboxylate anions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:535-542. [PMID: 25048288 DOI: 10.1016/j.saa.2014.06.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/19/2014] [Accepted: 06/08/2014] [Indexed: 06/03/2023]
Abstract
The infrared spectra of six aqueous carboxylate anions have been calculated at the M05-2X/cc-pVTZ level of theory with the SMD solvent model, and validated against experimental data from the literature over the region of 1700 cm(-1) to 1250 cm(-1); this region corresponds to the stretching modes of the carboxylate group, and is often interrogated when probing bonding of carboxylates to other species and surfaces. The anions studied here were formate, acetate, oxalate, succinate, glutarate and citrate. For the lowest energy conformer of each anion, the carboxylate moiety antisymmetric stretching peak was predicted with a mean signed error of only 4 cm(-1) using the SMD solvent model, while the symmetric peak was slightly overestimated. Performing calculations in vacuum and scaling was found to generally over-predict the antisymmetric vibrational frequencies and under predict the symmetric peak. Different conformers of the same anion were found to have only slightly different spectra in the studied region and the inclusion of explicit water molecules was not found to significantly change the calculated spectra when the implicit solvent model is used. Overall, the use of density functional theory in conjunction with an implicit solvent model was found to result in infra-red spectra that are the best reproduction of the features found experimentally for the aqueous carboxylate ions in the important 1700 cm(-1) to 1250 cm(-1) region. The development of validated model chemistries for simulating the stretching modes of aqueous carboxylate ions will be valuable for future studies that investigate how carboxylate anions complex with multivalent metal cations and related species in solution.
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Affiliation(s)
- Catherine C R Sutton
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010, Australia
| | - George V Franks
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010, Australia
| | - Gabriel da Silva
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010, Australia.
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44
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Novkovic L, Trmcic M, Rodic M, Bihelovic F, Zlatar M, Matovic R, Saicic RN. Synthesis of endoperoxides by domino reactions of ketones and molecular oxygen. RSC Adv 2015. [DOI: 10.1039/c5ra13476e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Domino reactions of ketones with molecular oxygen in the presence of potassium hydroxide and potassiumt-butoxide afford cyclic hydroperoxy acetals (3,5-dihydroxy-1,2-dioxanes).
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Affiliation(s)
- L. Novkovic
- Innovative Centre of the Faculty of Chemistry
- University of Belgrade
- Serbia
| | - M. Trmcic
- Innovative Centre of the Faculty of Chemistry
- University of Belgrade
- Serbia
| | - M. Rodic
- Department of Chemistry
- University of Novi Sad
- Novi Sad
- Serbia
| | - F. Bihelovic
- Faculty of Chemistry
- University of Belgrade
- 11158 Belgrade 118
- Serbia
| | - M. Zlatar
- ICTM Center for Chemistry
- Belgrade
- Serbia
| | | | - R. N. Saicic
- Faculty of Chemistry
- University of Belgrade
- 11158 Belgrade 118
- Serbia
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Hessz D, Hégely B, Kállay M, Vidóczy T, Kubinyi M. Solvation and protonation of coumarin 102 in aqueous media: a fluorescence spectroscopic and theoretical study. J Phys Chem A 2014; 118:5238-47. [PMID: 24945906 DOI: 10.1021/jp504496k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ground- and excited-state protonation of Coumarin 102 (C102), a fluorescent probe applied frequently in heterogeneous systems with an aqueous phase, has been studied in aqueous solutions by spectroscopic experiments and theoretical calculations. For the dissociation constant of the protonated form in the ground state, pKa = 1.61 was obtained from the absorption spectra; for the excited-state dissociation constant, pKa* = 2.19 was obtained from the fluorescence spectra. These values were closely reproduced by theoretical calculations via a thermodynamic cycle (the value of pKa* also by calculations via the Förster cycle) using an implicit–explicit solvation model (polarized continuum model + addition of a solvent molecule). The theoretical calculations indicated that (i) in the ground state, C102 occurs primarily as a hydrogen-bonded water complex, with the oxo group as the binding site, (ii) this hydrogen bond becomes stronger upon excitation, and (iii) in the ground state, the amino nitrogen atom is the protonation site, and in the excited state, the carboxy oxygen atom is the protonation site. A comprehensive analysis of fluorescence decay data yielded the values kpr = 3.27 × 10(10) M(–1) s(–1) for the rate constant of the excited-state protonation and kdpr = 2.78 × 10(8) s(–1) for the rate constant of the reverse process (kpr and kdpr were treated as independent parameters). This, considering the relatively long fluorescence lifetimes of neutral C102 (6.02 ns) and its protonated form (3.06 ns) in aqueous media, means that a quasi-equilibrium state of excited-state proton transfer is reached in strongly acidic solutions.
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Affiliation(s)
- Dóra Hessz
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , P.O. Box 286, 1519 Budapest, Hungary
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Riojas AG, Wilson AK. Solv-ccCA: Implicit Solvation and the Correlation Consistent Composite Approach for the Determination of pKa. J Chem Theory Comput 2014; 10:1500-10. [PMID: 26580366 DOI: 10.1021/ct400908z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct theoretical methods are advantageous for the prediction of pKa, as relative methods rely upon the experimental values of reference acid molecules that can limit application of the method to well-characterized systems. Here, a direct route is introduced, which incorporates the SMD universal solvation model1 within the correlation consistent Composite Approach (ccCA). This Solv-ccCA methodology has been used for the prediction of theoretical pKa values for nitrogen-containing species to within a mean absolute deviation (MAD) of 1.0 pKa unit from experimental values by utilizing a thermodynamic cycle that combines gas-phase and solution-phase calculations. Several density functionals, including B3LYP, B97-1, B97-2, B98, BMK, M06, and M06-2X, were also evaluated for use with SMD and for comparison to Solv-ccCA.
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Affiliation(s)
- Amanda G Riojas
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas , Denton, Texas 76203-5017, United States
| | - Angela K Wilson
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas , Denton, Texas 76203-5017, United States
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Lipophilicity assessment of ruthenium(II)-arene complexes by the means of reversed-phase thin-layer chromatography and DFT calculations. ScientificWorldJournal 2014; 2014:862796. [PMID: 24587761 PMCID: PMC3919081 DOI: 10.1155/2014/862796] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/28/2013] [Indexed: 11/18/2022] Open
Abstract
The lipophilicity of ten ruthenium(II)-arene complexes was assessed by reversed-phase thin-layer chromatography (RP-TLC) on octadecyl silica stationary phase. The binary solvent systems composed of water and acetonitrile were used as mobile phase in order to determine chromatographic descriptors for lipophilicity estimation. Octanol-water partition coefficient, logKOW, of tested complexes was experimentally determined using twenty-eight standard solutes which were analyzed under the same chromatographic conditions as target substances. In addition, ab initio density functional theory (DFT) computational approach was employed to calculate logKOW values from the differences in Gibbs' free solvation energies of the solute transfer from n-octanol to water. A good overall agreement between DFT calculated and experimentally determined logKOW values was established (R2 = 0.8024–0.9658).
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Xue XS, Yang C, Li X, Cheng JP. Computational Study on the pKa Shifts in Proline Induced by Hydrogen-Bond-Donating Cocatalysts. J Org Chem 2014; 79:1166-73. [DOI: 10.1021/jo402605n] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xiao-Song Xue
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Chen Yang
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Li
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Jin-Pei Cheng
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
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Abstract
Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.
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Xue XS, Yang C, Li X, Cheng JP. Computation of standard equilibrium acidity of C–H acids in ionic media: shedding light on predicting changes of chemical behavior by switching solvent system from molecular to ionic. Org Chem Front 2014. [DOI: 10.1039/c3qo00070b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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