1
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Spicher S, Plett C, Pracht P, Hansen A, Grimme S. Automated Molecular Cluster Growing for Explicit Solvation by Efficient Force Field and Tight Binding Methods. J Chem Theory Comput 2022; 18:3174-3189. [PMID: 35482317 DOI: 10.1021/acs.jctc.2c00239] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An automated and broadly applicable workflow for the description of solvation effects in an explicit manner is introduced. This method, termed quantum cluster growth (QCG), is based on the semiempirical GFN2-xTB/GFN-FF methods, enabling efficient geometry optimizations and MD simulations. Fast structure generation is provided using the intermolecular force field xTB-IFF. Additionally, the approach uses an efficient implicit solvation model for the electrostatic embedding of the growing clusters. The novel QCG procedure presents a robust cluster generation tool for subsequent application of higher-level (e.g., DFT) methods to study solvation effects on molecular geometries explicitly or to average spectroscopic properties over cluster ensembles. Furthermore, the computation of the solvation free energy with a supermolecular approach can be carried out with QCG. The underlying growing process is physically motivated by computing the leading-order solute-solvent interactions first and can account for conformational and chemical changes due to solvation for low-energy barrier processes. The conformational space is explored with the NCI-MTD algorithm as implemented in the CREST program, using a combination of metadynamics and MD simulations. QCG with GFN2-xTB yields realistic solution geometries and reasonable solvation free energies for various systems without introducing many empirical parameters. Computed IR spectra of some solutes with QCG show a better match to the experimental data compared to well-established implicit solvation models.
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Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Christoph Plett
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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2
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Bondanza M, Nottoli M, Cupellini L, Lipparini F, Mennucci B. Polarizable embedding QM/MM: the future gold standard for complex (bio)systems? Phys Chem Chem Phys 2020; 22:14433-14448. [DOI: 10.1039/d0cp02119a] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We provide a perspective of the induced dipole formulation of polarizable QM/MM, showing how efficient implementations will enable their application to the modeling of dynamics, spectroscopy, and reactivity in complex biosystems.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
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3
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Niether D, Wiegand S. Thermophoresis of biological and biocompatible compounds in aqueous solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:503003. [PMID: 31491783 DOI: 10.1088/1361-648x/ab421c] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.
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Affiliation(s)
- D Niether
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
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4
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Bedrov D, Piquemal JP, Borodin O, MacKerell AD, Roux B, Schröder C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem Rev 2019; 119:7940-7995. [PMID: 31141351 PMCID: PMC6620131 DOI: 10.1021/acs.chemrev.8b00763] [Citation(s) in RCA: 274] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Indexed: 11/30/2022]
Abstract
Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.
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Affiliation(s)
- Dmitry Bedrov
- Department
of Materials Science & Engineering, University of Utah, 122 South Central Campus Drive, Room 304, Salt Lake City, Utah 84112, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, CC137, 4 Place Jussieu, Tour 12-13, 4ème étage, 75252 Paris Cedex 05, France
- Institut
Universitaire de France, 75005, Paris Cedex 05, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Oleg Borodin
- Electrochemistry
Branch, Sensors and Electron Devices Directorate, Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20703, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, Gordon Center for Integrative
Science, University of Chicago, 929 57th Street, Chicago, Illinois 60637, United States
| | - Christian Schröder
- Department
of Computational Biological Chemistry, University
of Vienna, Währinger Strasse 17, A-1090 Vienna, Austria
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5
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Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. J Chem Phys 2019; 150:074103. [PMID: 30795653 DOI: 10.1063/1.5080384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl-. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.
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Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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6
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Polarizable ab initio QM/MM Study of the Reaction Mechanism of N- tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄]. Molecules 2018; 23:E2830. [PMID: 30384470 PMCID: PMC6278528 DOI: 10.3390/molecules23112830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
N-t e r t-butoxycarbonylation of amines in solution (water, organic solvents, or ionic liquids) is a common reaction for the preparation of drug molecules. To understand the reaction mechanism and the role of the solvent, quantum mechanical/molecular mechanical simulations using a polarizable multipolar force field with long⁻range electrostatic corrections were used to optimize the minimum energy paths (MEPs) associated with various possible reaction mechanisms employing the nudged elastic band (NEB) and the quadratic string method (QSM). The calculated reaction energies and energy barriers were compared with the corresponding gas-phase and dichloromethane results. Complementary Electron Localization Function (ELF)/NCI analyses provide insights on the critical structures along the MEP. The calculated results suggest the most likely path involves a sequential mechanism with the rate⁻limiting step corresponding to the nucleophilic attack of the aniline, followed by proton transfer and the release of CO 2 without the direct involvement of imidazolium cations as catalysts.
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Affiliation(s)
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA.
- The Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA.
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7
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Massarczyk M, Schlitter J, Kötting C, Rudack T, Gerwert K. Monitoring transient events in infrared spectra using local mode analysis. Proteins 2018; 86:1013-1019. [PMID: 30019772 DOI: 10.1002/prot.25536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 01/10/2023]
Abstract
Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.
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Affiliation(s)
| | - Jürgen Schlitter
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Till Rudack
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
| | - Klaus Gerwert
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
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8
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Sidler D, Meuwly M, Hamm P. An efficient water force field calibrated against intermolecular THz and Raman spectra. J Chem Phys 2018; 148:244504. [DOI: 10.1063/1.5037062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David Sidler
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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9
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Hassan I, Donati L, Stensitzki T, Keller BG, Heyne K, Imhof P. The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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11
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Thomsen B, Kawakami T, Shigemoto I, Sugita Y, Yagi K. Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6. J Phys Chem B 2017; 121:6050-6063. [DOI: 10.1021/acs.jpcb.7b00372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo Thomsen
- Theoretical
Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tomonori Kawakami
- Advanced
Materials Research Laboratories, Toray Industries, Inc., 2-1 Sonoyama 3-chome, Otsu, Shiga 520-0842, Japan
| | - Isamu Shigemoto
- Advanced
Materials Research Laboratories, Toray Industries, Inc., 2-1 Sonoyama 3-chome, Otsu, Shiga 520-0842, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Quantitative Biology Center, 6-7-1 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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12
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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13
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Massarczyk M, Rudack T, Schlitter J, Kuhne J, Kötting C, Gerwert K. Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details. J Phys Chem B 2017; 121:3483-3492. [PMID: 28092441 DOI: 10.1021/acs.jpcb.6b09343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call local mode analysis (LMA) for calculating IR spectra and assigning spectral IR-bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory. Through LMA the decoding of IR spectra no longer requires several simulations or optimizations. The novel approach correlates the motions of atoms of a single simulation with the corresponding IR bands and provides direct access to the structural information encoded in IR spectra. Either the contributions of a particular atom or atom group to the complete IR spectrum of the molecule are visualized, or an IR-band is selected to visualize the corresponding structural motions. Thus, LMA decodes the detailed information contained in IR spectra and provides an intuitive approach for structural biologists and biochemists. The unique feature of LMA is the bidirectional analysis connecting structural details to spectral features and vice versa spectral features to molecular motions.
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Affiliation(s)
- M Massarczyk
- Department of Biophysics, Ruhr-University , 44801 Bochum, Germany
| | - T Rudack
- Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS) , Shanghai 200031, China
| | - J Schlitter
- Department of Biophysics, Ruhr-University , 44801 Bochum, Germany
| | - J Kuhne
- Department of Biophysics, Ruhr-University , 44801 Bochum, Germany
| | - C Kötting
- Department of Biophysics, Ruhr-University , 44801 Bochum, Germany
| | - K Gerwert
- Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS) , Shanghai 200031, China
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