1
|
Sharma B, Tran VA, Pongratz T, Galazzo L, Zhurko I, Bordignon E, Kast SM, Neese F, Marx D. A Joint Venture of Ab Initio Molecular Dynamics, Coupled Cluster Electronic Structure Methods, and Liquid-State Theory to Compute Accurate Isotropic Hyperfine Constants of Nitroxide Probes in Water. J Chem Theory Comput 2021; 17:6366-6386. [PMID: 34516119 PMCID: PMC8515807 DOI: 10.1021/acs.jctc.1c00582] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Indexed: 01/11/2023]
Abstract
The isotropic hyperfine coupling constant (HFCC, Aiso) of a pH-sensitive spin probe in a solution, HMI (2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water, is computed using an ensemble of state-of-the-art computational techniques and is gauged against X-band continuous wave electron paramagnetic resonance (EPR) measurement spectra at room temperature. Fundamentally, the investigation aims to delineate the cutting edge of current first-principles-based calculations of EPR parameters in aqueous solutions based on using rigorous statistical mechanics combined with correlated electronic structure techniques. In particular, the impact of solvation is described by exploiting fully atomistic, RISM integral equation, and implicit solvation approaches as offered by ab initio molecular dynamics (AIMD) of the periodic bulk solution (using the spin-polarized revPBE0-D3 hybrid functional), embedded cluster reference interaction site model integral equation theory (EC-RISM), and polarizable continuum embedding (using CPCM) of microsolvated complexes, respectively. HFCCs are obtained from efficient coupled cluster calculations (using open-shell DLPNO-CCSD theory) as well as from hybrid density functional theory (using revPBE0-D3). Re-solvation of "vertically desolvated" spin probe configuration snapshots by EC-RISM embedding is shown to provide significantly improved results compared to CPCM since only the former captures the inherent structural heterogeneity of the solvent close to the spin probe. The average values of the Aiso parameter obtained based on configurational statistics using explicit water within AIMD and from EC-RISM solvation are found to be satisfactorily close. Using either such explicit or RISM solvation in conjunction with DLPNO-CCSD calculations of the HFCCs provides an average Aiso parameter for HMI in aqueous solution at 300 K and 1 bar that is in good agreement with the experimentally determined one. The developed computational strategy is general in the sense that it can be readily applied to other spin probes of similar molecular complexity, to aqueous solutions beyond ambient conditions, as well as to other solvents in the longer run.
Collapse
Affiliation(s)
- Bikramjit Sharma
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Van Anh Tran
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Tim Pongratz
- Physikalische
Chemie III, Technische Universität
Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Laura Galazzo
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, 44780 Bochum, Germany
| | - Irina Zhurko
- Laboratory
of Nitrogen Compounds, N.N. Vorozhtsov Novosibirsk Institute of Organic
Chemistry, NIOCH SB RAS, 9 Lavrentiev Avenue, 630090, Novosibirsk, Russia
| | - Enrica Bordignon
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, 44780 Bochum, Germany
| | - Stefan M. Kast
- Physikalische
Chemie III, Technische Universität
Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dominik Marx
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| |
Collapse
|
2
|
Kim J, Lee JY, Park HY, Kim H, Kang JH, Kim HJ, Jeong W. Combination of peptides with biological, organic, and inorganic materials for synergistically enhanced diagnostics and therapeutics. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joo‐Young Kim
- Department of Biological Engineering Inha University Incheon Republic of Korea
- Department of Biological Sciences and Bioengineering Inha University Incheon Republic of Korea
| | - Jae Yun Lee
- Department of Biological Engineering Inha University Incheon Republic of Korea
| | - Ha Yeon Park
- Department of Biological Engineering Inha University Incheon Republic of Korea
| | - Hyunji Kim
- Department of Biological Engineering Inha University Incheon Republic of Korea
| | - Jeon Hyeong Kang
- Department of Biological Engineering Inha University Incheon Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering Inha University Incheon Republic of Korea
- Department of Biological Sciences and Bioengineering Inha University Incheon Republic of Korea
| | - Woo‐Jin Jeong
- Department of Biological Engineering Inha University Incheon Republic of Korea
- Department of Biological Sciences and Bioengineering Inha University Incheon Republic of Korea
| |
Collapse
|
3
|
Monroe J, Barry M, DeStefano A, Aydogan Gokturk P, Jiao S, Robinson-Brown D, Webber T, Crumlin EJ, Han S, Shell MS. Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces. Annu Rev Chem Biomol Eng 2020; 11:523-557. [PMID: 32169001 DOI: 10.1146/annurev-chembioeng-120919-114657] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.
Collapse
Affiliation(s)
- Jacob Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Mikayla Barry
- Department of Materials, University of California, Santa Barbara, California 93106, USA
| | - Audra DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Pinar Aydogan Gokturk
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Dennis Robinson-Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Thomas Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| |
Collapse
|