1
|
Gräve C, Lindner J, Flesch S, Domenianni LI, Vöhringer P. Linear and Two-Dimensional Infrared Spectroscopy of the Multifunctional Vibrational Probe, 3-(4-Azidophenyl) Propiolonitrile. Deperturbing a Fermi Triad by Isotopic Substitution. Chemphyschem 2024:e202400818. [PMID: 39636750 DOI: 10.1002/cphc.202400818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 12/05/2024] [Accepted: 12/05/2024] [Indexed: 12/07/2024]
Abstract
Infrared probes are chemical moieties whose vibrational modes are used to obtain spectroscopic information about structural dynamics of complex systems; in particular, of biomacromolecules. Here, we explore the vibrational spectroscopy and dynamics of a reagent, 3-(4-azidophenyl)propiolonitrile (AzPPN), for selectively tagging thiols in protein environments with a multifunctional infrared probe containing both, an azide and a nitrile chromophore. The linear infrared spectrum of AzPPN is heavily perturbed in the antisymmetric azide stretching region as a result of accidental Fermi resonances. Isotopically labeling the azide group at the β-position deperturbs the spectrum considerably and reveals two combination tones that mix with the antisymmetric stretching fundamental into a Fermi triad of hybrid vibrational excitations. Moreover, two-dimensional infrared (2DIR) spectra were recorded for 15Nβ-labeled AzPPN, which reveal waiting-time-dependent spectral shifts of diagonal peaks and dynamic buildups of cross peaks. The 2DIR-spectral evolution is indicative of intramolecular distribution of the pump-induced excess vibrational energy into low-frequency modes of the molecule that are coupled to either the azide or the nitrile stretching transition dipoles. Finally, IR-pump/IR-probe spectra with selective narrowband excitation reveal a time constant of 2.3 ps for intramolecular vibrational redistribution (IVR) and 18 ps for the final energy dissipation into the solvent. The cross-peak dynamics corroborate a notion in which IVR within the AzPPN-molecule is an irreversible process.
Collapse
Affiliation(s)
- Claudia Gräve
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn
| | - Jörg Lindner
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn
| | - Stefan Flesch
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn
| | - Luis I Domenianni
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn
| | - Peter Vöhringer
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn
| |
Collapse
|
2
|
Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
Collapse
Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
3
|
Zhang J, Wang Z, Zhang R, Lei X, Wang G, Zou P. Hemicyanine-Phenothiazine Based Highly Selective Ratiometric Fluorescent Probes for Detecting Hypochlorite Ion in Fruits, Vegetables and Beverages. J Fluoresc 2024:10.1007/s10895-024-03694-w. [PMID: 38607530 DOI: 10.1007/s10895-024-03694-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Hypochloric acid (HClO) is a reactive oxygen species (ROS) that functions as a bacteriostatic and disinfectant in food production. Excessive levels of ClO-, however, have been linked to various health issues, including cardiovascular diseases (Halliwell and Gutteridge in Oxford University press, USA, 2015), arthritis, and neurodegenerative diseases (Heinzelmann and Bauer in Biol Chem. 391(6):675-693, 2010). Therefore, synthesizing highly selective and sensitive probes for rapidly detecting endogenous ClO- in daily foods is currently a popular research topic (Kalyanaraman et al. in Redox Biol. 15:347-362, 2018; Winterbourn in Nat Chem Biol. 4(5):278-286, 2008; Turrens in J Physiol. 552(2):335-344, 2003). Thus, we have developed two highly selective ratiometric fluorescent probes (Probe1 and Probe2) based on indole-phenothiazine to detect ClO- in common vegetables, fruits and beverages qualitatively and quantitatively. Moreover, Both Probe1 and Probe2 have shown good specificity and stability, with high fluorescence intensity and long duration (Feng et al. in Adv Sci. 5:1800397, 2018; Wei et al. in Angew Chem. 131(14):4595-4599, 2019; Baruah et al. in J Mater Chem B, 2022).
Collapse
Affiliation(s)
- Jinyang Zhang
- College of Science, Sichuan Agricultural University, Ya'an, 625014, People's Republic of China
| | - Zhe Wang
- College of Science, Sichuan Agricultural University, Ya'an, 625014, People's Republic of China
| | - Rui Zhang
- College of Science, Sichuan Agricultural University, Ya'an, 625014, People's Republic of China
| | - Xueli Lei
- College of Science, Sichuan Agricultural University, Ya'an, 625014, People's Republic of China
| | - Guangtu Wang
- College of Science, Sichuan Agricultural University, Ya'an, 625014, People's Republic of China.
| | - Ping Zou
- College of Science, Sichuan Agricultural University, Ya'an, 625014, People's Republic of China.
| |
Collapse
|
4
|
You M, Gao Z, Zhou L, Guo C, Guo Q. Investigation of the Vibrational Characteristics of 6-Isocyano-1-Methyl-1H-Indole: Utilizing the Isonitrile Group as an Infrared Probe. Molecules 2023; 28:6939. [PMID: 37836782 PMCID: PMC10574170 DOI: 10.3390/molecules28196939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Indole derivatives have garnered considerable attention in the realm of biochemistry due to their multifaceted properties. In this study, we undertake a systematic investigation of the vibrational characteristics of a model indole derivative, 6-isocyano-1-methyl-1H-indole (6ICMI), by employing a combination of FTIR, IR pump-probe spectroscopy, and theoretical calculations. Our findings demonstrate a strong dependence of the isonitrile stretching frequency of 6ICMI on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when the isonitrile group is bonded to aromatic groups. Both experimental and theoretical analyses unveil a significant correlation between the isonitrile stretch vibration of 6ICMI and the solvent acceptor number of alcohols. Furthermore, the polarization-controlled infrared pump-probe conducted on 6ICMI in dimethyl sulfoxide provides additional support for the potential use of the isonitrile stretching mode of 6ICMI as an effective infrared probe for local environments.
Collapse
Affiliation(s)
- Min You
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Zilin Gao
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China;
| | - Changyuan Guo
- Key Laboratory of Intelligent Air-Ground Cooperative Control for Universities in Chongqing, College of Automation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Qiang Guo
- Shanxi Province Key Laboratory of Higee-Oriented Chemical Engineering, School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
| |
Collapse
|
5
|
Cheng YY, Feng XZ, Zhan T, An QQ, Han GC, Chen Z, Kraatz HB. A facile indole probe for ultrasensitive immunosensor fabrication toward C-reactive protein sensing. Talanta 2023; 262:124696. [PMID: 37244246 DOI: 10.1016/j.talanta.2023.124696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/15/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
C-reactive protein (CRP) is a protein biomarker for acute phase response. Herein, we fabricate a highly sensitive electrochemical immunosensor for CRP on a screen-printed carbon electrode (SPCE) with indole as a novel electrochemical probe and Au nanoparticles for signal amplification. Amongst, indole appeared as transparent nanofilms on the electrode surface, and underwent a one-electron and one-proton transfer to form oxindole during the oxidation process. Upon optimization of experimental conditions, a logarithmic correlation between CRP concentration (0.0001-100 μg∙mL-1) and response current was revealed with a detection limit of 0.03 ng∙mL-1 and a sensitivity of 5.7055 μA∙μg-1∙mL∙cm-2. The sensor exhibited exceptionally distinction selectivity, reproducibility and stability of the electrochemical immunosensor studied. The recovery rate of CRP in human serum samples determined by the standard addition method, ranged between 98.2-102.2%. Overall, the developed immunosensor is promising, and has the potential for CRP detection in real human serum samples.
Collapse
Affiliation(s)
- Yun-Yun Cheng
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, PR China
| | - Xiao-Zhen Feng
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, PR China
| | - Tao Zhan
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, PR China
| | - Qi-Qi An
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, PR China
| | - Guo-Cheng Han
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, PR China.
| | - Zhencheng Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, PR China.
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada.
| |
Collapse
|
6
|
Roque JPL, Rosado MTS, Fausto R, Reva I. Dual Photochemistry of Benzimidazole. J Org Chem 2023; 88:2884-2897. [PMID: 36795993 PMCID: PMC9990075 DOI: 10.1021/acs.joc.2c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Monomers of benzimidazole trapped in an argon matrix at 15 K were characterized by vibrational spectroscopy and identified as 1H-tautomers exclusively. The photochemistry of matrix-isolated 1H-benzimidazole was induced by excitations with a frequency-tunable narrowband UV light and followed spectroscopically. Hitherto unobserved photoproducts were identified as 4H- and 6H-tautomers. Simultaneously, a family of photoproducts bearing the isocyano moiety was identified. Thereby, the photochemistry of benzimidazole was hypothesized to follow two reaction pathways: the fixed-ring and the ring-opening isomerizations. The former reaction channel results in the cleavage of the NH bond and formation of a benzimidazolyl radical and an H-atom. The latter reaction channel involves the cleavage of the five-membered ring and concomitant shift of the H-atom from the CH bond of the imidazole moiety to the neighboring NH group, leading to 2-isocyanoaniline and subsequently to the isocyanoanilinyl radical. The mechanistic analysis of the observed photochemistry suggests that detached H-atoms, in both cases, recombine with the benzimidazolyl or isocyanoanilinyl radicals, predominantly at the positions with the largest spin density (revealed using the natural bond analysis computations). The photochemistry of benzimidazole therefore occupies an intermediate position between the earlier studied prototype cases of indole and benzoxazole, which exhibit exclusively the fixed-ring and the ring-opening photochemistries, respectively.
Collapse
Affiliation(s)
- José P L Roque
- CQC-IMS, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | - Mário T S Rosado
- CQC-IMS, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | - Rui Fausto
- CQC-IMS, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | - Igor Reva
- CQC-IMS, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal.,CIEPQPF, Department of Chemical Engineering, University of Coimbra, Coimbra 3030-790, Portugal
| |
Collapse
|
7
|
Spange S, Weiß N, Mayerhöfer TG. The Global Polarity of Alcoholic Solvents and Water - Importance of the Collectively Acting Factors Density, Refractive Index and Hydrogen Bonding Forces. ChemistryOpen 2022; 11:e202200140. [PMID: 36284211 PMCID: PMC9596611 DOI: 10.1002/open.202200140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/26/2022] [Indexed: 11/05/2022] Open
Abstract
The DHBD quantity represents the hydroxyl group density of alcoholic solvents or water. DHBD is purely physically defined by the product of molar concentration of the solvent (N) and the factor Σn=n×f which reflects the number n and position (f-factor) of the alcoholic OH groups per molecule. Whether the hydroxyl group is either primary, secondary or tertiary is taken into account by f. Σn is clearly linearly correlated with the physical density or the refractive index of the alcohol derivative. Relationships of solvent-dependent UV/Vis absorption energies as ET (30) values, 129 Xe NMR shifts and kinetic data of 2-chloro-2-methylpropane solvolysis with DHBD are demonstrated. It can be shown that the ET (30) solvent parameter reflects the global polarity of the hydrogen bond network rather than specific H-bond acidity. Significant correlations of the log k1 rate constants of the solvolysis reaction of 2-chloro-2-methylpropane with DHBD show the physical reasoning of the approach.
Collapse
Affiliation(s)
- Stefan Spange
- Institute of ChemistryChemnitz University of TechnologyStraße der Nationen 6209111ChemnitzGermany
| | - Nadine Weiß
- Institute of ChemistryChemnitz University of TechnologyStraße der Nationen 6209111ChemnitzGermany
| | - Thomas G. Mayerhöfer
- Leibniz Institute of Photonic TechnologyAlbert-Einstein-Straße 907745JenaGermany
- Institute of Physical Chemistry and Abbe Center of PhotonicsFriedrich Schiller UniversityHelmholtzweg 4Jena07743Germany
| |
Collapse
|
8
|
Oram BK, Monu, Bandyopadhyay B. Impact of donor acidity on ν C≡N and ν O–H spectral shifts in O-H···N≡C H-bonded complexes between nitriles and alcohols: a combined IR spectroscopic and quantum chemical investigation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2061387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Binod Kumar Oram
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, India
| | - Monu
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, India
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, India
| |
Collapse
|
9
|
Thielges MC. Transparent window 2D IR spectroscopy of proteins. J Chem Phys 2021; 155:040903. [PMID: 34340394 PMCID: PMC8302233 DOI: 10.1063/5.0052628] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.
Collapse
Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington,
Indiana 47405, USA
| |
Collapse
|
10
|
|
11
|
Liu J, Huang X, Fan H, Su W, Chen X, Zhang W. Ester-derivatized indoles as sensitive infrared probes for local environment. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Kübel J, Lee G, Ooi SA, Westenhoff S, Han H, Cho M, Maj M. Ultrafast Chemical Exchange Dynamics of Hydrogen Bonds Observed via Isonitrile Infrared Sensors: Implications for Biomolecular Studies. J Phys Chem Lett 2019; 10:7878-7883. [PMID: 31794222 DOI: 10.1021/acs.jpclett.9b03144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Local probes are indispensable to study protein structure and dynamics with site-specificity. The isonitrile functional group is a highly sensitive and H-bonding interaction-specific probe. Isonitriles exhibit large spectral shifts and transition dipole moment changes upon H-bonding while being weakly affected by solvent polarity. These unique properties allow a clear separation of distinct subpopulations of interacting species and an elucidation of their ultrafast dynamics with two-dimensional infrared (2D-IR) spectroscopy. Here, we apply 2D-IR to quantify the picosecond chemical exchange dynamics of solute-solvent complexes forming between isonitrile-derivatized alanine and fluorinated ethanol, where the degree of fluorination controls their H-bond-donating ability. We show that the molecules undergo faster exchange in the presence of more acidic H-bond donors, indicating that the exchange process is primarily dependent on the nature of solvent-solvent interactions. We foresee isonitrile as a highly promising probe for studying of H-bonds dynamics in the active site of enzymes.
Collapse
Affiliation(s)
- Joachim Kübel
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| | - Giseong Lee
- Department of Chemistry , Korea University , Seoul 02841 , South Korea
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| | - Hogyu Han
- Department of Chemistry , Korea University , Seoul 02841 , South Korea
| | - Minhaeng Cho
- Department of Chemistry , Korea University , Seoul 02841 , South Korea
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science , Seoul 02841 , South Korea
| | - Michał Maj
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| |
Collapse
|