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B: Liquids, Chemical and Dynamical Processes in Solution, Spectroscopy in Solution
Rational Design of an Acetylenic Infrared Probe with Enhanced Dipole Strength and Increased Vibrational Lifetime Dorota Kossowska, Kwanghee Park, Jun Young Park, Chaiho Lim, Kyungwon Kwak, and Minhaeng Cho J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.9b04925 • Publication Date (Web): 25 May 2019 Downloaded from http://pubs.acs.org on May 30, 2019
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The Journal of Physical Chemistry
Rational Design of an Acetylenic Infrared Probe with Enhanced Dipole Strength and Increased Vibrational Lifetime Dorota Kossowska,†,‡ Kwanghee Park,† Jun Young Park,†,‡ Chaiho Lim,†,‡ Kyungwon Kwak,*,†,‡ and Minhaeng Cho*,†,‡
†Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea ‡
Department of Chemistry, Korea University, Seoul 02841, Korea
*Electronic mails:
[email protected] (M.C.),
[email protected] (K.K.)
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Abstract Developing infrared (IR) probes is of great interest in biomolecular imaging and spectroscopy. We report our attempt to improve the IR properties of alkyne-derivatized compounds. The vibrational properties of the alkyne (C≡C) stretch mode of aromatic silylacetylene 1 and aliphatic silylacetylene 2 were studied using FTIR and femtosecond IR pump−probe spectroscopies. We find that the insertion of silicon at the position adjacent to the alkyne group, separating it from the compound’s main body, causes an approximately 10-fold increase in the dipole strength of C≡C stretch mode and a lengthening of its vibrational lifetime from 5.6 ps for acetylenic compound without a silicon atom acting like a thermal insulator to 50.6 ps and 50.4 ps for 1 and 2, respectively. The enhanced dipole strength and the increased lifetime of 1 allowed us to measure the 2D-IR spectra for long waiting times up to 450 ps, which suggests that the dynamic observation range of 2D-IR spectroscopy with these IR probes can be extended into the subnanosecond range where protein skeletal movements occur.
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The Journal of Physical Chemistry
INTRODUCTION Recently, there has been growing interest in the development of small IR probes that can be site-specifically incorporated into proteins and biologically important molecules. In particular, linear and nonlinear vibrational spectroscopy of such IR probes provides important information on the structure, solvation energy and dynamics, local electric field, conformational transition rate and mechanism of biological macromolecules of interest.1-7 Ideal IR probes should be small in size to minimize possible steric perturbation to protein structure and function, should have a narrow bandwidth to avoid spectral overlaps with other absorption peaks, and be sensitive to the local electrostatic environment to facilitate the study of changes in the conformation and the extent of solvation. Furthermore, ideally, their vibrational frequencies fall within the transparent window (ca. 2000-2500 cm-1) to avoid congestive spectral overlap with protein amide bands and strong water absorption peaks.8 In addition to these desired properties for IR probes, large transition dipole moments and long vibrational lifetimes are prerequisite for improving detection sensitivity and expanding the dynamic range measurement in the time domain. Numerous attempts have been made over the past decade to develop an optimal vibrational probe. Deuteration has been found to be an attractive strategy that introduces nearly no perturbation to the structure and function of a given protein. For example, the −CD stretch mode9 is considered to be one of the minimal perturbation IR probes that is useful for studying local environment around the IR probe site-specifically incorporated into biological molecules. However, its weak dipole strength and short lifetime (~1.3 ps) limit its use for time-resolved IR spectroscopic investigation of deuterated proteins.10 Although various metal carbonyl (M(CO)n) compounds11-13 have shown to be exceptionally useful because they have large extinction 3 ACS Paragon Plus Environment
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coefficients (∼4000 M−1 cm−1) and reasonably long vibrational lifetimes (approximately 5-10 ps),11 researchers have been concerned that their bulkiness could impact undesired perturbation to structures and dynamics of native proteins. Azido-derivatized (−N3) compounds14-17 with large transition dipole moments (~4.8-12.9×10-2 D2) are useful; however, their short lifetime (~1.0-1.5 ps)18,19 limits the observation time window for molecular dynamics study of biomolecules with time-resolved IR spectroscopy. In addition, the azido stretch mode in aromatic compounds mix with other combination or overtone modes via Fermi resonance couplings, which prohibits a clear interpretation of vibrational spectroscopic data. The isonitrile stretch mode (−N≡C)19,20 with a fairly strong transition dipole strength (~2.2-2.7×10-2 D2) and comparatively longer lifetime (~5.510.5 ps) can be useful, but its chemical instability is prohibitive for wide application. Nitrile and thiocyanate stretch modes (−C≡N and −SC≡N)21-27 have been considered to be the most useful IR probes not only because they can be easily introduced into a protein using mutagenesis and chemical ligation methods but also because their vibrational frequencies are sensitive to the local electrostatic environment and the level of hydration. Unfortunately, due to the short vibrational lifetimes of −C≡N stretch modes (< 5.0 ps) and the relatively weak dipole strength (
