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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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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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Zhang J. Two-dimensional infrared spectral explorations into bilayer and monolayer self-assemblies of amphiphilic polypeptides. J Biomol Struct Dyn 2020; 39:9-19. [PMID: 31914853 DOI: 10.1080/07391102.2020.1713891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Poly(2-(3-((2-hydroxyethyl)amino)-3-oxopropyl)ethyleneamido) (PHAOE) is an amphiphilic polypeptide. The self-assembly is significant, but the ultrafast dynamic analyses of the peptide self-assembly are exiguous and worth further exploring. In this investigation, the temporal dynamic characteristics of the aggregates and unaggregated PHAOEs are mined by the two-dimensional infrared (2D IR) spectroscopy. The homogeneous and inhomogeneous diffusion processes of the carbonyl stretching modes of the unaggregated PHAOEs are slower than those of the self-assemblies. The inhomogeneous spectral diffusion proportion of the biopolymer PHAOE in methanol is greater than that in dimethyl sulfoxide (DMSO). The solvation shells surround the aggregates and unaggregated PHAOEs in the protic solvent methanol, but there are not any solvation shells around the aggregates or unaggregated PHAOEs in the dipolar solvent DMSO. The massive hydrogen-bonded monolayer self-assembly has merely an aggregate of PHAOEs and no solvation shell in DMSO. But the hydrogen-bonded bilayer self-assembly has a self-assembled methanol shell and an interior aggregate of PHAOEs in methanol. The self-assemblies of PHAOEs motivate the methanols to self-assemble. The large delocalized amide structure results in the fast spectral diffusion of the carbonyl stretching mode.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jun Zhang
- 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, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
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