Two-dimensional infrared spectroscopic study of cytochrome c peroxidase activity in deep eutectic solvent.

Deep eutectic solvents (DESs) prepared by mixing hydrogen-bond donor and acceptor molecules have been found to be of use in several applications. Recently, it was shown that DESs can enhance the peroxidation activity of cytochrome c. Here, to elucidate the effects of DESs on the peroxidase activity of cytochrome c, we carried out linear and nonlinear infrared spectroscopic studies of the CO stretch mode of carbon monoxide cytochrome c (COCytc) in ethylammonium chloride (EAC)/urea DES. The FTIR spectrum of COCytc shows a significant spectral shift upon addition of the DES. The broadening and red-shifting of the CO band are observed in both urea and DES solutions, which are induced by the change of the distal ligands around the heme. Although the FTIR study is sensitive to structural changes in the active site, it does not provide quantitative information about structural dynamics related to the catalytic activity itself. Thus, we carried out two-dimensional IR spectroscopy of the CO mode, which suggests that there is a different conformer that could be related to the enhanced catalytic activity in DES. In particular, the spectral diffusion dynamics of that conformer exhibits quite different behavior. The experimental results lead us to propose a hypothesis that the DES increases the population of the conformer with distal ligand lysines close to the reaction center through the combining effect of urea and EAC, which results in the enhancement of the peroxidase activity of cytochrome c. We anticipate that the present experimental work stimulates future investigations of the effects of DES on biocatalysis.

Simultaneous enhancement of transition dipole strength and vibrational lifetime of an alkyne IR probe viaπ-d backbonding and vibrational decoupling.

Alkyne infrared (IR) probes 1-6 with Si and S (or Se) atoms incorporated into the C[triple bond, length as m-dash]C bond were synthesized, and the vibrational properties of their C[triple bond, length as m-dash]C stretch mode were studied using Fourier transform infrared (FTIR) and femtosecond IR pump-probe (IR PP) spectroscopies in combination with quantum chemical calculations. From FTIR studies, the transition dipole strengths (in units of 10-2 D2) of 1-3 having the Si atom were measured to be 1.85, 3.32, and 2.52, whereas those of 4-6 having no Si atom were measured to be 0.13, 0.20, and 0.17, respectively, in CHCl3. Thus, the increase in the transition dipole strength of the C[triple bond, length as m-dash]C stretch mode upon incorporation of the Si atom into the C[triple bond, length as m-dash]C bond is by a factor of about 14 or higher. The large increase in the transition dipole strength of the C[triple bond, length as m-dash]C stretch mode upon such Si incorporation is attributed to π-d backbonding between the C[triple bond, length as m-dash]C group's π and Si atom's d orbitals. From IR PP experiments, the vibrational lifetimes of the C[triple bond, length as m-dash]C stretch mode in 1-3 having none, S, and Se atoms were determined to be 5.7 ± 0.7, 13.0 ± 1.1, and 94.2 ± 5.8 ps, respectively, in CHCl3. Thus, the increase in the vibrational lifetime of the C[triple bond, length as m-dash]C stretch mode upon incorporation of the S (or Se) atom between the phenyl ring and the C[triple bond, length as m-dash]C bond is by a factor of about 2 (or 16) or higher. The large increase in the vibrational lifetime of the C[triple bond, length as m-dash]C stretch mode upon such S (or Se) incorporation is attributed to its heavy atom effect impeding vibrational couplings between the C[triple bond, length as m-dash]C stretch and phenyl ring vibrations. From two-dimensional infrared (2DIR) experiments, the large transition dipole strength and long vibrational lifetime of 3 containing the Si and S (or Se) atoms were shown to enable the measurement of its 2DIR spectra up to 500 ps. The strongly absorbing alkynes with long vibrational lifetimes will be a promising probe of molecular dynamics in nonlinear vibrational spectroscopy and imaging on an extended time scale.

Rational Design of an Acetylenic Infrared Probe with Enhanced Dipole Strength and Increased Vibrational Lifetime.

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 Fourier transform infrared 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 the C≡C stretch mode and a lengthening of its vibrational lifetime from 5.6 ps for the acetylenic compound without a silicon atom acting like a thermal insulator to 50.6 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.

Do Osmolytes Impact the Structure and Dynamics of Myoglobin?

Osmolytes are small organic compounds that can affect the stability of proteins in living cells. The mechanism of osmolytes' protective effects on protein structure and dynamics has not been fully explained, but in general, two possibilities have been suggested and examined: a direct interaction of osmolytes with proteins (water replacement hypothesis), and an indirect interaction (vitrification hypothesis). Here, to investigate these two possible mechanisms, we studied myoglobin-osmolyte systems using FTIR, UV-vis, CD, and femtosecond IR pump-probe spectroscopy. Interestingly, noticeable changes are observed in both the lifetime of the CO stretch of CO-bound myoglobin and the spectra of UV-vis, CD, and FTIR upon addition of the osmolytes. In addition, the temperature-dependent CD studies reveal that the protein's thermal stability depends on molecular structure, hydrogen-bonding ability, and size of osmolytes. We anticipate that the present experimental results provide important clues about the complicated and intricate mechanism of osmolyte effects on protein structure and dynamics in a crowded cellular environment.

Cyanamide as an Infrared Reporter: Comparison of Vibrational Properties between Nitriles Bonded to N and C Atoms.

Infrared (IR) probes based on terminally blocked ß-cyanamidoalanine (AlaNHCN) 1 and p-cyanamidophenylalanine (PheNHCN) 2 were synthesized, and the vibrational properties of their CN stretch modes were studied using Fourier transform infrared (FTIR) and femtosecond IR pump-probe spectroscopies in combination with quantum chemical calculations. From FTIR studies, it is found that the transition dipole strengths of the cyanamide (NHCN) group in 1 and 2 are much larger than those of the nitrile (CN) group but comparable to those of the isonitrile (NC) and azido (N3) groups in their previously studied analogs. The CN stretch frequencies in 1 and 2 are red-shifted from those in their nitrile analogs but more blue-shifted from the NC and N3 stretch frequencies in their isonitrile and azido analogs. The much larger transition dipole strength and the red-shifted frequency of the cyanamide relative to nitrile group originates from the n → π* interaction between the N atom's nonbonding (n) and CN group's antibonding (π*) orbitals of the NHCN group. Unlike aliphatic cyanamide 1, aromatic cyanamide 2 shows a complicated line shape of the CN stretch spectra. Such a complicated line shape arises from the Fermi resonance between the CN stretch mode of the NHCN group and one of the overtones of the phenyl ring vibrations and can be substantially simplified by deuteration of the NHCN into NDCN group. From IR pump-probe experiments, the vibrational lifetimes of the CN stretch mode in 1 were determined to be 0.58 ± 0.04 ps in D2O and 0.89 ± 0.09 ps in H2O and those in 2 were determined to be 1.64 ± 0.13 ps in CH3OD/dimethyl sulfoxide and 0.30 ± 0.05 and 2.62 ± 0.26 ps in CH3OH. The short time component (0.30 ± 0.05 ps) observed for 2 in CH3OH is attributed to the vibrational relaxation through Fermi resonance. These vibrational lifetimes are close to those of the nitrile and azido groups but shorter than those of the isonitrile group. Consequently, cyanamide behaves like an apparent vibrational hybrid of nitrile and isonitrile in that cyanamide is similar to nitrile in vibrational frequency and lifetime but to isonitrile in transition dipole strength. It is believed that cyanamide has the potential to be a strongly absorbing IR reporter of the conformational and environmental structure and dynamics of biomolecules in comparison to nitrile, a weak absorber.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery.

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

ß-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes.

An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump-probe spectroscopy. It is found that the NC stretching mode is very sensitive to the hydrogen-bonding ability of solvent molecules. Moreover, its transition dipole strength is larger than that of nitrile (CN) in nitrile-derivatized IR probe 2. The vibrational lifetime of the NC stretching mode is found to be 5.5 ± 0.2 ps in both D2O and DMF solvents, which is several times longer than that of the azido (N3) stretching mode in azido-derivatized IR probe 3. Altogether these properties suggest that the NC group can be a very promising sensing moiety of IR probes for studying the solvation structure and dynamics of biomolecules.