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B: Liquids; Chemical and Dynamical Processes in Solution
Cyanamide as an Infrared Reporter: Comparison of Vibrational Properties between Nitriles Bonded to N and C Atoms Giseong Lee, Dorota Kossowska, JoonHyung Lim, Soobin Kim, Hogyu Han, Kyungwon Kwak, and Minhaeng Cho J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.8b00887 • Publication Date (Web): 08 Mar 2018 Downloaded from http://pubs.acs.org on March 11, 2018
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The Journal of Physical Chemistry
Cyanamide as an Infrared Reporter: Comparison of Vibrational Properties between Nitriles Bonded to N and C Atoms Giseong Lee,#,‡ Dorota Kossowska,#,†,‡ Joonhyung Lim,†,‡ Soobin Kim,† Hogyu Han,*,‡ 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
Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 02855, Korea
*Author to whom correspondence should be addressed:
[email protected] (H.H.) ,
[email protected] (K.K.), and
[email protected] (M.C.). #
These two authors contributed equally to this work.
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ABSTRACT Infrared (IR) probes based on terminally blocked β-cyanamidoalanine (AlaNHCN) 1 and pcyanamidophenylalanine (PheNHCN) 2 were synthesized and the vibrational properties of their CN stretch mode were studied using 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 is originated 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 lineshape of the CN stretch spectra. Such a complicated lineshape 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 to be 1.64 ± 0.13 ps in CH3OD/DMSO 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 complementary to nitrile, a weak absorber.
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The Journal of Physical Chemistry
I. INTRODUCTION Ultrafast infrared (IR) spectroscopy is a powerful tool for assessing the structural and environmental dynamics of biomolecules.1−6 Numerous IR probes based on biomolecules have been used to site-specifically interrogate their structure and dynamics.7−12 While many IR probes are found to be useful in FTIR spectroscopy, their use in the time-resolved nonlinear IR spectroscopy is often limited by the lack of some desired spectral properties. Such properties include large transition dipole moment, narrow bandwidth, long vibrational lifetime, and high environmental sensitivity. Moreover, the small size and high solvothermal stability of IR reporter incorporated into biomolecules are required. The stretch vibration of the nitrile (C≡N) group is a useful IR reporter of the structure and dynamics of local environment.13−29 In particular, the nitrile stretch frequency is sensitively blueshifted upon hydrogen-bonding, which is mainly due to the exchange-repulsion solute−solvent interaction.12 However, the nitrile stretch mode exhibits small transition dipole strength (5.0 ps) is longer than that of the nitrile and azido groups. Accordingly, isonitrile can be a better IR reporter of H-bonding structure and dynamics than nitrile and azide, despite its less chemical stability under acidic conditions. Here, we report novel IR probes based on terminally blocked cyanamide (NHCN)derivatized alanine 1 (Ac-Ala(NHCN)-NHMe, Figure 1) and phenylalanine 2 (Ac-Phe(NHCN)NHMe) containing cyanamide (HN−C≡N), a seemingly hybrid form of mainly C≡N and partially N≡C. It is noteworthy that there is a structural similarity between cyanamide (HN−C≡N) and azide (HN−N≡N ↔ HN=N=N). The vibrational properties of the CN stretch mode in 1 and 2 were investigated using FTIR and femtosecond IR pump−probe spectroscopies. It is found that the transition dipole strength of cyanamide is much larger than that of nitrile, but comparable to 4 ACS Paragon Plus Environment
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that of isonitrile and azide. The vibrational frequency of cyanamide is red-shifted from that of nitrile, but more blue-shifted from that of isonitrile and azide. The vibrational lifetime of cyanamide is close to that of nitrile and azide, but shorter than that of isonitrile. Consequently, cyanamide is similar to nitrile in vibrational frequency and lifetime, to isonitrile in transition dipole strength, and to azide in transition dipole strength and vibrational lifetime. Thus, cyanamide is believed to be a strongly absorbing IR reporter complementary to nitrile, a weak absorber. To explain the differences in vibrational properties between cyanamide and nitrile, quantum chemical calculations were performed. We found that such differences are associated with the occurrence of the n → π* interaction between the N atom’s nonbonding (n) and CN group’s antibonding (π*) orbitals only in cyanamide. Quantum chemical calculations also reveal that a complicated lineshape of the CN stretch spectra in aromatic cyanamide is attributed to the Fermi resonance not occurring in aromatic nitrile. II. EXPERIMENTAL AND COMPUTATIONAL METHODS II.A. Materials. Compounds 1 and 2 were synthesized and characterized (Scheme 1 and Section SII of the Supporting Information). All the solvents for IR spectroscopy were purchased from Sigma−Aldrich and used as received. To prepare deuterated samples, the samples were dissolved in D2O, dried, and then dissolved in deuterated solvents for FTIR studies, whereas they were directly dissolved in deuterated solvents for IR pump−probe experiments. The deuteration of the NHCN into NDCN group was monitored by disappearance of 1H NMR peaks around 6.81 and 10.05 ppm for 1 and 2 in DMSO-d6, respectively. To examine the solvothermal stability of the NHCN group, we performed TLC analyses for 1 and 2 subjected to various concentrations of methanolic HCl and methylamine solutions at varying temperatures with stirring. It is found that the chemical stability (
