1
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Dong T, Yu P, Zhao J, Wang J. Site specifically probing the unfolding process of human telomere i-motif DNA using vibrationally enhanced alkynyl stretch. Phys Chem Chem Phys 2024; 26:3857-3868. [PMID: 38224126 DOI: 10.1039/d3cp05328h] [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: 01/16/2024]
Abstract
The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5'E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations. The CC probe extended into the major groove of the i-motif was found using nonlinear IR results only to introduce a minor steric effect on both steady-state structure and local structure dynamics; however, its IR absorption profile effectively reports the cleavage of the hemi-protonated base pair of C1-C13 upon the unfolding with C1 remaining protonated. The temperature mid-point (Tm) of the local transition reported using the CC tag was slightly lower than the Tm of global transition, and the enthalpy of the former exceeds 60% of the global transition. It is shown that the base-pair unraveling is noncooperative, with outer base pairs breaking first and being likely the rate limiting step. Our results offered an in-depth understanding of the macroscopic unfolding characteristics of the i-motif DNA and provided a nonlinear IR approach to monitoring the local structural transition and dynamics of DNA and its complexes.
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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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2
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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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3
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Hu R, Ding X, Yu P, He X, Watts A, Zhao X, Wang J. Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin. J Am Chem Soc 2022; 144:22083-22092. [PMID: 36399663 DOI: 10.1021/jacs.2c09435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E-F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a 13C, 15N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the 13C, 15N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm-1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E-F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins.
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Affiliation(s)
- Rong Hu
- 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
| | - Xiaoyan Ding
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China.,Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Pengyun Yu
- 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
| | - Xuemei He
- 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
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Xin Zhao
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China
| | - Jianping Wang
- 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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4
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Zhou L, Tian L, Zhang WK. Experimental consideration of two-dimensional Fourier transform spectroscopy. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2007125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Lie Tian
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Wen-kai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
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5
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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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6
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Wu Y, Yu P, Chen Y, Zhao J, Liu H, Li Y, Wang J. Intensified C≡C Stretching Vibrator and Its Potential Role in Monitoring Ultrafast Energy Transfer in 2D Carbon Material by Nonlinear Vibrational Spectroscopy. J Phys Chem Lett 2019; 10:1402-1410. [PMID: 30848918 DOI: 10.1021/acs.jpclett.9b00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, an intensity-enhanced C≡C stretching infrared (IR) absorption is observed in hexakis[(trimethylsilyl)ethynyl]benzene (HTEB), whose IR transition dipole magnitude becomes comparable to that of a typical C═O stretch, and the enhancement is believed to be due to a joint effect of π-π conjugation and hyperconjugation associated with a terminal trimethylsilyl group. Using dynamical time-dependent two-dimensional infrared (2D IR) spectroscopy, a picosecond intramolecular energy redistribution process is observed between two nondegenerate C≡C stretching modes, whose symmetry breaking is attributed to a noncovalent halogen-bonding interaction between HTEB and solvent CH2Cl2. The rigid structure of HTEB and limited structural dynamics are also inferred from the insignificant initial spectral diffusion value extracted from the 2D IR spectra. This work provides the first nonlinear infrared investigation of the conventionally weak C≡C stretch. The methods outlined are particularly important for detailed understanding of the structure-related processes such as vibrational energy transfer in novel C≡C species containing materials such as graphdiyne.
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Affiliation(s)
- Yanzhou Wu
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Pengyun Yu
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Yanhuan Chen
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Juan Zhao
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Huibiao Liu
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Yuliang Li
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jianping Wang
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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7
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Feng M, Zhao J, Yu P, Wang J. Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute-Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution. J Phys Chem B 2018; 122:9225-9235. [PMID: 30200757 DOI: 10.1021/acs.jpcb.8b07247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, the solvation of a nitrosyl ruthenium complex, [(CH3)4N][RuCl3(qn)(NO)] (with qn = deprotonated 8-hydroxyquinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D2O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand-solvent hydrogen-bonding interactions, one N═O···D and particularly three Ru-Cl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump-probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D2O, confirming stronger solvent-solute interaction and also faster solvent structural dynamics in D2O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D2O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand-solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand-solvent interactions and show slower dynamics.
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Affiliation(s)
- Minjun Feng
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, 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, Institute of Chemistry, 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, Institute of Chemistry, 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, Institute of Chemistry, 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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8
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He X, Yu P, Zhao J, Wang J. Efficient Vibrational Energy Transfer through Covalent Bond in Indigo Carmine Revealed by Nonlinear IR Spectroscopy. J Phys Chem B 2017; 121:9411-9421. [DOI: 10.1021/acs.jpcb.7b06766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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
- 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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9
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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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10
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Yu P, Zhao Y, Yang F, Pan H, Wang J, Zhao J, Wang W, Wang H, Wang J. Differentiating Two Nitrosylruthenium Isomeric Complexes by Steady-State and Ultrafast Infrared Spectroscopies. J Phys Chem B 2016; 120:11502-11509. [PMID: 27755866 DOI: 10.1021/acs.jpcb.6b08060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The [Ru(II)-NO+] group affects the structure and chemical reactivity of nitrosylruthenium(II) complexes. A characteristic infrared absorption band due to the nitrosyl (NO) stretching motion is shown in the frequency region 1800-1900 cm-1. In this work, linear infrared (IR) and nonlinear IR methods, including pump-probe and two-dimensional (2D) IR, were utilized to study the structures and dynamics of two isomeric nitrosylruthenium complexes [Ru(OAc)(2mqn)2NO] (H2mqn = 2-methyl-8-quinolinol) in cis and trans isomeric configurations in a weak polar solvent (CDCl3). Using the NO stretching mode as a vibrational probe, information about local structural dynamics of the Ru complex as well as solvent fluctuation dynamics was obtained. In particular, a "structured" solvent environment is believed to form in the vicinity of the NO group in the case of the cis isomer with the aid of a neighboring OAc ligand, which is the reason for more efficient vibrational relaxation but more inhomogeneously distributed solvent and thus associated slower spectral diffusion. Our results also suggest a more anharmonic potential surface for the NO stretching mode in the less stable trans isomer.
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Affiliation(s)
- Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, the Chinese Academy of Sciences , Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences , Beijing 100049, P. R. China
| | - Yan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, the Chinese Academy of Sciences , Beijing, 100190, P. R. China.,Institute of Molecular Science, Shanxi University , Taiyuan, 030006, P. R. China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, the Chinese Academy of Sciences , Beijing, 100190, P. R. China
| | - Huifen Pan
- Institute of Molecular Science, Shanxi University , Taiyuan, 030006, P. R. China
| | - Jianru Wang
- Institute of Molecular Science, Shanxi University , Taiyuan, 030006, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, the Chinese Academy of Sciences , Beijing, 100190, P. R. China
| | - Wenming Wang
- Institute of Molecular Science, Shanxi University , Taiyuan, 030006, P. R. China
| | - Hongfei Wang
- Institute of Molecular Science, Shanxi University , Taiyuan, 030006, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, the Chinese Academy of Sciences , Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences , Beijing 100049, P. R. China
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11
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Zhao Y, Yang F, Wang J, Yu P, Pan H, Wang H, Wang J. Structural dynamics of nitrosylruthenium isomeric complexes studied with steady-state and transient pump-probe infrared spectroscopies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 166:62-67. [PMID: 27209490 DOI: 10.1016/j.saa.2016.04.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
The characteristic nitrosyl stretching (NO) in the region of 1800-1900cm(-1) was used to study the geometric and ligand effect on two nitrosylruthenium complexes, namely [Ru(OAc)(2QN)2NO] (QN=2-chloro-8-quinolinol (H2cqn) or QN=2-methyl-8-quinolinol (H2mqn)). The NO stretching frequency (νNO) was found in the following order: νcis-1 (2cqn)>νcis-2 (2cqn)>νcis-1 (2mqn)>νtrans (2mqn). The results exhibited a spectral sensitivity of the NO mode to both charge distribution and ligand arrangement, which was supported by ab initio computations and natural bond orbital (NBO) analyses. Further, the vibrational population of the vibrationally excited NO stretching mode was found to relax on the order of 7-10ps, showing less than 30% variation from one isomer to another, which were explained on the basis of NO local structures and solute-solvent interactions in these isomeric nitrosylruthenium complexes.
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Affiliation(s)
- Yan Zhao
- College of Physics & Electronics Engineering, Shanxi University, Taiyuan 030006, China; Molecular Reaction Dynamics Laboratory, Beijing National Laboratory for Molecular Sciences, Beijing 100190, China; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fan Yang
- Molecular Reaction Dynamics Laboratory, Beijing National Laboratory for Molecular Sciences, Beijing 100190, China; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianru Wang
- Institute of Opto-Electronics, Shanxi University, Taiyuan 030006, China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, Beijing National Laboratory for Molecular Sciences, Beijing 100190, China; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Huifen Pan
- Key Laboratory of Energy Conversion and Storage Materials of Shanxi Provence, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Hongfei Wang
- Key Laboratory of Energy Conversion and Storage Materials of Shanxi Provence, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, Beijing National Laboratory for Molecular Sciences, Beijing 100190, China; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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12
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Zhao J, Wang J. Uncovering the Sensitivity of Amide-II Vibration to Peptide–Ion Interactions. J Phys Chem B 2016; 120:9590-8. [DOI: 10.1021/acs.jpcb.6b05889] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Zhao
- Beijing
National Laboratory for Molecular Sciences and Molecular Reaction
Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory for Molecular Sciences and Molecular Reaction
Dynamics Laboratory, 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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13
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Feng MJ, Yang F, Wang JP. Vibrational and Structural Dynamics of Mn(CO)5Br and Re(CO)5Br Examined Using Nonlinear Infrared Spectroscopy. CHINESE J CHEM PHYS 2016. [DOI: 10.1063/1674-0068/29/cjcp1512253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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14
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Abstract
The vibrational properties of the amide-I modes of β-peptides in five helical conformations (8-helix, 10-helix, 12-helix, 14-helix, and 10/12-helix) from tetramer to heptamer were examined by ab initio calculations. The normal modes have been first decoupled into local modes, whose transition energies are found to be intrinsically sensitive to peptide structure and intramolecular hydrogen bonding interactions. By further removing the intramolecular hydrogen bonding interactions, pure local modes are obtained, whose transition energies still exhibit some conformational dependence in 8-helix and 10/12 hybrid helix, but not much in homogeneous 10-, 12-, and 14-helical conformations. This suggests that a set of nearly degenerated pure local-mode transitions can be specified when excitonic modeling the amide-I vibration in latter cases. The work provides important benchmark measurements for understanding the complexity of the amide-I absorption spectra of β-polypeptides.
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Affiliation(s)
- Juan Zhao
- Beijing National Laboratory for Molecular Sciences; Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, P. R. China
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15
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Yang F, Yu P, Zhao J, Shi J, Wang J. Ultrafast vibrational and structural dynamics of dimeric cyclopentadienyliron dicarbonyl examined by infrared spectroscopy. Phys Chem Chem Phys 2015; 17:14542-50. [DOI: 10.1039/c5cp00965k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Equilibrium and ultrafast structural dynamics of a classic transition metal carbonyl compound were revealed by linear and nonlinear infrared methods.
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Affiliation(s)
- Fan Yang
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
- P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
- P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
- P. R. China
| | - Jipei Shi
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
- P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
- P. R. China
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16
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Prampolini G, Yu P, Pizzanelli S, Cacelli I, Yang F, Zhao J, Wang J. Structure and Dynamics of Ferrocyanide and Ferricyanide Anions in Water and Heavy Water: An Insight by MD Simulations and 2D IR Spectroscopy. J Phys Chem B 2014; 118:14899-912. [DOI: 10.1021/jp511391b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Wang J, Yang F, Zhao Y, Yu P, Qiao X, Wang J, Wang H. Photoisomerization and structural dynamics of two nitrosylruthenium complexes: a joint study by NMR and nonlinear IR spectroscopies. Phys Chem Chem Phys 2014; 16:24045-54. [PMID: 25285659 DOI: 10.1039/c4cp02298j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, the photoisomerization and structural dynamics of two isomeric nitrosylruthenium(ii) complexes [Ru(OAc)(2cqn)2NO] (H2cqn = 2-chloro-8-quinolinol) in CDCl3 and DMSO are examined using NMR and IR spectroscopic methods. The two N atoms in the 2cqn ligand are in trans position in the synthesized cis-1 isomer, while they are in cis position in the cis-2 isomer. Kinetics monitored by NMR spectroscopy shows that the rate constant of photoisomerization from cis-2 to cis-1 isomer depends on the wavelength of irradiation and solvent polarity; it proceeds faster on irradiating near the absorption peak in the UV-Vis region, and also in more polar solvents (DMSO). Density functional theory computation indicates that the peculiarity of [Ru(ii)-NO(+)] group affects the structure and reactivity of the nitrosylruthenium complexes. Using the nitrosyl stretching (νNO) to be vibrational probe, the structural dynamics and structural distributions of the cis-1 and cis-2 isomers are examined by steady-state linear infrared and ultrafast two-dimensional infrared (2D IR) spectroscopies. The structural and photochemical aspects of the observed spectroscopic parameters are discussed in terms of solute-solvent interactions for the two nitrosylruthenium complexes.
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Affiliation(s)
- Jianru Wang
- State Key Lab of Quantum Optics and Quantum Optics Devices, Institute of Opto-Electronics, Shanxi University, Taiyuan 030006, China.
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Yu P, Yang F, Zhao J, Wang J. Hydration Dynamics of Cyanoferrate Anions Examined by Ultrafast Infrared Spectroscopy. J Phys Chem B 2014; 118:3104-14. [DOI: 10.1021/jp410614f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Pengyun Yu
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fan Yang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Juan Zhao
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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Yang F, Yu P, Shi J, Zhao J, He X, Wang J. Two‐Dimensional Infrared Spectroscopy of the Photoproduct of π‐Cyclopentadienyliron Dicarbonyl Dimer. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/06/721-728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Yang F, Yu P, Zhao J, Wang J. Simultaneously Probing Two Ultrafast Condensed-Phase Molecular Symmetry Breaking Events by Two-Dimensional Infrared Spectroscopy. Chemphyschem 2013; 14:2497-504. [DOI: 10.1002/cphc.201300094] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/16/2013] [Indexed: 11/09/2022]
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