1
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Pham BQ, Carrington L, Tiwari A, Leang SS, Alkan M, Bertoni C, Datta D, Sattasathuchana T, Xu P, Gordon MS. Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller-Plesset perturbation method. J Chem Phys 2023; 158:2887208. [PMID: 37114705 DOI: 10.1063/5.0143424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller-Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ∼0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | | | | | - Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Colleen Bertoni
- Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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2
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Clemente CM, Capece L, Martí MA. Best Practices on QM/MM Simulations of Biological Systems. J Chem Inf Model 2023; 63:2609-2627. [PMID: 37100031 DOI: 10.1021/acs.jcim.2c01522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
During the second half of the 20th century, following structural biology hallmark works on DNA and proteins, biochemists shifted their questions from "what does this molecule look like?" to "how does this process work?". Prompted by the theoretical and practical developments in computational chemistry, this led to the emergence of biomolecular simulations and, along with the 2013 Nobel Prize in Chemistry, to the development of hybrid QM/MM methods. QM/MM methods are necessary whenever the problem we want to address involves chemical reactivity and/or a change in the system's electronic structure, with archetypal examples being the studies of an enzyme's reaction mechanism and a metalloprotein's active site. In the last decades QM/MM methods have seen an increasing adoption driven by their incorporation in widely used biomolecular simulation software. However, properly setting up a QM/MM simulation is not an easy task, and several issues need to be properly addressed to obtain meaningful results. In the present work, we describe both the theoretical concepts and practical issues that need to be considered when performing QM/MM simulations. We start with a brief historical perspective on the development of these methods and describe when and why QM/MM methods are mandatory. Then we show how to properly select and analyze the performance of the QM level of theory, the QM system size, and the position and type of the boundaries. We show the relevance of performing prior QM model system (or QM cluster) calculations in a vacuum and how to use the corresponding results to adequately calibrate those derived from QM/MM. We also discuss how to prepare the starting structure and how to select an adequate simulation strategy, including those based on geometry optimizations as well as free energy methods. In particular, we focus on the determination of free energy profiles using multiple steered molecular dynamics (MSMD) combined with Jarzynski's equation. Finally, we describe the results for two illustrative and complementary examples: the reaction performed by chorismate mutase and the study of ligand binding to hemoglobins. Overall, we provide many practical recommendations (or shortcuts) together with important conceptualizations that we hope will encourage more and more researchers to incorporate QM/MM studies into their research projects.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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3
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Pham BQ, Alkan M, Gordon MS. Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions. J Chem Theory Comput 2023; 19:2213-2221. [PMID: 37011288 DOI: 10.1021/acs.jctc.2c01137] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
A framework to offload four-index two-electron repulsion integrals to graphical processing units (GPUs) using OpenMP is discussed. The method has been applied to the Fock build for low angular momentum s and p functions in both the restricted Hartree-Fock (RHF) and in the effective fragment molecular orbital (EFMO) framework. Benchmark calculations for the GPU code for the pure RHF method show an increasing speedup relative to the existing OpenMP CPU code in GAMESS from 1.04 to 52× for clusters of 70-569 water molecules. The parallel efficiency on 24 NVIDIA V100 GPU boards also increases when increasing the system size: from 75 to 94% for water clusters that contain 303-1120 molecules. In the EFMO framework, the GPU Fock build shows a high linear scalability up to 4608 V100s with a parallel efficiency of 96% for calculations on a solvated mesoporous silica nanoparticle system with ∼67,000 basis functions.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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4
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Lim H, Jeon HN, Rhee JK, Oh B, No KT. Quantum computational study of chloride attack on chloromethane for chemical accuracy and quantum noise effects with UCCSD and k-UpCCGSD ansatzes. Sci Rep 2022; 12:7495. [PMID: 35523939 PMCID: PMC9076662 DOI: 10.1038/s41598-022-11537-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
Quantum computing is expected to play an important role in solving the problem of huge computational costs in various applications by utilizing the collective properties of quantum states, including superposition, interference, and entanglement, to perform computations. Quantum mechanical (QM) methods are candidates for various applications and can provide accurate absolute energy calculations in structure-based methods. QM methods are powerful tools for describing reaction pathways and their potential energy surfaces (PES). In this study, we applied quantum computing to describe the PES of the bimolecular nucleophilic substitution (SN2) reaction between chloromethane and chloride ions. We performed noiseless and noise simulations using quantum algorithms and compared the accuracy and noise effects of the ansatzes. In noiseless simulations, the results from UCCSD and k-UpCCGSD are similar to those of full configurational interaction (FCI) with the same active space, which indicates that quantum algorithms can describe the PES of the SN2 reaction. In noise simulations, UCCSD is more susceptible to quantum noise than k-UpCCGSD. Therefore, k-UpCCGSD can serve as an alternative to UCCSD to reduce quantum noisy effects in the noisy intermediate-scale quantum era, and k-UpCCGSD is sufficient to describe the PES of the SN2 reaction in this work. The results showed the applicability of quantum computing to the SN2 reaction pathway and provided valuable information for structure-based molecular simulations with quantum computing.
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Affiliation(s)
- Hocheol Lim
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon, Republic of Korea.,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon, Republic of Korea.,Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hyeon-Nae Jeon
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | | | - Byungdu Oh
- Baobab AiBIO Co., Ltd., Incheon, Republic of Korea. .,SKKU Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, Republic of Korea.
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon, Republic of Korea. .,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon, Republic of Korea. .,Baobab AiBIO Co., Ltd., Incheon, Republic of Korea.
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5
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Raju DR, Kumar A, BK N, Shetty A, PS A, Kumar RP, Lalitha R, Sigamani G. Extensive modelling and quantum chemical study of sterol C-22 desaturase mechanism: A commercially important cytochrome P450 family. Catal Today 2021. [DOI: 10.1016/j.cattod.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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6
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Abstract
Computational methods for modeling biochemical processes implemented in GAMESS package are reviewed; in particular, quantum mechanics combined with molecular mechanics (QM/MM), semi-empirical, and fragmentation approaches. A detailed summary of capabilities is provided for the QM/MM implementation in QuanPol program and the fragment molecular orbital (FMO) method. Molecular modeling and visualization packages useful for biochemical simulations with GAMESS are described. GAMESS capabilities with corresponding references are tabulated for reader's convenience.
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7
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Current and Future Challenges in Modern Drug Discovery. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2114:1-17. [PMID: 32016883 DOI: 10.1007/978-1-0716-0282-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Drug discovery is an expensive, time-consuming, and risky business. To avoid late-stage failure, learnings from past projects and the development of new approaches are crucial. New modalities and emerging new target spaces allow the exploration of unprecedented indications or to address so far undrugable targets. Late-stage attrition is usually attributed to the lack of efficacy or to compound-related safety issues. Efficacy has been shown to be related to a strong genetic link to human disease, a better understanding of the target biology, and the availability of biomarkers to bridge from animals to humans. Compound safety can be improved by ligand optimization, which is becoming increasingly demanding for difficult targets. Therefore, new strategies include the design of allosteric ligands, covalent binders, and other modalities. Design methods currently heavily rely on artificial intelligence and advanced computational methods such as free energy calculations and quantum chemistry. Especially for quantum chemical methods, a more detailed overview is given in this chapter.
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8
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Kim Y, Bui Y, Tazhigulov RN, Bravaya KB, Slipchenko LV. Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database. J Chem Theory Comput 2020; 16:7735-7747. [PMID: 33236635 DOI: 10.1021/acs.jctc.0c00758] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as "flexible EFP", is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.
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Affiliation(s)
- Yongbin Kim
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yen Bui
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruslan N Tazhigulov
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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9
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Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method. Methods Mol Biol 2020. [PMID: 32016888 DOI: 10.1007/978-1-0716-0282-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent development of the fragment molecular orbital (FMO) method related to energy gradients, geometry optimization, transition state search, and chemical reaction mapping is summarized. The frozen domain formulation of FMO is introduced in detail, and the structure of related GAMESS input files for FMO is described.
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10
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Pham BQ, Gordon MS. Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid-Distributed/Shared Memory Programming Model. J Chem Theory Comput 2020; 16:1039-1054. [PMID: 31899632 DOI: 10.1021/acs.jctc.9b01082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The fully analytic gradient of the second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity (RI) approximation in the fragment molecular orbital (FMO) framework is derived and implemented using a hybrid multilevel parallel programming model, a combination of the general distributed data interface (GDDI) and the OpenMP API. The FMO/MP2 analytic gradient contains three parts, i.e., the internal fragment component, the electrostatic potential (ESP) component, and the response terms. The RI approximation is applied to the internal fragment MP2 gradient term, whose MP2 densities and monomer MP2 Lagrangians are shared with the ESP and the response terms. The FMO/RI-MP2 analytic gradient implementation is validated against the numerical gradient (with errors ∼10-6-10-5 Hartree/Bohr) and the energy conservation in molecular dynamics (MD) simulations using NVE ensembles. The RI approximation introduces an error of ∼10-5 Hartree/Bohr with a speedup of 4.0-8.0× compared with the currently available GDDI FMO/MP2 gradient. The node linear scaling of the fragmentation framework due to multilevel parallelism is well-preserved and is demonstrated in single-point gradient calculations of large water clusters (e.g., 1120 and 2165 molecules) using 300-800 KNL compute nodes with a parallel efficiency of more than 90%.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States
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11
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Gupta AK, Thapa B, Raghavachari K. Exploring Reaction Energy Profiles Using the Molecules-in-Molecules Fragmentation-Based Approach. J Chem Theory Comput 2019; 15:3991-4002. [PMID: 31181886 DOI: 10.1021/acs.jctc.9b00152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Molecules-in-Molecules (MIM) fragmentation-based approach has been successfully used in previous studies to obtain the energies, optimized geometries, and spectroscopic properties of large molecular systems. The present work delineates a protocol to study the potential energy profiles for multistep chemical reactions using the MIM methodology. In a complex multistep chemical reaction, the fragmentation scheme needs to be changed as the reacting species transition into a new reaction step, resulting in a discontinuity in the potential energy curve of the reaction. In our approach, the fragmentation scheme for a particular step in a reaction is chosen on the basis of the nature of the bonding changes associated with that step. Thus, the reactant, transition state, and product are treated consistently throughout the reaction step, leading to an accurate energy barrier for that step. The discontinuity now occurs in describing the energies of reaction intermediates at the transition point between two reaction steps that are treated by two different fragmentation schemes. To address this issue, we propose a systematic procedure for obtaining continuous potential energy curves that are least shifted from their initial positions. The corrected MIM potential energy curves are continuous with activation energies preserved. Following this approach, energy profiles of complex reactions involving large molecular species can be obtained at high levels of theory with a reasonable computational cost.
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Affiliation(s)
- Ankur Kumar Gupta
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Bishnu Thapa
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Krishnan Raghavachari
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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12
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Okiyama Y, Watanabe C, Fukuzawa K, Mochizuki Y, Nakano T, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies. J Phys Chem B 2018; 123:957-973. [PMID: 30532968 DOI: 10.1021/acs.jpcb.8b09326] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment molecular orbital (FMO) methodology in solution: coupling with an implicit solvent model based on the Poisson-Boltzmann surface area called as FMO-PBSA. We investigated the solvent effects on practical and heterogeneous targets with uneven exposure to solvents unlike deoxyribonucleic acid analyzed in our recent study. Interfragment interaction energy (IFIE) and its decomposition analyses by FMO-PBSA revealed solvent-screening mechanisms that affect local stability inside ubiquitin protein: the screening suppresses excessiveness in bare charge-charge interactions and enables an intuitive IFIE analysis. The electrostatic character and associated solvation free energy also give consistent results as a whole to previous studies on the explicit solvent model. Moreover, by using the estrogen receptor alpha (ERα) protein bound to ligands, we elucidated the importance of specific interactions that depend on the electric charge and activatability as agonism/antagonism of the ligand while estimating the influences of the implicit solvent on the ligand and helix-12 bindings. The predicted ligand-binding affinities of bioactive compounds to ERα also show a good correlation with their in vitro activities. The FMO-PBSA approach would thus be a promising tool both for biological and pharmaceutical research targeting proteins.
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Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Chiduru Watanabe
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,RIKEN Center for Biosystems Dynamics Research , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Faculty of Pharmaceutical Sciences , Hoshi University , 2-4-41 Ebara , Shinagawa-ku, Tokyo 142-8501 , Japan
| | - Yuji Mochizuki
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Department of Chemistry and Research Center for Smart Molecules, Faculty of Science , Rikkyo University , 3-34-1 Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Tatsuya Nakano
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics , Kobe University , 1-1 Rokkodai, Nada-ku, Kobe , Hyogo 657-8501 , Japan
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13
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Okiyama Y, Nakano T, Watanabe C, Fukuzawa K, Mochizuki Y, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study. J Phys Chem B 2018; 122:4457-4471. [DOI: 10.1021/acs.jpcb.8b01172] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tatsuya Nakano
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Chiduru Watanabe
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuji Mochizuki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
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14
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Xu P, Guidez EB, Bertoni C, Gordon MS. Perspective:Ab initioforce field methods derived from quantum mechanics. J Chem Phys 2018. [DOI: 10.1063/1.5009551] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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15
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Fedorov DG. The fragment molecular orbital method: theoretical development, implementation in
GAMESS
, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1322] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD‐FMat)National Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
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16
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Yan X, Li X, Zhang C, Xu Y, Cooks RG. Ambient Ionization Mass Spectrometry Measurement of Aminotransferase Activity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1175-1181. [PMID: 28144898 DOI: 10.1007/s13361-016-1591-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/03/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
A change in enzyme activity has been used as a clinical biomarker for diagnosis and is useful in evaluating patient prognosis. Current laboratory measurements of enzyme activity involve multi-step derivatization of the reaction products followed by quantitative analysis of these derivatives. This study simplified the reaction systems by using only the target enzymatic reaction and directly detecting its product. A protocol using paper spray mass spectrometry for identifying and quantifying the reaction product has been developed. Evaluation of the activity of aspartate aminotransferase (AST) was chosen as a proof-of-principle. The volume of sample needed is greatly reduced compared with the traditional method. Paper spray has a desalting effect that avoids sprayer clogging problems seen when examining serum samples by nanoESI. This very simple method does not require sample pretreatment and additional derivatization reactions, yet it gives high quality kinetic data, excellent limits of detection (60 ppb from serum), and coefficients of variation <10% in quantitation. Graphical Abstract ᅟ.
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Affiliation(s)
- Xin Yan
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Xin Li
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chengsen Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yang Xu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- College of Life Sciences, Jilin University, Changchun, China
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
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17
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Pruitt SR, Steinmann C. Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method. J Phys Chem A 2017; 121:1797-1807. [DOI: 10.1021/acs.jpca.6b12830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Spencer R. Pruitt
- Academic & Research Computing, Worcester Polytechnic Institute, Worcester, Massachusetts 01602, United States
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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18
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Nakata H, Fedorov DG. Efficient Geometry Optimization of Large Molecular Systems in Solution Using the Fragment Molecular Orbital Method. J Phys Chem A 2016; 120:9794-9804. [DOI: 10.1021/acs.jpca.6b09743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroya Nakata
- Department
of Fundamental Technology Research, R and D Center Kagoshima, Kyocera, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - Dmitri G. Fedorov
- Research
Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
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19
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Gurunathan PK, Acharya A, Ghosh D, Kosenkov D, Kaliman I, Shao Y, Krylov AI, Slipchenko LV. Extension of the Effective Fragment Potential Method to Macromolecules. J Phys Chem B 2016; 120:6562-74. [PMID: 27314461 DOI: 10.1021/acs.jpcb.6b04166] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.
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Affiliation(s)
| | - Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Debashree Ghosh
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Dmytro Kosenkov
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry and Physics, Monmouth University , West Long Branch, New Jersey 07764, United States
| | - Ilya Kaliman
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Yihan Shao
- Q-Chem Inc. , 6601 Owens Drive, Suite 105 Pleasanton, California 94588, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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20
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Nakata H, Fedorov DG, Nagata T, Kitaura K, Nakamura S. Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method. J Chem Theory Comput 2015; 11:3053-64. [DOI: 10.1021/acs.jctc.5b00277] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research
Cluster for Innovation, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Takeshi Nagata
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research
Cluster for Innovation, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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21
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Fedorov DG, Asada N, Nakanishi I, Kitaura K. The use of many-body expansions and geometry optimizations in fragment-based methods. Acc Chem Res 2014; 47:2846-56. [PMID: 25144610 DOI: 10.1021/ar500224r] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conspectus Chemists routinely work with complex molecular systems: solutions, biochemical molecules, and amorphous and composite materials provide some typical examples. The questions one often asks are what are the driving forces for a chemical phenomenon? How reasonable are our views of chemical systems in terms of subunits, such as functional groups and individual molecules? How can one quantify the difference in physicochemical properties of functional units found in a different chemical environment? Are various effects on functional units in molecular systems additive? Can they be represented by pairwise potentials? Are there effects that cannot be represented in a simple picture of pairwise interactions? How can we obtain quantitative values for these effects? Many of these questions can be formulated in the language of many-body effects. They quantify the properties of subunits (fragments), referred to as one-body properties, pairwise interactions (two-body properties), couplings of two-body interactions described by three-body properties, and so on. By introducing the notion of fragments in the framework of quantum chemistry, one obtains two immense benefits: (a) chemists can finally relate to quantum chemistry, which now speaks their language, by discussing chemically interesting subunits and their interactions and (b) calculations become much faster due to a reduced computational scaling. For instance, the somewhat academic sounding question of the importance of three-body effects in water clusters is actually another way of asking how two hydrogen bonds affect each other, when they involve three water molecules. One aspect of this is the many-body charge transfer (CT), because the charge transfers in the two hydrogen bonds are coupled to each other (not independent). In this work, we provide a generalized view on the use of many-body expansions in fragment-based methods, focusing on the general aspects of the property expansion and a contraction of a many-body expansion in a formally two-body series, as exemplified in the development of the fragment molecular orbital (FMO) method. Fragment-based methods have been very successful in delivering the properties of fragments, as well as the fragment interactions, providing insights into complex chemical processes in large molecular systems. We briefly review geometry optimizations performed with fragment-based methods and present an efficient geometry optimization method based on the combination of FMO with molecular mechanics (MM), applied to the complex of a subunit of protein kinase 2 (CK2) with a ligand. FMO results are discussed in comparison with experimental and MM-optimized structures.
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Affiliation(s)
- Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Naoya Asada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kinki University, 3-4-1,
Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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22
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Derivatives of the approximated electrostatic potentials in unrestricted Hartree–Fock based on the fragment molecular orbital method and an application to polymer radicals. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1477-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Luehr N, Markland TE, Martínez TJ. Multiple time step integrators in ab initio molecular dynamics. J Chem Phys 2014; 140:084116. [DOI: 10.1063/1.4866176] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Christensen AS, Steinmann C, Fedorov DG, Jensen JH. Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method. PLoS One 2014; 9:e88800. [PMID: 24558430 PMCID: PMC3928295 DOI: 10.1371/journal.pone.0088800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.
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Affiliation(s)
| | - Casper Steinmann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Dmitri G. Fedorov
- Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Jan H. Jensen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Sanchez-Martinez M, Marcos E, Tauler R, Field M, Crehuet R. Conformational Compression and Barrier Height Heterogeneity in the N-Acetylglutamate Kinase. J Phys Chem B 2013; 117:14261-72. [DOI: 10.1021/jp407016v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Melchor Sanchez-Martinez
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Enrique Marcos
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Romà Tauler
- Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Martin Field
- Institut de Biologie Structurale Jean-Pierre Ebel (CEA, CNRS UMR5075, Université Joseph Fourier - Grenoble I), 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
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