1
|
Iyengar SS, Schlegel HB, Sumner I, Li J. Rare Events Sampling Methods for Quantum and Classical Ab Initio Molecular Dynamics. J Phys Chem A 2024; 128:5386-5397. [PMID: 38951489 DOI: 10.1021/acs.jpca.3c07385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
We provide an approach to sample rare events during classical ab initio molecular dynamics and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of freedom are introduced that may harmonically interact with the electronic and nuclear degrees of freedom to steer the dynamics in a conservative fashion toward energetically forbidden regions. A similar approach when introduced for quantum wavepacket dynamics has the effect of biasing the trajectory of the wavepacket centroid toward the regions of the potential surface that are difficult to sample. The approach is demonstrated for a phenol-amine system, which is a prototypical problem for condensed phase-proton transfer, and for model potentials undergoing wavepacket dynamics. In all cases, the approach yields trajectories that conserve energy while sampling rare events.
Collapse
Affiliation(s)
- Srinivasan S Iyengar
- Department of Chemistry, Department of Physics, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit 48202, Michigan, United States
| | - Isaiah Sumner
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg 22807, Virginia, United States
| | - Junjie Li
- Texas Advanced Computing Center, The University of Texas at Austin, Austin 78758, Texas, United States
| |
Collapse
|
2
|
Zhang JH, Ricard TC, Haycraft C, Iyengar SS. Weighted-Graph-Theoretic Methods for Many-Body Corrections within ONIOM: Smooth AIMD and the Role of High-Order Many-Body Terms. J Chem Theory Comput 2021; 17:2672-2690. [PMID: 33891416 DOI: 10.1021/acs.jctc.0c01287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a weighted-graph-theoretic approach to adaptively compute contributions from many-body approximations for smooth and accurate post-Hartree-Fock (pHF) ab initio molecular dynamics (AIMD) of highly fluxional chemical systems. This approach is ONIOM-like, where the full system is treated at a computationally feasible quality of treatment (density functional theory (DFT) for the size of systems considered in this publication), which is then improved through a perturbative correction that captures local many-body interactions up to a certain order within a higher level of theory (post-Hartree-Fock in this publication) described through graph-theoretic techniques. Due to the fluxional and dynamical nature of the systems studied here, these graphical representations evolve during dynamics. As a result, energetic "hops" appear as the graphical representation deforms with the evolution of the chemical and physical properties of the system. In this paper, we introduce dynamically weighted, linear combinations of graphs, where the transition between graphical representations is smoothly achieved by considering a range of neighboring graphical representations at a given instant during dynamics. We compare these trajectories with those obtained from a set of trajectories where the range of local many-body interactions considered is increased, sometimes to the maximum available limit, which yields conservative trajectories as the order of interactions is increased. The weighted-graph approach presents improved dynamics trajectories while only using lower-order many-body interaction terms. The methods are compared by computing dynamical properties through time-correlation functions and structural distribution functions. In all cases, the weighted-graph approach provides accurate results at a lower cost.
Collapse
Affiliation(s)
- Juncheng Harry Zhang
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Timothy C Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
3
|
DeGregorio N, Iyengar SS. Challenges in constructing accurate methods for hydrogen transfer reactions in large biological assemblies: rare events sampling for mechanistic discovery and tensor networks for quantum nuclear effects. Faraday Discuss 2020; 221:379-405. [DOI: 10.1039/c9fd00071b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present two methods that address the computational complexities arising in hydrogen transfer reactions in enzyme active sites.
Collapse
Affiliation(s)
- Nicole DeGregorio
- Department of Chemistry
- Department of Physics
- Indiana University
- Bloomington
- USA
| | | |
Collapse
|
4
|
Hu S, Offenbacher AR, Lu ED, Klinman JP. Comparative kinetic isotope effects on first- and second-order rate constants of soybean lipoxygenase variants uncover a substrate-binding network. J Biol Chem 2019; 294:18069-18076. [PMID: 31624150 PMCID: PMC6885649 DOI: 10.1074/jbc.ra119.010826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/14/2019] [Indexed: 01/08/2023] Open
Abstract
Lipoxygenases are widespread enzymes found in virtually all eukaryotes, including fungi, and, more recently, in prokaryotes. These enzymes act on long-chain polyunsaturated fatty acid substrates (C18 to C20), raising questions regarding how the substrate threads its way from solvent to the active site. Herein, we report a comparison of the temperature dependence of isotope effects on first- and second-order rate constants among single-site variants of the prototypic plant enzyme soybean lipoxygenase-1 substituted at amino acid residues inferred to impact substrate binding. We created 10 protein variants including four amino acid positions, Val-750, Ile-552, Ile-839, and Trp-500, located within a previously proposed substrate portal. The conversion of these bulky hydrophobic side chains to smaller side chains is concluded to increase the mobility of flanking helices, giving rise to increased off rates for substrate dissociation from the enzyme. In this manner, we identified a specific "binding network" that can regulate movement of the substrate from the solvent to the active site. Taken together with our previous findings on C-H and O2 activation of soybean lipoxygenase-1, these results support the emergence of multiple complementary networks within a single protein scaffold that modulate different steps along the enzymatic reaction coordinate.
Collapse
Affiliation(s)
- Shenshen Hu
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Adam R Offenbacher
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720; Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Edbert D Lu
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720.
| |
Collapse
|
5
|
Kumar A, Iyengar SS. Fragment-Based Electronic Structure for Potential Energy Surfaces Using a Superposition of Fragmentation Topologies. J Chem Theory Comput 2019; 15:5769-5786. [DOI: 10.1021/acs.jctc.9b00608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Anup Kumar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana-47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana-47405, United States
| |
Collapse
|
6
|
Mason JL, Topolski JE, Ewigleben J, Iyengar SS, Jarrold CC. Photoelectrons Are Not Always Quite Free. J Phys Chem Lett 2019; 10:144-149. [PMID: 30569715 DOI: 10.1021/acs.jpclett.8b03253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The photoelectron spectra of Sm2O- obtained over a range of photon energies exhibit anomalous changes in relative excited-state band intensities. Specifically, the excited-state transition intensities increase relative to the transition to the neutral ground state with decreasing photon energy, the opposite of what is expected from threshold effects. This phenomenon was previously observed in studies on several Sm-rich homo- and heterolanthanide oxides collected with two different harmonic outputs of a Nd:YAG (2.330 and 3.495 eV) [ J. Chem. Phys. 2017, 146, 194310]. We relate these anomalous intensities to populations of ground and excited anionic and neutrals states through the inspection of time-dependent perturbation theory within the adiabatic and sudden limits and for the first time show that transition intensities in photoelectron spectroscopy have a deep significance in gauging participation from excited states. We believe our results will have significance in the study of other electron-rich systems that have especially high density of accessible spin states.
Collapse
Affiliation(s)
- Jarrett L Mason
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| | - Josey E Topolski
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| | - Joshua Ewigleben
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| | - Srinivasan S Iyengar
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| | - Caroline Chick Jarrold
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| |
Collapse
|
7
|
Li P, Soudackov AV, Hammes-Schiffer S. Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer. J Phys Chem Lett 2018; 9:6444-6449. [PMID: 30359035 PMCID: PMC6402330 DOI: 10.1021/acs.jpclett.8b02945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Soybean lipoxygenase catalyzes a proton-coupled electron transfer (PCET) reaction and serves as a prototype for hydrogen tunneling in enzymes due to the unusually high kinetic isotope effect and significant modulation of the rate constant and kinetic isotope effect by mutation. Herein these experimental observations are interpreted in the context of changes to the substrate binding pocket in microsecond molecular dynamics simulations of wild-type and mutant soybean lipoxygenase. The binding pocket exhibits an hourglass shape with residues L546 and L754 bracketing the bottleneck, positioning the linoleic acid substrate for PCET. Mutation of I553 to less bulky residues slightly increases the width of the bottleneck and the volume of the binding pocket. Mutating L546 or L754 to a smaller residue also enlarges this width and volume, and mutating both has an even more dramatic effect. This analysis illustrates how mutation of the substrate binding pocket can be used as a strategy to tune the kinetics.
Collapse
Affiliation(s)
- Pengfei Li
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Alexander V. Soudackov
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| |
Collapse
|
8
|
Sankaralingam M, Lee YM, Karmalkar DG, Nam W, Fukuzumi S. A Mononuclear Non-heme Manganese(III)–Aqua Complex as a New Active Oxidant in Hydrogen Atom Transfer Reactions. J Am Chem Soc 2018; 140:12695-12699. [DOI: 10.1021/jacs.8b07772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Deepika G. Karmalkar
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Faculty of Science and Engineering, Meijo University, Nagoya, Aichi 468-8502, Japan
| |
Collapse
|
9
|
Li P, Soudackov AV, Hammes-Schiffer S. Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations. J Am Chem Soc 2018; 140:3068-3076. [PMID: 29392938 PMCID: PMC5849423 DOI: 10.1021/jacs.7b13642] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton donor-acceptor (C-O) distance and the proton coordinate, and the potential of mean force is computed as a function of the C-O distance, inherently including anharmonicity. The simulation results are used to calculate the kinetic isotope effects for the wild-type enzyme (WT) and the L546A/L754A double mutant (DM), which have been measured experimentally to be ∼80 and ∼700, respectively. The PCET reaction is found to be exoergic for WT and slightly endoergic for the DM, and the equilibrium C-O distance for the reactant is found to be ∼0.2 Å greater for the DM than for WT. The larger equilibrium distance for the DM, which is due mainly to less optimal substrate binding in the expanded binding cavity, is primarily responsible for its higher kinetic isotope effect. The calculated potentials of mean force are anharmonic and relatively soft at shorter C-O distances, allowing efficient thermal sampling of the shorter distances required for effective hydrogen tunneling. The primarily local electrostatic field at the transferring hydrogen is ∼100 MV/cm in the direction to facilitate proton transfer and increases dramatically as the C-O distance decreases. These simulations suggest that the overall protein environment is important for conformational sampling of active substrate configurations aligned for proton transfer, but the PCET reaction is influenced primarily by local electrostatic effects that facilitate conformational sampling of shorter proton donor-acceptor distances required for effective hydrogen tunneling.
Collapse
Affiliation(s)
- Pengfei Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave, Urbana, Illinois 61801; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Alexander V. Soudackov
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave, Urbana, Illinois 61801; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave, Urbana, Illinois 61801; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| |
Collapse
|
10
|
DeGregorio N, Iyengar SS. Efficient and Adaptive Methods for Computing Accurate Potential Surfaces for Quantum Nuclear Effects: Applications to Hydrogen-Transfer Reactions. J Chem Theory Comput 2017; 14:30-47. [DOI: 10.1021/acs.jctc.7b00927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole DeGregorio
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
11
|
Tikhonov IV, Moskalenko IV, Pliss EM, Fomich MA, Bekish AV, Shmanai VV. Kinetic isotope H/D effect in the oxidation of ethers of linoleic acid in solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793117030113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
12
|
Haycraft C, Li J, Iyengar SS. Efficient, “On-the-Fly”, Born–Oppenheimer and Car–Parrinello-type Dynamics with Coupled Cluster Accuracy through Fragment Based Electronic Structure. J Chem Theory Comput 2017; 13:1887-1901. [DOI: 10.1021/acs.jctc.6b01107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
13
|
Mittal M, Kumar RB, Balagunaseelan N, Hamberg M, Jegerschöld C, Rådmark O, Haeggström JZ, Rinaldo-Matthis A. Kinetic investigation of human 5-lipoxygenase with arachidonic acid. Bioorg Med Chem Lett 2016; 26:3547-51. [DOI: 10.1016/j.bmcl.2016.06.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 11/16/2022]
|
14
|
Li J, Haycraft C, Iyengar SS. Hybrid Extended Lagrangian, Post-Hartree–Fock Born–Oppenheimer ab Initio Molecular Dynamics Using Fragment-Based Electronic Structure. J Chem Theory Comput 2016; 12:2493-508. [DOI: 10.1021/acs.jctc.6b00001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| |
Collapse
|
15
|
Li J, Iyengar SS. Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique. J Chem Theory Comput 2015; 11:3978-91. [DOI: 10.1021/acs.jctc.5b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
| |
Collapse
|