251
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Mehaffey MR, Cammarata MB, Brodbelt JS. Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2018; 90:839-846. [PMID: 29188992 PMCID: PMC5750083 DOI: 10.1021/acs.analchem.7b03591] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex interplay of dynamic protein plasticity and specific side-chain interactions with substrate molecules that allows enzymes to catalyze reactions has yet to be fully unraveled. Top-down ultraviolet photodissociation (UVPD) mass spectrometry is used to track snapshots of conformational fluctuations in the phosphotransferase adenylate kinase (AK) throughout its active reaction cycle by characterization of complexes containing AK and each of four different adenosine phosphate ligands. Variations in efficiencies of UVPD backbone cleavages were consistently observed for three α-helices and the adenosine binding regions for AK complexes representing different steps of the catalytic cycle, implying that these stretches of the protein sample various structural microstates as the enzyme undergoes global open-to-closed transitions. Focusing on the conformational impact of recruiting or releasing the Mg2+ cofactor highlights two loop regions for which fragmentation increases upon UVPD, signaling an increase in loop flexibility as the metal cation disrupts the loop interactions with the substrate ligands. Additionally, the observation of holo ions and variations in UVPD backbone cleavage efficiency at R138 implicate this conserved active site residue in stabilizing the donor phosphoryl group during catalysis. This study showcases the utility of UVPD-MS to provide insight into conformational fluctuations of single residues for active enzymes.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
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252
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Dudev T, Ilieva S, Doudeva L. How an electric field can modulate the metal ion selectivity of protein binding sites: insights from DFT/PCM calculations. Phys Chem Chem Phys 2018; 20:24633-24640. [DOI: 10.1039/c8cp04050h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An electric field (internal or external) is a potent force that can modulate the metal selectivity of a protein binding site.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| | - Sonia Ilieva
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| | - Lyudmila Doudeva
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
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253
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Wang L, Shen Y, Yang Y, Lu W, Li W, Wei F, Zheng G, Zhou Y, Zheng W, Cao Y. Stern-Layer Adsorption of Oligonucleotides on Lamellar Cationic Lipid Bilayer Investigated by Polarization-Resolved SFG-VS. ACS OMEGA 2017; 2:9241-9249. [PMID: 30023605 PMCID: PMC6045418 DOI: 10.1021/acsomega.7b01214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
The molecular interaction between the oligonucleotides and lipid membranes is the key to the functions of virus, aptamer, and various oligonucleotide-based materials. In this study, the conformational changes of oligonucleotides (dT25) on lamellar cationic 1,2-dimyristoyl-3-trimethylammonium-propane (DMTAP) bilayer were investigated by polarization-resolved sum frequency generation vibrational spectroscopy (SFG-VS) in situ. The SFG-VS spectra within different wavenumber ranges were analyzed to give conformation details of thymine groups, phosphate groups, and OD/OH groups and to provide a comprehensive and fundamental understanding of the oligonucleotide adsorption on a model bilayer. It is shown that the adsorption of dT25 on DMTAP bilayer reaches maximum at CdT ≈ 500 nM. And the conformation of dT25 molecules change significantly when surface charge of DMTAP bilayer reaches the point of zero charge (PZC) at CdT ≈ 100 nM. Combined spectroscopic evidences also indicate that the formation of electric double layer at the DMTAP/dT25 surface follows the Gouy-Chapman-Stern model. The analysis results also show that the symmetric PO2- stretching mode of oligonucleotide molecules can serve as a sensitive vibration molecular probe for quantifying the oligonucleotide/lipid charge ratio and determine the point of zero charge (PZC) of lipid bilayer surface, which may help researchers to control the layer-by-layer assembly of oligonucleotide-lipid complexes and to improve the efficiency genetic therapy against cancer and viral infections.
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Affiliation(s)
- Liqun Wang
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Yang Shen
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Yanbo Yang
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Wangting Lu
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Wenhui Li
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Feng Wei
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Guang Zheng
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Youhua Zhou
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
| | - Wanquan Zheng
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
- Institut
des Sciences Moléculaires d’Orsay, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Yuancheng Cao
- Institution
for Interdisciplinary Research, & Key Laboratory
of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Life
Science, School of Physics and Information Engineering, and School of Chemical and Environmental
Engineering, Jianghan University, 430056 Wuhan, Hubei, P. R. China
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254
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Wang XW, Zhang JZH, He X. Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1709169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xian-wei Wang
- College of Science, Zhejiang University of Technology, Hangzhou 310023, China
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- Zhejiang Provincial Collaborative Innovation Center of High-end Laser Manufacturing Equipment, Hangzhou 310014, China
| | - John Z. H. Zhang
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York 10003, USA
| | - Xiao He
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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255
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Torii H. Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins. J Phys Chem B 2017; 122:154-164. [PMID: 29192780 DOI: 10.1021/acs.jpcb.7b10791] [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
For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe2+ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, Faculty of Education and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan
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256
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Tao Y, Zou W, Cremer D, Kraka E. Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity. J Comput Chem 2017; 39:293-306. [PMID: 29143968 DOI: 10.1002/jcc.25109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/16/2017] [Accepted: 10/22/2017] [Indexed: 01/24/2023]
Abstract
Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yunwen Tao
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas, 75275-0314
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, Xi'an, Shaanxi, 710127, People's Republic of China
| | - Dieter Cremer
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas, 75275-0314
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas, 75275-0314
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257
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Ghosh A, Mukherjee P, Deb S, Bhargava R. Mapping Solvation Environments in Porous Metal-Organic Frameworks with Infrared Chemical Imaging. J Phys Chem Lett 2017; 8:5325-5330. [PMID: 29023128 DOI: 10.1021/acs.jpclett.7b02104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report here the first mesoscale characterization of solvent environments in the metal-organic framework (MOF) Cu3(BTC)2 using infrared imaging. Two characteristic populations of the MOF structures corresponding to the carboxylate binding to the Cu(II) (metal) ions were observed, which reflect a regular solvated MOF structure with axial solvents in the binuclear copper paddlewheel and an unsolvated defect mode that lacks axial solvent coordination. Infrared imaging also shows strong correlation between solvent localization and the spatial distribution of the solvated population within the MOF. This is a vital result as any remnant solvent molecules adsorbed inside of MOFs can render them less effective. We propose fast IR imaging as a potential characterization technique that can measure adsorbate and defect distributions in MOFs.
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Affiliation(s)
- Ayanjeet Ghosh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Prabuddha Mukherjee
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Sanghamitra Deb
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Departments of Bioengineering, Chemical and Biomolecular Engineering, Electrical and Computer Engineering, Mechanical Science and Engineering and Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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258
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Antipov SV, Bhattacharyya S, El Hage K, Xu ZH, Meuwly M, Rothlisberger U, Vaníček J. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061509. [PMID: 29376107 PMCID: PMC5758379 DOI: 10.1063/1.4996559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.
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Affiliation(s)
- Sergey V Antipov
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Swarnendu Bhattacharyya
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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259
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Hamm P, Meuwly M, Johnson SL, Beaud P, Staub U. Perspective: THz-driven nuclear dynamics from solids to molecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061601. [PMID: 29308420 PMCID: PMC5741436 DOI: 10.1063/1.4992050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Recent years have seen dramatic developments in the technology of intense pulsed light sources in the THz frequency range. Since many dipole-active excitations in solids and molecules also lie in this range, there is now a tremendous potential to use these light sources to study linear and nonlinear dynamics in such systems. While several experimental investigations of THz-driven dynamics in solid-state systems have demonstrated a variety of interesting linear and nonlinear phenomena, comparatively few efforts have been made to drive analogous dynamics in molecular systems. In the present Perspective article, we discuss the similarities and differences between THz-driven dynamics in solid-state and molecular systems on both conceptual and practical levels. We also discuss the experimental parameters needed for these types of experiments and thereby provide design criteria for a further development of this new research branch. Finally, we present a few recent examples to illustrate the rich physics that may be learned from nonlinear THz excitations of phonons in solids as well as inter-molecular vibrations in liquid and gas-phase systems.
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Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Steve L Johnson
- Institute for Quantum Electronics, ETH Zurich, Zurich, Switzerland
| | - Paul Beaud
- Paul Scherrer Institute, Villigen, Switzerland
| | - Urs Staub
- Paul Scherrer Institute, Villigen, Switzerland
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260
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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261
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Olson CM, Grofe A, Huber CJ, Spector IC, Gao J, Massari AM. Enhanced vibrational solvatochromism and spectral diffusion by electron rich substituents on small molecule silanes. J Chem Phys 2017; 147:124302. [PMID: 28964044 PMCID: PMC5848733 DOI: 10.1063/1.5003908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/08/2017] [Indexed: 01/14/2023] Open
Abstract
Fourier transform infrared and two-dimensional IR (2D-IR) spectroscopies were applied to two different silanes in three different solvents. The selected solutes exhibit different degrees of vibrational solvatochromism for the Si-H vibration. Density functional theory calculations confirm that this difference in sensitivity is the result of higher mode polarization with more electron withdrawing ligands. This mode sensitivity also affects the extent of spectral diffusion experienced by the silane vibration, offering a potential route to simultaneously optimize the sensitivity of vibrational probes in both steady-state and time-resolved measurements. Frequency-frequency correlation functions obtained by 2D-IR show that both solutes experience dynamics on similar time scales and are consistent with a picture in which weakly interacting solvents produce faster, more homogeneous fluctuations. Molecular dynamics simulations confirm that the frequency-frequency correlation function obtained by 2D-IR is sensitive to the presence of hydrogen bonding dynamics in the surrounding solvation shell.
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Affiliation(s)
- Courtney M Olson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, USA
| | - Adam Grofe
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, USA
| | | | - Ivan C Spector
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, USA
| | - Aaron M Massari
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, USA
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262
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Neri G, Donaldson PM, Cowan AJ. The Role of Electrode-Catalyst Interactions in Enabling Efficient CO 2 Reduction with Mo(bpy)(CO) 4 As Revealed by Vibrational Sum-Frequency Generation Spectroscopy. J Am Chem Soc 2017; 139:13791-13797. [PMID: 28895400 DOI: 10.1021/jacs.7b06898] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Group 6 metal carbonyl complexes ([M(bpy)(CO)4], M = Cr, Mo, W) are potentially promising CO2 reduction electrocatalysts. However, catalytic activity onsets at prohibitively negative potentials and is highly dependent on the nature of the working electrode. Here we report in situ vibrational SFG (VSFG) measurements of the electrocatalyst [Mo(bpy)(CO)4] at platinum and gold electrodes. The greatly improved onset potential for electrocatalytic CO2 reduction at gold electrodes is due to the formation of the catalytically active species [Mo(bpy)(CO)3]2- via a second pathway at more positive potentials, likely avoiding the need for the generation of [Mo(bpy)(CO)4]2-. VSFG studies demonstrate that the strength of the interaction between initially generated [Mo(bpy)(CO)4]•- and the electrode is critical in enabling the formation of the active catalyst via the low energy pathway. By careful control of electrode material, solvent and electrolyte salt, it should therefore be possible to attain levels of activity with group 6 complexes equivalent to their much more widely studied group 7 analogues.
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Affiliation(s)
- Gaia Neri
- Department of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool , L69 7ZD Liverpool, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, STFC Rutherford Appleton Laboratory , Harwell, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Alexander J Cowan
- Department of Chemistry and Stephenson Institute for Renewable Energy, University of Liverpool , L69 7ZD Liverpool, United Kingdom
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263
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Hussain A, Huse N, Vendrell O. Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:054102. [PMID: 28966931 PMCID: PMC5612798 DOI: 10.1063/1.5003404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/05/2017] [Indexed: 05/26/2023]
Abstract
Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN). Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.
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Affiliation(s)
- Abid Hussain
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, 22761 Hamburg, Germany
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264
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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265
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Agostini F, Völler J, Koksch B, Acevedo‐Rocha CG, Kubyshkin V, Budisa N. Biocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology. Angew Chem Int Ed Engl 2017; 56:9680-9703. [DOI: 10.1002/anie.201610129] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Federica Agostini
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Jan‐Stefan Völler
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | | | - Vladimir Kubyshkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
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266
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Boxer SG. Comment on "Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes". J Phys Chem B 2017; 121:7395-7396. [PMID: 28689400 DOI: 10.1021/acs.jpcb.7b02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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267
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Mani T, Grills DC. Probing Intermolecular Electron Delocalization in Dimer Radical Anions by Vibrational Spectroscopy. J Phys Chem B 2017; 121:7327-7335. [PMID: 28678501 DOI: 10.1021/acs.jpcb.7b02559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Delocalization of charges is one of the factors controlling charge transport in conjugated molecules. It is considered to play an important role in the performance of a wide range of molecular technologies, including organic solar cells and organic electronics. Dimerization reactions are well-suited as a model to investigate intermolecular spatial delocalization of charges. While dimerization reactions of radical cations are well investigated, studies on radical anions are still scarce. Upon dimerization of radical anions with neutral counterparts, an electron is considered to delocalize over the two molecules. Here, by using time-resolved infrared (TRIR) detection coupled with pulse radiolysis, we show that radical anions of 4-n-hexyl-4'-cyanobiphenyl (6CB) undergo such dimerization reactions, with an electron equally delocalized over the two molecules. We have recently demonstrated that nitrile ν(C≡N) vibrations respond to the degree of electron localization of nitrile-substituted anions: we can quantify the changes in the electronic charges from the neutral to the anion states in the nitriles by monitoring the ν(C≡N) IR shifts. In the first part of this article, we show that the sensitivity of the ν(C≡N) IR shifts does not depend on solvent polarity. In the second part, we describe how probing the shifts of the nitrile IR vibrational band unambiguously confirms the formation of dimer radical anions, with Kdim = 3 × 104 M-1. IR findings are corroborated by electronic absorption spectroscopy and electronic structure calculations. We find that the presence of a hexyl chain and the formation of π-π interactions are both crucial for dimerization of radical anions of 6CB with neutral 6CB. The present study provides clear evidence of spatial delocalization of electrons over two molecular fragments.
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Affiliation(s)
- Tomoyasu Mani
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060, United States.,Chemistry Division, Brookhaven National Laboratory , Upton, New York 11973-5000, United States
| | - David C Grills
- Chemistry Division, Brookhaven National Laboratory , Upton, New York 11973-5000, United States
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268
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Biokatalyse mit nicht‐natürlichen Aminosäuren: Enzymologie trifft Xenobiologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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269
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Laage D, Elsaesser T, Hynes JT. Perspective: Structure and ultrafast dynamics of biomolecular hydration shells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044018. [PMID: 28470026 PMCID: PMC5398927 DOI: 10.1063/1.4981019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 05/25/2023]
Abstract
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
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Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Départment de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
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270
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Abstract
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.
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Affiliation(s)
- Stephen D Fried
- Proteins and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305;
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271
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Salna B, Benabbas A, Russo D, Champion PM. Tunneling Kinetics and Nonadiabatic Proton-Coupled Electron Transfer in Proteins: The Effect of Electric Fields and Anharmonic Donor–Acceptor Interactions. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b05570] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Bridget Salna
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - Douglas Russo
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - Paul M. Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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272
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Basom EJ, Manifold BA, Thielges MC. Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam. Biochemistry 2017; 56:3248-3256. [PMID: 28581729 DOI: 10.1021/acs.biochem.7b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
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Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bryce A Manifold
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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273
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Rajeshwar T R, Krishnan M. Direct Determination of Site-Specific Noncovalent Interaction Strengths of Proteins from NMR-Derived Fast Side Chain Motional Parameters. J Phys Chem B 2017; 121:5174-5186. [PMID: 28452484 DOI: 10.1021/acs.jpcb.7b01402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel approach to accurately determine residue-specific noncovalent interaction strengths (ξ) of proteins from NMR-measured fast side chain motional parameters (Oaxis2) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ξ, Oaxis2, conformational entropy (Sconf), conformational barriers, and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ξ and that for each residue type there exists a critical range of ξ, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with Oaxis2 ∼ 0) to highly restricted (with Oaxis2 ∼ 1) by increasing ξ by ∼3 kcal/mol. Beyond this critical range of ξ, both side chain flexibility and conformational entropy are insensitive to ξ. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.
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Affiliation(s)
- Rajitha Rajeshwar T
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
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274
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Błasiak B, Londergan CH, Webb LJ, Cho M. Vibrational Probes: From Small Molecule Solvatochromism Theory and Experiments to Applications in Complex Systems. Acc Chem Res 2017; 50:968-976. [PMID: 28345879 DOI: 10.1021/acs.accounts.7b00002] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies. To fully utilize IR probe functional groups for quantitative bioassays, a variety of biological and chemical techniques have been developed to site-specifically introduce vibrational probe groups into proteins and nucleic acids. These IR-probe-labeled biomolecules and chemically reactive systems are subject to linear and nonlinear vibrational spectroscopic investigations and provide information on the local electric field, conformational changes, site-site protein contacts, and/or function-defining features of biomolecules. A rapidly expanding library of data from such experiments requires an interpretive method with atom-level chemical accuracy. However, despite prolonged efforts to develop an all-encompassing theory for describing vibrational solvatochromism and electrochromism as well as dynamic fluctuations of instantaneous vibrational frequencies, purely empirical and highly approximate theoretical models have often been used to interpret experimental results. They are, in many cases, based on the simple assumption that the vibrational frequency of an IR reporter is solely dictated by electric potential or field distribution around the vibrational chromophore. Such simplified description of vibrational solvatochromism generally referred to as vibrational Stark effect theory has been considered to be quite appealing and, even in some cases, e.g., carbonyl stretch modes in amide, ester, ketone, and carbonate compounds or proteins, it works quantitatively well, which makes it highly useful in determining the strength of local electric field around the IR chromophore. However, noting that the vibrational frequency shift results from changes of solute-solvent intermolecular interaction potential along its normal coordinate, Pauli exclusion repulsion, polarization, charge transfer, and dispersion interactions, in addition to the electrostatic interaction between distributed charges of both vibrational chromophore and solvent molecules, are to be properly included in the theoretical description of vibrational solvatochromism. Since the electrostatic and nonelectrostatic intermolecular interaction components have distinctively different distance and orientation dependences, they affect the solvatochromic vibrational properties in a completely different manner. Over the past few years, we have developed a systematic approach to simulating vibrational solvatochromic data based on the effective fragment potential approach, one of the most accurate and rigorous theories on intermolecular interactions. We have further elucidated the interplay of local electric field with the general vibrational solvatochromism of small IR probes in either solvents or complicated biological systems, with emphasis on contributions from non-Coulombic intermolecular interactions to vibrational frequency shifts and fluctuations. With its rigorous foundation and close relation to quantitative interpretation of experimental data, this and related theoretical approaches and experiments will be of use in studying and quantifying the structure and dynamics of biomolecules with unprecedented time and spatial resolution when combined with time-resolved vibrational spectroscopy and chemically sensitive vibrational imaging techniques.
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Affiliation(s)
- Bartosz Błasiak
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Casey H. Londergan
- Department
of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - 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, 105
E. 24th Street, STOP A5300, Austin, Texas 78712, United States
| | - Minhaeng Cho
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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275
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Bhowmick A, Sharma SC, Head-Gordon T. The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase. J Am Chem Soc 2017; 139:5793-5800. [DOI: 10.1021/jacs.6b12265] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Teresa Head-Gordon
- Chemical
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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276
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Kashid SM, Jin GY, Chakrabarty S, Kim YS, Bagchi S. Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics. J Phys Chem Lett 2017; 8:1604-1609. [PMID: 28326785 DOI: 10.1021/acs.jpclett.7b00270] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast two-dimensional infrared spectroscopy experiments. Our results demonstrate the cosolvent-concentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute-solvent interactions is the key to the anomalous behavior.
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Affiliation(s)
- Somnath M Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil, Ulsan 44919, Korea
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil, Ulsan 44919, Korea
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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277
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Koch M, Myahkostupov M, Oblinsky DG, Wang S, Garakyaraghi S, Castellano FN, Scholes GD. Charge Localization after Ultrafast Photoexcitation of a Rigid Perylene Perylenediimide Dyad Visualized by Transient Stark Effect. J Am Chem Soc 2017; 139:5530-5537. [DOI: 10.1021/jacs.7b01630] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Koch
- Department
of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Mykhaylo Myahkostupov
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Daniel G. Oblinsky
- Department
of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Siwei Wang
- Department
of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Sofia Garakyaraghi
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Felix N. Castellano
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Gregory D. Scholes
- Department
of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
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278
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Abaskharon RM, Brown SP, Zhang W, Chen J, Smith AB, Gai F. Isotope-Labeled Aspartate Sidechain as a Non-Perturbing Infrared Probe: Application to Investigate the Dynamics of a Carboxylate Buried Inside a Protein. Chem Phys Lett 2017; 683:193-198. [PMID: 29033461 DOI: 10.1016/j.cplett.2017.03.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13C=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum. Applicability of this site-specific vibrational probe is demonstrated by using it to assess the dynamics of an aspartate ion buried inside a small protein via two-dimensional infrared spectroscopy.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Stephen P Brown
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Wenkai Zhang
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Jianxin Chen
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.,Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
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279
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Stevenson P, Tokmakoff A. Ultrafast Fluctuations of High Amplitude Electric Fields in Lipid Membranes. J Am Chem Soc 2017; 139:4743-4752. [DOI: 10.1021/jacs.6b12412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paul Stevenson
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Ave., Cambridge, Massachusetts 02139, United States
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
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280
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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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281
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Wang H, Yao K, Parkhill JA, Schultz ZD. Detection of electron tunneling across plasmonic nanoparticle-film junctions using nitrile vibrations. Phys Chem Chem Phys 2017; 19:5786-5796. [PMID: 28180214 PMCID: PMC5325176 DOI: 10.1039/c6cp08168a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The significant electric field enhancements that occur in plasmonic nanogap junctions are instrumental in boosting the performance of spectroscopy, optoelectronics and catalysis. Electron tunneling, associated with quantum effects in small junctions, is reported to limit the electric field enhancement. However, observing and quantitatively determining how tunneling alters the electric fields within small gaps is challenging due to the nanoscale dimensions and heterogeneity present experimentally. Here, we report the use of a nitrile probe placed in the nanoparticle-film gap junctions to demonstrate that the change in the nitrile stretching band associated with the vibrational Stark effect can be directly correlated with the local electric field environment modulated by gap size variations. The emergence of Stark shifts correlates with plasmon resonance shifts associated with electron tunneling across the gap junction. Time dependent changes in the nitrile band with extended illumination further support a build up of charge associated with optical rectification in the coupled plasmon system. Computational models agree with our experimental observations that the frequency shifts arise from a vibrational Stark effect. Large local electric fields associated with the smallest gap junctions give rise to significant Stark shifts. These results indicate that nitrile Stark probes can measure the local field strengths in plasmonic junctions and monitor the subtle changes in the local electric fields resulting from electron tunneling.
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Affiliation(s)
- Hao Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | - John A Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
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282
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Völler JS, Biava H, Hildebrandt P, Budisa N. An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy. Biochim Biophys Acta Gen Subj 2017; 1861:3053-3059. [PMID: 28229928 DOI: 10.1016/j.bbagen.2017.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics. GENERAL SIGNIFICANCE Mapping the electrostatics in proteins will improve our understanding of natural catalytic processes and, in beyond, will be helpful for biocatalyst engineering. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Jan-Stefan Völler
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany.
| | - Hernan Biava
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany; Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany.
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283
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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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284
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Park Y, Kang H, Kang H. Brute Force Orientation of Matrix-Isolated Molecules: Reversible Reorientation of Formaldehyde in an Argon Matrix toward Perfect Alignment. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Youngwook Park
- Department of Chemistry; Seoul National University; 1 Gwanak-ro Seoul 151-747 Republic of Korea
| | - Hani Kang
- Department of Chemistry; Seoul National University; 1 Gwanak-ro Seoul 151-747 Republic of Korea
| | - Heon Kang
- Department of Chemistry; Seoul National University; 1 Gwanak-ro Seoul 151-747 Republic of Korea
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285
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Park Y, Kang H, Kang H. Brute Force Orientation of Matrix-Isolated Molecules: Reversible Reorientation of Formaldehyde in an Argon Matrix toward Perfect Alignment. Angew Chem Int Ed Engl 2017; 56:1046-1049. [PMID: 27996190 DOI: 10.1002/anie.201610948] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Indexed: 11/10/2022]
Abstract
Brute force orientation by an electric field is a promising way of controlling the orientation of polar molecules in the gas phase, but its application to condensed-phase molecules has been very limited. We studied the reorientation of formaldehyde molecules in a solid Ar matrix under the influence of a strong electric field using reflection absorption infrared spectroscopy. Asymptotically perfect alignment of the formaldehyde molecules along the field was achieved at field strengths exceeding 1×108 V m-1 . The vibrational bands of the aligned molecules exhibited a unidirectional Stark shift proportional to the field strength. The reorientation of the molecules was reversible despite the cryogenic solid environment of the system.
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Affiliation(s)
- Youngwook Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul, 151-747, Republic of Korea
| | - Hani Kang
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul, 151-747, Republic of Korea
| | - Heon Kang
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul, 151-747, Republic of Korea
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286
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Xue RJ, Grofe A, Yin H, Qu Z, Gao J, Li H. Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules. J Chem Theory Comput 2017; 13:191-201. [PMID: 28068771 DOI: 10.1021/acs.jctc.6b00733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linear and two-dimensional infrared (IR) spectroscopy of site-specific probe molecules provides an opportunity to gain a molecular-level understanding of the local hydrogen-bonding network, conformational dynamics, and long-range electrostatic interactions in condensed-phase and biological systems. A challenge in computation is to determine the time-dependent vibrational frequencies that incorporate explicitly both nuclear quantum effects of vibrational motions and an electronic structural representation of the potential energy surface. In this paper, a nuclear quantum vibrational perturbation (QVP) method is described for efficiently determining the instantaneous vibrational frequency of a chromophore in molecular dynamics simulations. Computational efficiency is achieved through the use of (a) discrete variable representation of the vibrational wave functions, (b) a perturbation theory to evaluate the vibrational energy shifts due to solvent dynamic fluctuations, and (c) a combined QM/MM potential for the systems. It was found that first-order perturbation is sufficiently accurate, enabling time-dependent vibrational frequencies to be obtained on the fly in molecular dynamics. The QVP method is illustrated in the mode-specific linear and 2D-IR spectra of the H-Cl stretching frequency in the HCl-water clusters and the carbonyl stretching vibration of acetone in aqueous solution. To further reduce computational cost, a hybrid strategy was proposed, and it was found that the computed vibrational spectral peak position and line shape are in agreement with experimental results. In addition, it was found that anharmonicity is significant in the H-Cl stretching mode, and hydrogen-bonding interactions further enhance anharmonic effects. The present QVP method complements other computational approaches, including path integral-based molecular dynamics, and represents a major improvement over the electrostatics-based spectroscopic mapping procedures.
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Affiliation(s)
- Rui-Jie Xue
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Adam Grofe
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street, SE, Minneapolis, Minnesota 55455, United States
| | - He Yin
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Zexing Qu
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Jiali Gao
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street, SE, Minneapolis, Minnesota 55455, United States
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
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287
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You M, Liu L, Zhang W. The covalently bound diazo group as an infrared probe for hydrogen bonding environments. Phys Chem Chem Phys 2017; 19:19420-19426. [DOI: 10.1039/c7cp01867c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bandwidth or position of diazo groups can probe the polarizability and HBA, or density of HBD groups.
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Affiliation(s)
- Min You
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
| | - Liyuan Liu
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
| | - Wenkai Zhang
- Center for Advanced Quantum Studies
- Department of Physics and Applied Optics Beijing Area Major Laboratory
- Beijing Normal University
- Beijing
- China
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288
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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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289
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Kraack JP, Hamm P. Surface-Sensitive and Surface-Specific Ultrafast Two-Dimensional Vibrational Spectroscopy. Chem Rev 2016; 117:10623-10664. [DOI: 10.1021/acs.chemrev.6b00437] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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290
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Shaik S, Mandal D, Ramanan R. Oriented electric fields as future smart reagents in chemistry. Nat Chem 2016; 8:1091-1098. [DOI: 10.1038/nchem.2651] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022]
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291
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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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292
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Wu Y, Boxer SG. A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase. J Am Chem Soc 2016; 138:11890-5. [PMID: 27545569 PMCID: PMC5063566 DOI: 10.1021/jacs.6b06843] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with ΔG(⧧) in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations. A linear relationship is observed between the electric field and ΔG(⧧) that interpolates between wild-type and more drastic conventional mutations, reinforcing the evaluation of the electrostatic contribution to catalysis in KSI. A simplified model and calculation are developed to estimate changes in the electric field accompanying changes in the extended hydrogen-bond network in the active site. The results are consistent with a model in which the O-H group of a key active site tyrosine functions by imposing a static electrostatic potential onto the carbonyl bond. The model suggests that the contribution to catalysis from the active site hydrogen bonds is of similar weight to the distal interactions from the rest of the protein. A similar linear correlation was also observed between the proton affinity of KSI's active site and the catalytic rate, suggesting a direct connection between the strength of the H-bond and the electric field it exerts.
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Affiliation(s)
- Yufan Wu
- 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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293
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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: 56] [Impact Index Per Article: 7.0] [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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294
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Torii H. Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile. J Phys Chem A 2016; 120:7137-44. [DOI: 10.1021/acs.jpca.6b06607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hajime Torii
- Department
of Chemistry,
Faculty of Education, and Department of Optoelectronics and Nanostructure
Science, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
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295
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Wei L, Hu F, Chen Z, Shen Y, Zhang L, Min W. Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes. Acc Chem Res 2016; 49:1494-502. [PMID: 27486796 PMCID: PMC5704954 DOI: 10.1021/acs.accounts.6b00210] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Innovations in light microscopy have tremendously revolutionized the way researchers study biological systems with subcellular resolution. In particular, fluorescence microscopy with the expanding choices of fluorescent probes has provided a comprehensive toolkit to tag and visualize various molecules of interest with exquisite specificity and high sensitivity. Although fluorescence microscopy is currently the method of choice for cellular imaging, it faces fundamental limitations for studying the vast number of small biomolecules. This is because common fluorescent labels, which are relatively bulky, could introduce considerable perturbation to or even completely alter the native functions of vital small biomolecules. Hence, despite their immense functional importance, these small biomolecules remain largely undetectable by fluorescence microscopy. To address this challenge, a bioorthogonal chemical imaging platform has recently been introduced. By coupling stimulated Raman scattering (SRS) microscopy, an emerging nonlinear Raman microscopy technique, with tiny and Raman-active vibrational probes (e.g., alkynes and stable isotopes), bioorthogonal chemical imaging exhibits superb sensitivity, specificity, and biocompatibility for imaging small biomolecules in live systems. In this Account, we review recent technical achievements for visualizing a broad spectrum of small biomolecules, including ribonucleosides and deoxyribonucleosides, amino acids, fatty acids, choline, glucose, cholesterol, and small-molecule drugs in live biological systems ranging from individual cells to animal tissues and model organisms. Importantly, this platform is compatible with live-cell biology, thus allowing real-time imaging of small-molecule dynamics. Moreover, we discuss further chemical and spectroscopic strategies for multicolor bioorthogonal chemical imaging, a valuable technique in the era of "omics". As a unique tool for biological discovery, this platform has been applied to studying various metabolic processes under both physiological and pathological states, including protein synthesis activity of neuronal systems, protein aggregations in Huntington disease models, glucose uptake in tumor xenografts, and drug penetration through skin tissues. We envision that the coupling of SRS microscopy with vibrational probes would do for small biomolecules what fluorescence microscopy of fluorophores has done for larger molecular species.
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Affiliation(s)
- Lu Wei
- Department of Chemistry, Columbia University, New York, 10027
| | - Fanghao Hu
- Department of Chemistry, Columbia University, New York, 10027
| | - Zhixing Chen
- Department of Chemistry, Columbia University, New York, 10027
| | - Yihui Shen
- Department of Chemistry, Columbia University, New York, 10027
| | - Luyuan Zhang
- Department of Chemistry, Columbia University, New York, 10027
| | - Wei Min
- Department of Chemistry, Columbia University, New York, 10027
- Kavli Institute for Brain Science, Columbia University, New York, 10027
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296
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Doughty B, Yin P, Ma YZ. Adsorption, Ordering, and Local Environments of Surfactant-Encapsulated Polyoxometalate Ions Probed at the Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8116-22. [PMID: 27452922 DOI: 10.1021/acs.langmuir.6b01643] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The continued development and application of surfactant-encapsulated polyoxometalates (SEPs) relies on understanding the ordering and organization of species at their interface and how these are impacted by the various local environments to which they are exposed. Here, we report on the equilibrium properties of two common SEPs adsorbed to the air-water interface and probed with surface-specific vibrational sum-frequency generation (SFG) spectroscopy. These results reveal clear shifts in vibrational band positions, the magnitude of which scales with the charge of the SEP core, which is indicative of a static field effect on the surfactant coating and the associated local chemical environment. This static field also induces ordering in surrounding water molecules that is mediated by charge screening via the surface-bound surfactants. From these SFG measurements, we are able to show that Mo132-based SEPs are more polar than Mo72V30 SEPs. Disorder in the surfactant chain packing at the highly curved SEP surfaces is attributed to large conic volumes that can be sampled without interactions with neighboring chains. Measurements of adsorption isotherms yield free energies of adsorption to the air-water interface of -46.8 ± 0.4 and -44.8 ± 1.2 kJ/mol for the Mo132 and Mo72V30 SEPs, respectively, indicating a strong propensity for the fluid surface. The influence of intermolecular interactions on the surface adsorption energies is discussed.
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Affiliation(s)
- Benjamin Doughty
- Chemical Sciences Division, ‡Chemical and Engineering Materials Division, Neutron Sciences Directorate, and §Shull Wollan Center, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Panchao Yin
- Chemical Sciences Division, ‡Chemical and Engineering Materials Division, Neutron Sciences Directorate, and §Shull Wollan Center, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Ying-Zhong Ma
- Chemical Sciences Division, ‡Chemical and Engineering Materials Division, Neutron Sciences Directorate, and §Shull Wollan Center, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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297
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Loukova GV, Vasiliev VP, Milov AA, Smirnov VA, Minkin VI. Unraveling electronic properties of an organometallic solute: Lippert-Mataga and quantum-chemical extensive study. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.04.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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298
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Haldar T, Kashid SM, Deb P, Kesh S, Bagchi S. Pick and Choose the Spectroscopic Method to Calibrate the Local Electric Field inside Proteins. J Phys Chem Lett 2016; 7:2456-2460. [PMID: 27295386 DOI: 10.1021/acs.jpclett.6b00852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrostatic interactions in proteins play a crucial role in determining the structure-function relation in biomolecules. In recent years, fluorescent probes have been extensively employed to interrogate the polarity in biological cavities through dielectric constants or semiempirical polarity scales. A choice of multiple spectroscopic methods, not limited by fluorophores, along with a molecular level description of electrostatics involving solute-solvent interactions, would allow more flexibility to pick and choose the experimental technique to determine the local electrostatics within protein interiors. In this work we report that ultraviolet/visible-absorption, infrared-absorption, or (13)C NMR can be used to calibrate the local electric field in both hydrogen bonded and non-hydrogen bonded protein environments. The local electric field at the binding site of a serum protein has been determined using the absorption wavelength as well as the carbonyl stretching frequency of its natural steroid substrate, testosterone. Excellent agreement is observed in the results obtained from two independent spectroscopic techniques.
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Affiliation(s)
- 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
| | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sandeep Kesh
- 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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299
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Dinpajooh M, Matyushov DV. Dielectric constant of water in the interface. J Chem Phys 2016; 145:014504. [DOI: 10.1063/1.4955203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, USA
| | - Dmitry V. Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, USA
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300
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Dahms F, Costard R, Pines E, Fingerhut BP, Nibbering ETJ, Elsaesser T. The Hydrated Excess Proton in the Zundel Cation H5
O2
+
: The Role of Ultrafast Solvent Fluctuations. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Dahms
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Rene Costard
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Ehud Pines
- Department of Chemistry; Ben Gurion University of the Negev; P.O.B. 653 Beersheva 84105 Israel
| | - Benjamin P. Fingerhut
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Erik T. J. Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Thomas Elsaesser
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
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