Search

The development of novel vibrational reporters (VR), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (

We present the analysis of formaldehyde (HCHO) in anhydrous methanol (CH3OH) as a case study to quantify HCHO in non-aqueous samples. At higher concentrations (C > 0.07 M), we detect a product of HCHO, methoxy methanol (MM, CH3OCH2OH), by Fourier transform infrared spectroscopy, FTIR. Formaldehyde reacts with CH3OH, CD3OH, and CD3OD as shown by FTIR with a characteristic spectral feature around 1,195 cm−1 for CH3OH used for the qualitative detection of MM, a formaldehyde derivative in neat methanol. Ab initio calculations support this assignment. The extinction coefficient for 1,195 cm−1 is in the order of 1.4 × 102 M−1cm−1, which makes the detection limit by FTIR in the order of 0.07 M. For lower concentrations, we performed the quantitative analysis of non-aqueous samples by derivatization with dinitrophenylhydrazine (DNPH). The derivatization uses an aqueous H2SO4 solution to yield the formaldehyde derivatized hydrazone. Ba(OH)2 removes sulfate ions from the derivatized samples and a final extraction with isobutyl acetate to yield a 1:1 methanol: isobutyl acetate solvent for injection for electrospray ionization (ESI). The ESI analysis gave a linear calibration curve for concentrations from 10 to 200 µM with a time-of-flight analyzer (TOF). The detection and quantification limits are 7.8 and 26 μM, respectively, for a linear correlation with R2 > 0.99. We propose that the formaldehyde in CH3OH is in equilibrium with the MM species, without evidence of HCHO in solution. In the presence of water, the peaks for MM become less resolved, as expected from the well-known equilibria of HCHO that favors the formation of methylene glycol and polymeric species. Our results show that HCHO, in methanol does not exist in the aldehyde form as the main chemical species. Still, HCHO is in equilibrium between the production of MM and the formation of hydrated species in the presence of water. We demonstrate the ESI-MS analysis of HCHO from a non-aqueous TiO2 suspension in methanol. Detection of HCHO after illumination of the colloid indicates that methanol photooxidation yields formaldehyde in equilibrium with the solvent.

A concise synthesis of protected 5-cyano-l-tryptophan (Trp5CN ) has been developed for 2D IR spectroscopic investigations within either peptides or proteins. To assess the potential of differently substituted cyano-tryptophans, several model cyano-indole systems were characterized using IR spectroscopy. Upon assessment of their spectroscopic properties, Trp5CN was integrated into a model peptide sequence, Trp5CN -Gly-Phe4CN , to elucidate its structure. This peptide demonstrates the capability of this probe to capture structural information by 2D IR spectroscopy. The 2D IR spectrum of the peptide in water was simulated to reveal a unique spectral signature resulting from the presence of dipolar coupling. The coupling strength between cyano labels was determined to be 1.4 cm-1 by matching the slopes along the max contour for the simulated and experimental spectrum. Using transition dipole coupling, a distance between the two probes of 13 A was calculated.

The newly synthesized Eu(III) and Yb(III) complexes with the new carbazole-based ligands CPAD(2−) and CPAP(4−) display the characteristic long-lived metal-centered emission upon one- and two-photon excitation. The Eu(III) complexes show the expected narrow emission bands in the red region, with emission lifetimes between 0.382 and 1.464 ms, and quantum yields between 2.7 and 35.8%, while the Yb(III) complexes show the expected emission in the NIR region, with emission lifetimes between 0.52 and 37.86 μs, and quantum yields between 0.028 and 1.12 %. Two-photon absorption cross sections (σ(2PA)) as high as 857 GM were measured for the two ligands. The complexes showed a strong dependence of the one- and two-photon sensitized emission intensity on solvent viscosity in the range 0.5 – 200 cP in the visible and NIR region.

The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2'-azido-5-cyano-2'-deoxyuridine (N3CNdU) are examined by two-dimensional infrared (2D IR) spectroscopy. At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational transitions along the diagonal and off-diagonal cross peaks indicating vibrational coupling. The coupling strength is determined from the off-diagonal anharmonicity to be 66 cm(-1) for the intramolecular distance of ∼7.9 Å, based on a structural map generated for this model system. In addition, the frequency-frequency correlation decay is detected, monitoring the solvent dynamics around each individual probe position. Overall, these vibrational reporters can be utilized in tandem to simultaneously track global structural information and fast structural fluctuations.

Plant-insect interactions are ubiquitous, and have been studied intensely because of their relevance to damage and pollination in agricultural plants, and to the ecology and evolution of biodiversity. Variation within species can affect the outcome of these interactions, such as whether an insect successfully develops on a plant species. Whereas specific genes and chemicals that mediate these interactions have been identified, studies of genome-or metabolome-wide intraspecific variation might be necessary to better explain patterns of host-plant use and adaptation often observed in the wild. Here, we present such a study. Specifically, we assess the consequences of genome-wide genetic variation in the model plantMedicago truncatulaforLycaeides melissacaterpillar growth and survival (i.e., larval performance). Using a rearing experiment and a whole-genome SNP data set (>5 million SNPs), we show that polygenic variation inM. truncatulaexplains 9–41% of the observed variation in caterpillar growth and survival. We detect genetic correlations among caterpillar performance and other plant traits, such as structural defenses and some anonymous chemical features; these genetic correlations demonstrate that multipleM. truncatulaalleles have pleiotropic effects on plant traits and caterpillar growth or survival (or that there is substantial linkage disequilibrium among loci affecting these traits). We further show that a moderate proportion of the genetic effect ofM. truncatulaalleles onL. melissaperformance can be explained by the effect of these alleles on the plant traits we measured, especially leaf toughness. Taken together, our results show that intraspecific genetic variation inM. truncatulahas a substantial effect on the successful development ofL. melissacaterpillars (i.e., on a plant-insect interaction), and further point toward traits mediating this genetic effect.

Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.

Within this work, the family of cyanophenylalanine spectroscopic reporters is extended by showing the ortho and meta derivatives have intrinsic photophysical properties that are useful for studies of protein structure and dynamics. The molar absorptivities of 2-cyanophenylalanine and 3-cyanophenylalanine are shown to be comparable to that of 4-cyanophenylalanine with similar spectral features in their absorbance and emission profiles, demonstrating that these probes can be utilized interchangeably. The fluorescence quantum yields are also on the same scale as commonly used fluorophores in peptides and proteins, tyrosine and tryptophan. These new cyano-fluorophores can be paired with either 4-cyanophenylalanine or tryptophan to capture distances in peptide structure through Förster resonance energy transfer. Additionally, the spectroscopic properties of these chromophores can report the local solvent environment via changes in fluorescence emission intensity as a result of hydrogen bonding and/or hydration. A decrease in the quantum yield is also observed in basic environments due to photoinduced electron transfer from a deprotonated amine in the free PheCN species and at the N-terminus of a short peptide, providing an avenue to detect pH in biological systems. Our results show the potential of these probes, 2-cyanophenylalanine and 3-cyanophenylalanine, to be incorporated into a single peptide chain, either individually or in tandem with 4-cyanophenylalanine, tryptophan, or tyrosine, in order to obtain information about peptide structure and dynamics.

Two novel 2′-deoxyadenosine (dA) analogues, Si2–dA–SCN and Si2–dA–SeCN, and two novel phenylalanine (Phe) analogues, Boc–Me–PheCH2SCN and Boc–Me–PheCH2SeCN, have been synthesized and the thiocyanate (SCN) and selenocyanate (SeCN) functional groups evaluated as vibrational reporters. The syntheses of Si2–dA–SCN and Si2–dA–SeCN were accomplished in three steps in 16% and 32% overall yields, respectively, and the syntheses of Boc–Me–PheCH2SCN and Boc–Me–PheCH2SeCN were completed in four steps in 8.9% and 2.3% overall yields, respectively. The SCN and SeCN stretch vibrational modes were shown to be sensitive to the local environment by frequency shifts and full-width half-maximum (fwhm) changes in response to tetrahydrofuran (THF) and THF/water solvent mixtures. The vibrational lifetimes of the Si2–dA–SeCN (237 ± 12 ps) and Boc–Me–PheCH2SeCN (295 ± 31 ps) in THF solution were determined by ultrafast infrared pump-probe spectroscopy to be 1.5 to 3 times longer than those for Si2–dA–SCN (140 ± 6 ps) and Boc–Me–PheCH2SCN (102 ± 4 ps). The longer lifetimes for the SeCN analogues were attributed to the better insulating effects of the heavier selenium atom compared to the sulfur atom. The solvent sensitivity and longer vibrational lifetimes compared to other vibrational reporters suggest that SCN and SeCN vibrational reporters are well suited to studying several dynamic processes including protein and nucleic acid hydration and conformational changes, however stability issues may require post-synthetic modification methods to incorporate these reporters into biomacromolecules.

The ability to detect changes in the local environment of proteins is pivotal to determining their dynamic nature during many biological processes. For this purpose, the utility of the tyrosine ring breathing vibration as a sensitive infrared reporter for measuring the local electric field in protein is investigated. Variations in the bandwidth of this vibrational transition in a variety of solvents indicate differences in microenvironment affect the inhomogeneous broadening and thus the frequency distribution. The ring mode is influenced by direct and indirect interactions associated with the charge distribution of the surrounding solvent molecules. Molecular dynamics simulations were implemented to obtain a correlation between the electric field induced by the solvent on the mode and the observed vibrational bandwidth. Moreover, the Trp-cage was synthesized as a model peptide system to access the efficacy of the correlation to predict the electric field strength within the hydrophobic core of the native and denatured states of the protein. The 2D IR spectra of tyrosine in dimethyl sulfoxide (DMSO) and water (D

Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035–4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.