1
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Zhou L, Feng RR, Zhang W, Gai F. Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences. J Phys Chem Lett 2024; 15:187-200. [PMID: 38156972 DOI: 10.1021/acs.jpclett.3c02619] [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: 01/03/2024]
Abstract
Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.
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Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- 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
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2
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Bai Y, Camargo CM, Glasauer SMK, Gifford R, Tian X, Longhini AP, Kosik KS. Single-cell mapping of lipid metabolites using an infrared probe in human-derived model systems. Nat Commun 2024; 15:350. [PMID: 38191490 PMCID: PMC10774263 DOI: 10.1038/s41467-023-44675-0] [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: 04/03/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Understanding metabolic heterogeneity is the key to uncovering the underlying mechanisms of metabolic-related diseases. Current metabolic imaging studies suffer from limitations including low resolution and specificity, and the model systems utilized often lack human relevance. Here, we present a single-cell metabolic imaging platform to enable direct imaging of lipid metabolism with high specificity in various human-derived 2D and 3D culture systems. Through the incorporation of an azide-tagged infrared probe, selective detection of newly synthesized lipids in cells and tissue became possible, while simultaneous fluorescence imaging enabled cell-type identification in complex tissues. In proof-of-concept experiments, newly synthesized lipids were directly visualized in human-relevant model systems among different cell types, mutation status, differentiation stages, and over time. We identified upregulated lipid metabolism in progranulin-knockdown human induced pluripotent stem cells and in their differentiated microglia cells. Furthermore, we observed that neurons in brain organoids exhibited a significantly lower lipid metabolism compared to astrocytes.
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Affiliation(s)
- Yeran Bai
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
- Photothermal Spectroscopy Corp., Santa Barbara, CA, USA.
| | - Carolina M Camargo
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Stella M K Glasauer
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Raymond Gifford
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Xinran Tian
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Andrew P Longhini
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
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3
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Taniguchi T, Agbo DO. Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region. Phys Chem Chem Phys 2023; 25:28567-28575. [PMID: 37861094 DOI: 10.1039/d3cp04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
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4
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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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5
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Dong T, Yu P, Zhao J, Wang J. Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching. Phys Chem Chem Phys 2022; 24:29988-29998. [PMID: 36472165 DOI: 10.1039/d2cp03920f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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6
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Akhiyarov AA, Lobov AN, Chernikova IB, Ivanov SP. Acid-Base Properties of 6-Methyluracil-5-carbonitrile and Its N-Methyl Derivatives. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Taniguchi T, Zubir MZM, Harada N, Monde K. Exploration of chromophores for a VCD couplet in a spectrally transparent infrared region for biomolecules. Phys Chem Chem Phys 2021; 23:27525-27532. [PMID: 34874381 DOI: 10.1039/d1cp04074j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Interactions of two chromophores such as carbonyl groups yield a strong VCD couplet that reflects the molecular structures. The use of VCD couplets for biomacromolecular structural studies has been hampered by severe signal overlap caused by numerous functional groups that originally exist in biomacromolecules. Nitrile, isonitrile, alkyne, and azido groups show characteristic IR absorption in the 2300-2000 cm-1 region, where biomolecules do not strongly absorb. We herein examined the usefulness of these functional groups as chromophores to observe a strong VCD couplet that can be readily interpreted using theoretical calculations. Studies on a chiral binaphthyl scaffold possessing two identical chromophores showed that nitrile and isonitrile groups generate moderately-strong but complex VCD signals due to anharmonic contributions. The nature of their anharmonic VCD patterns is discussed by comparison with the VCD spectrum of a mono-chromophoric molecule and by anharmonic DFT calculations. On the other hand, through studies on diazido binaphthyl and diazido monosaccharide, we demonstrated that the azido group is more promising for structural analysis of larger molecules due to its simple, strong VCD couplet whose spectral patterns are readily predicted by harmonic DFT calculations.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
| | | | - Nobuyuki Harada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
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9
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Fica-Contreras SM, Daniels R, Yassin O, Hoffman DJ, Pan J, Sotzing G, Fayer MD. Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis. J Phys Chem B 2021; 125:8907-8918. [PMID: 34339200 DOI: 10.1021/acs.jpcb.1c04939] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast infrared vibrational spectroscopy is widely used for the investigation of dynamics in systems from water to model membranes. Because the experimental observation window is limited to a few times the probe's vibrational lifetime, a frequent obstacle for the measurement of a broad time range is short molecular vibrational lifetimes (typically a few to tens of picoseconds). Five new long-lifetime aromatic selenocyanate vibrational probes have been synthesized and their vibrational properties characterized. These probes are compared to commercial phenyl selenocyanate. The vibrational lifetimes range between ∼400 and 500 ps in complex solvents, which are some of the longest room-temperature vibrational lifetimes reported to date. In contrast to vibrations that are long-lived in simple solvents such as CCl4, but become much shorter in complex solvents, the probes discussed here have ∼400 ps lifetimes in complex solvents and even longer in simple solvents. One of them has a remarkable lifetime of 1235 ps in CCl4. These probes have a range of molecular sizes and geometries that can make them useful for placement into different complex materials due to steric reasons, and some of them have functionalities that enable their synthetic incorporation into larger molecules, such as industrial polymers. We investigated the effect of a range of electron-donating and electron-withdrawing para-substituents on the vibrational properties of the CN stretch. The probes have a solvent-independent linear relationship to the Hammett substituent parameter when evaluated with respect to the CN vibrational frequency and the ipso 13C NMR chemical shift.
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Affiliation(s)
| | - Robert Daniels
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Omer Yassin
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - David J Hoffman
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Junkun Pan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Gregory Sotzing
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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10
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Acharyya A, Mukherjee D, Gai F. Assessing the Effect of Hofmeister Anions on the Hydrogen-Bonding Strength of Water via Nitrile Stretching Frequency Shift. J Phys Chem B 2020; 124:11783-11792. [PMID: 33346656 DOI: 10.1021/acs.jpcb.0c06299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The temperature dependence of the peak frequency (νmax) of the C≡N stretching vibrational spectrum of a hydrogen-bonded C≡N species is known to be a qualitative measure of its hydrogen-bonding strength. Herein, we show that within a two-state framework, this dependence can be analyzed in a more quantitative manner to yield the enthalpy and entropy changes (ΔHHB and ΔSHB) for the corresponding hydrogen-bonding interactions. Using this method, we examine the effect of ten common anions on the strength of the hydrogen-bond(s) formed between water and the C≡N group of an unnatural amino acid, p-cyanophenylalanine (PheCN). We find that based on the ΔHHB values, these anions can be arranged in the following order: HPO42- > OAc- > F- > SO42- ≈ Cl- ≈ (H2O) ≈ ClO4- ≈ NO3- > Br- > SCN- ≈ I-, which differs from the corresponding Hofmeister series. Because PheCN has a relatively small size, the finding that anions having very different charge densities (e.g., SO42- and ClO4-) act similarly suggests that this ranking order is likely the result of specific ion effects. Since proteins contain different backbone and side-chain units, our results highlight the need to assess their individual contributions toward the overall Hofmeister effect in order to achieve a microscopic understanding of how ions affect the physical and chemical properties of such macromolecules. In addition, the analytical method described in the present study is applicable for analyzing the spectral evolution of any vibrational spectra composed of two highly overlapping bands.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Debopreeti Mukherjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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11
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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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12
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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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13
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Cai K, Liu J, Liu Y, Chen F, Yan G, Lin H. Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117681. [PMID: 31685425 DOI: 10.1016/j.saa.2019.117681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ37-42 and N3-Aβ37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ37-42 and N3-Aβ37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China.
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China
| | - Ya'nan Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China
| | - Feng Chen
- Fujian Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde, 352100, PR China
| | - Guiyang Yan
- Fujian Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde, 352100, PR China
| | - Huiqiu Lin
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China
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14
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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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15
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Beć KB, Grabska J, Czarnecki MA, Huck CW, Wójcik MJ, Nakajima T, Ozaki Y. IR Spectra of Crystalline Nucleobases: Combination of Periodic Harmonic Calculations with Anharmonic Corrections Based on Finite Models. J Phys Chem B 2019; 123:10001-10013. [DOI: 10.1021/acs.jpcb.9b06285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krzysztof B. Beć
- Institute of Analytical Chemistry, University of Innsbruck, A6020 Innsbruck, Austria
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Justyna Grabska
- Institute of Analytical Chemistry, University of Innsbruck, A6020 Innsbruck, Austria
| | - Mirosław A. Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Christian W. Huck
- Institute of Analytical Chemistry, University of Innsbruck, A6020 Innsbruck, Austria
| | - Marek J. Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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16
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Chatterjee S, Ghosh D, Haldar T, Deb P, Sakpal SS, Deshmukh SH, Kashid SM, Bagchi S. Hydrocarbon Chain-Length Dependence of Solvation Dynamics in Alcohol-Based Deep Eutectic Solvents: A Two-Dimensional Infrared Spectroscopic Investigation. J Phys Chem B 2019; 123:9355-9363. [DOI: 10.1021/acs.jpcb.9b08954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Deborin Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sushil S. Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samadhan H. Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Somnath M. Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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17
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Ng Pack G, Rotondaro MC, Shah PP, Mandal A, Erramilli S, Ziegler LD. Two-dimensional infrared spectroscopy from the gas to liquid phase: density dependent J-scrambling, vibrational relaxation, and the onset of liquid character. Phys Chem Chem Phys 2019; 21:21249-21261. [PMID: 31538165 DOI: 10.1039/c9cp04101j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast 2DIR spectra and pump-probe responses of the N2O ν3 asymmetric stretch in SF6 as a function of density from the gas to supercritical phase and liquid are reported. 2DIR spectra unequivocally reveal free rotor character at all densities studied in the gas and supercritical region. Analysis of the 2DIR spectra determines that J-scrambling or rotational relaxation in N2O is highly efficient, occurring in ∼1.5 to ∼2 collisions with SF6 at all non-liquid densities. In contrast, N2O ν3 vibrational energy relaxation requires ∼15 collisions, and complete vibrational equilibrium occurs on the ∼ns scale at all densities. An independent binary collision model is sufficient to describe these supercritical state point dynamics. The N2O ν3 in liquid SF6 2DIR spectrum shows no evidence of free rotor character or spectral diffusion. Using these 2DIR results, hindered rotor or liquid-like character is found in gas and all supercritical solutions for SF6 densities ≥ρ* = 0.3, and increases with SF6 density. 2DIR spectral analysis offers direct time domain evidence of critical slowing for SF6 solutions closest to the critical point density. Applications of 2DIR to other high density and supercritical solution dynamics and descriptions are discussed.
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Affiliation(s)
- Greg Ng Pack
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and Photonics Center, Boston University, Boston, MA 02215, USA
| | - Matthew C Rotondaro
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and Photonics Center, Boston University, Boston, MA 02215, USA
| | - Parth P Shah
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and Photonics Center, Boston University, Boston, MA 02215, USA
| | - Aritra Mandal
- Department of Chemistry, University of Colorado, Boulder, CO 80309, USA
| | - Shyamsunder Erramilli
- Photonics Center, Boston University, Boston, MA 02215, USA and Department of Physics, Boston University, Boston, MA 02215, USA
| | - L D Ziegler
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and Photonics Center, Boston University, Boston, MA 02215, USA
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18
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Abstract
Despite the key roles of proteins and nucleic acids in biology, understanding their labile structures and hydrogen bond interactions with guest molecules has posed a critical challenge to the scientific community. In this report, I have used dimethylformamide as a model amide to account for amide hydrogen bond interactions of protein. To quantify hydrogen bond conformation and the structural change, I have monitored the amide I infrared (IR) stretching frequencies while varying the pKa of phenol derivatives. For all phenol derivatives, amide I has formed one hydrogen bond and two hydrogen bond conformation. It has been observed that the formation constant for one hydrogen bond is higher than that of two hydrogen bonds for all phenol derivatives. During the formation of hydrogen bond with amide I, IR absorbance of C═C transition is enhanced for all phenol derivatives. Enhancement of the IR absorbance of the C═C transition indicates hydrogen bond-assisted vibrational coupling between the amide I and phenol ring transition. The relative coupling constant is estimated to be higher for single hydrogen-bonded conformer than the double hydrogen-bonded conformer. This is an intriguing result as the frequency difference between the two coupled transitions predicts otherwise. Using IR absorption spectroscopy, a delicate interplay between hydrogen bonding conformations and intermolecular vibrational coupling between amide I and H-bond donor phenol molecules has been shown. This study can be used as a point of reference for understanding the structural information of proteins, peptides, and nucleosides having hydrogen bond interaction with any drug or ligand molecules. My results as well provide an insight into the vibrational coupling of carbonyl and C═C transition of nucleobases.
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Affiliation(s)
- Anup Ghosh
- Department of Condensed Matter Physics and Materials Sciences , S. N. Bose National Centre for Basic Sciences , JD Block, Sector-III, Salt Lake City , Kolkata 700 106 , India
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19
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Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. 4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules 2019; 24:E602. [PMID: 30744004 PMCID: PMC6384856 DOI: 10.3390/molecules24030602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 11/16/2022] Open
Abstract
Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA⁻protein interactions.
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Affiliation(s)
- Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Christina M Eng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jeffrey M Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Verma PK, Kundu A, Cho M. How Molecular Crowding Differs from Macromolecular Crowding: A Femtosecond Mid-Infrared Pump-Probe Study. J Phys Chem Lett 2018; 9:6584-6592. [PMID: 30380875 DOI: 10.1021/acs.jpclett.8b03153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Crowding is an inherent property of living systems in which biochemical processes occur in highly concentrated solutions of various finite-sized species of both low (molecular crowding) and high (macromolecular crowding) molecular weights. Is molecular crowding fundamentally different from macromolecular crowding? To answer this question, we use a femtosecond mid-infrared pump-probe technique with three vibrational probes in molecular (diethylene glycol) and macromolecular (polyethylene glycol) solutions. In less crowded media, both molecular and macromolecular crowders fail to affect the dynamics of interstitial bulk-like water molecules and those at the crowder/water interface. In highly crowded media, interstitial water dynamics strongly depends on molecular crowding, but macromolecular crowding does not alter the bulk-like hydration dynamics and has a modest crowding effect on water at the crowder/water interface. The results of this study provide a molecular level understanding of the structural and dynamic changes to water and the water-mediated cross-linking of crowders.
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Affiliation(s)
- Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
- Department of Chemistry, Institute of Science , Banaras Hindu University , Varanasi 221005 , India
| | - Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
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21
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Pandey HD, Leitner DM. Vibrational States and Nitrile Lifetimes of Cyanophenylalanine Isotopomers in Solution. J Phys Chem A 2018; 122:6856-6863. [DOI: 10.1021/acs.jpca.8b06300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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22
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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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23
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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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24
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He X, Xu F, Yu P, Wu Y, Wang F, Zhao Y, Wang J. Solvent-dependent structural dynamics of an azido-platinum complex revealed by linear and nonlinear infrared spectroscopy. Phys Chem Chem Phys 2018; 20:9984-9996. [PMID: 29619447 DOI: 10.1039/c7cp08606g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The vibrational and anisotropic relaxation dynamics and structural dynamics of a potential anticancer prodrug, trans,trans,trans-[Pt(N3)2(OH)2(py)2], were investigated using time-resolved infrared pump-probe spectroscopy and ultrafast two-dimensional infrared (2D IR) spectroscopy. Herein, two representative bio-friendly solvents, H2O and DMSO, were used, in which the local structural and dynamical variations were monitored using the antisymmetric linear combination of the two N3 stretching vibrational modes as an infrared probe. It was found that the vibrational relaxation process of the N3 antisymmetric stretching (as) mode in H2O is two to three times faster than that in DMSO. The anisotropic relaxation process of the anticancer prodrug was observed to be hindered in DMSO; this indicated a tighter solvent environment around the sample molecule in this solvent. The vibrational frequency time correlation of the N3 antisymmetric stretching mode in H2O decays with a time constant of 1.94 ps, in agreement with the hydrogen bond formation and breaking times of water. In DMSO, the frequency time correlation of the N3 as mode decays on a much longer time scale; this further indicates its sensitivity to the out-layer DMSO structural dynamics, which are relatively static in the experimental time window.
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Affiliation(s)
- Xuemei He
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
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25
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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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26
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Rodgers JM, Abaskharon RM, Ding B, Chen J, Zhang W, Gai F. Fermi resonance as a means to determine the hydrogen-bonding status of two infrared probes. Phys Chem Chem Phys 2018; 19:16144-16150. [PMID: 28604875 DOI: 10.1039/c7cp02442h] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The C[double bond, length as m-dash]O/C[triple bond, length as m-dash]N stretching vibration arising from a carbonyl/nitrile functional group in various molecular systems has been frequently used to assess, for example, local hydrogen-bonding interactions, among other applications. However, in practice it is not always easy to ascertain whether the carbonyl or nitrile group in question is engaged in such interactions. Herein, we use 4-cyanoindole and cyclopentanone as models to show that, when a fundamental C[double bond, length as m-dash]O or C[triple bond, length as m-dash]N stretching mode is involved in Fermi resonance, the underlying vibrational coupling constant (W) is a convenient reporter of the hydrogen-bonding status of the corresponding carbonyl or nitrile group. Specifically, we find that for both groups a W value of 7.7 cm-1 or greater is indicative of their involvement in hydrogen-bonding interactions. Furthermore, we find that, as observed in similar studies, the Fermi resonance coupling leads to quantum beats in the two-dimensional infrared spectra of 4-cyanoindole in isopropanol, with a period of about 1.9 ps.
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Affiliation(s)
- Jeffrey M Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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27
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Zang J, Feng M, Zhao J, Wang J. Micellar and bicontinuous microemulsion structures show different solute–solvent interactions: a case study using ultrafast nonlinear infrared spectroscopy. Phys Chem Chem Phys 2018; 20:19938-19949. [DOI: 10.1039/c8cp01024b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using aqueous and organic probes to simultaneously explore the structural dynamics of reverse micellar and bicontinuous microemulsion structures.
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Affiliation(s)
- Jinger Zang
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Minjun Feng
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
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28
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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29
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Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
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30
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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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