1
|
Judd KD, Parsons SW, Eremin DB, Fokin VV, Dawlaty JM. Visualizing partial solvation at the air-water interface. Chem Sci 2024; 15:8346-8354. [PMID: 38846382 PMCID: PMC11151832 DOI: 10.1039/d4sc01311e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 04/08/2024] [Indexed: 06/09/2024] Open
Abstract
Despite significant research, the mechanistic nuances of unusual reactivity at the air-water interface, especially in microdroplets, remain elusive. The likely contributors include electric fields and partial solvation at the interface. To reveal these intricacies, we measure the frequency shift of a well-defined azide vibrational probe at the air-water interface, while independently controlling the surface charge density by introducing surfactants. First, we establish the response of the probe in the bulk and demonstrate that it is sensitive to both electrostatics and hydrogen bonding. From interfacial spectroscopy we infer that the azide is neither fully hydrated nor in a completely aprotic dielectric environment; instead, it experiences an intermediate environment. In the presence of hydrogen bond-accepting sulphate surfactants, competition arises for interfacial water with the azide. However, the dominant influence stems from the electrostatic effect of their negative heads, resulting in a significant blue-shift. Conversely, for the positive ammonium surfactants, our data indicate a balanced interplay between electrostatics and hydrogen bonding, leading to a minimal shift in the probe. Our results demonstrate partial solvation at the interface and highlights that both hydrogen bonding and electrostatics may assist or oppose each other in polarizing a reactant, intermediate, or product at the interface, which is important for understanding and tuning interfacial reactivity.
Collapse
Affiliation(s)
- Kenneth D Judd
- Department of Chemistry, The University of Southern California Los Angeles CA 90089 USA
| | - Sean W Parsons
- Department of Chemistry, The University of Southern California Los Angeles CA 90089 USA
| | - Dmitry B Eremin
- Department of Chemistry, The University of Southern California Los Angeles CA 90089 USA
| | - Valery V Fokin
- Department of Chemistry, The University of Southern California Los Angeles CA 90089 USA
| | - Jahan M Dawlaty
- Department of Chemistry, The University of Southern California Los Angeles CA 90089 USA
| |
Collapse
|
2
|
Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
Collapse
Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
3
|
Taniguchi T, Agbo DO. Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region. Phys Chem Chem Phys 2023; 25:28567-28575. [PMID: 37861094 DOI: 10.1039/d3cp04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.
Collapse
Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
| |
Collapse
|
4
|
You M, Gao Z, Zhou L, Guo C, Guo Q. Investigation of the Vibrational Characteristics of 6-Isocyano-1-Methyl-1H-Indole: Utilizing the Isonitrile Group as an Infrared Probe. Molecules 2023; 28:6939. [PMID: 37836782 PMCID: PMC10574170 DOI: 10.3390/molecules28196939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Indole derivatives have garnered considerable attention in the realm of biochemistry due to their multifaceted properties. In this study, we undertake a systematic investigation of the vibrational characteristics of a model indole derivative, 6-isocyano-1-methyl-1H-indole (6ICMI), by employing a combination of FTIR, IR pump-probe spectroscopy, and theoretical calculations. Our findings demonstrate a strong dependence of the isonitrile stretching frequency of 6ICMI on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when the isonitrile group is bonded to aromatic groups. Both experimental and theoretical analyses unveil a significant correlation between the isonitrile stretch vibration of 6ICMI and the solvent acceptor number of alcohols. Furthermore, the polarization-controlled infrared pump-probe conducted on 6ICMI in dimethyl sulfoxide provides additional support for the potential use of the isonitrile stretching mode of 6ICMI as an effective infrared probe for local environments.
Collapse
Affiliation(s)
- Min You
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Zilin Gao
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China;
| | - Changyuan Guo
- Key Laboratory of Intelligent Air-Ground Cooperative Control for Universities in Chongqing, College of Automation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Qiang Guo
- Shanxi Province Key Laboratory of Higee-Oriented Chemical Engineering, School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
| |
Collapse
|
5
|
Chowdhury T, Chatterjee S, Deshmukh SH, Bagchi S. A Systematic Study on the Role of Hydrogen Bond Donors in Dictating the Dynamics of Choline-Based Deep Eutectic Solvents. J Phys Chem B 2023; 127:7299-7308. [PMID: 37561654 DOI: 10.1021/acs.jpcb.3c02191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Deep eutectic solvents, promising green alternatives to conventional solvents, consist of a hydrogen bond donor and a hydrogen bond acceptor. The hydrogen bonding components in deep eutectic solvents form an extended hydrogen bonding network, which can be tuned to specific applications by changing the hydrogen bond donors. In this work, we have changed the hydrogen bond donor from a diol to a dicarboxylic acid by systematically replacing a hydroxyl group with an acid group one at a time to investigate the solvation structure and dynamics of the deep eutectic systems. Using a combination of ultrafast vibrational spectroscopy and molecular dynamics simulations, we compared the spectral diffusion and orientational relaxation dynamics of three deep eutectic systems using the vibrational responses of a dissolved anion. Our results indicate that although the solvation structures are marginally different across the systems, distinct differences are present in the solvent fluctuation and solute reorientation dynamics. This work provides a detailed molecular understanding of carboxylic-acid-based deep eutectic systems and how they differ from alcohol-based deep eutectic systems.
Collapse
Affiliation(s)
- Tubai Chowdhury
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samadhan H Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
6
|
Hassani M, Mallon CJ, Monzy JN, Schmitz AJ, Brewer SH, Fenlon EE, Tucker MJ. Inhibition of vibrational energy flow within an aromatic scaffold via heavy atom effect. J Chem Phys 2023; 158:224201. [PMID: 37309893 PMCID: PMC10275622 DOI: 10.1063/5.0153760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
The regulation of intramolecular vibrational energy redistribution (IVR) to influence energy flow within molecular scaffolds provides a way to steer fundamental processes of chemistry, such as chemical reactivity in proteins and design of molecular diodes. Using two-dimensional infrared (2D IR) spectroscopy, changes in the intensity of vibrational cross-peaks are often used to evaluate different energy transfer pathways present in small molecules. Previous 2D IR studies of para-azidobenzonitrile (PAB) demonstrated that several possible energy pathways from the N3 to the cyano-vibrational reporters were modulated by Fermi resonance, followed by energy relaxation into the solvent [Schmitz et al., J. Phys. Chem. A 123, 10571 (2019)]. In this work, the mechanisms of IVR were hindered via the introduction of a heavy atom, selenium, into the molecular scaffold. This effectively eliminated the energy transfer pathway and resulted in the dissipation of the energy into the bath and direct dipole-dipole coupling between the two vibrational reporters. Several structural variations of the aforementioned molecular scaffold were employed to assess how each interrupted the energy transfer pathways, and the evolution of 2D IR cross-peaks was measured to assess the changes in the energy flow. By eliminating the energy transfer pathways through isolation of specific vibrational transitions, through-space vibrational coupling between an azido (N3) and a selenocyanato (SeCN) probe is facilitated and observed for the first time. Thus, the rectification of this molecular circuitry is accomplished through the inhibition of energy flow using heavy atoms to suppress the anharmonic coupling and, instead, favor a vibrational coupling pathway.
Collapse
Affiliation(s)
- Majid Hassani
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | | | - Judith N. Monzy
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Andrew J. Schmitz
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| |
Collapse
|
7
|
Chatterjee S, Chowdhury T, Bagchi S. Does variation in composition affect dynamics when approaching the eutectic composition? J Chem Phys 2023; 158:114203. [PMID: 36948840 DOI: 10.1063/5.0139153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Deep eutectic solvent is a mixture of two or more components, mixed in a certain molar ratio, such that the mixture melts at a temperature lower than individual substances. In this work, we have used a combination of ultrafast vibrational spectroscopy and molecular dynamics simulations to investigate the microscopic structure and dynamics of a deep eutectic solvent (1:2 choline chloride: ethylene glycol) at and around the eutectic composition. In particular, we have compared the spectral diffusion and orientational relaxation dynamics of these systems with varying compositions. Our results show that although the time-averaged solvent structures around a dissolved solute are comparable across compositions, both the solvent fluctuations and solute reorientation dynamics show distinct differences. We show that these subtle changes in solute and solvent dynamics with changing compositions arise from the variations in the fluctuations of the different intercomponent hydrogen bonds.
Collapse
Affiliation(s)
- Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Tubai Chowdhury
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| |
Collapse
|
8
|
Haldar T, Chatterjee S, Alam MN, Maity P, Bagchi S. Blue Fluorescence of Cyano-tryptophan Predicts Local Electrostatics and Hydrogen Bonding in Biomolecules. J Phys Chem B 2022; 126:10732-10740. [PMID: 36511763 DOI: 10.1021/acs.jpcb.2c05848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cyano-tryptophan is an unnatural fluorescent amino acid that emits in the visible region. Along with the structural similarity with tryptophan, the unique photophysical properties of this fluorophore make it an ideal probe for biophysical research. Herein, combining fluorescence spectroscopy, infrared spectroscopy, and molecular dynamics simulations, we show that the cyano-tryptophan's emission energy quantifies the underlying bond-specific noncovalent interactions in terms of the electric field. We further report the use of fluorophore's emission energy to predict its hydrogen bond characteristics. We demonstrate that combining experiments with molecular dynamics simulations can provide the hydrogen bonding status of the nitrile moiety. In addition, we report a method to differentiate between aqueous and nonaqueous hydrogen-bonding partners. Using a phenomenological approach, we demonstrate that the presence of the cyano-indole moiety is responsible for the distinct correlations between the fluorophore's emission and the electrostatic forces on the nitrile bond. As indole is a privileged scaffold for both native amino acids and nucleobases, cyano-indoles will have many multifaceted applications.
Collapse
Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Md Nirshad Alam
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Pradip Maity
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| |
Collapse
|
9
|
Dereka B, Lewis NHC, Keim JH, Snyder SA, Tokmakoff A. Characterization of Acetonitrile Isotopologues as Vibrational Probes of Electrolytes. J Phys Chem B 2021; 126:278-291. [PMID: 34962409 PMCID: PMC8762666 DOI: 10.1021/acs.jpcb.1c09572] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acetonitrile has emerged as a solvent candidate for novel electrolyte formulations in metal-ion batteries and supercapacitors. It features a bright local C≡N stretch vibrational mode whose infrared (IR) signature is sensitive to battery-relevant cations (Li+, Mg2+, Zn2+, Ca2+) both in pure form and in the presence of water admixture across a full possible range of concentrations from the dilute to the superconcentrated regime. Stationary and time-resolved IR spectroscopy thus emerges as a natural tool to study site-specific intermolecular interactions from the solvent perspective without introducing an extrinsic probe that perturbs solution morphology and may not represent the intrinsic dynamics in these electrolytes. The metal-coordinated acetonitrile, water-separated metal-acetonitrile pair, and free solvent each have a distinct vibrational signature that allows their unambiguous differentiation. The IR band frequency of the metal-coordinated acetonitrile depends on the ion charge density. To study the ion transport dynamics, it is necessary to differentiate energy-transfer processes from structural interconversions in these electrolytes. Isotope labeling the solvent is a necessary prerequisite to separate these processes. We discuss the design principles and choice of the CD313CN label and characterize its vibrational spectroscopy in these electrolytes. The Fermi resonance between 13C≡N and C-D stretches complicates the spectral response but does not prevent its effective utilization. Time-resolved two-dimensional (2D) IR spectroscopy can be performed on a mixture of acetonitrile isotopologues and much can be learned about the structural dynamics of various species in these formulations.
Collapse
Affiliation(s)
- Bogdan Dereka
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60637, United States
| | - Nicholas H C Lewis
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60637, United States
| | - Jonathan H Keim
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Scott A Snyder
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60637, United States
| |
Collapse
|
10
|
Vinogradov I, Feng Y, Kumar SKK, Guo C, Udagawa NS, Ge NH. Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy. J Chem Phys 2021; 155:035102. [PMID: 34293882 DOI: 10.1063/5.0054428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.
Collapse
Affiliation(s)
- Ilya Vinogradov
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Yuan Feng
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - S K Karthick Kumar
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Chenxu Guo
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Nina Saki Udagawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| |
Collapse
|
11
|
Thielges MC. Transparent window 2D IR spectroscopy of proteins. J Chem Phys 2021; 155:040903. [PMID: 34340394 PMCID: PMC8302233 DOI: 10.1063/5.0052628] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.
Collapse
Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington,
Indiana 47405, USA
| |
Collapse
|
12
|
Choi S, Park J, Kwak K, Cho M. Substituent Effects on the Vibrational Properties of the CN Stretch Mode of Aromatic Nitriles: IR Probes Useful for Time-resolved IR Spectroscopy. Chem Asian J 2021; 16:2626-2632. [PMID: 34288497 DOI: 10.1002/asia.202100657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Indexed: 11/10/2022]
Abstract
Developing ideal IR probes is essential to understand the structure and dynamics of biomolecules with time-resolved IR spectroscopies and imaging techniques. Especially, nitrile (CN) group has recently been proposed to serve as IR probes of the local environment of proteins. Herein, we investigated the effect of a substituent on the vibrational properties of the benzonitrile. The electron-donating and withdrawing character of p-substituent on benzonitrile are expected to modulate the vibrational frequency, molar extinction coefficient, and vibrational lifetime of CN probe. FT-IR revealed the positive correlation between electron-donating character and the molar extinction coefficient of CN stretch mode. Infrared pump-probe (IR-PP) measurements showed that the vibrational lifetime of CN stretch mode exhibits a relatively weak correlation with the electron-donating strength. Among the investigated samples, 4-dimethylamino benzonitrile with the strongest electron-donating strength shows enhanced absorption and extended vibrational lifetime. Utilizing substituent effects will be a practical strategy to improve the performance of the IR probe.
Collapse
Affiliation(s)
- Suin Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Junyoung Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| |
Collapse
|
13
|
Park JY, Kwon HJ, Mondal S, Han H, Kwak K, Cho M. Two-dimensional IR spectroscopy reveals a hidden Fermi resonance band in the azido stretch spectrum of β-azidoalanine. Phys Chem Chem Phys 2020; 22:19223-19229. [PMID: 32812969 DOI: 10.1039/d0cp02693j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Azido stretch modes in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local electrostatic environments. The vibrational bands of azide probes are often accompanied by complex line shapes with shoulder peaks, which may arise either from incomplete background subtraction, Fermi resonance, or multiple conformers. The isotope substitution in the infrared probe has thus been introduced to remove Fermi resonances without causing a significant perturbation to the structure. Here, we synthesized and labeled the mid-N atoms of aliphatic azide derivatives with 15N to study the effects of isotope labelling on their vibrational properties. The FT-IR spectra of the aliphatic azide with asymmetric lineshape became a single symmetric band upon isotope substitution, which might be an indication of the removal of the hidden Fermi resonance from the system. We also noticed that the 2D-IR spectrum of unlabeled aliphatic azide has cross-peaks, even though it is not apparently identifiable. The 1D slice spectra obtained from the 2D-IR spectra reveal the existence of a hidden Fermi resonance peak. Furthermore, we show that this weak Fermi resonance does not produce discernible oscillatory beating patterns in the IR pump-probe spectrum, which has been used as evidence of the Fermi resonance. Therefore, we confirm that isotope labelling combined with 2D-IR spectroscopy is the most efficient and incisive way to identify the origin of small shoulder peaks in the linear and nonlinear vibrational spectra of various IR probe molecules.
Collapse
Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
14
|
Park JY, Mondal S, Kwon HJ, Sahu PK, Han H, Kwak K, Cho M. Effect of isotope substitution on the Fermi resonance and vibrational lifetime of unnatural amino acids modified with IR probe: A 2D-IR and pump-probe study of 4-azido-L-phenyl alanine. J Chem Phys 2020; 153:164309. [DOI: 10.1063/5.0025289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Prabhat Kumar Sahu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| |
Collapse
|
15
|
|
16
|
Schmitz AJ, Pandey HD, Chalyavi F, Shi T, Fenlon EE, Brewer SH, Leitner DM, Tucker MJ. Tuning Molecular Vibrational Energy Flow within an Aromatic Scaffold via Anharmonic Coupling. J Phys Chem A 2019; 123:10571-10581. [PMID: 31735035 DOI: 10.1021/acs.jpca.9b08010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
From guiding chemical reactivity in synthesis or protein folding to the design of energy diodes, intramolecular vibrational energy redistribution harnesses the power to influence the underlying fundamental principles of chemistry. To evaluate the ability to steer these processes, the mechanism and time scales of intramolecular vibrational energy redistribution through aromatic molecular scaffolds have been assessed by utilizing two-dimensional infrared (2D IR) spectroscopy. 2D IR cross peaks reveal energy relaxation through an aromatic scaffold from the azido- to the cyano-vibrational reporters in para-azidobenzonitrile (PAB) and para-(azidomethyl)benzonitrile (PAMB) prior to energy relaxation into the solvent. The rates of energy transfer are modulated by Fermi resonances, which are apparent by the coupling cross peaks identified within the 2D IR spectrum. Theoretical vibrational mode analysis allowed the determination of the origins of the energy flow, the transfer pathway, and a direct comparison of the associated transfer rates, which were in good agreement with the experimental results. Large variations in energy-transfer rates, approximately 1.9 ps for PAB and 23 ps for PAMB, illustrate the importance of strong anharmonic coupling, i.e., Fermi resonance, on the transfer pathways. In particular, vibrational energy rectification is altered by Fermi resonances of the cyano- and azido-modes allowing control of the propensity for energy flow.
Collapse
Affiliation(s)
- Andrew J Schmitz
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Hari Datt Pandey
- Department of Chemistry , University of California , Riverside , California 92521 , United States
| | - Farzaneh Chalyavi
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Tianjiao Shi
- Department of Chemistry , Franklin & Marshall College , Lancaster , Pennsylvania 17604-3003 , United States
| | - Edward E Fenlon
- Department of Chemistry , Franklin & Marshall College , Lancaster , Pennsylvania 17604-3003 , United States
| | - Scott H Brewer
- Department of Chemistry , Franklin & Marshall College , Lancaster , Pennsylvania 17604-3003 , United States
| | - David M Leitner
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| |
Collapse
|
17
|
Kossowska D, Park K, Park JY, Lim C, Kwak K, Cho M. Rational Design of an Acetylenic Infrared Probe with Enhanced Dipole Strength and Increased Vibrational Lifetime. J Phys Chem B 2019; 123:6274-6281. [DOI: 10.1021/acs.jpcb.9b04925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Chaiho Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| |
Collapse
|
18
|
You M, Zhou L, Huang X, Wang Y, Zhang W. Isonitrile-Derivatized Indole as an Infrared Probe for Hydrogen-Bonding Environments. Molecules 2019; 24:molecules24071379. [PMID: 30965674 PMCID: PMC6480494 DOI: 10.3390/molecules24071379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/24/2019] [Accepted: 03/30/2019] [Indexed: 11/18/2022] Open
Abstract
The isonitrile (NC) group has been shown to be a promising infrared probe for studying the structure and dynamics of biomolecules. However, there have been no systematic studies performed on the NC group as an infrared probe, when it is bonded to an indole ring. Here, we systematically study the NC stretching mode of two model compounds, 5-isocyano-1H-indole (5ICI) and 5-isocyano-1-methyl-1H-indole (NM5ICI), using Fourier transform infrared (FTIR) spectroscopy. The NC stretching frequency is shown to be strongly dependent on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when NC is bonded to an indole ring. Infrared pump–probe studies of 5ICI in DMSO and in EtOH further support that the NC stretching mode could be used as a site-specific infrared probe for local environments when NC is bonded to an indole ring.
Collapse
Affiliation(s)
- Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Xinyue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Yang Wang
- Department of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| |
Collapse
|
19
|
Kossowska D, Lee G, Han H, Kwak K, Cho M. Simultaneous enhancement of transition dipole strength and vibrational lifetime of an alkyne IR probe via π-d backbonding and vibrational decoupling. Phys Chem Chem Phys 2019; 21:24919-24925. [DOI: 10.1039/c9cp04356j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne IR probes 1–6 with Si and S (or Se) atoms incorporated into the CC bond were synthesized, and the vibrational properties of their CC stretch mode were studied using FTIR and femtosecond IR PP spectroscopies and quantum chemical calculations.
Collapse
Affiliation(s)
- Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 02841
- Korea
- Department of Chemistry
| | - Giseong Lee
- Department of Chemistry
- Korea University
- Seoul 02841
- Korea
| | - Hogyu Han
- Department of Chemistry
- Korea University
- Seoul 02841
- Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 02841
- Korea
- Department of Chemistry
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 02841
- Korea
- Department of Chemistry
| |
Collapse
|
20
|
Huang XY, You M, Ran GL, Fan HR, Zhang WK. Ester-Derivatized indoles as fluorescent and infrared probes for hydration environments. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1805118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-yue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Guang-liu Ran
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Hao-ran Fan
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wen-kai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
21
|
Chalyavi F, Gilmartin PH, Schmitz AJ, Fennie MW, Tucker MJ. Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure. Angew Chem Int Ed Engl 2018; 57:7528-7532. [PMID: 29710418 PMCID: PMC6002807 DOI: 10.1002/anie.201803849] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Indexed: 12/20/2022]
Abstract
A concise synthesis of protected 5-cyano-l-tryptophan (Trp5CN ) has been developed for 2D IR spectroscopic investigations within either peptides or proteins. To assess the potential of differently substituted cyano-tryptophans, several model cyano-indole systems were characterized using IR spectroscopy. Upon assessment of their spectroscopic properties, Trp5CN was integrated into a model peptide sequence, Trp5CN -Gly-Phe4CN , to elucidate its structure. This peptide demonstrates the capability of this probe to capture structural information by 2D IR spectroscopy. The 2D IR spectrum of the peptide in water was simulated to reveal a unique spectral signature resulting from the presence of dipolar coupling. The coupling strength between cyano labels was determined to be 1.4 cm-1 by matching the slopes along the max contour for the simulated and experimental spectrum. Using transition dipole coupling, a distance between the two probes of 13 Å was calculated.
Collapse
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Philip H Gilmartin
- Department of Chemistry, University of Scranton, 204 Monroe Ave., Scranton, PA, 18510, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Michael W Fennie
- Department of Chemistry, University of Scranton, 204 Monroe Ave., Scranton, PA, 18510, USA
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| |
Collapse
|
22
|
Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
23
|
Lee G, Kossowska D, Lim J, Kim S, Han H, Kwak K, Cho M. Cyanamide as an Infrared Reporter: Comparison of Vibrational Properties between Nitriles Bonded to N and C Atoms. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00887] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giseong Lee
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Joonhyung Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Soobin Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| |
Collapse
|
24
|
Ghosh A, Ostrander JS, Zanni MT. Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy. Chem Rev 2017; 117:10726-10759. [PMID: 28060489 PMCID: PMC5500453 DOI: 10.1021/acs.chemrev.6b00582] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.
Collapse
Affiliation(s)
| | - Joshua S. Ostrander
- 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
| |
Collapse
|
25
|
Le Sueur AL, Ramos S, Ellefsen JD, Cook S, Thielges MC. Evaluation of p-(13C,15N-Cyano)phenylalanine as an Extended Time Scale 2D IR Probe of Proteins. Anal Chem 2017; 89:5254-5260. [DOI: 10.1021/acs.analchem.6b04650] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Amanda L. Le Sueur
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Sashary Ramos
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Jonathan D. Ellefsen
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Silas Cook
- 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
| |
Collapse
|
26
|
Ramos S, Scott KJ, Horness RE, Le Sueur AL, Thielges MC. Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine. Phys Chem Chem Phys 2017; 19:10081-10086. [PMID: 28367555 PMCID: PMC6252261 DOI: 10.1039/c7cp00403f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of dynamics to the function of proteins is well appreciated, but the difficulty in their measurement impedes investigation into their precise role(s). 2D IR spectroscopy is a developing approach for the study of dynamics and has motivated efforts to develop spectrally resolved IR probe groups that enable its application for measuring the dynamics at specific sites in a protein. A challenge with this approach is that the timescales accessible are limited by the vibrational lifetimes of the probes. Toward development of better probes for 2D IR spectroscopy of protein dynamics, we report the characterization of p-cyano-seleno-phenylalanine (CNSePhe), a derivative of the well established IR probe p-cyano-phenylalanine (CNPhe), by FT IR, pump-probe, and 2D IR spectroscopy. The incorporation of the heavy Se atom decouples the CN vibration from the rest in the molecule. Although this leads to a reduction of the transition dipole strength, and thus a reduction in signal intensity, it also dramatically increases the vibrational lifetime, enabling collection of 2D IR spectra for analysis of molecular dynamics on much longer timescales. Interestingly, we also find that the lifetime for CNSePhe shows increased sensitivity to the presence of hydrogen bonding interactions with the CN, suggesting that the probe should be useful for interpretation of CN spectra and possibly for the study of solvation.
Collapse
Affiliation(s)
- S. Ramos
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - K. J. Scott
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - R. E. Horness
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - A. L. Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - M. C. Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| |
Collapse
|
27
|
Kundu A, Verma PK, Ha JH, Cho M. Studying Water Hydrogen-Bonding Network near the Lipid Multibilayer with Multiple IR Probes. J Phys Chem A 2017; 121:1435-1441. [DOI: 10.1021/acs.jpca.6b12152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Achintya Kundu
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jeong-Hyon Ha
- Space-Time
Resolved Molecular Imaging Research Team, Korea Basic Science Institute (KBSI), Seoul 136-075, Republic of Korea
| | - Minhaeng Cho
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
28
|
Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
29
|
Du MR, Zhang XB, Si SM, Yang F, Wang L. Theoretical insights into C–C bond formation through isonitrile insertion into a Cp*Ti complex. RSC Adv 2017. [DOI: 10.1039/c7ra05680j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reaction of Cp*(Cl)Ti(2,3-dimethylbutadiene) with isonitriles is studied using DFT, detailed elementary reaction steps and N-substitution effects of isonitrile are examined.
Collapse
Affiliation(s)
- Ming-Ran Du
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan 232001
- People's Republic of China
| | - Xiang-Biao Zhang
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan 232001
- People's Republic of China
| | - Sheng-Meng Si
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan 232001
- People's Republic of China
| | - Feng Yang
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan 232001
- People's Republic of China
| | - Lei Wang
- Department of Chemistry
- Huaibei Normal University
- Huaibei
- People's Republic of China
| |
Collapse
|
30
|
Du MR, Zhang XB, Si SM, Wang L. Theoretical insights into the reaction of Cp*(Cl)Hf(diene) with isonitriles. RSC Adv 2017. [DOI: 10.1039/c7ra08981c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The reaction of Cp*(Cl)Hf(2,3-dimethylbutadiene) with isonitriles is theoretically investigated, and detailed elementary reactions and the substitution effects are examined.
Collapse
Affiliation(s)
- Ming-Ran Du
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan
- People's Republic of China
| | - Xiang-Biao Zhang
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan
- People's Republic of China
| | - Sheng-Meng Si
- School of Chemical Engineering
- Anhui University of Science and Technology
- Huainan
- People's Republic of China
| | - Lei Wang
- Department of Chemistry
- Huaibei Normal University
- Huaibei
- People's Republic of China
| |
Collapse
|
31
|
Okuda M, Ohta K, Tominaga K. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies. J Chem Phys 2016. [DOI: 10.1063/1.4962344] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Masaki Okuda
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| |
Collapse
|
32
|
Maj M, Ahn C, Błasiak B, Kwak K, Han H, Cho M. Isonitrile as an Ultrasensitive Infrared Reporter of Hydrogen-Bonding Structure and Dynamics. J Phys Chem B 2016; 120:10167-10180. [DOI: 10.1021/acs.jpcb.6b04319] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Changwoo Ahn
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Bartosz Błasiak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hogyu Han
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| |
Collapse
|
33
|
Kundu A, Kwak K, Cho M. Water Structure at the Lipid Multibilayer Surface: Anionic Versus Cationic Head Group Effects. J Phys Chem B 2016; 120:5002-7. [PMID: 27171689 DOI: 10.1021/acs.jpcb.6b02340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane water interface is a potential reaction site for many biochemical reactions. Therefore, a molecular level understanding of water structure and dynamics that strongly depend on the chemical structure of lipid is prerequisite for elucidating the role of water in biological reactions on membrane surface. Recently, we carried out femtosecond infrared pump-probe studies of water structure and dynamics at multibilayer surfaces of zwitterionic phosphatidylcholine-analogue lipid ( J. Phys. Chem. Lett. 2016 , 7 , 741 ). Here, to further elucidate the anionic and cationic headgroup effects on water, we study vibrational dynamics of water on lipid multibilayers formed by anionic phospho-glycerol lipid molecules as well as by cationic choline-derivatized lipid molecules. We observed two significantly different vibrational lifetime components (very fast 0.5 ps and slow 1.9 ps) of the OD stretch mode of HOD molecules at the negatively charged phospho-lipid multibilayer whereas only one vibrational lifetime component (1.6 ps) was observed at the positively charged choline-derivatized lipid multibilayer. From the detailed analyses about the vibrational energy and rotational relaxations of HOD molecules in lipid multibilayers composed of anionic lipid with phosphate and cationic lipid without phosphate, the role of phosphate group in structuring water molecules at phospholipid membrane interface is revealed.
Collapse
Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| |
Collapse
|
34
|
Levin DE, Schmitz AJ, Hines SM, Hines KJ, Tucker MJ, Brewer SH, Fenlon EE. Synthesis and Evaluation of the Sensitivity and Vibrational Lifetimes of Thiocyanate and Selenocyanate Infrared Reporters. RSC Adv 2016; 43:36231-36237. [PMID: 27114820 DOI: 10.1039/c5ra27363c] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two novel 2'-deoxyadenosine (dA) analogues, Si2-dA-SCN and Si2-dA-SeCN, and two novel phenylalanine (Phe) analogues, Boc-Me-PheCH2SCN and Boc-Me-PheCH2SeCN, have been synthesized and the thiocyanate (SCN) and selenocyanate (SeCN) functional groups evaluated as vibrational reporters. The syntheses of Si2-dA-SCN and Si2-dA-SeCN were accomplished in three steps in 16% and 32% overall yields, respectively, and the syntheses of Boc-Me-PheCH2SCN and Boc-Me-PheCH2SeCN were completed in four steps in 8.9% and 2.3% overall yields, respectively. The SCN and SeCN stretch vibrational modes were shown to be sensitive to the local environment by frequency shifts and full-width half-maximum (fwhm) changes in response to tetrahydrofuran (THF) and THF/water solvent mixtures. The vibrational lifetimes of the Si2-dA-SeCN (237±12 ps) and Boc-Me-PheCH2SeCN (295±31 ps) in THF solution were determined by ultrafast infrared pump-probe spectroscopy to be 1.5 to 3 times longer than those for Si2-dA-SCN (140±6 ps) and Boc-Me-PheCH2SCN (102±4 ps). The longer lifetimes for the SeCN analogues were attributed to the better insulating effects of the heavier selenium atom compared to the sulfur atom. The solvent sensitivity and longer vibrational lifetimes compared to other vibrational reporters suggest that SCN and SeCN vibrational reporters are well suited to studying several dynamic processes including protein and nucleic acid hydration and conformational changes, however stability issues may require post-synthetic modification methods to incorporate these reporters into biomacromolecules.
Collapse
Affiliation(s)
- Daniel E Levin
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA
| | - Shawn M Hines
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Kevin J Hines
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Edward E Fenlon
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| |
Collapse
|
35
|
Fang B, Wang T, Chen X, Jin T, Zhang R, Zhuang W. Modeling Vibrational Spectra of Ester Carbonyl Stretch in Water and DMSO Based on Molecular Dynamics Simulation. J Phys Chem B 2015; 119:12390-6. [PMID: 26335032 DOI: 10.1021/acs.jpcb.5b06541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of molecular dynamics simulation, we model the ester carbonyl stretch FTIR signals of methyl acetate in D2O and DMSO. An ab initio map is constructed at the B3LYP/6-311++G** level to relate the carbonyl stretch frequency to the external electric field. Using this map, fluctuating Hamiltonian of the carbonyl stretch is constructed from the MD simulation trajectory. The IR spectra calculated based on this Hamiltonian are found to be in good agreement with the experiment. For methyl acetate in D2O, hydrogen bonding on alkoxy oxygen causes a blue shift of frequency, while that on carbonyl oxygen causes a red shift. Two peaks observed in FTIR signals originate from the balance of these two effects. Furthermore, in both D2O and DMSO solutions, correlations are found between the instantaneous electric field on C═O and the frequencies. Broader line width of the signal in D2O suggests a more inhomogeneous electric field distribution due to the complicated hydrogen-bonding environment.
Collapse
Affiliation(s)
- Bin Fang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Tianjun Wang
- Department of Chemistry, ShanghaiTech University , 19 Yueyang Road, Shanghai 200031, China
| | - Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University , 2699 Qianjin Street, ChangChun 130012, China
| | - Tan Jin
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| |
Collapse
|