1
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Elhajj S, Gozem S. First and Second Reductions in an Aprotic Solvent: Comparing Computational and Experimental One-Electron Reduction Potentials for 345 Quinones. J Chem Theory Comput 2024; 20:6227-6240. [PMID: 38970475 PMCID: PMC11270834 DOI: 10.1021/acs.jctc.4c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
Using reference reduction potentials of quinones recently measured relative to the saturated calomel electrode (SCE) in N,N-dimethylformamide (DMF), we benchmark absolute one-electron reduction potentials computed for 345 Q/Q•- and 265 Q•-/Q2- half-reactions using adiabatic electron affinities computed with density functional theory and solvation energies computed with four continuum solvation models: IEF-PCM, C-PCM, COSMO, and SM12. Regression analyses indicate a strong linear correlation between experimental and absolute computed Q/Q•- reduction potentials with Pearson's correlation coefficient (r) between 0.95 and 0.96 and the mean absolute error (MAE) relative to the linear fit between 83.29 and 89.51 mV for different solvation methods when the slope of the regression is constrained to 1. The same analysis for Q•-/Q2- gave a linear regression with r between 0.74 and 0.90 and MAE between 95.87 and 144.53 mV, respectively. The y-intercept values obtained from the linear regressions are in good agreement with the range of absolute reduction potentials reported in the literature for the SCE but reveal several sources of systematic error. The y-intercepts from Q•-/Q2- calculations are lower than those from Q/Q•- by around 320-410 mV for IEF-PCM, C-PCM, and SM12 compared to 210 mV for COSMO. Systematic errors also arise between molecules having different ring sizes (benzoquinones, naphthoquinones, and anthraquinones) and different substituents (titratable vs nontitratable). SCF convergence issues were found to be a source of random error that was slightly reduced by directly optimizing the solute structure in the continuum solvent reaction field. While SM12 MAEs were lower than those of the other solvation models for Q/Q•-, SM12 had larger MAEs for Q•-/Q2- pointing to a larger error when describing multiply charged anions in DMF. Altogether, the results highlight the advantages of, and further need for, testing computational methods using a large experimental data set that is not skewed (e.g., having more titratable than nontitratable substituents on different parent groups or vice versa) to help further distinguish between sources of random and systematic errors in the calculations.
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Affiliation(s)
- Sarah Elhajj
- Department of Chemistry, Georgia
State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia
State University, Atlanta, Georgia 30302, United States
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2
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Duque-Prata A, Serpa C, Caridade PJSB. Full theoretical protocol for the design of metal-free organic electron donor-spacer-acceptor systems. Phys Chem Chem Phys 2023; 25:27854-27865. [PMID: 37814945 DOI: 10.1039/d3cp03323f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
A user-friendly (time-dependent) density functional theory based algorithm is proposed to design new donor-spacer-acceptor systems for electron transfer reactions. This algorithm is focused on metal-free organic compounds, most of which contain aromatic or alkene moieties. The oxidation and reduction potentials are calculated, together with the excited-state energy difference including the zero-point energy and the structural properties required to calculate an electron transfer Gibbs free energy change. The proposed algorithm has been tested on well-known systems, while two new compounds are suggested for photoinduced intramolecular electron transfer reactions using this scheme. The methodology here presented is intended to be a tool for synthetic physical-chemists, allowing them to evaluate the properties of hypothetical systems before the synthesis, enabling the study of limitless combinations of donor-spacer-acceptor arrangements.
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Affiliation(s)
- Amílcar Duque-Prata
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-545 Coimbra, Portugal.
| | - Carlos Serpa
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-545 Coimbra, Portugal.
| | - Pedro J S B Caridade
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-545 Coimbra, Portugal.
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3
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Fedorov R, Gryn’ova G. Unlocking the Potential: Predicting Redox Behavior of Organic Molecules, from Linear Fits to Neural Networks. J Chem Theory Comput 2023; 19:4796-4814. [PMID: 37463673 PMCID: PMC10414033 DOI: 10.1021/acs.jctc.3c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 07/20/2023]
Abstract
Redox-active organic molecules, i.e., molecules that can relatively easily accept and/or donate electrons, are ubiquitous in biology, chemical synthesis, and electronic and spintronic devices, such as solar cells and rechargeable batteries, etc. Choosing the best candidates from an essentially infinite chemical space for experimental testing in a target application requires efficient screening approaches. In this Review, we discuss modern in silico techniques for predicting reduction and oxidation potentials of organic molecules that go beyond conventional first-principles computations and thermodynamic cycles. Approaches ranging from simple linear fits based on molecular orbital energy approximation and energy difference approximation to advanced regression and neural network machine learning algorithms employing complex descriptors of molecular compositions, geometries, and electronic structures are examined in conjunction with relevant literature examples. We discuss the interplay between ab initio data and machine learning (ML), i.e., whether it is better to base predictions on low-level quantum-chemical results corrected with ML or to bypass first-principles computations entirely and instead rely on elaborate deep learning architectures. Finally, we list currently available data sets of redox-active organic molecules and their experimental and/or computed properties to facilitate the development of screening platforms and rational design of redox-active organic molecules.
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Affiliation(s)
- Rostislav Fedorov
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing, Heidelberg
University, 69120 Heidelberg, Germany
| | - Ganna Gryn’ova
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing, Heidelberg
University, 69120 Heidelberg, Germany
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4
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Reznichenko O, Leclercq D, Franco Pinto J, Mouawad L, Gabelica V, Granzhan A. Optimization of G-Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones). Chemistry 2023; 29:e202202427. [PMID: 36286608 PMCID: PMC10099395 DOI: 10.1002/chem.202202427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/06/2022]
Abstract
G-quadruplexes (G4s), secondary structures adopted by guanine-rich DNA and RNA sequences, are implicated in numerous biological processes and have been suggested as potential drug targets. Accordingly, there is an increasing interest in developing high-throughput methods that allow the generation of congeneric series of G4-targeting molecules ("ligands") and investigating their interactions with the targets. We have developed an operationally simple method of parallel synthesis to generate "ready-to-screen" libraries of cationic acylhydrazones, a motif that we have previously identified as a promising scaffold for potent, biologically active G4 ligands. Combined with well-established screening techniques, such as fluorescence melting, this method enables the rapid synthesis and screening of combinatorial libraries of potential G4 ligands. Following this protocol, we synthesized a combinatorial library of 90 bis(acylhydrazones) and screened it against five different nucleic acid structures. This way, we were able to analyze the structure-activity relationships within this series of G4 ligands, and identified three novel promising ligands whose interactions with G4-DNAs of different topologies were studied in detail by a combination of several biophysical techniques, including native mass spectrometry, and molecular modeling.
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Affiliation(s)
- Oksana Reznichenko
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Denis Leclercq
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Jaime Franco Pinto
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Liliane Mouawad
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Valérie Gabelica
- Univ. BordeauxCNRS, INSERM, ARNAUMR 5320, U1212, IECB33600PessacFrance
| | - Anton Granzhan
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
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5
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Yan Y, Vaid TP, Sanford MS. Bis(diisopropylamino)cyclopropenium-arene Cations as High Oxidation Potential and High Stability Catholytes for Non-aqueous Redox Flow Batteries. J Am Chem Soc 2020; 142:17564-17571. [DOI: 10.1021/jacs.0c07464] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yichao Yan
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Joint Center for Energy Storage Research (JCESR), 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Thomas P. Vaid
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Joint Center for Energy Storage Research (JCESR), 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Melanie S. Sanford
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Joint Center for Energy Storage Research (JCESR), 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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6
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Ortiz-Rodríguez JC, Santana JA, Méndez-Hernández DD. Linear correlation models for the redox potential of organic molecules in aqueous solutions. J Mol Model 2020; 26:70. [PMID: 32146589 DOI: 10.1007/s00894-020-4331-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/23/2020] [Indexed: 01/11/2023]
Abstract
In this study, we use the molecular orbital energy approximation (MOEA) and the energy difference approximation (EDA) to build linear correlation models for the redox potentials of 53 organic compounds in aqueous solutions. The molecules evaluated include nitroxides, phenols, and amines. Both the MOEA and EDA methods yield similar correlation models, however, the MOEA method is less computationally expensive. Correlation coefficients (R2) below 0.3 and mean absolute errors above 0.25 V were found for correlation models built without solvent effects. When explicit water molecules and a continuum solvent model are added to the calculations, correlation coefficients close to 0.8 are reached, and mean absolute errors below 0.18 V are obtained. The incorporation of solvent effects is necessary for good correlation models, particularly for redox processes of charged molecules in aqueous solutions. A comparison of the correlation models from different methodologies is provided. Graphical abstract.
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Affiliation(s)
| | - Juan A Santana
- Department of Chemistry, University of Puerto Rico at Cayey, Cayey, PR, 00736, USA
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7
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Grimm ML, Suleman NK, Hancock AN, Spencer JN, Dudding T, Rowshanpour R, Castagnoli N, Tanko JM. Stereoelectronic and Resonance Effects on the Rate of Ring Opening of N-Cyclopropyl-Based Single Electron Transfer Probes. J Am Chem Soc 2020; 142:2640-2652. [PMID: 31913031 DOI: 10.1021/jacs.9b12617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Cyclopropyl-N-methylaniline (5) is a poor probe for single electron transfer (SET) because the corresponding radical cation undergoes cyclopropane ring opening with a rate constant of only 4.1 × 104 s-1, too slow to compete with other processes such as radical cation deprotonation. The sluggish rate of ring opening can be attributed to either (i) a resonance effect in which the spin and charge of the radical cation in the ring-closed form is delocalized into the phenyl ring, and/or (ii) the lowest energy conformation of the SET product (5•+) does not meet the stereoelectronic requirements for cyclopropane ring opening. To resolve this issue, a new series of N-cyclopropylanilines were designed to lock the cyclopropyl group into the required bisected conformation for ring opening. The results reveal that the rate constant for ring opening of radical cations derived from 1'-methyl-3',4'-dihydro-1'H-spiro[cyclopropane-1,2'-quinoline] (6) and 6'-chloro-1'-methyl-3',4'-dihydro-1'H-spiro[cyclopropane-1,2'-quinoline] (7) are 3.5 × 102 s-1 and 4.1 × 102 s-1, effectively ruling out the stereoelectronic argument. In contrast, the radical cation derived from 4-chloro-N-methyl-N-(2-phenylcyclopropyl)aniline (8) undergoes cyclopropane ring opening with a rate constant of 1.7 × 108 s-1, demonstrating that loss of the resonance energy associated with the ring-closed form of these N-cyclopropylanilines can be amply compensated by incorporation of a radical-stabilizing phenyl substituent on the cyclopropyl group. Product studies were performed, including a unique application of EC-ESI/MS (Electrochemistry/ElectroSpray Ionization Mass Spectrometry) in the presence of 18O2 and H218O to elucidate the mechanism of ring opening of 7•+ and trapping of the resulting distonic radical cation.
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Affiliation(s)
- Michelle L Grimm
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - N Kamrudin Suleman
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Amber N Hancock
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Jared N Spencer
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Travis Dudding
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Rozhin Rowshanpour
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Neal Castagnoli
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - James M Tanko
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
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8
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Gieseking RLM, Ratner MA, Schatz GC. Benchmarking Semiempirical Methods To Compute Electrochemical Formal Potentials. J Phys Chem A 2018; 122:6809-6818. [DOI: 10.1021/acs.jpca.8b05143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rebecca L. M. Gieseking
- Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - George C. Schatz
- Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208, United States
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9
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Emanuelsson R, Sterby M, Strømme M, Sjödin M. An All-Organic Proton Battery. J Am Chem Soc 2017; 139:4828-4834. [DOI: 10.1021/jacs.7b00159] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rikard Emanuelsson
- Nanotechnology and Functional
Materials, Department of Engineering Sciences, The Ångström
Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden
| | - Mia Sterby
- Nanotechnology and Functional
Materials, Department of Engineering Sciences, The Ångström
Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden
| | - Maria Strømme
- Nanotechnology and Functional
Materials, Department of Engineering Sciences, The Ångström
Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden
| | - Martin Sjödin
- Nanotechnology and Functional
Materials, Department of Engineering Sciences, The Ångström
Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden
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10
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Sanderson JN, Dominey AP, Percy JM. Iron-Catalyzed Isopropylation of Electron-Deficient Aryl and Heteroaryl Chlorides. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- James N. Sanderson
- GlaxoSmithKline; Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY U.K
- Pure and Applied Chemistry; University of Strathclyde; Thomas Graham Building, 295 Cathedral Street Glasgow G1 1XL U.K
| | - Andrew P. Dominey
- GlaxoSmithKline; Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY U.K
| | - Jonathan M. Percy
- Pure and Applied Chemistry; University of Strathclyde; Thomas Graham Building, 295 Cathedral Street Glasgow G1 1XL U.K
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11
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Borioni JL, Puiatti M, Vera DMA, Pierini AB. In search of the best DFT functional for dealing with organic anionic species. Phys Chem Chem Phys 2017; 19:9189-9198. [DOI: 10.1039/c6cp06163j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
“And the winner is…” This work assesses the ability of different Density Functional Theory (DFT) functionals for a proper treatment of organic anionic species.
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Affiliation(s)
- José L. Borioni
- INFIQC – CONICET
- Instituto de Investigaciones en Físicoquímica de Córdoba
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad Nacional de Córdoba
| | - Marcelo Puiatti
- INFIQC – CONICET
- Instituto de Investigaciones en Físicoquímica de Córdoba
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad Nacional de Córdoba
| | - D. Mariano A. Vera
- QUIAMM-IMBIOTEC-Departamento de Química
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Mar del Plata
- Mar del Plata
- Argentina
| | - Adriana B. Pierini
- INFIQC – CONICET
- Instituto de Investigaciones en Físicoquímica de Córdoba
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad Nacional de Córdoba
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12
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Finke AD, Jahn BO, Saithalavi A, Dahlstrand C, Nauroozi D, Haberland S, Gisselbrecht JP, Boudon C, Mijangos E, Schweizer WB, Ott S, Ottosson H, Diederich F. The 6,6-Dicyanopentafulvene Core: A Template for the Design of Electron-Acceptor Compounds. Chemistry 2015; 21:8168-76. [DOI: 10.1002/chem.201500379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 02/04/2023]
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13
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Méndez‐Hernández DD, Gillmore JG, Montano LA, Gust D, Moore TA, Moore AL, Mujica V. Building and testing correlations for the estimation of one‐electron reduction potentials of a diverse set of organic molecules. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3413] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Dalvin D. Méndez‐Hernández
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
| | - Jason G. Gillmore
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
- Department of Chemistry Hope College Holland MI 49423 USA
| | - Luis A. Montano
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
| | - Devens Gust
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
| | - Thomas A. Moore
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
| | - Ana L. Moore
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
| | - Vladimiro Mujica
- Center for Bio‐Inspired Solar Fuel Production, Department of Chemistry and Biochemistry Arizona State University Tempe AZ 85287‐1604 USA
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14
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Prediction of the reduction potential of tris(2,2′-bipyridinyl)iron(III/II) derivatives. J Comput Chem 2014; 36:33-41. [DOI: 10.1002/jcc.23766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/17/2014] [Accepted: 10/06/2014] [Indexed: 11/07/2022]
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15
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Abstract
We show that the general anesthetics xenon, sulfur hexafluoride, nitrous oxide, and chloroform cause rapid increases of different magnitude and time course in the electron spin content of Drosophila. With the exception of CHCl3, these changes are reversible. Anesthetic-resistant mutant strains of Drosophila exhibit a different pattern of spin responses to anesthetic. In two such mutants, the spin response to CHCl3 is absent. We propose that these spin changes are caused by perturbation of the electronic structure of proteins by general anesthetics. Using density functional theory, we show that general anesthetics perturb and extend the highest occupied molecular orbital of a nine-residue α-helix. The calculated perturbations are qualitatively in accord with the Meyer-Overton relationship and some of its exceptions. We conclude that there may be a connection between spin, electron currents in cells, and the functioning of the nervous system.
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16
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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17
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Curpăn R, Avram S, Vianello R, Bologa C. Exploring the biological promiscuity of high-throughput screening hits through DFT calculations. Bioorg Med Chem 2014; 22:2461-8. [PMID: 24656802 DOI: 10.1016/j.bmc.2014.02.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 11/28/2022]
Abstract
The goal of this study is the understanding of biologically promiscuous compounds (frequent hitters) in HTS outcomes through their chemical behavior estimated via reactivity descriptors. Chemical reactivity is often an undesirable property due to the lack in biological selectivity of compounds comprised in HTS libraries. In this study the reactivity indexes have been computed within the DFT formalism, at different levels of theory, for two classes of representative compounds compiled from PubChem database, one comprising frequent hitters and the second one comprising rare hitters (biologically more selective compounds). We found that frequent hitters exert increased reactivity, mainly due to their electrophilic character, compared to the more selective class of compounds.
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Affiliation(s)
- Ramona Curpăn
- Department of Computational Chemistry, Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania.
| | - Sorin Avram
- Department of Computational Chemistry, Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania
| | - Robert Vianello
- Quantum Organic Chemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb HR-10000, Croatia
| | - Cristian Bologa
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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18
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Radtke V, Himmel D, Pütz K, Goll SK, Krossing I. The Protoelectric Potential Map (PPM): An Absolute Two-Dimensional Chemical Potential Scale for a Global Understanding of Chemistry. Chemistry 2014; 20:4194-211. [DOI: 10.1002/chem.201302473] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Sanina NA, Krivenko AG, Manzhos RA, Emel'yanova NS, Kozub GI, Korchagin DV, Shilov GV, Kondrat'eva TA, Ovanesyan NS, Aldoshin SM. Influence of aromatic ligand on the redox activity of neutral binuclear tetranitrosyl iron complexes [Fe2(μ-SR)2(NO)4]: experiments and quantum-chemical modeling. NEW J CHEM 2014. [DOI: 10.1039/c3nj00704a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Seto K, Nakayama T, Uno B. Formal redox potentials of organic molecules in ionic liquids on the basis of quaternary nitrogen cations as adiabatic electron affinities. J Phys Chem B 2013; 117:10834-45. [PMID: 24021019 DOI: 10.1021/jp402457k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formal redox potentials E°' involving neutral species R and radical anions R(•-) in ionic liquids (ILs) composed of ammonium, pyridinium, and imidazolium cations are discussed from the point of view of the adiabatic electron affinity as a molecular property. The dependence of the 1,4-benzoquinone (BQ)/BQ(•-) redox process in CH2Cl2 and CH3CN is primarily investigated over a wide concentration range of ILs as the supporting electrolyte. A logarithmic relationship involving a positive shift of E°' with increasing concentration is obtained when the concentration is changed from 0.01 to 1.0 M. The relationship of E°' at IL concentrations greater than 1.0 M gradually reaches a plateau and remains there even for the neat ILs. It is found that the E°' values in the neat ILs are not influenced by the measurement conditions, and that they remain considerably dependent on the nature and concentration of the electrolyte when measured using the traditional method involving molecular solvents combined with a supporting electrolyte (0.1-0.5 M). The difference in the E°' values observed in the ammonium and pyridinium ILs is only several millivolts. In addition, ESR and self-consistent isodensity polarized continuum model calculation results reveal that the potential shift toward positive values upon the transition from molecular solvents containing ILs to neat ILs is adequately accounted for by changes in the electrostatic interaction of R(•-) taken into the cavity composed of the solvent and IL. On the other hand, the first reduction waves of quinones, electron-accepting molecules, and polynuclear aromatic hydrocarbons are reversibly or quasi-reversibly observed in the ILs. The electrochemical stability of the ILs is exploited in the facile measurement of these quasi-reversible waves at quite negative potentials, such as for the naphthalene (NP)/NP(•-) couple. Notably, the E°' values obtained in the ammonium ILs correlate well with the calculated standard redox potentials and are linearly fitted with high correlation over all classes of compounds using a single regression equation based on Koopmans' theorem.
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Affiliation(s)
- Kunimasa Seto
- United Graduate School of Drug Discovery and Medical Information, Gifu University , Yanagido, Gifu 501-1194, Japan
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21
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Redox properties of [Fe2(SC6H5)2(NO)4]: an experimental study and quantum chemical modeling. Russ Chem Bull 2013. [DOI: 10.1007/s11172-012-0259-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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22
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Cheng GJ, Song LJ, Yang YF, Zhang X, Wiest O, Wu YD. Computational Studies on the Mechanism of the Copper-Catalyzed sp3-CH Cross-Dehydrogenative Coupling Reaction. Chempluschem 2013; 78:943-951. [DOI: 10.1002/cplu.201300117] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Indexed: 11/09/2022]
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23
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Comparison of pure and hybrid DFT functionals for geometry optimization and calculation of redox potentials for iron nitrosyl complexes with “μ-SCN” bridging ligands. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1316-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Méndez-Hernández DD, Tarakeshwar P, Gust D, Moore TA, Moore AL, Mujica V. Simple and accurate correlation of experimental redox potentials and DFT-calculated HOMO/LUMO energies of polycyclic aromatic hydrocarbons. J Mol Model 2012; 19:2845-8. [PMID: 23224940 DOI: 10.1007/s00894-012-1694-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/12/2012] [Indexed: 11/30/2022]
Abstract
The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements for large systems. Methodologies that yield strong linear correlations between calculations and experimental data have been reported, however the balance between accuracy and computational cost is always a major issue. In this work, linear correlations (with an R(2) value of up to 0.9990) between DFT-calculated HOMO/LUMO energies and 70 redox potentials from a series of 51 polycyclic aromatic hydrocarbons (obtained from the literature) are presented. The results are compared to previously reported linear correlations that were obtained with a more expensive computational methodology based on a Born-Haber thermodynamic cycle. It is shown in this article that similar or better correlations can be obtained with a simple and cheaper calculation.
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Pollock BJ, Sikes CA, Ter Louw RP, Hawken SR, Speelman AL, Lynch EJ, Stanford DJ, Wheeler KA, Gillmore JG. Synthesis and Structural Investigation of an “Oxazinoquinolinespirohexadienone” That Only Exists as Its Long-Wavelength Ring-Opened Quinonimine Isomer. J Org Chem 2012; 77:8689-95. [DOI: 10.1021/jo3016083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin J. Pollock
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
- Department
of Chemistry, Harper College, 1200 West
Algonquin Road, Palatine,
Illinois 60067, United States
| | - Christos A. Sikes
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
- Department
of Chemistry, Harper College, 1200 West
Algonquin Road, Palatine,
Illinois 60067, United States
| | - Ryan P. Ter Louw
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
| | - Scott R. Hawken
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
| | - Amy L. Speelman
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
| | - Eugene J. Lynch
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
| | - Daniel J. Stanford
- Department
of Chemistry, Harper College, 1200 West
Algonquin Road, Palatine,
Illinois 60067, United States
| | - Kraig A. Wheeler
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston,
Illinois 61920, United States
| | - Jason G. Gillmore
- Department of Chemistry, Hope College,
35 East 12th Street, Holland, Michigan
49423, United States
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Sun H, Putta A, Billion M. Arene trifluoromethylation: an effective strategy to obtain air-stable n-type organic semiconductors with tunable optoelectronic and electron transfer properties. J Phys Chem A 2012; 116:8015-22. [PMID: 22780095 DOI: 10.1021/jp301718j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Modulation of organic semiconductor band gap, electron affinities (EA), ionization potentials (IP), and reorganization energies (λ) associated with charge transfer is critical for its applications. We report here that trifluoromethylation not only increases both IP and EA significantly as expected but also narrows the HOMO-LUMO band gaps and increases considerably the air-stability of arene-based n-type organic semiconductors. The increased air-stability results from relatively high EA energies and a change in oxidation mechanism. Calculated EAs and IPs show that trifluoromethylated arenes are excellent candidates for n-type semiconductor materials; though a moderate increase of inner-sphere reorganization energy (λi) associated with charge transfer is the penalty for the improved performance of the trifluoromethylated compounds. However, since λi decreases as the π conjugation increases, a rational design to produce air-stable n-type semiconductor materials with reasonably small λi is simply to prepare trifluoromethylated arenes with extended π conjugation. Furthermore, we found that structural isomerization can fine-tune the optoelectronic and electronic transfer properties of the corresponding aromatics.
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Affiliation(s)
- Haoran Sun
- Department of Chemistry, University of South Dakota , Vermillion, South Dakota 57069, United States
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Lynch EJ, Speelman AL, Curry BA, Murillo CS, Gillmore JG. Expanding and Testing a Computational Method for Predicting the Ground State Reduction Potentials of Organic Molecules on the Basis of Empirical Correlation to Experiment. J Org Chem 2012; 77:6423-30. [DOI: 10.1021/jo300853k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Eugene J. Lynch
- Department of Chemistry, Hope College, 35 E. 12th Street, Holland,
Michigan 49423, United States
| | - Amy L. Speelman
- Department of Chemistry, Hope College, 35 E. 12th Street, Holland,
Michigan 49423, United States
| | - Bryce A. Curry
- Department of Chemistry, Hope College, 35 E. 12th Street, Holland,
Michigan 49423, United States
| | - Charles S. Murillo
- Department of Chemistry, Hope College, 35 E. 12th Street, Holland,
Michigan 49423, United States
| | - Jason G. Gillmore
- Department of Chemistry, Hope College, 35 E. 12th Street, Holland,
Michigan 49423, United States
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28
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Wang LP, Van Voorhis T. A Polarizable QM/MM Explicit Solvent Model for Computational Electrochemistry in Water. J Chem Theory Comput 2012; 8:610-7. [DOI: 10.1021/ct200340x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
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Häussler M, King S, Eng M, Haque S, Bilic A, Watkins S, Wilson G, Chen M, Scully A. Photo-spectroscopic properties of benzothiadiazole-containing pendant polymers for photovoltaic applications. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.03.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tugsuz T. DFT Study on the Standard Electrode Potentials of Imidazole, Tetrathiafulvalene, and Tetrathiafulvalene−Imidazole. J Phys Chem B 2010; 114:17092-101. [DOI: 10.1021/jp106705d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tugba Tugsuz
- Department of Chemistry, Hacettepe University, Beytepe, Ankara 06800, Turkey
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Davis AP, Fry AJ. Experimental and Computed Absolute Redox Potentials of Polycyclic Aromatic Hydrocarbons are Highly Linearly Correlated Over a Wide Range of Structures and Potentials. J Phys Chem A 2010; 114:12299-304. [DOI: 10.1021/jp106088n] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony P. Davis
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Albert J. Fry
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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32
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Electrocatalysis of oxygen reduction by quinones adsorbed on highly oriented pyrolytic graphite electrodes. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2010.06.055] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Synthesis and photochemistry of two quinoline analogs of the perimidinespirohexadienone family of photochromes. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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