1
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Zhu X, Iyengar SS. Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol. J Chem Theory Comput 2022; 18:5125-5144. [PMID: 35994592 DOI: 10.1021/acs.jctc.1c01241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over a series of publications we have introduced a graph-theoretic description for molecular fragmentation. Here, a system is divided into a set of nodes, or vertices, that are then connected through edges, faces, and higher-order simplexes to represent a collection of spatially overlapping and locally interacting subsystems. Each such subsystem is treated at two levels of electronic structure theory, and the result is used to construct many-body expansions that are then embedded within an ONIOM-scheme. These expansions converge rapidly with many-body order (or graphical rank) of subsystems and have been previously used for ab initio molecular dynamics (AIMD) calculations and for computing multidimensional potential energy surfaces. Specifically, in all these cases we have shown that CCSD and MP2 level AIMD trajectories and potential surfaces may be obtained at density functional theory cost. The approach has been demonstrated for gas-phase studies, for condensed phase electronic structure, and also for basis set extrapolation-based AIMD. Recently, this approach has also been used to derive new quantum-computing algorithms that enormously reduce the quantum circuit depth in a circuit-based computation of correlated electronic structure. In this publication, we introduce (a) a family of neural networks that act in parallel to represent, efficiently, the post-Hartree-Fock electronic structure energy contributions for all simplexes (fragments), and (b) a new k-means-based tessellation strategy to glean training data for high-dimensional molecular spaces and minimize the extent of training needed to construct this family of neural networks. The approach is particularly useful when coupled cluster accuracy is desired and when fragment sizes grow in order to capture nonlocal interactions accurately. The unique multidimensional k-means tessellation/clustering algorithm used to determine our training data for all fragments is shown to be extremely efficient and reduces the needed training to only 10% of data for all fragments to obtain accurate neural networks for each fragment. These fully connected dense neural networks are then used to extrapolate the potential energy surface for all molecular fragments, and these are then combined as per our graph-theoretic procedure to transfer the learning process to a full system energy for the entire AIMD trajectory at less than one-tenth the cost as compared to a regular fragmentation-based AIMD calculation.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
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2
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Dean JLS, Fournier JA. Vibrational Dynamics of the Intramolecular H-Bond in Acetylacetone Investigated with Transient and 2D IR Spectroscopy. J Phys Chem B 2022; 126:3551-3562. [PMID: 35536173 DOI: 10.1021/acs.jpcb.2c00793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acetylacetone (AcAc) has proven to be a fruitful but highly challenging model system for the experimental and computational interrogation of strong intramolecular hydrogen bonds. Key questions remain, however, regarding the identity of the minimum-energy structure of AcAc and the dynamics of intramolecular proton transfer. Here, we investigate the OH/OD stretch and bend regions of the enol tautomer of AcAc and its deuterated isotopologue with transient absorption and 2D IR spectroscopy. The OH bend region reveals a single dominant diagonal transition near 1625 cm-1 with intense cross peaks to lower-frequency modes, demonstrating highly mixed fingerprint transitions that contain OH bend character. The anharmonic coupling of the OH bend results in a highly elongated OH bend excited-state absorption transition that indicates a large manifold of OH bend overtone/combination bands in the OH stretch region that leads to strong bend-stretch Fermi resonance interactions. The OH and OD stretch regions consist of broad ground-state bleach signals, but there is no clear evidence of ω21 excited-state absorptions due to rapid population relaxation arising from strong intramolecular coupling to bending, fingerprint, and low-frequency H-bond modes. Orientational relaxation dynamics persist for timescales longer than the vibrational lifetimes, with polarization anisotropy components decaying within approximately 2 and 10 periods of the O-O oscillation for the OH and OD stretch, respectively. The significant isotopic dependence of the orientational dynamics is discussed in the context of intramolecular mode coupling, diffusional processes, and contributions from proton/deuteron transfer dynamics.
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Affiliation(s)
- Jessika L S Dean
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, United States 63130
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, United States 63130
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3
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Walker AR, Wu B, Meisner J, Fayer MD, Martínez TJ. Proton Transfer from a Photoacid to a Water Wire: First Principles Simulations and Fast Fluorescence Spectroscopy. J Phys Chem B 2021; 125:12539-12551. [PMID: 34743512 DOI: 10.1021/acs.jpcb.1c07254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We investigate photoinduced proton transfer between the photoacid 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular dynamics simulations. Photoexcitation causes rapid proton release from the HPTS hydroxyl. Previous experiments on HPTS/water described the progress from photoexcitation to proton diffusion using kinetic equations with two time constants. The shortest time constant has been interpreted as protonated and photoexcited HPTS evolving into an "associated" state, where the proton is "shared" between the HPTS hydroxyl and an originally hydrogen bonded water. The longer time constant has been interpreted as indicating evolution to a "solvent separated" state where the shared proton undergoes long distance diffusion. In this work, we refine the previous experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS. We find that the initial excitation results in rapid rearrangement of water, forming a strong hydrogen bonded network (a "water wire") around HPTS. HPTS then deprotonates in ≤3 ps, resulting in a proton that migrates back and forth along the wire before localizing on a single water molecule. We find a near linear relationship between the emission wavelength and proton-HPTS distance over the simulated time scale, suggesting that the emission wavelength can be used as a ruler for the proton distance. Our simulations reveal that the "associated" state corresponds to a water wire with a mobile proton and that the diffusion of the proton away from this water wire (to a generalized "solvent-separated" state) corresponds to the longest experimental time constant.
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Affiliation(s)
- Alice R Walker
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Boning Wu
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jan Meisner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Todd J Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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4
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Kumar A, DeGregorio N, Iyengar SS. Graph-Theory-Based Molecular Fragmentation for Efficient and Accurate Potential Surface Calculations in Multiple Dimensions. J Chem Theory Comput 2021; 17:6671-6690. [PMID: 34623129 DOI: 10.1021/acs.jctc.1c00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a multitopology molecular fragmentation approach, based on graph theory, to calculate multidimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory but at the density functional theory cost. A molecular assembly is coarse-grained into a set of graph-theoretic nodes that are then connected with edges to represent a collection of locally interacting subsystems up to an arbitrary order. Each of the subsystems is treated at two levels of electronic structure theory, the result being used to construct many-body expansions that are embedded within an ONIOM scheme. These expansions converge rapidly with the many-body order (or graphical rank) of subsystems and capture many-body interactions accurately and efficiently. However, multiple graphs, and hence multiple fragmentation topologies, may be defined in molecular configuration space that may arise during conformational sampling or from reactive, bond breaking and bond formation, events. Obtaining the resultant potential surfaces is an exponential scaling proposition, given the number of electronic structure computations needed. We utilize a family of graph-theoretic representations within a variational scheme to obtain multidimensional potential surfaces at a reduced cost. The fast convergence of the graph-theoretic expansion with increasing order of many-body interactions alleviates the exponential scaling cost for computing potential surfaces, with the need to only use molecular fragments that contain a fewer number of quantum nuclear degrees of freedom compared to the full system. This is because the dimensionality of the conformational space sampled by the fragment subsystems is much smaller than the full molecular configurational space. Additionally, we also introduce a multidimensional clustering algorithm, based on physically defined criteria, to reduce the number of energy calculations by orders of magnitude. The molecular systems benchmarked include coupled proton motion in protonated water wires. The potential energy surfaces and multidimensional nuclear eigenstates obtained are shown to be in very good agreement with those from explicit post-Hartree-Fock calculations that become prohibitive as the number of quantum nuclear dimensions grows. The developments here provide a rigorous and efficient alternative to this important chemical physics problem.
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Affiliation(s)
- Anup Kumar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - 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
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5
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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.
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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
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6
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Nava M, Makri N. Quantum-Classical Path Integral Simulation of Excess Proton Dynamics in a Water Dimer Embedded in the Gramicidin Channel. J Chem Theory Comput 2021; 17:627-638. [PMID: 33494606 DOI: 10.1021/acs.jctc.0c01012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use the quantum-classical path integral (QCPI) methodology to investigate the relaxation dynamics of an excess proton that has been inserted in a water dimer embedded in the gramicidin A channel at room temperature. We obtain one-dimensional potential slices for the quantum degree of freedom through a proper transformation to internal coordinates. Our results indicate that the proton transfer is driven by the oscillation of the oxygen pair, and that the transfer occurs primarily at single-well or nearby low-barrier configurations. Yet, we find that tunneling and zero-point energy lead to a significant acceleration of the proton transfer dynamics.
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Affiliation(s)
- Marco Nava
- Department of Chemistry, University of Illinois, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Nancy Makri
- Department of Chemistry, University of Illinois, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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7
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Li C, Requist R, Gross EKU. Density functional theory of electron transfer beyond the Born-Oppenheimer approximation: Case study of LiF. J Chem Phys 2018; 148:084110. [DOI: 10.1063/1.5011663] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chen Li
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany
| | - Ryan Requist
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany
| | - E. K. U. Gross
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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8
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Kumar A, Jash A, Dubey A, Bajpai A, Philip D, Bhargava K, Singh SK, Das M, Banerjee SS. Water mediated dielectric polarizability and electron charge transport properties of high resistance natural fibers. Sci Rep 2018; 8:2726. [PMID: 29426905 PMCID: PMC5807519 DOI: 10.1038/s41598-018-20313-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/18/2017] [Indexed: 11/09/2022] Open
Abstract
Recent studies showed that silk and human hair fibers develop thermoelectric properties at optimal water, temperature and light conditions. The nature of charge carriers and the role of water in mediating charge conduction in these fibers is an unexplored issue. By studying four different classes of natural fibers, viz., silk cocoon, human hair, jute and corn silk, we uncover their common electrical transport properties and its dependence on water concentration and temperature. All these fibers uniformly exhibit nonlinear, hysteretic current - voltage characteristics, which scale with water concentration. The optimal electrical conductivity shows thermally activated hopping transport mechanism. Scanning tunneling microscope (STM) and dielectric measurements of silk cocoon fibers showed the electronic density of states and dielectric properties of the hydrated medium enhances with water concentration. Electron paramagnetic resonance (EPR) study reveals that the charge carriers in these membranes are electronic in nature. Our results are explained through the mechanism of hopping of a Polaron, which is an electron surrounded by positive charge fluctuations created by water molecules. The mechanism unravels the peculiar role water plays in mediating electrical activity in these membranes and also opens the possibility for exploring such charge transport mechanism in other biological membranes.
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Affiliation(s)
- Ankit Kumar
- Department of Physics, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India
| | - Amit Jash
- Department of Physics, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India
| | - Amarish Dubey
- Design Program, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India
| | - Alok Bajpai
- Psychiatrist, Medical Centre, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India.
| | - Deepu Philip
- Design Program, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India.,Industrial and Management Engineering, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
| | | | | | - Mainak Das
- Design Program, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India. .,Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India.
| | - S S Banerjee
- Department of Physics, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India.
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9
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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
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10
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Rossi M, Ceriotti M, Manolopoulos DE. Nuclear Quantum Effects in H(+) and OH(-) Diffusion along Confined Water Wires. J Phys Chem Lett 2016; 7:3001-3007. [PMID: 27440483 DOI: 10.1021/acs.jpclett.6b01093] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The diffusion of protons and hydroxide ions along water wires provides an efficient mechanism for charge transport that is exploited by biological membrane channels and shows promise for technological applications such as fuel cells. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we focus on two aspects of this process that are often disregarded because of their high computational cost: the use of first-principles potential energy surfaces and the treatment of the nuclei as quantum particles. We consider proton and hydroxide ions in finite water wires using density functional theory augmented with an apolar cylindrical confining potential. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition that takes explicitly into account the delocalization of the charge in the Grotthus-like mechanism. We include nuclear quantum effects (NQEs) through the thermostated ring polymer molecular dynamics method and model finite system size effects by considering Langevin dynamics on the potential of mean force of the charged species, allowing us to extract the same "universal" diffusion coefficient from simulations with different wire sizes. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate water-water distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire.
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Affiliation(s)
- Mariana Rossi
- Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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11
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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
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12
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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
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13
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Isaev AN. Structure of a proton wire in the harmonic model with allowance for the interproton interaction for the first and second neighbors. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414120103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Theoretical investigation of hydrogen bonding interaction in H3O+(H2O)9 complex. J Mol Model 2014; 20:2480. [DOI: 10.1007/s00894-014-2480-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/28/2014] [Indexed: 11/24/2022]
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15
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Yamada A, Kojima H, Okazaki S. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water. J Chem Phys 2014; 141:084509. [DOI: 10.1063/1.4893933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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17
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Desai D, Wong B, Huang Y, Ye Q, Tang D, Guo H, Huang M, Timmins P. Surfactant-Mediated Dissolution of Metformin Hydrochloride Tablets: Wetting Effects Versus Ion Pairs Diffusivity. J Pharm Sci 2014; 103:920-6. [DOI: 10.1002/jps.23852] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/06/2013] [Accepted: 12/20/2013] [Indexed: 11/08/2022]
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18
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Karahka ML, Kreuzer HJ. Charge transport along proton wires. Biointerphases 2013; 8:13. [DOI: 10.1186/1559-4106-8-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/07/2013] [Indexed: 11/10/2022] Open
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19
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20
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Decornez H, Hammes-Schiffer S. Effects of Model Protein Environments on the Dynamics of Proton Wires. Isr J Chem 2013. [DOI: 10.1002/ijch.199900045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Chen D, Wei GW. Quantum dynamics in continuum for proton transport--generalized correlation. J Chem Phys 2012; 136:134109. [PMID: 22482542 DOI: 10.1063/1.3698598] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As a key process of many biological reactions such as biological energy transduction or human sensory systems, proton transport has attracted much research attention in biological, biophysical, and mathematical fields. A quantum dynamics in continuum framework has been proposed to study proton permeation through membrane proteins in our earlier work and the present work focuses on the generalized correlation of protons with their environment. Being complementary to electrostatic potentials, generalized correlations consist of proton-proton, proton-ion, proton-protein, and proton-water interactions. In our approach, protons are treated as quantum particles while other components of generalized correlations are described classically and in different levels of approximations upon simulation feasibility and difficulty. Specifically, the membrane protein is modeled as a group of discrete atoms, while ion densities are approximated by Boltzmann distributions, and water molecules are represented as a dielectric continuum. These proton-environment interactions are formulated as convolutions between number densities of species and their corresponding interaction kernels, in which parameters are obtained from experimental data. In the present formulation, generalized correlations are important components in the total Hamiltonian of protons, and thus is seamlessly embedded in the multiscale/multiphysics total variational model of the system. It takes care of non-electrostatic interactions, including the finite size effect, the geometry confinement induced channel barriers, dehydration and hydrogen bond effects, etc. The variational principle or the Euler-Lagrange equation is utilized to minimize the total energy functional, which includes the total Hamiltonian of protons, and obtain a new version of generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation. A set of numerical algorithms, such as the matched interface and boundary method, the Dirichlet to Neumann mapping, Gummel iteration, and Krylov space techniques, is employed to improve the accuracy, efficiency, and robustness of model simulations. Finally, comparisons between the present model predictions and experimental data of current-voltage curves, as well as current-concentration curves of the Gramicidin A channel, verify our new model.
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Affiliation(s)
- Duan Chen
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, USA
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22
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Qi SF, Wang XN, Yang ZZ, Xu XH. Evidence of direct formation of C8 adducts in carcinogenic reactions of arylnitrenium ions with purine nucleosides: Theoretical study of C8 deprotonation process. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.01.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Arabi AA, Matta CF. Effects of external electric fields on double proton transfer kinetics in the formic acid dimer. Phys Chem Chem Phys 2011; 13:13738-48. [DOI: 10.1039/c1cp20175a] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Isaev AN. The geometry and electronic structure of the ionic defect in a chain of water molecules between a donor and an acceptor. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2010. [DOI: 10.1134/s0036024410030179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Isaev AN. Quantum-chemical calculations of a long proton wire. Application of a harmonic model to analysis of the structure of an ionic defect in a water chain with an excess proton. J Phys Chem A 2010; 114:2201-12. [PMID: 20085360 DOI: 10.1021/jp908259p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum-chemical calculations of molecular complexes (NH(3))(3)Zn(2+)...(H(2)O)(n)...NH(3) (C(n), n = 11, 16, 21, and 30) simulating a proton wire donor-water chain-acceptor were carried out. Earlier found periodicity in the length of the O-H bonds in water chain is explained within the framework of a one-component harmonic model. In complexes C(n), the geometry and electronic structure of ionic defect in water chain with an excess proton were studied. Calculations carried out at ab initio (B3LYP/6-31+G**) and semiempirical (PM3) levels of theory predict different patterns of distribution of the O-H bonds lengths and positive charge on the H-bond hydrogen atoms in the region of ionic defect. The obtained data show how a length of water chain and position of a protonated water link in the chain influence the ionic defect structure. To describe the observed structures of ionic defect, the harmonic model was used and the role of parameters of the H-bonded chain was investigated. The performed analysis explains different mechanisms (concerted and stepwise) of proton transfer along the H-bonded chain derived from ab initio and semiempirical calculation schemes.
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Affiliation(s)
- Alexander N Isaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, 119991 Moscow, Russia.
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26
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Prakash M, Subramanian V, Gadre SR. Stepwise Hydration of Protonated Carbonic Acid: A Theoretical Study. J Phys Chem A 2009; 113:12260-75. [DOI: 10.1021/jp904576u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Prakash
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| | - Shridhar R. Gadre
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
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27
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Phillips LR, Cole CD, Hendershot RJ, Cotten M, Cross TA, Busath DD. Noncontact dipole effects on channel permeation. III. Anomalous proton conductance effects in gramicidin. Biophys J 2008; 77:2492-501. [PMID: 20540928 DOI: 10.1016/s0006-3495(99)77085-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/1998] [Accepted: 08/04/1999] [Indexed: 11/25/2022] Open
Abstract
Proton transport on water wires, of interest for many problems in membrane biology, is analyzed in side-chain analogs of gramicidin A channels. In symmetrical 0.1N HCl solutions, fluorination of channel Trp(11), Trp-(13), or Trp(15) side chains is found to inhibit proton transport, and replacement of one or more Trps with Phe enhances proton transport, the opposite of the effects on K(+) transport in lecithin bilayers. The current-voltage relations are superlinear, indicating that some membrane field-dependent process is rate limiting. The interfacial dipole effects are usually assumed to affect the rate of cation translocation across the channel. For proton conductance, however, water reorientation after proton translocation is anticipated to be rate limiting. We propose that the findings reported here are most readily interpreted as the result of dipole-dipole interactions between channel waters and polar side chains or lipid headgroups. In particular, if reorientation of the water column begins with the water nearest the channel exit, this hypothesis explains the negative impact of fluorination and the positive impact of headgroup dipole on proton conductance.
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Affiliation(s)
- L R Phillips
- Zoology Department, Brigham Young University, Provo, Utah 84062, USA
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28
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Dudev T, Lim C. Metal binding affinity and selectivity in metalloproteins: insights from computational studies. Annu Rev Biophys 2008; 37:97-116. [PMID: 18573074 DOI: 10.1146/annurev.biophys.37.032807.125811] [Citation(s) in RCA: 182] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review highlights insights gained from computational studies on protein-metal recognition. We systematically dissect the various factors governing metal binding affinity and selectivity in proteins starting from (a) the intrinsic properties of the metal and neighboring metal cations (if present), to (b) the primary coordination sphere, (c) the second coordination shell, (d) the protein matrix, (e) the bulk solvent, and (f) competing non-protein ligands from the surrounding biological environment. The results herein reveal the fundamental principles and the molecular bases underlying protein-metal recognition, which serve as a guide to engineer novel metalloproteins with programmed properties.
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
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29
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Vendrell O, Gelabert R, Moreno M, Lluch JM. A Potential Energy Function for Heterogeneous Proton-Wires. Ground and Photoactive States of the Proton-Wire in the Green Fluorescent Protein. J Chem Theory Comput 2008; 4:1138-50. [DOI: 10.1021/ct800075w] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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30
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Thomaeus A, Naworyta A, Mowbray SL, Widersten M. Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability. Protein Sci 2008; 17:1275-84. [PMID: 18515642 DOI: 10.1110/ps.034173.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro(186), Leu(266), His(269), and the His(153) imidazole. The hydroxyl of Tyr(149) is also an integrated component of the chain, which leads to the hydroxyl of Tyr(154). Available data suggest that Tyr(154) functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 A resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k (cat)/K (M) was similar or slightly increased compared with the wild-type reactions. k (cat) for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K (M). Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k (cat) but lowered thermostability.
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Affiliation(s)
- Ann Thomaeus
- Department of Biochemistry and Organic Chemistry, Uppsala University, SE-751 23 Uppsala, Sweden
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31
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Li X, Moore DT, Iyengar SS. Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: Case study of the proton-bound dimethyl ether dimer. J Chem Phys 2008; 128:184308. [DOI: 10.1063/1.2903446] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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32
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Stoyanov E, Stoyanova I, Reed C. IR Spectroscopic Properties of H(MeOH)n+ Clusters in the Liquid Phase: Evidence for a Proton Wire. Chemistry 2008; 14:3596-604. [DOI: 10.1002/chem.200701746] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Isaev AN. Cooperative interactions of hydrogen bonds in proton-transfer processes involving water molecules. Simulation of biochemical systems. RUSS J GEN CHEM+ 2008. [DOI: 10.1134/s1070363208040324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Yamada A, Okazaki S. A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics. J Chem Phys 2008; 128:044507. [DOI: 10.1063/1.2825611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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The Study of Dynamically Averaged Vibrational Spectroscopy of Atmospherically Relevant Clusters Using Ab Initio Molecular Dynamics in Conjunction with Quantum Wavepackets. ADVANCES IN QUANTUM CHEMISTRY 2008. [DOI: 10.1016/s0065-3276(07)00216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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36
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Vendrell O, Meyer HD. A proton between two waters: insight from full-dimensional quantum-dynamics simulations of the [H2O–H–OH2]+ cluster. Phys Chem Chem Phys 2008; 10:4692-703. [DOI: 10.1039/b807317a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Isaev AN. The wave nature of the protonic conductivity mechanism in the active site of carboanhydrase. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407060155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Vendrell O, Meyer HD. Proton conduction along a chain of water molecules. Development of a linear model and quantum dynamical investigations using the multiconfiguration time-dependent Hartree method. J Chem Phys 2006; 122:104505. [PMID: 15836330 DOI: 10.1063/1.1859274] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Proton transfer along a chain of water molecules is discussed. A linear model for such a chain is developed and its parameters are determined by comparison to quantum chemistry calculations. Fully quantum mechanical dynamical simulations on the translocation process are performed for different chain lengths, with up to five water molecules. We found that tunneling is important for the proton-transfer process. Furthermore, translocation is accomplished through a strongly correlated motion involving both hydrogen and oxygen atoms. An approximate treatment, which limits or even neglects this correlation, may lead to severely incorrect results.
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Affiliation(s)
- Oriol Vendrell
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany.
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39
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Yamada A, Okazaki S. A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: An analysis of tunneling and thermal activation. J Chem Phys 2006; 124:94110. [PMID: 16526848 DOI: 10.1063/1.2172595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.
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Affiliation(s)
- Atsushi Yamada
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
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40
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Li G, Cui Q. Direct determination of reaction paths and stationary points on potential of mean force surfaces. J Mol Graph Model 2005; 24:82-93. [PMID: 16005650 DOI: 10.1016/j.jmgm.2005.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2005] [Indexed: 11/23/2022]
Abstract
A simulation approach is introduced for directly determining reaction paths and stationary points on potential of mean force (PMF) surfaces associated with molecular events that occur in complex environments. The nudged elastic band approach was employed to search for steepest descent paths on the PMF surface using the relevant PMF derivatives from a series of local simulations. The steepest descent path on the PMF surface corresponds to the minimum PMF path (i.e. the path with the lowest local PMF barrier), which contains important information about stationary points (e.g. saddle points) on the PMF surface, which in turn can provide useful insights into the thermodynamics and kinetics for the process of interest. By working with the PMF defined in a low-dimensional sub-space rather than a potential energy function of full molecular dimensionality, the main features of the process under study are concisely represented and the orthogonal degrees of freedom are adequately sampled with the appropriate canonical distribution at the desired temperature (e.g. 300 K). Therefore, minimum PMF paths carry statistically meaningful mechanistic information and are complementary to reaction paths of full molecular dimensionality proposed in previous studies. The NEB based path optimization method is direct in the sense that no information regarding the global PMF surface is necessary for the determination of the local reaction path and stationary points along this path. Since only low-dimensional quantities (paths) are searched for, the PMF-path method is expected to scale better in terms of dimension of the PMF sub-space than those aims to fully explore multi-dimensional PMF surfaces. Test applications on simple molecular systems, the alanine di-peptide in vacuum and in solution and a micro-solvated proton-wire, indicate that reliable PMF paths can be determined for both conformational isomerization and chemical reaction processes. However, highly accurate PMF derivatives are required for determining more quantitative observables, such as the free energy profile along the minimum PMF path. Therefore, effective numerical algorithms for calculating local PMF derivatives and systematic protocols for defining the relevant sub-space are the main focus in the near future. Finally, we emphasize that the minimum PMF path defined here includes thermal (e.g. entropic) effects associated with the orthogonal degrees of freedom, but finite kinetic energies associated with the PMF degrees of freedom are not included; this can be improved by adopting a different definition of the reaction path, such as the maximum flux path, on the PMF surface, or thermally sampling all degrees of freedom orthogonal to the one-dimensional path.
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Affiliation(s)
- Guohui Li
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
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41
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Iyengar SS. Dynamical effects on vibrational and electronic spectra of hydroperoxyl radical water clusters. J Chem Phys 2005; 123:084310. [PMID: 16164294 DOI: 10.1063/1.2006674] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We have carried out ab initio molecular-dynamics studies on hydroperoxyl water clusters. Our studies are complemented by optimization, frequency, and excited-state calculations. The three main results we obtained are (a) the dynamically averaged energy gap between the highest-occupied molecular orbital and the lowest-unoccupied molecular orbital monotonically decreases as the number of water molecules is increased in a hydroperoxyl water cluster system, (b) the dynamical averaging of the potential-energy surface at finite temperature broadens the electronic excitation spectrum and changes the infrared spectrum in nontrivial ways, and (c) the structural analysis of our dynamics simulation indicates that the oxygen-oxygen distance in a solvated hydroperoxyl-water cluster is very similar to that found in protonated water clusters (Zundel: H5O2+) inspite of the fact that the latter possesses a positive charge and the hydroperoxyl-water cluster does not. Dynamical charge analysis and the weak acidity of HO2 are used to justify this result.
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Affiliation(s)
- Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA.
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42
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Iyengar SS, Petersen MK, Day TJF, Burnham CJ, Teige VE, Voth GA. The properties of ion-water clusters. I. The protonated 21-water cluster. J Chem Phys 2005; 123:084309. [PMID: 16164293 DOI: 10.1063/1.2007628] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ab initio atom-centered density-matrix propagation approach and the multistate empirical valence bond method have been employed to study the structure, dynamics, and rovibrational spectrum of a hydrated proton in the "magic" 21 water cluster. In addition to the conclusion that the hydrated proton tends to reside on the surface of the cluster, with the lone pair on the protonated oxygen pointing "outwards," it is also found that dynamical effects play an important role in determining the vibrational properties of such clusters. This result is used to analyze and complement recent experimental and theoretical studies.
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Affiliation(s)
- Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, USA.
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43
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Moss ML, Moss-Salentijn L, Hasselgren G, Ling H. A quantum biological hypothesis of human secondary dentinogenesis. Med Hypotheses 2004; 64:479-86. [PMID: 15617853 DOI: 10.1016/j.mehy.2004.07.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 07/05/2004] [Indexed: 11/30/2022]
Abstract
It is hypothesized that human coronal secondary dentin (SD) is a final classical mechanical (CM) response to a chain of prior quantum mechanical (QM) transductions of the information of initial CM occlusal loadings of enamel. Such CM energy is transduced into QM quanta (as protons) that are translocated centripetally via clustered water (CW), (as "proton wires"), that is structurally related to both enamel prism sheath and hydroxyapatite crystal hydration shells. These quanta pass into odontoblastic cell processes (OP), lying within dentinal tubules (DT). OP's contain abundant parallel arrays of cylindrical microtubules (MT). These are the sites of two further CW-related QM events: (i) proton translocation associated with conformal changes of MT tubulin protein dimers; and (ii) coherent energetic oscillations within the CW filling the MT's hollow cores. Finally, these quanta pass into the odontoblastic soma, where QM wave function collapse transduces this information into a final CM state that initiates the processes of SD formation. A critical portion of this hypothesis may be experimentally tested.
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Affiliation(s)
- M L Moss
- College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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44
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Chou T. Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport. Biophys J 2004; 86:2827-36. [PMID: 15111400 PMCID: PMC1304152 DOI: 10.1016/s0006-3495(04)74335-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A discrete multistate kinetic model for water-wire proton transport is constructed and analyzed using Monte Carlo simulations. In the model, each water molecule can be in one of three states: oxygen lone-pairs pointing leftward, pointing rightward, or protonated (H(3)O(+)). Specific rules for transitions among these states are defined as protons hop across successive water oxygens. Our model also includes water-channel interactions that preferentially align the water dipoles, nearest-neighbor dipolar coupling interactions, and Coulombic repulsion. Extensive Monte Carlo simulations were performed and the observed qualitative physical behaviors discussed. We find the parameters that allow the model to exhibit superlinear and sublinear current-voltage relationships, and show why alignment fields, whether generated by interactions with the pore interior or by membrane potentials, always decrease the proton current. The simulations also reveal a "lubrication" mechanism that suppresses water dipole interactions when the channel is multiply occupied by protons. This effect can account for an observed sublinear-to-superlinear transition in the current-voltage relationship.
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Affiliation(s)
- Tom Chou
- Department of Biomathematics and the Institute for Pure and Applied Mathematics, Los Angeles, California 90095-1766, USA.
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45
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Theoretical Study of Multidimensional Proton Tunnelling in Benzoic Acid Dimer. Int J Mol Sci 2003. [DOI: 10.3390/i4070422] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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46
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Abstract
Proton channels exist in a wide variety of membrane proteins where they transport protons rapidly and efficiently. Usually the proton pathway is formed mainly by water molecules present in the protein, but its function is regulated by titratable groups on critical amino acid residues in the pathway. All proton channels conduct protons by a hydrogen-bonded chain mechanism in which the proton hops from one water or titratable group to the next. Voltage-gated proton channels represent a specific subset of proton channels that have voltage- and time-dependent gating like other ion channels. However, they differ from most ion channels in their extraordinarily high selectivity, tiny conductance, strong temperature and deuterium isotope effects on conductance and gating kinetics, and insensitivity to block by steric occlusion. Gating of H(+) channels is regulated tightly by pH and voltage, ensuring that they open only when the electrochemical gradient is outward. Thus they function to extrude acid from cells. H(+) channels are expressed in many cells. During the respiratory burst in phagocytes, H(+) current compensates for electron extrusion by NADPH oxidase. Most evidence indicates that the H(+) channel is not part of the NADPH oxidase complex, but rather is a distinct and as yet unidentified molecule.
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Affiliation(s)
- Thomas E Decoursey
- Department of Molecular Biophysics and Physiology, Rush Presbyterian St. Luke's Medical Center, Chicago, Illinois 60612, USA.
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47
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Zhang C, Lindan PJD. Multilayer water adsorption on rutile TiO2(110): A first-principles study. J Chem Phys 2003. [DOI: 10.1063/1.1543983] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Cui Q, Karplus M. Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase. J Phys Chem B 2003. [DOI: 10.1021/jp021931v] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, and Laboratoire de Chimie Biophysique, ISIS, Universitè Louis Pasteur, 67000 Strasbourg, France
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, and Laboratoire de Chimie Biophysique, ISIS, Universitè Louis Pasteur, 67000 Strasbourg, France
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49
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Wójcik MJ, Tatara W, Ikeda S. Theoretical study of multidimensional proton tunneling in the hydrogen carbonate dimer ion [(HCO3)2]2−. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(02)00251-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Pomès R, Roux B. Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophys J 2002; 82:2304-16. [PMID: 11964221 PMCID: PMC1302023 DOI: 10.1016/s0006-3495(02)75576-8] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The conduction of protons in the hydrogen-bonded chain of water molecules (or "proton wire") embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a "hop-and-turn" or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H+) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H+ is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H+, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.
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Affiliation(s)
- Régis Pomès
- Structural Biology and Biochemistry, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1X8, Canada.
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