1
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Sarangi R, Maity S, Acharya A. Machine Learning Approach to Vertical Energy Gap in Redox Processes. J Chem Theory Comput 2024. [PMID: 39044422 DOI: 10.1021/acs.jctc.4c00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
A straightforward approach to calculating the free energy change (ΔG) and reorganization energy of a redox process is linear response approximation (LRA). However, accurate prediction of redox properties is still challenging due to difficulties in conformational sampling and vertical energy-gap sampling. Expensive hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are typically employed in sampling energy gaps using conformations from simulations. To alleviate the computational cost associated with the expensive QM method in the QM/MM calculation, we propose machine learning (ML) methods to predict the vertical energy gaps (VEGs). We tested several ML models to predict the VEGs and observed that simple models like linear regression show excellent performance (mean absolute error ∼0.1 eV) in predicting VEGs in all test systems, even when using features extracted from cheaper semiempirical methods. Our best ML model (extra trees regressor) shows a mean absolute error of around 0.1 eV while using features from the cheapest QM method. We anticipate our approach can be generalized to larger macromolecular systems with more complex redox centers.
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Affiliation(s)
- Ronit Sarangi
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Suman Maity
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Atanu Acharya
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, United States
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2
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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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3
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Uddin IA, Stec E, Papadantonakis GA. Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs. Chemphyschem 2024; 25:e202300946. [PMID: 38381922 DOI: 10.1002/cphc.202300946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
Gas-phase and aqueous vertical ionization potentials, vIPgas and vIPaq respectively and measurements of the molecular electrostatic and local ionization maps calculated at the DFT/B3LYP-D3/ 6-311+G** level of theory and the C-PCM reaction field model for single- and double-stranded CpG and 5MeCpG pairs show that the vIPaq for single- and double-stranded pairs of C-G and 5MeC-G are practically the same, in the range of 5.79 to 5.81 eV. The aqueous adiabatic ionization potentials for single-stranded CpG and 5MeCpG are 5.52 eV and 5.51 eV respectively and they reflect the nuclear reorganization that takes place after the abstraction of the electron. The aqueous adiabatic ionization energy values that correspond to the CpG+. radical cation and the hydrated electron, e-,, being at infinite distance, adIPaq+Vo, are 3.92 eV and 3.91 eV respectively with (Vo=-1.6 eV) Analysis of data suggest that the HOMO-LUMO energy gap in the hard/soft-acid/base (HSAB) concept cannot be used a priori to determine the effect of cytosine methylation on the guanine enhanced oxidative damage in DNA.
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Affiliation(s)
- Ismihan A Uddin
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
| | - Ewa Stec
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
| | - George A Papadantonakis
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
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4
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Slipchenko LV. Detangling Solvatochromic Effects by the Effective Fragment Potential Method. J Phys Chem A 2024; 128:656-669. [PMID: 38193780 DOI: 10.1021/acs.jpca.3c06194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Understanding molecular interactions in complex systems opens avenues for the efficient design of new materials with target properties. Energy decomposition methods provide a means to obtain a detailed picture of intermolecular interactions. This work introduces a molecular modeling approach for decomposing the solvatochromic shifts of the electronic excited states into the contributions of the individual molecular fragments of the environment surrounding the chromophore. The developed approach is implemented for the QM/EFP (quantum mechanics/effective fragment potential) model that provides a rigorous first-principles-based description of the electronic states of the chromophores in complex polarizable environments. On the example of two model systems, water pentamer and hydrated uracil, we show how the decomposition of the solvatochromic shifts into the contributions of individual solvent water molecules provides a detailed picture of the intermolecular interactions in the ground and excited states of these systems. The analysis also demonstrates the nonadditivity of solute-solvent interactions and the significant contribution of solute polarization to the total values of solvatochromic shifts.
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Affiliation(s)
- Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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5
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Boichenko AN, Bochenkova AV. Accurate Vertical Electron Detachment Energies and Multiphoton Resonant Photoelectron Spectra of Biochromophore Anions in Aqueous Solution. J Chem Theory Comput 2023. [PMID: 37146177 DOI: 10.1021/acs.jctc.2c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We introduce a new methodology for calculating vertical electron detachment energies (VDEs) of biologically relevant chromophores in their deprotonated anionic forms in aqueous solution. It combines a large-scale mixed DFT/EFP/MD approach with the high-level multireference perturbation theory XMCQDPT2 and the Effective Fragment Potential (EFP) method. The methodology includes a multiscale flexible treatment of inner (∼1000 water molecules) and outer (∼18000 water molecules) water shells around a charged solute, capturing both the effects of specific solvation and the properties of bulk water. VDEs are calculated as a function of system size for getting a converged value at the DFT/EFP level of theory. The XMCQDPT2/EFP approach, adapted for calculating VDEs, supports the DFT/EFP results. When corrected for a solvent polarization contribution, the XMCQDPT2/EFP method yields the most accurate estimate to date of the first VDE for aqueous phenolate (7.3 ± 0.1 eV), which agrees well with liquid-jet X-ray photoelectron spectroscopy data (7.1 ± 0.1 eV). We show that the geometry of the water shell and its size are essential for accurate VDE calculations of aqueous phenolate and its biologically relevant derivatives. By simulating photoelectron spectra of aqueous phenolate upon two-photon excitation at wavelengths resonant with the S0 → S1 transition, we also provide interpretation of recent multiphoton UV liquid-microjet photoelectron spectroscopy experiments. We show that its first VDE is consistent with our estimate of 7.3 eV, when experimental two-photon binding energies are corrected for the resonant contribution.
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Affiliation(s)
- Anton N Boichenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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6
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Yifrach Y, Rahimi R, Baraban JH, Bar I. Ionization energies and ionization-induced structural changes in 2-phenylethylamine and its monohydrate. J Chem Phys 2023; 158:114305. [PMID: 36948812 DOI: 10.1063/5.0138002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
We report the resonance-enhanced two-photon ionization combined with various detection approaches and quantum chemical calculations of biologically relevant neurotransmitter prototypes, the most stable conformer of 2-phenylethylamine (PEA), and its monohydrate, PEA-H2O, to reveal the possible interactions between the phenyl ring and amino group in the neutral and ionic species. Extracting the ionization energies (IEs) and appearance energy was achieved by measuring the photoionization and photodissociation efficiency curves of the PEA parent and photofragment ions, together with velocity and kinetic energy-broadened spatial map images of photoelectrons. We obtained coinciding upper bounds for the IEs for PEA and PEA-H2O of 8.63 ± 0.03 and 8.62 ± 0.04 eV, within the range predicted by quantum calculations. The computed electrostatic potential maps show charge separation, corresponding to a negative charge on phenyl and a positive charge on the ethylamino side chain in the neutral PEA and its monohydrate; in the cations, the charge distributions naturally become positive. The significant changes in geometries upon ionization include switching of the amino group orientation from pyramidal to nearly planar in the monomer but not in the monohydrate, lengthening of the N-H⋯π hydrogen bond (HB) in both species, Cα-Cβ bond in the side chain of the PEA+ monomer, and the intermolecular O-H⋯N HB in PEA-H2O cations, leading to distinct exit channels.
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Affiliation(s)
- Yair Yifrach
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Joshua H Baraban
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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7
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Sarangi R, Nanda KD, Krylov AI. Charge-transfer-to-solvent states provide a sensitive spectroscopic probe of the local solvent structure around anions. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2148582] [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]
Affiliation(s)
- Ronit Sarangi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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8
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Heindel JP, Hao H, LaCour RA, Head-Gordon T. Spontaneous Formation of Hydrogen Peroxide in Water Microdroplets. J Phys Chem Lett 2022; 13:10035-10041. [PMID: 36264238 DOI: 10.1021/acs.jpclett.2c01721] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
There is accumulating evidence that many chemical reactions are accelerated by several orders of magnitude in micrometer-sized aqueous or organic liquid droplets compared to their corresponding bulk liquid phase. However, the molecular origin of the enhanced rates remains unclear as in the case of spontaneous appearance of 1 μM hydrogen peroxide in water microdroplets. In this Letter, we consider the range of ionization energies and whether interfacial electric fields of a microdroplet can feasibly overcome the high energy step from hydroxide ions (OH-) to hydroxyl radicals (OH•) in a primary H2O2 mechanism. We find that the vertical ionization energies (VIEs) of partially solvated OH- ions are greatly lowered relative to the average VIE in the bulk liquid, unlike the case of the Cl- anion which shows no reduction in the VIEs regardless of solvation environment. Overall reduced hydrogen-bonding and undercoordination of OH- are structural features that are more readily present at the air-water interface, where the energy scale for ionization can be matched by statistically probable electric field values.
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Affiliation(s)
- Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
| | - R Allen LaCour
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Departments of Bioengineering and Chemical and Biomolecular EngineeringUniversity of California, Berkeley, California94720, United States
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9
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Carter-Fenk K, Herbert JM. Appraisal of dispersion damping functions for the effective fragment potential method. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2055504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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10
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Liebenthal M, Vu NH, DePrince E. Equation-of-motion cavity quantum electrodynamics coupled-cluster theory for electron attachment. J Chem Phys 2022; 156:054105. [DOI: 10.1063/5.0078795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Nam Hoang Vu
- Chemistry & Biochemistry, Florida State University, United States of America
| | - Eugene DePrince
- Chemistry and Biochemistry, Florida State University, United States of America
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11
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 451] [Impact Index Per Article: 150.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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12
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Bruce JP, Zhang K, Balasubramani SG, Haines AR, Galhenage RP, Voora VK, Furche F, Hemminger JC. Exploring the Solvation of Acetic Acid in Water Using Liquid Jet X-ray Photoelectron Spectroscopy and Core Level Electron Binding Energy Calculations. J Phys Chem B 2021; 125:8862-8868. [PMID: 34339193 DOI: 10.1021/acs.jpcb.1c03520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Liquid jet X-ray photoelectron spectroscopy was used to investigate changes in the local electronic structure of acetic acid in the bulk of aqueous solutions induced by solvation effects. These effects manifest themselves as shifts in the difference in the carbon 1s binding energy (ΔBE) between the methyl and carboxyl carbons of acetic acid. Furthermore, molecular dynamics simulations, coupled with correlated electronic structure calculations of the first solvation sphere, provide insight into the number of water molecules directly interacting with the carboxyl group that are required to match the ΔBE from the photoelectron spectroscopy experiments. This comparison shows that a single water molecule in the first solvation shell describes the photoelectron ΔBE of acetic acid while at least 20 water molecules are required for the conjugate base, acetate, in aqueous solutions.
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Affiliation(s)
- Jared P Bruce
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Kimberly Zhang
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | | | - Amanda R Haines
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Randima P Galhenage
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Vamsee K Voora
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - John C Hemminger
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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13
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Weng G, Vlček V. Efficient treatment of molecular excitations in the liquid phase environment via stochastic many-body theory. J Chem Phys 2021; 155:054104. [PMID: 34364336 DOI: 10.1063/5.0058410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurate predictions of charge excitation energies of molecules in the disordered condensed phase are central to the chemical reactivity, stability, and optoelectronic properties of molecules and critically depend on the specific environment. Herein, we develop a stochastic GW method for calculating these charge excitation energies. The approach employs maximally localized electronic states to define the electronic subspace of a molecule and the rest of the system, both of which are randomly sampled. We test the method on three solute-solvent systems: phenol, thymine, and phenylalanine in water. The results are in excellent agreement with the previous high-level calculations and available experimental data. The stochastic calculations for supercells containing up to 1000 electrons representing the solvated systems are inexpensive and require ≤1000 central processing unit hrs. We find that the coupling with the environment accounts for ∼40% of the total correlation energy. The solvent-to-solute feedback mechanism incorporated in the molecular correlation term causes up to 0.6 eV destabilization of the quasiparticle energy. Simulated photo-emission spectra exhibit red shifts, state-degeneracy lifting, and lifetime shortening. Our method provides an efficient approach for an accurate study of excitations of large molecules in realistic condensed phase environments.
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Affiliation(s)
- Guorong Weng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
| | - VojtĚch Vlček
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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14
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Paul SK, Herbert JM. Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface. J Am Chem Soc 2021; 143:10189-10202. [PMID: 34184532 DOI: 10.1021/jacs.1c03131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, but the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. We have computed aqueous-phase VIEs for a set of inorganic anions, using a combination of molecular dynamics simulations and electronic structure calculations, with results that are in excellent agreement with experiment regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk aqueous solution. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in both environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that the surface activity of soft anions is largely a second or third solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding.
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Affiliation(s)
- Suranjan K Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Kostal V, Brezina K, Marsalek O, Jungwirth P. Benzene Radical Anion Microsolvated in Ammonia Clusters: Modeling the Transition from an Unbound Resonance to a Bound Species. J Phys Chem A 2021; 125:5811-5818. [PMID: 34165987 DOI: 10.1021/acs.jpca.1c04594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The benzene radical anion, well-known in organic chemistry as the first intermediate in the Birch reduction of benzene in liquid ammonia, exhibits intriguing properties from the point of view of quantum chemistry. Notably, it has the character of a metastable shape resonance in the gas phase, while measurements in solution find it to be experimentally detectable and stable. In this light, our previous calculations performed in bulk liquid ammonia explicitly reveal that solvation leads to stabilization. Here, we focus on the transition of the benzene radical anion from an unstable gas-phase ion to a fully solvated bound species by explicit ionization calculations of the radical anion solvated in molecular clusters of increasing size. The computational cost of the largest systems is mitigated by combining density functional theory with auxiliary methods including effective fragment potentials or approximating the bulk by polarizable continuum models. Using this methodology, we obtain the cluster size dependence of the vertical binding energy of the benzene radical anion converging to the value of -2.3 eV at a modest computational cost.
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Affiliation(s)
- Vojtech Kostal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Krystof Brezina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.,Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Ondrej Marsalek
- Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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16
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Abstract
We present an EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) study on the electron attachment process to solvated cytosine. The electron attachment in the bulk solvated cytosine occurs through a doorway mechanism, where the initial electron is localized on water. The electron is subsequently transferred to cytosine by the mixing of electronic and nuclear degrees of freedom, which occurs on an ultrafast time scale. The bulk water environment stabilizes the cytosine-bound anion by an extensive hydrogen-bond network and drastically enhances the electron transfer rate from that observed in the gas phase. Microhydration studies cannot reproduce the effect of the bulk water environment on the electron attachment process, and one needs to include a large number of water molecules in the calculation to obtain converged results. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.
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Affiliation(s)
- Pooja Verma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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17
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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18
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Mukherjee M, Tripathi D, Brehm M, Riplinger C, Dutta AK. Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study. J Chem Theory Comput 2020; 17:105-116. [DOI: 10.1021/acs.jctc.0c00655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Divya Tripathi
- Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Martin Brehm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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19
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Kim Y, Bui Y, Tazhigulov RN, Bravaya KB, Slipchenko LV. Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database. J Chem Theory Comput 2020; 16:7735-7747. [PMID: 33236635 DOI: 10.1021/acs.jctc.0c00758] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as "flexible EFP", is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.
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Affiliation(s)
- Yongbin Kim
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yen Bui
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruslan N Tazhigulov
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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20
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Viquez Rojas CI, Slipchenko LV. Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding. J Chem Theory Comput 2020; 16:6408-6417. [PMID: 32786899 DOI: 10.1021/acs.jctc.9b01156] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hybrid quantum mechanical and molecular mechanical (QM/MM) approaches facilitate computational modeling of large biological and materials systems. Typically, in QM/MM, a small region of the system is modeled with an accurate quantum mechanical method and its surroundings with a more efficient alternative, such as a classical force field or the effective fragment potential (EFP). The reliability of QM/MM calculations depends largely on the treatment of interactions between the two subregions, also known as embedding. The polarizable embedding, which allows mutual polarization between solvent and solute, is considered to be essential for describing electronic excitations in polar solvents. In this work, we employ the QM/EFP model and extend the polarizable embedding by incorporating two short-range terms-a charge penetration correction to the electrostatic term and the exchange-repulsion term-both of which are modeled with one-electron contributions to the quantum Hamiltonian. We evaluate the accuracy of these terms by computing excitation energies across 37 molecular clusters consisting of biologically relevant chromophores surrounded by polar solvent molecules. QM/EFP excitation energies are compared to the fully quantum mechanical calculations with the configuration interaction singles (CIS) method. We find that the charge penetration correction diminishes the accuracy of the QM/EFP calculations. On the other hand, while the effect of exchange-repulsion is negligible for most ππ* transitions, the exchange-repulsion significantly improves description of nπ* transitions with blue solvatochromic shifts. As a result, addition of the exchange-repulsion term improves the overall accuracy of QM/EFP. Performances of QM/EFP models remain similar when excitation energies are modeled with cc-pVDZ and aug-cc-pVDZ basis sets.
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Affiliation(s)
- Claudia I Viquez Rojas
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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21
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Huang SR, Tureček F. Cation Radicals of Hachimoji Nucleobases. Canonical Purine and Noncanonical Pyrimidine Forms Generated in the Gas Phase and Characterized by UV–Vis Photodissociation Action Spectroscopy. J Phys Chem A 2020; 124:7101-7112. [DOI: 10.1021/acs.jpca.0c06227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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22
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A computational investigation of cytosine and 5-methyl cytosine reactivity by means of ionization potentials and one specific methylation pathway. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Fabrizio A, Meyer B, Corminboeuf C. Machine learning models of the energy curvature vs particle number for optimal tuning of long-range corrected functionals. J Chem Phys 2020; 152:154103. [DOI: 10.1063/5.0005039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Benjamin Meyer
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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24
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Ranga S, Mukherjee M, Dutta AK. Interactions of Solvated Electrons with Nucleobases: The Effect of Base Pairing. Chemphyschem 2020; 21:1019-1027. [DOI: 10.1002/cphc.202000133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/23/2020] [Indexed: 01/30/2023]
Affiliation(s)
- Santosh Ranga
- Department of ChemistryIndian Institute of Technology (IIT), Bombay Powai Maharastra 400076 India
| | - Madhubani Mukherjee
- Department of ChemistryIndian Institute of Technology (IIT), Bombay Powai Maharastra 400076 India
| | - Achintya Kumar Dutta
- Department of ChemistryIndian Institute of Technology (IIT), Bombay Powai Maharastra 400076 India
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25
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Kim Y, Morozov D, Stadnytskyi V, Savikhin S, Slipchenko LV. Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex. J Phys Chem Lett 2020; 11:1636-1643. [PMID: 32013435 DOI: 10.1021/acs.jpclett.9b03486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.
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Affiliation(s)
- Yongbin Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
| | - Valentyn Stadnytskyi
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
- Laboratory of Chemical Physics, National Institute of Diabetes, Digestion and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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26
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Tóth Z, Kubečka J, Muchová E, Slavíček P. Ionization energies in solution with the QM:QM approach. Phys Chem Chem Phys 2020; 22:10550-10560. [PMID: 32010902 DOI: 10.1039/c9cp06154a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We discuss a fragment-based QM:QM scheme as a practical way to access the energetics of vertical electronic processes in the condensed phase. In the QM:QM scheme, we decompose the large molecular system into small fragments, which interact solely electrostatically. The energies of the fragments are calculated in a self-consistent field generated by the other fragments and the total energy of the system is calculated as a sum of the fragment energies. We show on two test cases (cytosine and a sodium cation) that the method allows one to accurately simulate the shift of vertical ionization energies (VIE) while going from the gas phase to the bulk. For both examples, the predicted solvent shifts and peak widths estimated at the DFT level agree well with the experimental observations. We argue that the QM:QM approach is more suitable than either an electrostatic embedding based QM/MM approach, a full quantum description at the DFT level with a generally used functional or a combination of both. We also discuss the potential scope of the applicability for other electronic processes such as Auger decay.
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Affiliation(s)
- Zsuzsanna Tóth
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic.
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27
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Caricato M. Coupled cluster theory in the condensed phase within the singles‐T density scheme for the environment response. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marco Caricato
- Department of Chemistry University of Kansas Lawrence Kansas
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28
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Izsák R. Single‐reference coupled cluster methods for computing excitation energies in large molecules: The efficiency and accuracy of approximations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1445] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Róbert Izsák
- Max‐Planck‐Institut für Kohlenforschung Mülheim an der Ruhr Germany
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29
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Lu SI. Discrete Solvent Reaction Field Calculations for One- and Two-Photon Absorptions of Solution-Phase Dimethylaminonitrostilbene Molecule. J Phys Chem A 2019; 123:5334-5340. [PMID: 31242735 DOI: 10.1021/acs.jpca.9b04041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on the configurations generated by molecular dynamics (MD) simulations using the on-the-fly density-functional tight-bonding (DFTB) force field, we investigated performance of the discrete solvent reaction field (DRF) model coupled to time-dependent density functional theory (TD-DFT) for solvatochromic effect of one- and two-photon absorption phenomena. Dimethylaminonitrostilbene (DANS) molecule solvated in chloroform, dichloromethane, and dimethyl sulfoxide solvents was selected as a model system for our research purpose. For every selected MD/DFTB configuration, within the context of the DRF, solute molecule is represented by TD-DFT and solvent molecules are described by atomic charges and polarizabilities. The calculated one-photon absorption energies reproduce well the positive solvatochromic behavior of solvated DANS and are in good agreement with available experimental data. For the two-photon absorption cross section, even though our approach overshot the experimental data by about 20% in absolute magnitude, experimentally observed solvatochromic change was captured qualitatively in this work. At last, we examined the contributions of atomic charges and polarizabilities of solvent molecules to the solvatochromic shifts of properties of interest.
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Affiliation(s)
- Shih-I Lu
- Department of Chemistry Soochow University No. 70 Lin-Shih Road , Taipei City , 111 , Taiwan
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30
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Bhattacharyya D, Zhang Y, Elles CG, Bradforth SE. Electronic Structure of Liquid Methanol and Ethanol from Polarization-Dependent Two-Photon Absorption Spectroscopy. J Phys Chem A 2019; 123:5789-5804. [DOI: 10.1021/acs.jpca.9b04040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dhritiman Bhattacharyya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Yuyuan Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Christopher G. Elles
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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31
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Tazhigulov RN, Gurunathan PK, Kim Y, Slipchenko LV, Bravaya KB. Polarizable embedding for simulating redox potentials of biomolecules. Phys Chem Chem Phys 2019; 21:11642-11650. [PMID: 31116217 PMCID: PMC6611676 DOI: 10.1039/c9cp01533g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The approach is tested on simulating reduction potential of cryptochrome 1 protein from Arabidopsis thaliana. The theoretical estimate (0.07 V) of the midpoint reduction potential is in good agreement with available experimental data (-0.15 V).
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Affiliation(s)
- Ruslan N Tazhigulov
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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32
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Barrozo A, Xu B, Gunina AO, Jacobs MI, Wilson K, Kostko O, Ahmed M, Krylov AI. To Be or Not To Be a Molecular Ion: The Role of the Solvent in Photoionization of Arginine. J Phys Chem Lett 2019; 10:1860-1865. [PMID: 30933520 DOI: 10.1021/acs.jpclett.9b00494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Application of photoionization mass spectroscopy, a technique capable of assessing protonation states in complex molecules in the gas phase, is challenging for arginine due to its fragility. We report photoionization efficiencies in the valence region of aqueous aerosol particles produced from arginine solutions under various pH and vaporization conditions. By using ab initio calculations, we investigate the stability of different conformers. Our results show that neutral arginine fragments upon ionization in the gas phase but solvation stabilizes the molecular ion, resulting in different photoionization dynamics. We also report the valence-band photoelectron spectra of the aerosol solutions obtained at different pH values.
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Affiliation(s)
- Alexandre Barrozo
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-0482 , United States
| | - Bo Xu
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Anastasia O Gunina
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-0482 , United States
| | - Michael I Jacobs
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Kevin Wilson
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Oleg Kostko
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Musahid Ahmed
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Anna I Krylov
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-0482 , United States
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149 , 22671 Hamburg , Germany
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33
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Haldar S, Riplinger C, Demoulin B, Neese F, Izsak R, Dutta AK. Multilayer Approach to the IP-EOM-DLPNO-CCSD Method: Theory, Implementation, and Application. J Chem Theory Comput 2019; 15:2265-2277. [DOI: 10.1021/acs.jctc.8b01263] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Soumi Haldar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | | | - Baptiste Demoulin
- Max-Planck-Institut
für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
| | - Robert Izsak
- Max-Planck-Institut
für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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34
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Muchová E, Slavíček P. Beyond Koopmans' theorem: electron binding energies in disordered materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:043001. [PMID: 30524069 DOI: 10.1088/1361-648x/aaf130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The topical review focuses on calculating ionization energies (IE), or electronic polarons in quasi-particle terminology, in large disordered systems, e.g. for a solute dissolved in a molecular solvent. The simplest estimate of the ionization energy is provided by one-electron energies in the Hartree-Fock theory, but the calculated quantities are not accurate. Density functional theory as many-body theory provides a principal opportunity for calculating one-electron energies including correlation and relaxation effects, i.e. the true energies of electronic polarons. We argue that such a principal possibility materializes within the concept of optimally tuned range-separated hybrid functionals (OT-RSH). We describe various schemes for optimal tuning. Importantly, the OT-RSH scheme is investigated for systems capped with dielectric continuum, providing a consistent picture on the QM/dielectric boundary. Finally, some limitations and open issues of the OT-RSH approach are addressed.
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Affiliation(s)
- Eva Muchová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
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35
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Zhang Y, Xie P, Yang S, Han K. Ionization and Electron Attachment for Nucleobases in Water. J Phys Chem B 2019; 123:1237-1247. [DOI: 10.1021/acs.jpcb.8b09435] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao, Binhai Road 72, Qingdao 266237, China
| | - Peng Xie
- School of Chemistry & Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
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36
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Nanda KD, Krylov AI. The effect of polarizable environment on two-photon absorption cross sections characterized by the equation-of-motion coupled-cluster singles and doubles method combined with the effective fragment potential approach. J Chem Phys 2018; 149:164109. [DOI: 10.1063/1.5048627] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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37
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Viquez Rojas CI, Fine J, Slipchenko LV. Exchange-repulsion energy in QM/EFP. J Chem Phys 2018; 149:094103. [PMID: 30195305 DOI: 10.1063/1.5043107] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The effective fragment potential (EFP) is a quantum mechanics (QM)-based model designed to accurately describe intermolecular interactions. Hybrid QM/EFP calculations combine quantum mechanical methods with an EFP embedding to study complex systems in which many-body effects are relevant. As in EFP-only calculations, non-bonded interactions between the QM region and EFP fragments are computed as a sum of electrostatic, polarization, dispersion, and exchange-repulsion energies. The exchange-repulsion term is a computational bottleneck of the EFP calculations. Here, we present a general procedure for computing the QM/EFP exchange-repulsion interactions based on one-electron contributions to the QM Hamiltonian, by using Gaussian functions to represent localized molecular orbitals of the effective fragments. The accuracy of the exchange-repulsion and total QM/EFP interaction energies is evaluated on a diverse set of dimers, including complexes from the S22 dataset of non-covalent interactions. In most cases, the QM/EFP energies are at least as accurate as corresponding EFP energies. A simple and computationally efficient form of the introduced QM/EFP exchange-repulsion term will facilitate further developments and applications of QM/EFP methods.
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Affiliation(s)
| | - Jonathan Fine
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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38
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Caricato M. Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response. J Chem Phys 2018; 148:134113. [DOI: 10.1063/1.5021781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Marco Caricato
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, USA
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39
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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40
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Dang A, Nguyen HTH, Ruiz H, Piacentino E, Ryzhov V, Tureček F. Experimental Evidence for Noncanonical Thymine Cation Radicals in the Gas Phase. J Phys Chem B 2017; 122:86-97. [DOI: 10.1021/acs.jpcb.7b09872] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andy Dang
- Department
of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Huong T. H. Nguyen
- Department
of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Heather Ruiz
- Department
of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Elettra Piacentino
- Department
of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Victor Ryzhov
- Department
of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - František Tureček
- Department
of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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41
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Chakraborty R, Bose S, Ghosh D. Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study. J Comput Chem 2017; 38:2528-2537. [PMID: 28856705 DOI: 10.1002/jcc.24913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 11/11/2022]
Abstract
Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide. In this work, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) approach with effective fragment potential as the MM method of choice and equation-of-motion coupled-cluster for ionization potential with singles and doubles (EOM-IP-CCSD) as the QM method. The performance of the hybrid scheme with respect to the full QM method shows an accuracy of ≤ 0.02-0.04 eV. The lowest few ionizations of the nucleotide are found to be from different parts of the moiety, that is, the nucleic acid base, phosphate, or sugar, and these ionization energies are very closely spaced giving rise to a very complicated spectrum. Furthermore, microsolvation has large effects on these ionizations and can lead to red or blue shift depending on the position of the water molecule. Even a single water molecule can change the order of ionized states in the nucleotide. The VIEs of the bulk solvated chromophores are predicted and compared to existing experimental spectra. The predominant role of polarization in the solvatochromic shift is noticed. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rahul Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Samik Bose
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debashree Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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42
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Bose S, Ghosh D. An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase. J Comput Chem 2017; 38:2248-2257. [DOI: 10.1002/jcc.24875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/06/2017] [Accepted: 06/19/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Samik Bose
- Physical and Materials Chemistry Division; CSIR-National Chemical Laboratory; Pune 411008 India
| | - Debashree Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Kolkata 700032 India
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43
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Sadybekov A, Krylov AI. Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine. J Chem Phys 2017; 147:014107. [DOI: 10.1063/1.4990564] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Arman Sadybekov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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44
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Dubinets N, Slipchenko LV. Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments. J Phys Chem A 2017; 121:5301-5312. [DOI: 10.1021/acs.jpca.7b01701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikita Dubinets
- Department
of Condensed Matter Physics, National Research Nuclear University “MEPhI”, 31 Kashirskoe Highway, Moscow, 115409, Russia
- Federal Research
Center “Crystallography and Photonics”, Photochemistry
Center RAS, 7a Novatorov Str., Moscow, 119421, Russia
| | - Lyudmila V. Slipchenko
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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45
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Khattab M, Wang F, Clayton AHA. Micro-solvation of tyrosine-kinase inhibitor AG1478 explored with fluorescence spectroscopy and computational chemistry. RSC Adv 2017. [DOI: 10.1039/c7ra04435f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Fluorescence quenching of the anticancer AG1478, by at least three explicit water molecules, can be exploited to probe drug–protein binding interactions.
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Affiliation(s)
- Muhammad Khattab
- Centre for Micro-Photonics
- Faculty of Science, Engineering and Technology
- Swinburne University of Technology
- Melbourne
- Australia
| | - Feng Wang
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- School of Science
- Faculty of Science, Engineering and Technology
- Swinburne University of Technology
| | - Andrew H. A. Clayton
- Centre for Micro-Photonics
- Faculty of Science, Engineering and Technology
- Swinburne University of Technology
- Melbourne
- Australia
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Ren S, Harms J, Caricato M. An EOM-CCSD-PCM Benchmark for Electronic Excitation Energies of Solvated Molecules. J Chem Theory Comput 2016; 13:117-124. [PMID: 27973775 DOI: 10.1021/acs.jctc.6b01053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we benchmark the equation of motion coupled cluster with single and double excitations (EOM-CCSD) method combined with the polarizable continuum model (PCM) for the calculation of electronic excitation energies of solvated molecules. EOM-CCSD is one of the most accurate methods for computing one-electron excitation energies, and accounting for the solvent effect on this property is a key challenge. PCM is one of the most widely employed solvation models due to its adaptability to virtually any solute and its efficient implementation with density functional theory methods (DFT). Our goal in this work is to evaluate the reliability of EOM-CCSD-PCM, especially compared to time-dependent DFT-PCM (TDDFT-PCM). Comparisons between calculated and experimental excitation energies show that EOM-CCSD-PCM consistently overestimates experimental results by 0.4-0.5 eV, which is larger than the expected EOM-CCSD error in vacuo. We attribute this decrease in accuracy to the approximated solvation model. Thus, we investigate a particularly important source of error: the lack of H-bonding interactions in PCM. We show that this issue can be addressed by computing an energy shift, ΔHB, from bare-PCM to microsolvation + PCM at DFT level. Our results show that such a shift is independent of the functional used, contrary to the absolute value of the excitation energy. Hence, we suggest an efficient protocol where the EOM-CCSD-PCM transition energy is corrected by ΔHB(DFT), which consistently improves the agreement with the experimental measurements.
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Affiliation(s)
- Sijin Ren
- Department of Chemistry, University of Kansas , 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, United States
| | - Joseph Harms
- Lawrence High School , 1901 Louisiana St., Lawrence, Kansas 66046, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas , 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, United States
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Chakraborty R, Ghosh D. The effect of sequence on the ionization of guanine in DNA. Phys Chem Chem Phys 2016; 18:6526-33. [PMID: 26864778 DOI: 10.1039/c5cp07804k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.
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Affiliation(s)
- Rahul Chakraborty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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Ghosh D. Hybrid Equation-of-Motion Coupled-Cluster/Effective Fragment Potential Method: A Route toward Understanding Photoprocesses in the Condensed Phase. J Phys Chem A 2016; 121:741-752. [DOI: 10.1021/acs.jpca.6b08263] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune, India 411008
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Gurunathan PK, Acharya A, Ghosh D, Kosenkov D, Kaliman I, Shao Y, Krylov AI, Slipchenko LV. Extension of the Effective Fragment Potential Method to Macromolecules. J Phys Chem B 2016; 120:6562-74. [PMID: 27314461 DOI: 10.1021/acs.jpcb.6b04166] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.
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Affiliation(s)
| | - Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Debashree Ghosh
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Dmytro Kosenkov
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry and Physics, Monmouth University , West Long Branch, New Jersey 07764, United States
| | - Ilya Kaliman
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Yihan Shao
- Q-Chem Inc. , 6601 Owens Drive, Suite 105 Pleasanton, California 94588, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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50
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Tazhigulov RN, Bravaya KB. Free Energies of Redox Half-Reactions from First-Principles Calculations. J Phys Chem Lett 2016; 7:2490-2495. [PMID: 27295124 DOI: 10.1021/acs.jpclett.6b00893] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values.
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Affiliation(s)
- Ruslan N Tazhigulov
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
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