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Acta Phys. -Chim. Sin.  2017, Vol. 33 Issue (1): 40-62    DOI: 10.3866/PKU.WHXB201609192
REVIEW     
Determining 3D Molecular Conformations with Ultrafast Multiple-Dimensional Vibrational Spectroscopy
Hai-Long CHEN2,Hong-Tao BIAN3,Jun-Rong ZHENG1,*()
1 Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
2 Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, P. R. China
3 School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
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Abstract  

In recent years, ultrafast multiple-dimensional vibrational spectroscopy has been widely applied to studies of molecular structures and ultrafast dynamics in various condensed phases, and is expected to become a new generation of routine analytical tool for determining microstructures and ultrafast behaviors in molecular systems. In this review, we introduce in detail a method of determining three-dimensional (3D) molecular conformations with ultrafast multiple-dimensional vibrational spectroscopy. The introduction of our research follows two directions:(1) obtaining relative spatial orientations of different groups in a molecular system and finally determining molecular conformations by measuring cross angles of vibrational transition dipole moments; and (2) exploring the nature of vibrational energy transfers and determining molecular distances with experimentally measured vibrational energy transfer rates.



Key wordsMultiple-dimensional vibrational spectroscopy      Ultrafast spectroscopy      2D infrared spectroscopy      Molecular conformation      Vibrational energy transfer     
Received: 22 July 2016      Published: 19 September 2016
MSC2000:  O649  
Fund:  The project was supported by the AFOSR YIP Award, USA(FA9550-11-1-0070);and an AFOSR MURI grant, USA(FA9550-15-1-0022);the Welch Foundation, USA(C-1752);NSF USA(CHE-1503865);ACS PRF, USA;Packard fellowship, USA;and Sloan fellowship, USA
Corresponding Authors: Jun-Rong ZHENG     E-mail: junrong@pku.edu.cn
Cite this article:

Hai-Long CHEN,Hong-Tao BIAN,Jun-Rong ZHENG. Determining 3D Molecular Conformations with Ultrafast Multiple-Dimensional Vibrational Spectroscopy. Acta Phys. -Chim. Sin., 2017, 33(1): 40-62.

URL:

http://www.whxb.pku.edu.cn/10.3866/PKU.WHXB201609192     OR     http://www.whxb.pku.edu.cn/Y2017/V33/I1/40

Fig 1 Laser setup of ultrafast multiple-dimensional vibrational spectroscopy and the measured spectra of detection beam 64 (A) laser setup. The mid-IR mode-specific-pump pulse is generated from the ps optical parametric amplifier (OPA) and ps difference frequency generation (DFG) setup pumped by the ps amplifier. The mid-IR and terahertz super-continuum pulse is generated from the optical setup shown in the dashed box, acting as the ultrabroadband-probe pulse. (B) spectrum of the super-continuum pulse in the high frequency range measured with a liquid-nitrogen-cooled mercury-cadmium-telluride (MCT) array detector. The low-frequency cutoff is caused by the low efficiencies of the grating and the MCT detector. (C) spectrum of the super-continuum in the low frequency range measured with the air-biased-coherent-detection (ABCD) method.
Fig 2 Multiple-dimensional vibrational spectrum of 1-cyanovinyl acetate at a waiting time of 0.2 ps 69
Fig 3 Molecular conformations of 4′-methyl-2′-nitroacetanilide (MNA) in (A) the white crystal, and (B) the yellow crystal 64
Fig 4 (A) Fourier transform infrared (FTIR) spectrum of MNA in the white crystal; (B) illustration of how the vibrational cross angle between two modes being experimentally determined 64
Fig 5 Determine cross angles between different vibrational modes 64 (A) multiple-mode 2D IR spectrum of a polycrystalline sample of the MNA white crystal at waiting time 0.2 ps with the detection beam perpendicular to the excitation beam. The relative intensities of peaks are adjusted to be comparably visible by multiplying the raw data with constants which are listed in the supporting materials; (B) enlarged 2D-IR spectrum for the cross peak pair between vs(NO2) (ω1) and v(C=O) (ω3) frequency range; (C) enlarged 2D-IR spectrum for the cross peak pair between v(NH) (ω1) and v(C=O) (ω3) frequency range; (D) a slice cut along ω1=1362 cm-1 of Fig.5(B) with the polarization of the excitation both parallel (‖) and perpendicular (⊥) to the polarization of the detection beam and (E) a slice cut along ω1=3260 cm-1 of Fig.5(C) with the polarization of the excitation both parallel (‖) and perpendicular (⊥) to the polarization of the detection beam. The solid lines denote Gaussian peak fits.
Fig 6 Average Er(x, y) values with different ∠CC/NO and ∠CC/NC dihedral angles for (A) MNA-W, (B) MNA-Y1, and (C) MNA-Y2 64 The z-axis is the amplitude of Er(x, y). The minimum Er(x, y) values of each MNA species are labeled with white boxes, which correspond to the most possible molecular conformations in the crystal, as depicted in the right panels. The dihedral angles of red dots are determined by XRD. color online
Fig 7 Molecular conformations of MNA in liquids 64 (A) the average difference Er(x, y) between the experimental and calculated vibrational cross angles of MNA conformations with different ∠CC/NC and ∠CC/NO dihedral angles for the four liquid samples. The z-axis is the amplitude of Er(x, y); (B) the MNA molecular conformation corresponding to the dihedral angles of the Er(x, y) minima in all four liquid samples; (C) conformational distributions of liquid samples 2-4 from MD simulations. The z-axis is the relative population of each conformation with a pair of ∠CC/NC and ∠CC/NO dihedral angles as the x-and y-axis.
Fig 8 Molecular conformation and vibrational dynamics of 4-mercaptophenol on the 3.5 nm gold nanoparticle surface probed with multiple-mode multiple-dimensional infrared spectroscopy 68
Fig 9 Determining the molecular conformation of HOC6H4-S (Au)2 on the surface of 3.5 nm Au nanoparticle 68 (A) The most probable conformation of HOC6H4-S (Au)2 on the surface of 3.5 nm Au nanoparticle determined by experiments. α, β, and γ are the dihedral angles as defined. (B) Experimental and calculated vibrational cross angle deviation Er vs the CC/OH dihedral angle C (2) C (3)/O (12) H (13) at different dihedral angles of C (5) C (6)/S (11) Au (15) (β) from 0° to 90°. Er reaches the global minimum when α=-120° and β=20°.
Fig 10 Molecular conformations of crystalline l-cysteine determined with vibrational cross angle measurements 63
Fig 11 Relative intermolecular orientation probed via molecular heat transport
Fig 12 Observation of ultrafast nonresonant energy transfer 72 (A) a snapshot of a 1.8 mol·L-1 KSCN aqueous solution obtained from MD simulation, with O (red), H (white), C (light blue), N (deep blue), K (green), and S (yellow). Some water molecules are removed to better display the cluster structure; (B) FTIR spectrum of the CN and 13C15N stretches of SCN- and S13C15N- of a 10 mol·L-1 KSCN/KS13C15N~1/1 aqueous solution; (C) the waiting time-dependent 2D IR spectra of the 10 mol·L-1 solution. As Tw increases, the off-diagonal peaks appear due to vibrational energy exchange between SCN- and S13C15N-. color online
Fig 13 Waiting time-dependent intensities of peaks 1, 3, 5, and 7 in Fig. 12(C) 72 Dots are experimental data, and curves are calculated results based on the kinetic model.
Fig 14 Anisotropy decay data (dots) of the 13C≡15N stretch pump/probe signal of S13C15N- in 10 mol·L-1 aqueous solutions with different KS13C15N/KSCN molar ratios 72
Fig 15 Molecular distances in KSCN crystal determined with vibrational energy transfers 59
Fig 16 Multiple-dimensional vibrational spectra of KSCN/KS13C15N (1 : 1 (molar ratio)) aqueous solutions with different concentrations at three different waiting times 72
c(KSCN)/(mol·L-1)Experimental cluster percentage/%MD cluster percentage/%ntotrDA/nm
10.095±199.718±30.51
8.892±113±20.50
6.570±49±20.48
4.067±479.55±20.46
1.835±531.44±10.44
1.027±63±10.43
Table 1 Experimental and MD simulation results of ion cluster properties in KSCN aqueous solutions at different concentrations 60, 72
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