1
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Gwak S, Park JY, Cho M, Kwon HJ, Han H. Efficient and Inexpensive Synthesis of 15N-Labeled 2-Azido-1,3-dimethylimidazolinium Salts Using Na 15NO 2 Instead of Na 15NNN. ACS OMEGA 2024; 9:6556-6560. [PMID: 38371833 PMCID: PMC10870284 DOI: 10.1021/acsomega.3c07147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 02/20/2024]
Abstract
15N-Labeled azides are important probes for infrared and magnetic resonance spectroscopy and imaging. They can be synthesized by reaction of primary amines with a 15N-labeled diazo-transfer reagent. We present the synthesis of 15N-labeled 2-azido-1,3-dimethylimidazolinium salts 1 as a 15N-labeled diazo-transfer reagent. Nitrosation of 1,3-dimethylimidazolinium-2-yl hydrazine (2) with Na15NO2 under acidic conditions gave 1 as a 1:1 mixture of α- and γ-15N-labeled azides, α- and γ-1, rather than γ-1 alone. The isotopomeric mixture thus obtained was then subjected to the diazo-transfer reaction with primary amines 3 to afford azides 4 as a 1:1 mixture of β-15N-labeled azides β-4 and unlabeled ones 4'. The efficient and inexpensive synthesis of 1 as a 1:1 mixture of α- and γ-1 using Na15NO2 instead of Na15NNN facilitates their wide use as a 15N-labeled diazo-transfer reagent for preparing 15N-labeled azides as molecular probes.
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Affiliation(s)
- Sungduk Gwak
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Jun Young Park
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hyeok-Jun Kwon
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Hogyu Han
- Department
of Chemistry, Korea University, Seoul 02841, Korea
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2
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Hu J, Bi J, Tuyizere E, Men Z. Investigating local field tuning Fermi resonance of CS 2 by Raman spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123881. [PMID: 38277784 DOI: 10.1016/j.saa.2024.123881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
In the spectroscopic study of polyatomic molecules, Fermi resonance (FR) is a vibrational coupling and energy transfer phenomenon that widely exists intra- and intermolecular. In particular, the FR coupling between the fundamental mode ν1 and the doubling mode 2ν2 of the CS2 molecule has attracted extensive research. In this work, we investigate the effect of local field on tuning the FR of CS2. By analyzing the Raman spectra of CS2 mixed with methanol and ethanol with different mole fractions, the results indicated that weak HBs interactions in binary solutions can be reflected by the linear frequency shift of the C-H bond vibrations (in methanol and ethanol) with different molar concentrations. Furthermore, the geometrical structure was optimized using DFT simulation, and the vibration analysis and interaction energy were carried out. The simulated Raman spectra are in good agreement with the experiments. In addition, high-pressure Raman spectra of CS2 were obtained by diamond anvil cell technique (up to 9.19 GPa) and a pressure-induced phase transition was observed at 1.71 GPa. The results demonstrated that the pressure-induced polymerization phase transition of CS2 molecules causes the close packing and more orderly arrangement of molecules, resulting in the enhancement of FR coupling. HB and high pressure tune the FR of the CS2 molecule differently.
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Affiliation(s)
- Junying Hu
- Key Laboratory of Physics and Technology for Advanced Batteries of Ministry of Education, College of Physics, Jilin University, Changchun 130012, China
| | - Jingkai Bi
- Institute of Quantum Materials and Physics, Henan Academy of Sciences, Zhengzhou 450046, China
| | - Emmanuel Tuyizere
- Key Laboratory of Physics and Technology for Advanced Batteries of Ministry of Education, College of Physics, Jilin University, Changchun 130012, China
| | - Zhiwei Men
- Key Laboratory of Physics and Technology for Advanced Batteries of Ministry of Education, College of Physics, Jilin University, Changchun 130012, China.
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3
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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4
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Perera SM, Aikawa T, Shaner SE, Moran SD, Wang L. Effects of the Intramolecular Group and Solvent on Vibrational Coupling Modes and Strengths of Fermi Resonances in Aryl Azides: A DFT Study of 4-Azidotoluene and 4-Azido- N-phenylmaleimide. J Phys Chem A 2023; 127:8911-8921. [PMID: 37819373 DOI: 10.1021/acs.jpca.3c06312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The high transition dipole strength of the azide asymmetric stretch makes aryl azides good candidates as vibrational probes (VPs). However, aryl azides have complex absorption profiles due to Fermi resonances (FRs). Understanding the origin and the vibrational modes involved in FRs of aryl azides is critically important toward developing them as VPs for studies of protein structures and structural changes in response to their surroundings. As such, we studied vibrational couplings in 4-azidotoluene and 4-azido-N-phenylmaleimide in two solvents, N,N-dimethylacetamide and tetrahydrofuran, to explore the origin and the effects of intramolecular group and solvent on the FRs of aryl azides using density functional theory (DFT) calculations with the B3LYP functional and seven basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). Two combination bands consisting of the azide symmetric stretch and another mode form strong FRs with the azide asymmetric stretch for both molecules. The FR profile was altered by replacing the methyl group with maleimide. Solvents change the relative peak position and intensity more significantly for 4-azido-N-phenylmaleimide, which makes it a more sensitive VP. Furthermore, the DFT results indicate that a comparison among the results from different basis sets can be used as a means to predict more reliable vibrational spectra.
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Affiliation(s)
- Sathya M Perera
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Tenyu Aikawa
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Sarah E Shaner
- Department of Chemistry and Physics, Southeast Missouri State University, Cape Girardeau, Missouri 63701, United States
| | - Sean D Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Lichang Wang
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
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5
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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.
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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
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6
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Lee B, Papoutsis BM, Wong NY, Piacentini J, Kearney C, Huggins NA, Cruz N, Ng TT, Hao KH, Kramer JS, Fenlon EE, Nerenberg PS, Phillips-Piro CM, Brewer SH. Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine. J Phys Chem B 2022; 126:8957-8969. [PMID: 36317866 PMCID: PMC10234312 DOI: 10.1021/acs.jpcb.2c05954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a multifaceted approach to effectively probe complex local protein environments utilizing the vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNPhe) in the model system superfolder green fluorescent protein (sfGFP). This approach combines temperature-dependent infrared (IR) spectroscopy, X-ray crystallography, and molecular dynamics (MD) simulations to provide a molecular interpretation of the local environment of the nitrile group in the protein. Specifically, a two-step enantioselective synthesis was developed that provided an 87% overall yield of pCNPhe in high purity without the need for chromatography. It was then genetically incorporated individually at three unique sites (74, 133, and 149) in sfGFP to probe these local protein environments. The incorporation of the UAA site-specifically in sfGFP utilized an engineered, orthogonal tRNA synthetase in E. coli using the Amber codon suppression protocol, and the resulting UAA-containing sfGFP constructs were then explored with this approach. This methodology was effectively utilized to further probe the local environments of two surface sites (sites 133 and 149) that we previously explored with room temperature IR spectroscopy and X-ray crystallography and a new interior site (site 74) featuring a complex local environment around the nitrile group of pCNPhe. Site 133 was found to be solvent-exposed, while site 149 was partially buried. Site 74 was found to consist of three distinct local environments around the nitrile group including nonspecific van der Waals interactions, hydrogen-bonding to a structural water, and hydrogen-bonding to a histidine side chain.
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Affiliation(s)
- ByungUk Lee
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Brianna M. Papoutsis
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Nathan Y. Wong
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Juliana Piacentini
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Nia A. Huggins
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | - Nicole Cruz
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | - Tracey T. Ng
- Department of Physics and Astronomy, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | - Kexin Heather Hao
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Jeremy S. Kramer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Paul S. Nerenberg
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
- Department of Physics and Astronomy, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | | | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
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7
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Kwon HJ, Gwak S, Park JY, Cho M, Han H. TfNN 15N: A γ- 15N-Labeled Diazo-Transfer Reagent for the Synthesis of β- 15N-Labeled Azides. ACS OMEGA 2022; 7:293-298. [PMID: 35036700 PMCID: PMC8757338 DOI: 10.1021/acsomega.1c04679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Azides are infrared (IR) probes that are important for structure and dynamics studies of proteins. However, they often display complex IR spectra owing to Fermi resonances and multiple conformers. Isotopic substitution of azides weakens the Fermi resonance, allowing more accurate IR spectral analysis. Site-specifically 15N-labeled aromatic azides, but not aliphatic azides, are synthesized through nitrosation. Both 15N-labeled aromatic and aliphatic azides are synthesized through nucleophilic substitution or diazo-transfer reaction but as an isotopomeric mixture. We present the synthesis of TfNN15N, a γ-15N-labeled diazo-transfer reagent, and its use to prepare β-15N-labeled aliphatic as well as aromatic azides.
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Affiliation(s)
- Hyeok-Jun Kwon
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Sungduk Gwak
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Jun Young Park
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hogyu Han
- Department
of Chemistry, Korea University, Seoul 02841, Korea
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8
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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.
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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
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9
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Cao X, Xing L, Wang Y, Wang S, Sun C, Men Z. Determination of temperature-dependent Fermi resonance in acetonitrile-water binary solution by two-dimensional correlation Raman spectroscopy. J Chem Phys 2021; 155:124302. [PMID: 34598585 DOI: 10.1063/5.0060969] [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
Acetonitrile (AN), as an organic solvent, has a wide range of applications. The C≡N stretching vibration mode (ν2) and the combination mode (ν3 + ν4) are coupled by Fermi resonance (FR). In this work, the phase transition and the interaction mechanism of the 60% AN-water binary solution (AN-Water) were analyzed by calculating FR parameters and two-dimensional correlation Raman spectroscopy (2DCRS). The change in the ν2 band and the base bands ν3 and ν4 caused energy transfer by anharmonic interaction, which led to a change in FR parameters. With a reduced temperature, the energy transfer was caused by microheterogeneity and the energy transfer effect (293-273 K), the phase separation (263-233 K), and the phase transition of AN (223-173 K). The 2DCRS and Gaussian deconvolution provided more information on FR, which revealed the interaction mechanism of the Fermi doublet. The polarity and binding modes of molecules provided a new perspective for analyzing the transmission of electrons and ions in the electrolyte at different temperatures.
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Affiliation(s)
- Xianwen Cao
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Lu Xing
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Ying Wang
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Shenghan Wang
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Chenglin Sun
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun 130012, China
| | - Zhiwei Men
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
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10
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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.
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Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington,
Indiana 47405, USA
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11
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Kurttila M, Stucki-Buchli B, Rumfeldt J, Schroeder L, Häkkänen H, Liukkonen A, Takala H, Kottke T, Ihalainen JA. Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy. Phys Chem Chem Phys 2021; 23:5615-5628. [PMID: 33656023 DOI: 10.1039/d0cp06553f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Signal propagation in photosensory proteins is a complex and multidimensional event. Unraveling such mechanisms site-specifically in real time is an eligible but a challenging goal. Here, we elucidate the site-specific events in a red-light sensing phytochrome using the unnatural amino acid azidophenylalanine, vibrationally distinguishable from all other protein signals. In canonical phytochromes, signal transduction starts with isomerization of an excited bilin chromophore, initiating a multitude of processes in the photosensory unit of the protein, which eventually control the biochemical activity of the output domain, nanometers away from the chromophore. By implementing the label in prime protein locations and running two-color step-scan FTIR spectroscopy on the Deinococcus radiodurans bacteriophytochrome, we track the signal propagation at three specific sites in the photosensory unit. We show that a structurally switchable hairpin extension, a so-called tongue region, responds to the photoconversion already in microseconds and finalizes its structural changes concomitant with the chromophore, in milliseconds. In contrast, kinetics from the other two label positions indicate that the site-specific changes deviate from the chromophore actions, even though the labels locate in the chromophore vicinity. Several other sites for labeling resulted in impaired photoswitching, low structural stability, or no changes in the difference spectrum, which provides additional information on the inner dynamics of the photosensory unit. Our work enlightens the multidimensionality of the structural changes of proteins under action. The study also shows that the signaling mechanism of phytochromes is accessible in a time-resolved and site-specific approach by azido probes and demonstrates challenges in using these labels.
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Affiliation(s)
- Moona Kurttila
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Brigitte Stucki-Buchli
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Jessica Rumfeldt
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Lea Schroeder
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Heikki Häkkänen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Alli Liukkonen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Heikki Takala
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Janne A Ihalainen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
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12
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Novak U, Grdadolnik J. Infrared spectra of hydrogen bond network in lamellar perfluorocarboxylic acid monohydrates. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119551. [PMID: 33610100 DOI: 10.1016/j.saa.2021.119551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
The infrared spectra of the long-chain perfluorocarboxylic acid monohydrates differ markedly from those of the anhydrous dimers. Consequently, the structure of the solid perfluorocarboxylic acid monohydrates must differ from any known dimer-containing carboxylic acid crystals. Consideration of the significant features of the infrared spectra of the long-chain perfluorocarboxylic acid monohydrates, supplemented by their Raman spectra, and comparison with the spectra of auxiliary substances have led us to conclude that the rather strong neutral carboxyl-hydroxyl to water bonding can best explain the observations. The infrared spectra indicate the presence of fairly short hydrogen bonds connecting the water molecules to the carbonyl groups. In the construction of the hydrogen bonding pattern of the perfluorocarboxylic acid monohydrates, the oxalic acid dihydrate plays the key role. The striking similarity between the infrared spectra of the oxalic acid dihydrates and the perfluorocarboxylic acid monohydrates in the regions characteristic of water and OH⋯O vibration suggests that the structure of the hydrated carboxyl groups is the same in both crystals. These regions are characterized by the sharp doublet at 3539 cm-1 and 3464 cm-1, which is due to the H2O ν1 and ν3 stretching vibrations, respectively, and the broad absorption between 3000 cm-1 and 1500 cm-1 with the intense band at 1970 cm-1, both associated with the vibration of the OH⋯O group. The later peak consists of two band components at near 1980 cm-1 and 2020 cm-1. These band components show different behaviour when the temperature, polarization or deuteration is changed. In general, the infrared spectra of long-chain perfluorocarboxylic acids represent the system with very short hydrogen bonds connecting the water molecules to the carboxylates. This hydrogen bond pattern should be very similar to that found in the crystals of α-oxalic acid dihydrate.
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Affiliation(s)
- Urban Novak
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
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13
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Abstract
The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN3) in lysozyme are characterized. It is found that AlaN3 is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ2 range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ0 ∼ 0 ps-1) or to a remaining, static contribution of ∼0.5 ps-1 (corresponding to 2.5 cm-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.
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Affiliation(s)
- Seyedeh Maryam Salehi
- 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
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14
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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.
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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.
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15
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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
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16
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Chalyavi F, Schmitz AJ, Fetto NR, Tucker MJ, Brewer SH, Fenlon EE. Extending the vibrational lifetime of azides with heavy atoms. Phys Chem Chem Phys 2020; 22:18007-18013. [PMID: 32749405 DOI: 10.1039/d0cp02814b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of novel vibrational reporters (VRs), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (<2 ps) have limited their full potential. Herein we report that the vibrational lifetimes of azides can be increased by attaching them to heavy atoms and by using heavy 15N isotopes. Three group 14 atom triphenyl azides (Ph3CN3, Ph3SiN3, Ph3SnN3), and their triple-15N isotopomers, were synthesized in good yields. Tributyltin azide and its heavy isotopomer (Bu3Sn15N3) were also prepared to probe the effect of molecular scaffolding. The extinction coefficients for the natural abundance azides were determined, ranging from 900 to 1500 M-1 cm-1. The vibrational lifetimes of all azides were measured by pump-probe IR spectroscopy and each showed a major component with a short-to-moderate vibrational lifetime and a minor component with a much longer vibrational lifetime. Based on these results, the lifetime, aka the observation window, of an azide reporter can be extended from ∼2 ps to as long as ∼300 ps by a combination of isotopic labeling and heavy atom effect. 2D IR measurements of these compounds further confirmed the ability to observe these azide transitions at much longer timescales showing their utility to capture dynamic processes from tens to hundreds of picoseconds.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Natalie R Fetto
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, 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. ,
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17
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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18
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Chalyavi F, Adeyiga O, Weiner JM, Monzy JN, Schmitz AJ, Nguyen JK, Fenlon EE, Brewer SH, Odoh SO, Tucker MJ. 2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks. J Chem Phys 2020; 152:074201. [PMID: 32087671 PMCID: PMC7028433 DOI: 10.1063/1.5138654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Olajumoke Adeyiga
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Julia M. Weiner
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Judith N. Monzy
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Andrew J. Schmitz
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Justin K. Nguyen
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Edward E. Fenlon
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Samuel O. Odoh
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
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19
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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.
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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
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20
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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
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21
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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.
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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.
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22
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Cao X, Gong N, Zhao H, Li Z, Sun C, Men Z. Raman spectroscopic study of nonlinear modulation on Fermi resonance of acetonitrile by hydrogen-bonding network. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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24
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Krause BS, Kaufmann JCD, Kuhne J, Vierock J, Huber T, Sakmar TP, Gerwert K, Bartl FJ, Hegemann P. Tracking Pore Hydration in Channelrhodopsin by Site-Directed Infrared-Active Azido Probes. Biochemistry 2019; 58:1275-1286. [DOI: 10.1021/acs.biochem.8b01211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Benjamin S. Krause
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Joel C. D. Kaufmann
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jens Kuhne
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Johannes Vierock
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Thomas Huber
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge, Sweden
| | - Klaus Gerwert
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Franz J. Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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25
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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26
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Zhang J, Wang L, Zhang J, Zhu J, Pan X, Cui Z, Wang J, Fang W, Li Y. Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine. J Phys Chem B 2018; 122:8122-8133. [DOI: 10.1021/acs.jpcb.8b03887] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Li Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jin Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Xin Pan
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- College of Physics and Electric Information, Anhui Normal University, Wuhu 241000, People’s Republic of China
| | - Zhifeng Cui
- College of Physics and Electric Information, Anhui Normal University, Wuhu 241000, People’s Republic of China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Weihai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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27
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Varner C, Zhou X, Saxman ZK, Leger JD, Jayawickramarajah J, Rubtsov IV. Azido alkanes as convenient reporters for mobility within lipid membranes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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28
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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.
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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
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29
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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]
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30
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Balakrishnan G, Barnett GV, Kar SR, Das TK. Detection and Identification of the Vibrational Markers for the Quantification of Methionine Oxidation in Therapeutic Proteins. Anal Chem 2018; 90:6959-6966. [PMID: 29741878 DOI: 10.1021/acs.analchem.8b01238] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Methionine oxidation is a major degradation pathway in therapeutic proteins which can impact the structure and function of proteins as well as risk to drug product quality. Detecting Met oxidation in proteins by peptide mapping followed by liquid chromatography with mass spectrometry (LC-MS) is the industry standard but is also labor intensive and susceptible to artifacts. In this work, vibrational difference spectroscopy in combination with 18O isotopic shift enabled us to demonstrate the application of Raman and FTIR techniques for the detection and quantification of Met oxidation in various therapeutic proteins, including mAbs, fusion proteins, and antibody drug conjugate. Vibrational markers of Met oxidation products, such as sulfoxide and sulfone, corresponding to S═O and C-S═O stretching frequencies were unequivocally identified based 18O isotoptic shifts. The intensity of the isolated νC-S Raman band at 702 cm-1 was successfully applied to quantify the average Met oxidation level in multiple proteins. These results are further corroborated by oxidation levels measured by tryptic peptide mapping, and thus the confirmed Met oxidation levels derived from Raman and mass spectrometry are indeed consistent with each other. Thus, we demonstrate the broader application of vibrational spectroscopy to detect the subtle spectral changes associated with various chemical or physical degradation of proteins, including Met oxidation as well as higher order structural changes.
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Affiliation(s)
- Gurusamy Balakrishnan
- Molecular and Analytical Development , Bristol-Myers Squibb , 311 Pennington Rocky Hill Road , Pennington , New Jersey 08534 , United States
| | - Gregory V Barnett
- Molecular and Analytical Development , Bristol-Myers Squibb , 311 Pennington Rocky Hill Road , Pennington , New Jersey 08534 , United States
| | - Sambit R Kar
- Molecular and Analytical Development , Bristol-Myers Squibb , 311 Pennington Rocky Hill Road , Pennington , New Jersey 08534 , United States
| | - Tapan K Das
- Molecular and Analytical Development , Bristol-Myers Squibb , 311 Pennington Rocky Hill Road , Pennington , New Jersey 08534 , United States
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31
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Bag SS, De S. Multipurpose isothiocyanyl alanine/lysine: Use as solvatochromic IR probes and in site specific labeling/ligation of short peptides. Bioorg Med Chem Lett 2018; 28:1404-1409. [PMID: 29555154 DOI: 10.1016/j.bmcl.2018.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/27/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022]
Abstract
The solvatochromic IR responsivity of small side chain -NCS in two unexplored unnatural amino acids, isothiocyanyl alanine (NCSAla = Ita) and lysine (NCSLys = Itl), without perturbing the conformation is demonstrated in two designed short tripeptide (BocAla-NCSAla-Ala-OMe) and hexapeptide (BocLeu-Val-Phe-Phe-NCSLys-Gly-OMe). Demonstration of site specific fluorescent labeling in both the peptides and ligation type reaction in NCSLys indicates the novelty of these two amino acids as alternative to the available canonical amino acids.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bioorganic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Suranjan De
- Bioorganic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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32
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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
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33
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Delor M, Archer SA, Keane T, Meijer AJHM, Sazanovich IV, Greetham GM, Towrie M, Weinstein JA. Directing the path of light-induced electron transfer at a molecular fork using vibrational excitation. Nat Chem 2017; 9:1099-1104. [DOI: 10.1038/nchem.2793] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/05/2017] [Indexed: 11/09/2022]
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34
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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
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35
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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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36
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Archer SA, Keane T, Delor M, Meijer AJHM, Weinstein JA. (13)C or Not (13)C: Selective Synthesis of Asymmetric Carbon-13-Labeled Platinum(II) cis-Acetylides. Inorg Chem 2016; 55:8251-3. [PMID: 27504991 DOI: 10.1021/acs.inorgchem.6b01287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asymmetric isotopic labeling of parallel and identical electron- or energy-transfer pathways in symmetrical molecular assemblies is an extremely challenging task owing to the inherent lack of isotopic selectivity in conventional synthetic methods. Yet, it would be a highly valuable tool in the study and control of complex light-matter interactions in molecular systems by exclusively and nonintrusively labeling one of otherwise identical reaction pathways, potentially directing charge and energy transport along a chosen path. Here we describe the first selective synthetic route to asymmetrically labeled organometallic compounds, on the example of charge-transfer platinum(II) cis-acetylide complexes. We demonstrate the selective (13)C labeling of one of two acetylide groups. We further show that such isotopic labeling successfully decouples the two ν(C≡C) in the mid-IR region, permitting independent spectroscopic monitoring of two otherwise identical electron-transfer pathways, along the (12)C≡(12)C and (13)C≡(13)C coordinates. Quantum-mechanical mixing leads to intriguing complex features in the vibrational spectra of such species, which we successfully model by full-dimensional anharmonically corrected DFT calculations, despite the large size of these systems. The synthetic route developed and demonstrated herein should lead to a great diversity of asymmetric organometallic complexes inaccessible otherwise, opening up a plethora of opportunities to advance the fundamental understanding and control of light-matter interactions in molecular systems.
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Affiliation(s)
- Stuart A Archer
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Theo Keane
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Milan Delor
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Anthony J H M Meijer
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Julia A Weinstein
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
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37
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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
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38
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Schmitz AJ, Hogle DG, Gai XS, Fenlon EE, Brewer SH, Tucker MJ. Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside. J Phys Chem B 2016; 120:9387-94. [PMID: 27510724 DOI: 10.1021/acs.jpcb.6b07212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2'-azido-5-cyano-2'-deoxyuridine (N3CNdU) are examined by two-dimensional infrared (2D IR) spectroscopy. At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational transitions along the diagonal and off-diagonal cross peaks indicating vibrational coupling. The coupling strength is determined from the off-diagonal anharmonicity to be 66 cm(-1) for the intramolecular distance of ∼7.9 Å, based on a structural map generated for this model system. In addition, the frequency-frequency correlation decay is detected, monitoring the solvent dynamics around each individual probe position. Overall, these vibrational reporters can be utilized in tandem to simultaneously track global structural information and fast structural fluctuations.
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Affiliation(s)
- Andrew J Schmitz
- Department of Chemistry, University of Nevada , Reno, Nevada 89557, United States
| | - David G Hogle
- Department of Chemistry, University of Nevada , Reno, Nevada 89557, United States
| | - Xin Sonia Gai
- 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
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada , Reno, Nevada 89557, United States
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39
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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.
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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
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40
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Tookmanian EM, Phillips-Piro CM, Fenlon EE, Brewer SH. Azidoethoxyphenylalanine as a Vibrational Reporter and Click Chemistry Partner in Proteins. Chemistry 2015; 21:19096-103. [PMID: 26608683 PMCID: PMC4815431 DOI: 10.1002/chem.201503908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 11/08/2022]
Abstract
An unnatural amino acid, 4-(2-azidoethoxy)-L-phenylalanine (AePhe, 1), was designed and synthesized in three steps from known compounds in 54% overall yield. The sensitivity of the IR absorption of the azide of AePhe was established by comparison of the frequency of the azide asymmetric stretch vibration in water and dimethyl sulfoxide. AePhe was successfully incorporated into superfolder green fluorescent protein (sfGFP) at the 133 and 149 sites by using the amber codon suppression method. The IR spectra of these sfGFP constructs indicated that the azide group at the 149 site was not fully solvated despite the location in sfGFP and the three-atom linker between the azido group and the aromatic ring of AePhe. An X-ray crystal structure of sfGFP-149-AePhe was solved at 1.45 Å resolution and provides an explanation for the IR data as the flexible linker adopts a conformation which partially buries the azide on the protein surface. Both sfGFP-AePhe constructs efficiently undergo a bioorthogonal strain-promoted click cycloaddition with a dibenzocyclooctyne derivative.
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Affiliation(s)
- Elise M Tookmanian
- Department of Chemistry Franklin & Marshall College, P.O. Box 3003, Lancaster, PA 17604 (USA)
| | | | - Edward E Fenlon
- Department of Chemistry Franklin & Marshall College, P.O. Box 3003, Lancaster, PA 17604 (USA).
| | - Scott H Brewer
- Department of Chemistry Franklin & Marshall College, P.O. Box 3003, Lancaster, PA 17604 (USA).
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41
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Wahsner J, Seitz M. Nonradiative Deactivation of Lanthanoid Excited States by Inner-Sphere Carboxylates. Inorg Chem 2015; 54:10841-8. [DOI: 10.1021/acs.inorgchem.5b01920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jessica Wahsner
- Inorganic
Chemistry I, Department of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Michael Seitz
- Institute of Inorganic Chemistry, University of Tübingen, Auf
der Morgenstelle 18, 72076 Tübingen, Germany
- Inorganic
Chemistry I, Department of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
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42
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Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
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Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
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43
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Czurlok D, Torres-Alacan J, Vöhringer P. Ultrafast 2DIR spectroscopy of ferric azide precursors for high-valent iron. Vibrational relaxation, spectral diffusion, and dynamic symmetry breaking. J Chem Phys 2015; 142:212402. [DOI: 10.1063/1.4914154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Denis Czurlok
- Abteilung für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Joel Torres-Alacan
- Abteilung für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Peter Vöhringer
- Abteilung für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
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44
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Li T, Cui Y, Mathaga J, Kumar R, Kuroda DG. Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine). J Chem Phys 2015; 142:212438. [PMID: 26049458 PMCID: PMC4425731 DOI: 10.1063/1.4919795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/23/2015] [Indexed: 12/20/2022] Open
Abstract
Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm(-1) region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ∼0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters.
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Affiliation(s)
- Tanping Li
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
| | - Yaowen Cui
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
| | - John Mathaga
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
| | - Revati Kumar
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
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45
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Abstract
Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
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46
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Maj M, Ahn C, Kossowska D, Park K, Kwak K, Han H, Cho M. β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes. Phys Chem Chem Phys 2015; 17:11770-8. [DOI: 10.1039/c5cp00454c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump–probe spectroscopy.
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Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Changwoo Ahn
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Kyungwon Kwak
- Department of Chemistry
- Chung-Ang University
- Seoul 156-756, Korea
| | - Hogyu Han
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
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Tookmanian EM, Fenlon EE, Brewer SH. Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids. RSC Adv 2014; 5:1274-1281. [PMID: 26478813 PMCID: PMC4603873 DOI: 10.1039/c4ra14244f] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.
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Affiliation(s)
- Elise M. Tookmanian
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Edward E. Fenlon
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Scott H. Brewer
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
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Chen Z, Paley DW, Wei L, Weisman AL, Friesner RA, Nuckolls C, Min W. Multicolor live-cell chemical imaging by isotopically edited alkyne vibrational palette. J Am Chem Soc 2014; 136:8027-33. [PMID: 24849912 PMCID: PMC4063185 DOI: 10.1021/ja502706q] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Vibrational imaging such as Raman microscopy is a powerful technique for visualizing a variety of molecules in live cells and tissues with chemical contrast. Going beyond the conventional label-free modality, recent advance of coupling alkyne vibrational tags with stimulated Raman scattering microscopy paves the way for imaging a wide spectrum of alkyne-labeled small biomolecules with superb sensitivity, specificity, resolution, biocompatibility, and minimal perturbation. Unfortunately, the currently available alkyne tag only processes a single vibrational "color", which prohibits multiplex chemical imaging of small molecules in a way that is being routinely practiced in fluorescence microscopy. Herein we develop a three-color vibrational palette of alkyne tags using a (13)C-based isotopic editing strategy. We first synthesized (13)C isotopologues of EdU, a DNA metabolic reporter, by using the newly developed alkyne cross-metathesis reaction. Consistent with theoretical predictions, the mono-(13)C ((13)C≡(12)C) and bis-(13)C ((13)C≡(13)C) labeled alkyne isotopologues display Raman peaks that are red-shifted and spectrally resolved from the originally unlabeled ((12)C≡(12)C) alkynyl probe. We further demonstrated three-color chemical imaging of nascent DNA, RNA, and newly uptaken fatty-acid in live mammalian cells with a simultaneous treatment of three different isotopically edited alkynyl metabolic reporters. The alkyne vibrational palette presented here thus opens up multicolor imaging of small biomolecules, enlightening a new dimension of chemical imaging.
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Affiliation(s)
- Zhixing Chen
- Department of Chemistry, ‡Department of Applied Physics and Applied Mathematics, and §Kavli Institute for Brain Science, Columbia University , New York, New York 10027, United States
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Wolfshorndl MP, Baskin R, Dhawan I, Londergan CH. Covalently Bound Azido Groups Are Very Specific Water Sensors, Even in Hydrogen-Bonding Environments. J Phys Chem B 2012; 116:1172-9. [DOI: 10.1021/jp209899m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Marta P. Wolfshorndl
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Rachel Baskin
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Ishita Dhawan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
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50
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Kuroda DG, Hochstrasser RM. Dynamic structures of aqueous oxalate and the effects of counterions seen by 2D IR. Phys Chem Chem Phys 2012; 14:6219-24. [DOI: 10.1039/c2cp23892f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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