51
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Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B 2017; 121:2331-2338. [PMID: 28225620 DOI: 10.1021/acs.jpcb.7b00537] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D2O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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52
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Sorenson SA, Patrow JG, Dawlaty JM. Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy. J Am Chem Soc 2017; 139:2369-2378. [DOI: 10.1021/jacs.6b11940] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shayne A. Sorenson
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Joel G. Patrow
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Jahan M. Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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53
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Boda M, Naresh Patwari G. Insights into acid dissociation of HCl and HBr with internal electric fields. Phys Chem Chem Phys 2017; 19:7461-7464. [DOI: 10.1039/c6cp08870h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A critical electric field exerted by the solvent on the ionizable group leads to acid dissociation.
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Affiliation(s)
- Manjusha Boda
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
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54
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Mohamed NA, Bradshaw RT, Essex JW. Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field. J Comput Chem 2016; 37:2749-2758. [PMID: 27757978 PMCID: PMC5111595 DOI: 10.1002/jcc.24500] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 01/24/2023]
Abstract
The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field. Although AMOEBA results give mean errors close to "chemical accuracy," GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non-potential-specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Noor Asidah Mohamed
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Richard T. Bradshaw
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Jonathan W. Essex
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
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55
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Albaugh A, Bradshaw RT, Demerdash O, Dziedzic J, Mao Y, Margul DT, Swails J, Boateng HA, Case DA, Eastman P, Essex JW, Head-Gordon M, Pande VS, Ponder J, Shao Y, Skylaris C, Todorov IT, Tuckerman ME, Zeng Q, Head-Gordon T. Advanced Potential Energy Surfaces for Molecular Simulation. J Phys Chem B 2016; 120:9811-32. [PMID: 27513316 PMCID: PMC9113031 DOI: 10.1021/acs.jpcb.6b06414] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
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Affiliation(s)
- Alex Albaugh
- Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Richard T. Bradshaw
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Omar Demerdash
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Daniel T. Margul
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Jason Swails
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey 08854-8066, United States
| | - Henry A. Boateng
- Department of Mathematics, Bates College, 2 Andrews Road, Lewiston, ME 04240
| | - David A. Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey 08854-8066, United States
| | - Peter Eastman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | | | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588
| | - Chris Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Illian T. Todorov
- STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA
- NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai, Shanghai 200062, China
| | - Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA 94720
- Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Bioengineering, University of California, Berkeley, CA 94720
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56
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Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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57
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Schneider SH, Boxer SG. Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site. J Phys Chem B 2016; 120:9672-84. [PMID: 27541577 DOI: 10.1021/acs.jpcb.6b08133] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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58
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Bradshaw RT, Essex JW. Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field. J Chem Theory Comput 2016; 12:3871-83. [PMID: 27341007 DOI: 10.1021/acs.jctc.6b00276] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard but showed substantially worse results than those using the fixed-point-charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 data set, we evaluate the cumulative effects of a series of incremental improvements in parametrization protocol, including both solute and solvent model changes. Ultimately, the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein-ligand binding studies.
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Affiliation(s)
- Richard T Bradshaw
- School of Chemistry, University of Southampton, Highfield Campus , Southampton SO17 1BJ, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield Campus , Southampton SO17 1BJ, U.K
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59
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Pan X, Schwartz SD. Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models. J Phys Chem B 2016; 120:6612-20. [PMID: 27347759 DOI: 10.1021/acs.jpcb.6b05119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate. Recent isotope-edited IR spectroscopy suggests that conformational heterogeneity exists within the Michaelis complex of LDH, and this heterogeneity affects the propensity toward the on-enzyme chemical step for each Michaelis substate. By combining molecular dynamics simulations with Markov and hidden Markov models, we obtained a detailed kinetic network of the substates of the Michaelis complex of LDH. The ensemble-average electric fields exerted onto the vibrational probe were calculated to provide a direct comparison with the vibrational spectroscopy. Structural features of the Michaelis substates were also analyzed on atomistic scales. Our work not only clearly demonstrates the conformational heterogeneity in the Michaelis complex of LDH and its coupling to the reactivities of the substates, but it also suggests a methodology to simultaneously resolve kinetics and structures on atomistic scales, which can be directly compared with the vibrational spectroscopy.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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60
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Sen S, Boda M, Venkat Lata S, Naresh Patwari G. Internal electric fields in small water clusters [(H2O)n; n = 2-6]. Phys Chem Chem Phys 2016; 18:16730-7. [PMID: 27270616 DOI: 10.1039/c6cp02803a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by the donor O-H of a particular water molecule due to the hydrogen bonding network. The red-shifts in O-H stretching frequencies show a spread of about ±100 cm(-1) against the corresponding electric fields. Deviations from linearity were marked in the region of 100-160 MV cm(-1), which can be attributed to the strain in the hydrogen bonding network, especially for structures with DDAA and DDA motifs. The linear Stark effect holds up to 200 MV cm(-1) of internal electric field for the average red-shifts in the O-H stretching frequencies, with a Stark tuning rate of 2.4 cm(-1) (MV cm(-1))(-1), suggesting the validity of the classical model in small water clusters.
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Affiliation(s)
- Saumik Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manjusha Boda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - S Venkat Lata
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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61
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Shelton DP. Orientation correlation and local field in liquid nitrobenzene. J Chem Phys 2016; 144:234506. [PMID: 27334178 DOI: 10.1063/1.4953794] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- David P. Shelton
- Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154-4002, USA
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62
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Deb P, Haldar T, Kashid SM, Banerjee S, Chakrabarty S, Bagchi S. Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. J Phys Chem B 2016; 120:4034-46. [DOI: 10.1021/acs.jpcb.6b02732] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Subhrashis Banerjee
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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63
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Tamimi A, Fayer MD. Ionic Liquid Dynamics Measured with 2D IR and IR Pump–Probe Experiments on a Linear Anion and the Influence of Potassium Cations. J Phys Chem B 2016; 120:5842-54. [DOI: 10.1021/acs.jpcb.6b00409] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amr Tamimi
- Department
of Chemistry Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry Stanford University, Stanford, California 94305, United States
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64
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Shi R, Wang Y. Dual Ionic and Organic Nature of Ionic Liquids. Sci Rep 2016; 6:19644. [PMID: 26782660 PMCID: PMC4726069 DOI: 10.1038/srep19644] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 12/16/2015] [Indexed: 12/20/2022] Open
Abstract
Inherited the advantages of inorganic salts and organic solvents, ionic liquids (ILs) exhibit many superior properties allowing them promising green solvents for the future. Although it has been widely acknowledged that the unique features of ILs originate from their dual ionic and organic nature, its microscopic physical origin still remains blurry. In this work, by comparing the ion/molecule cage structures obtained from molecular dynamics simulations for seven prototypic liquids--a molten inorganic salt, four ILs, a strongly polar organic solvent, and a weakly polar organic solvent, we have revealed that the depth of the cage energy landscape characterizes the ionic nature of ILs, whereas the slope and curvature of its mimimum determine the organic nature of ILs. This finding advances our understanding of ILs and thus will help their efficient utilization as well as the systematic design of novel functionalized ILs.
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Affiliation(s)
- Rui Shi
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, 55 East Zhongguancun Road, P. O. Box 2735, Beijing, 100190 China
| | - Yanting Wang
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, 55 East Zhongguancun Road, P. O. Box 2735, Beijing, 100190 China
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65
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Błasiak B, Ritchie AW, Webb LJ, Cho M. Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach. Phys Chem Chem Phys 2016; 18:18094-111. [DOI: 10.1039/c6cp01578f] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Systematic probing of local environments around biopolymers is important for understanding their functions.
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Affiliation(s)
- Bartosz Błasiak
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
| | - Andrew W. Ritchie
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Lauren J. Webb
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Minhaeng Cho
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
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66
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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67
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Śmiechowski M. Molecular hydrogen solvated in water – A computational study. J Chem Phys 2015; 143:244505. [DOI: 10.1063/1.4938571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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68
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List NH, Beerepoot MTP, Olsen JMH, Gao B, Ruud K, Jensen HJA, Kongsted J. Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone. J Chem Phys 2015; 142:034119. [PMID: 25612701 DOI: 10.1063/1.4905909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Bin Gao
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
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69
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Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J Chem Theory Comput 2015; 11:3696-713. [PMID: 26574453 DOI: 10.1021/acs.jctc.5b00255] [Citation(s) in RCA: 6632] [Impact Index Per Article: 736.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
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Affiliation(s)
- James A Maier
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Carmenza Martinez
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Koushik Kasavajhala
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lauren Wickstrom
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Kevin E Hauser
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
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70
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Masunov AE, Anderson D, Freidzon AY, Bagaturyants AA. Symmetry-Breaking in Cationic Polymethine Dyes: Part 2. Shape of Electronic Absorption Bands Explained by the Thermal Fluctuations of the Solvent Reaction Field. J Phys Chem A 2015; 119:6807-15. [DOI: 10.1021/acs.jpca.5b03877] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Alexandra Ya. Freidzon
- Photochemistry
Center RAS, ul. Novatorov 7a, Moscow, 119421, Russia
- National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow, 115409, Russia
| | - Alexander A. Bagaturyants
- Photochemistry
Center RAS, ul. Novatorov 7a, Moscow, 119421, Russia
- National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow, 115409, Russia
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71
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Rebane A, Wicks G, Drobizhev M, Cooper T, Trummal A, Uudsemaa M. Two-photon voltmeter for measuring a molecular electric field. Angew Chem Int Ed Engl 2015; 54:7582-6. [PMID: 25958849 PMCID: PMC4510705 DOI: 10.1002/anie.201502157] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 11/09/2022]
Abstract
We present a new approach for determining the strength of the dipolar solute-induced reaction field, along with the ground- and excited-state electrostatic dipole moments and polarizability of a solvated chromophore, using exclusively one-photon and two-photon absorption measurements. We verify the approach on two benchmark chromophores N,N-dimethyl-6-propionyl-2-naphthylamine (prodan) and coumarin 153 (C153) in a series of toluene/dimethyl sulfoxide (DMSO) mixtures and find that the experimental values show good quantitative agreement with literature and our quantum-chemical calculations. Our results indicate that the reaction field varies in a surprisingly broad range, 0-10(7) V cm(-1) , and that at close proximity, on the order of the chromophore radius, the effective dielectric constant of the solute-solvent system displays a unique functional dependence on the bulk dielectric constant, offering new insight into the close-range molecular interaction.
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Affiliation(s)
- Aleksander Rebane
- Deptartment of Physics, Montana State University, 264 EPS, Bozeman, MT 59717 (USA). .,National Institute of Chemical Physics and Biophysics, Tallinn (Estonia).
| | - Geoffrey Wicks
- Deptartment of Physics, Montana State University, 264 EPS, Bozeman, MT 59717 (USA)
| | - Mikhail Drobizhev
- Deptartment of Physics, Montana State University, 264 EPS, Bozeman, MT 59717 (USA)
| | - Thomas Cooper
- Air Force Research Lab, Wright Patterson Air Force Base, Dayton, OH (USA)
| | - Aleksander Trummal
- National Institute of Chemical Physics and Biophysics, Tallinn (Estonia)
| | - Merle Uudsemaa
- National Institute of Chemical Physics and Biophysics, Tallinn (Estonia).,Tallinn Institute of Technology, Tallinn (Estonia)
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72
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Rebane A, Wicks G, Drobizhev M, Cooper T, Trummal A, Uudsemaa M. Two-Photon Voltmeter for Measuring a Molecular Electric Field. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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73
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Fried SD, Boxer SG. Measuring electric fields and noncovalent interactions using the vibrational stark effect. Acc Chem Res 2015; 48:998-1006. [PMID: 25799082 DOI: 10.1021/ar500464j] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past decade, we have developed a spectroscopic approach to measure electric fields inside matter with high spatial (<1 Å) and field (<1 MV/cm) resolution. The approach hinges on exploiting a physical phenomenon known as the vibrational Stark effect (VSE), which ultimately provides a direct mapping between observed vibrational frequencies and electric fields. Therefore, the frequency of a vibrational probe encodes information about the local electric field in the vicinity around the probe. The VSE method has enabled us to understand in great detail the underlying physical nature of several important biomolecular phenomena, such as drug-receptor selectivity in tyrosine kinases, catalysis by the enzyme ketosteroid isomerase, and unidirectional electron transfer in the photosynthetic reaction center. Beyond these specific examples, the VSE has provided a conceptual foundation for how to model intermolecular (noncovalent) interactions in a quantitative, consistent, and general manner. The starting point for research in this area is to choose (or design) a vibrational probe to interrogate the particular system of interest. Vibrational probes are sometimes intrinsic to the system in question, but we have also devised ways to build them into the system (extrinsic probes), often with minimal perturbation. With modern instruments, vibrational frequencies can increasingly be recorded with very high spatial, temporal, and frequency resolution, affording electric field maps correspondingly resolved in space, time, and field magnitude. In this Account, we set out to explain the VSE in broad strokes to make its relevance accessible to chemists of all specialties. Our intention is not to provide an encyclopedic review of published work but rather to motivate the underlying framework of the methodology and to describe how we make and interpret the measurements. Using certain vibrational probes, benchmarked against computer models, it is possible to use the VSE to measure absolute electric fields in arbitrary environments. The VSE approach provides an organizing framework for thinking generally about intermolecular interactions in a quantitative way and may serve as a useful conceptual tool for molecular design.
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Affiliation(s)
- Stephen D. Fried
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
| | - Steven G. Boxer
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
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74
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Fried SD, Bagchi S, Boxer SG. Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science 2015; 346:1510-4. [PMID: 25525245 DOI: 10.1126/science.1259802] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI's rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme's catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA
| | - Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA.
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75
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Abstract
Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
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76
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Kashid SM, Bagchi S. Experimental Determination of the Electrostatic Nature of Carbonyl Hydrogen-Bonding Interactions Using IR-NMR Correlations. J Phys Chem Lett 2014; 5:3211-3215. [PMID: 26276334 DOI: 10.1021/jz501613p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrogen-bonding plays a fundamental role in the structure, function, and dynamics of various chemical and biological systems. Understanding the physical nature of interactions and the role of electrostatics in hydrogen-bonding has been the focus of several theoretical and computational research. We present an experimental approach involving IR-(13)C NMR correlations to determine the electrostatic nature of carbonyl hydrogen-bonding interactions. This report provides a direct experimental evidence of the classical nature of hydrogen-bonding interaction in carbonyls, independent of any theoretical approximation. These results have important implications in chemistry and biology and can be applied to probe the reaction mechanisms involving carbonyl activation/stabilization by hydrogen bonds using spectroscopic techniques.
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Affiliation(s)
- Somnath M Kashid
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Sayan Bagchi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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77
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Liu CT, Layfield JP, Stewart RJ, French JB, Hanoian P, Asbury JB, Hammes-Schiffer S, Benkovic SJ. Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase. J Am Chem Soc 2014; 136:10349-60. [PMID: 24977791 PMCID: PMC4183630 DOI: 10.1021/ja5038947] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Electrostatic interactions play an
important role in enzyme catalysis
by guiding ligand binding and facilitating chemical reactions. These
electrostatic interactions are modulated by conformational changes
occurring over the catalytic cycle. Herein, the changes in active
site electrostatic microenvironments are examined for all enzyme complexes
along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation
of thiocyanate probes at two site-specific locations in the active
site. The electrostatics and degree of hydration of the microenvironments
surrounding the probes are investigated with spectroscopic techniques
and mixed quantum mechanical/molecular mechanical (QM/MM) calculations.
Changes in the electrostatic microenvironments along the catalytic
environment lead to different nitrile (CN) vibrational stretching
frequencies and 13C NMR chemical shifts. These environmental
changes arise from protein conformational rearrangements during catalysis.
The QM/MM calculations reproduce the experimentally measured vibrational
frequency shifts of the thiocyanate probes across the catalyzed hydride
transfer step, which spans the closed and occluded conformations of
the enzyme. Analysis of the molecular dynamics trajectories provides
insight into the conformational changes occurring between these two
states and the resulting changes in classical electrostatics and specific
hydrogen-bonding interactions. The electric fields along the CN axes
of the probes are decomposed into contributions from specific residues,
ligands, and solvent molecules that make up the microenvironments
around the probes. Moreover, calculation of the electric field along
the hydride donor–acceptor axis, along with decomposition of
this field into specific contributions, indicates that the cofactor
and substrate, as well as the enzyme, impose a substantial electric
field that facilitates hydride transfer. Overall, experimental and
theoretical data provide evidence for significant electrostatic changes
in the active site microenvironments due to conformational motion
occurring over the catalytic cycle of ecDHFR.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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78
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Pazos IM, Ghosh A, Tucker MJ, Gai F. Ester carbonyl vibration as a sensitive probe of protein local electric field. Angew Chem Int Ed Engl 2014; 53:6080-4. [PMID: 24788907 PMCID: PMC4104746 DOI: 10.1002/anie.201402011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/20/2014] [Indexed: 11/10/2022]
Abstract
The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
| | - Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street, Philadelphia, PA 19104, United States
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79
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Pazos IM, Ghosh A, Tucker MJ, Gai F. Ester Carbonyl Vibration as a Sensitive Probe of Protein Local Electric Field. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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80
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Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B 2014; 118:6456-65. [PMID: 24484473 PMCID: PMC4065202 DOI: 10.1021/jp411671a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The charge distribution of halogen
atoms on organochlorine compounds
can be highly anisotropic and even display a so-called σ-hole,
which leads to strong halogen bonds with electron donors. In this
paper, we have systematically investigated a series of chloromethanes
with one to four chloro substituents using a polarizable multipole-based
molecular mechanics model. The atomic multipoles accurately reproduced
the ab initio electrostatic potential around chloromethanes, including
CCl4, which has a prominent σ-hole on the Cl atom.
The van der Waals parameters for Cl were fitted to the experimental
density and heat of vaporization. The calculated hydration free energy,
solvent reaction fields, and interaction energies of several homo-
and heterodimer of chloromethanes are in good agreement with experimental
and ab initio data. This study suggests that sophisticated electrostatic
models, such as polarizable atomic multipoles, are needed for accurate
description of electrostatics in organochlorine compounds and halogen
bonds, although further improvement is necessary for better transferability.
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Affiliation(s)
- Xiaojiao Mu
- Department of Biomedical Engineering, ‡Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Texas 78712, United States
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