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Pliego JR. Hybrid Cluster-Continuum Method for Single-Ion Solvation Free Energy in Acetonitrile Solvent. J Phys Chem A 2024; 128:6440-6449. [PMID: 39052560 PMCID: PMC11317976 DOI: 10.1021/acs.jpca.4c03593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
A new hybrid discrete-continuum approach named the cluster-continuum static approximation (CCSA) has been proposed for acetonitrile solvent. The continuum part uses the conductor-like polarizable continuum model for electrostatic and a surface area-dependent term for nonelectrostatic solvation. The CCSA includes only one explicit acetonitrile solvent molecule and a damping function, which makes the CCSA method reduce to pure continuum solvation in the case of weaker potential of mean force for solute-solvent interaction. The performance of the model was tested for 22 anions and 22 cations, including challenge species that cannot be adequately described by pure continuum solvation. A comparison was done with the widely used solvent model density (SMD) model. For anions, the CCSA reduces to pure continuum solvation and the method has the same performance as the SMD model, with a standard deviation of the mean signed error (SD-MSE) of 2.7 kcal mol-1 for both models. However, the CCSA method for cations considerably outperforms the SMD model, with an SD-MSE of 3.3 kcal mol-1 for the former and 8.4 kcal mol-1 for the latter. The method can be automated, and the present study suggests that continuum solvation models could be parameterized taking into account the explicit solvation as proposed in this work.
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Affiliation(s)
- Josefredo R. Pliego
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, São João del-Rei, Minas Gerais 36301-160, Brazil
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2
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Car-Parrinello molecular dynamics study of CuF, AgF, CuPF6 and AgPF6 in acetonitrile solvent and Cluster-Continuum calculation of the solvation free energy of Cu(I), Ag(I) and Li(I). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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3
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Pliego JR. Copper-Catalyzed Aromatic Fluorination of 2-(2-bromophenyl)pyridine via Cu(I)/Cu(III) Mechanism in Acetonitrile Solvent: Cluster-Continuum Free Energy Profile and Microkinetic Analysis. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Bensberg M, Türtscher PL, Unsleber JP, Reiher M, Neugebauer J. Solvation Free Energies in Subsystem Density Functional Theory. J Chem Theory Comput 2022; 18:723-740. [PMID: 34985890 DOI: 10.1021/acs.jctc.1c00864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise the scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and solvent. The key for the scalability is the performance of subsystem DFT for increasing numbers of subsystems. We investigate molecular dynamics and stationary point sampling of solvent configurations and compare the resulting (Gibbs) free energies to experiment and theoretical methods. We can show that with our hybrid model reaction barriers and reaction energies are accurately reproduced compared to experimental data.
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Affiliation(s)
- Moritz Bensberg
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Paul L Türtscher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jan P Unsleber
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
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Rufino VC, Pliego JR. Single-ion solvation free energy: A new cluster-continuum approach based on the cluster expansion method. Phys Chem Chem Phys 2021; 23:26902-26910. [PMID: 34825676 DOI: 10.1039/d1cp03517g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate calculation of the solvation free energy of single ions remains an important goal, involving development in the dielectric continuum solvation models, and statistical mechanics with explicit solvent and hybrid discrete-continuum methods. In the last case, many of the research studies involve a quasi-chemical approach using the monomer cycle or the cluster cycle to calculate the solvation free energy of single ions. In this work, a different cluster-continuum approach based on the cluster expansion method was tested for solvation of 16 cations and 32 anions in aqueous solution. The SMD model was used for the dielectric continuum part and three explicit water molecules were introduced in the region of the solute with the highest interaction energy. Harmonic frequency calculations and molecular dynamics sampling of configurations are not required. An empirical γN parameter for cations and another for anions is introduced. The method produces a substantial improvement of the SMD model with a mean absolute deviation of 2.3 kcal mol-1 for cations and 2.9 kcal mol-1 for anions. The analysis of the correlation between theoretical and experimental data produces a linear regression line with a slope of 1.09 for cations and 1.01 for anions. The good results of this approximated cluster expansion approach suggest that the method could be further improved by including more solvent molecules and sampling the configurations.
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Affiliation(s)
- Virgínia C Rufino
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei 36301-160, São João del-Rei, MG, Brazil.
| | - Josefredo R Pliego
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei 36301-160, São João del-Rei, MG, Brazil.
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Basdogan Y, Groenenboom MC, Henderson E, De S, Rempe SB, Keith JA. Machine Learning-Guided Approach for Studying Solvation Environments. J Chem Theory Comput 2019; 16:633-642. [PMID: 31809056 DOI: 10.1021/acs.jctc.9b00605] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular-level understanding and characterization of solvation environments are often needed across chemistry, biology, and engineering. Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics-based cluster-continuum approach for calculating single-ion solvation free energies. This approach uses a global optimization procedure to identify low-energy molecular clusters with different numbers of explicit solvent molecules and then employs the smooth overlap for atomic positions learning kernel to quantify the similarity between different low-energy solute environments. From these data, we use sketch maps, a nonlinear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. After testing this approach on different ions having charges 2+, 1+, 1-, and 2-, we find that the solvation environment around each ion can be seen to usually become more similar in hand with its calculated single-ion solvation free energy. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies within 5% of experimental measurements for most cases, and it should be transferable for the study of other systems where dynamics simulations are not easily carried out.
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Affiliation(s)
- Yasemin Basdogan
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Mitchell C Groenenboom
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Ethan Henderson
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Sandip De
- Laboratory of Computational Science and Modelling, Institute of Materials , École Polytechnique Fédérale de Lausanne , Lausanne 1015 , Switzerland
| | - Susan B Rempe
- Department of Nanobiology , Sandia National Laboratories , Albuquerque 87185 , New Mexico , United States
| | - John A Keith
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
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Pliego JR, Riveros JM. Hybrid discrete‐continuum solvation methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1440] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Josefredo R. Pliego
- Departamento de Ciências Naturais Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Jose M. Riveros
- Departamento de Química Fundamental Instituto de Química, Universidade de São Paulo São Paulo Brazil
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8
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Affiliation(s)
- Belinda L. Slakman
- Department of Chemical Engineering Northeastern University Boston Massachusetts
| | - Richard H. West
- Department of Chemical Engineering Northeastern University Boston Massachusetts
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9
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Lisboa FM, Pliego JR. Infinite dilution activity coefficient from SMD calculations: accuracy and performance for predicting liquid-liquid equilibria. J Mol Model 2018; 24:56. [DOI: 10.1007/s00894-018-3597-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/26/2018] [Indexed: 12/15/2022]
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Silva CM, Dias IC, Pliego JR. The role of ammonia oxide in the reaction of hydroxylamine with carboxylic esters. Org Biomol Chem 2015; 13:6217-24. [DOI: 10.1039/c5ob00300h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hydroxylamine can form a stable zwitterionic isomer that is a key for its high reactivity.
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Affiliation(s)
- Carlos M. Silva
- Departamento de Ciências Naturais
- Universidade Federal de São João del-Rei 36301-160
- São João del-Rei
- Brazil
| | - Isabela C. Dias
- Departamento de Ciências Naturais
- Universidade Federal de São João del-Rei 36301-160
- São João del-Rei
- Brazil
| | - Josefredo R. Pliego
- Departamento de Ciências Naturais
- Universidade Federal de São João del-Rei 36301-160
- São João del-Rei
- Brazil
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11
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Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile. J Comput Aided Mol Des 2014; 29:217-24. [DOI: 10.1007/s10822-014-9814-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
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12
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Miguel ELM, Silva PL, Pliego JR. Theoretical Prediction of pKa in Methanol: Testing SM8 and SMD Models for Carboxylic Acids, Phenols, and Amines. J Phys Chem B 2014; 118:5730-9. [DOI: 10.1021/jp501379p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Elizabeth L. M. Miguel
- Departamento de Ciências
Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
| | - Poliana L. Silva
- Departamento de Ciências
Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
| | - Josefredo R. Pliego
- Departamento de Ciências
Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
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13
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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14
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Duarte HA, Vankova N, Ferreira IP, Paniago EB, Heine T. Chemical Speciation of Metal Complexes from Chemical Shift Calculations: The Interaction of 2-Amino- N-hydroxypropanamide with V(V) in Aqueous Solution. J Phys Chem B 2013; 117:11670-80. [DOI: 10.1021/jp403744y] [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]
Affiliation(s)
- Hélio Anderson Duarte
- Grupo de Pesquisa
em Química Inorgânica Teórica−GPQIT, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, 31.270-901 Belo
Horizonte, MG, Brazil
| | - Nina Vankova
- School
of Engineering and Science, Jacobs University Bremen, D-28759 Bremen, Germany
| | - Isabella Pires Ferreira
- Grupo de Pesquisa
em Química Inorgânica Teórica−GPQIT, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, 31.270-901 Belo
Horizonte, MG, Brazil
| | - Eucler B. Paniago
- Grupo de Pesquisa
em Química Inorgânica Teórica−GPQIT, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, 31.270-901 Belo
Horizonte, MG, Brazil
| | - Thomas Heine
- School
of Engineering and Science, Jacobs University Bremen, D-28759 Bremen, Germany
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15
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Riccardi D, Guo HB, Parks JM, Gu B, Liang L, Smith JC. Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations. J Chem Theory Comput 2012; 9:555-69. [DOI: 10.1021/ct300296k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Demian Riccardi
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville,
Tennessee 37996, United States
| | - Hao-Bo Guo
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
| | - Baohua Gu
- Environmental Science Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Liyuan Liang
- Environmental Science Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville,
Tennessee 37996, United States
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16
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New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcata.2012.07.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Bryantsev VS. Calculation of solvation free energies of Li+ and O2 − ions and neutral lithium–oxygen compounds in acetonitrile using mixed cluster/continuum models. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1250-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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de Lima GF, Pliego JR, Duarte HA. Stability of hydroxylamine isomers in aqueous solution: Ab initio study using continuum, cluster-continuum and Shells Theory of Solvation. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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