Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations

In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na+, Ca2+, Mg2+, and Zn2+) with backbone (amide CO) and C-terminal carboxylate (COO–) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PPII) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone–cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH3+ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn2+) can specifically coordinate to the COO– group in bidentate and pseudo-bridging forms simultaneously. For Zn2+, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides

Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute–Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution

In this work, the solvation of a nitrosyl ruthenium complex, [(CH3)4N]­[RuCl3­(qn)­(NO)] (with qn = deprotonated 8-hydroxy­quinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D2O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand–solvent hydrogen-bonding interactions, one NO···D and particularly three RuCl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump–probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D2O, confirming stronger solvent–solute interaction and also faster solvent structural dynamics in D2O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D2O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand–solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand–solvent interactions and show slower dynamics

Intensified CC Stretching Vibrator and Its Potential Role in Monitoring Ultrafast Energy Transfer in 2D Carbon Material by Nonlinear Vibrational Spectroscopy

In this work, an intensity-enhanced CC stretching infrared (IR) absorption is observed in hexakis­[(trimethylsilyl)­ethynyl]­benzene (HTEB), whose IR transition dipole magnitude becomes comparable to that of a typical CO stretch, and the enhancement is believed to be due to a joint effect of π–π conjugation and hyperconjugation associated with a terminal trimethylsilyl group. Using dynamical time-dependent two-dimensional infrared (2D IR) spectroscopy, a picosecond intramolecular energy redistribution process is observed between two nondegenerate CC stretching modes, whose symmetry breaking is attributed to a noncovalent halogen-bonding interaction between HTEB and solvent CH2Cl2. The rigid structure of HTEB and limited structural dynamics are also inferred from the insignificant initial spectral diffusion value extracted from the 2D IR spectra. This work provides the first nonlinear infrared investigation of the conventionally weak CC stretch. The methods outlined are particularly important for detailed understanding of the structure-related processes such as vibrational energy transfer in novel CC species containing materials such as graphdiyne

Structure and Dynamics of Ferrocyanide and Ferricyanide Anions in Water and Heavy Water: An Insight by MD Simulations and 2D IR Spectroscopy

Combined computational and experimental techniques were employed to investigate at the microscopic level the structural and dynamic properties of ferro- and ferricyanide ions in aqueous solution. The characterization of the structural patterns and multiscale dynamics taking place within the first solvation spheres in water and heavy water solvents was first achieved through extensive molecular dynamics simulations, performed with refined force fields, specifically parametrized for the cyanide ions under investigation. The information gained about the solute–solvent interactions is then validated through the successful comparison of computed and measured waiting-time-dependent 2D IR spectra. The vibrational patterns resulting from 2D IR measurements were rationalized in terms of the interaction between the ion and the neighboring water molecules described by simulation. It was found that, within the first solvation sphere, the stronger interactions of the solvent with the ferro species are responsible for a delay in the relaxation dynamics, which becomes more and more evident on longer time scales

Structural Dynamics of (RGD)₄PGC Peptides in Solvated and Au Nanorod Surface-Bound Forms Examined by Ultrafast 2D IR Spectroscopy

Arginine (R)-glycine (G)-aspartate (D) (RGD)-containing oligopeptides are known to be very effective in increasing the biocompatibility and bioconnectivity of gold nanorods (AuNRs), where the conformation of the RGD peptide plays a critical role. In this work, Fourier-transform infrared (FTIR) and circular dichroism (CD) spectroscopies are used to characterize the secondary structure of a typical RGD peptide, namely, (RGD)4PGC, in its solvated state and the AuNRs’ surface-bound state (AuNRs@RGD) at neutral pH. It is shown that such a 15-mer RGD contains a β-turn on its C-terminus (residue DPGC), a short β-strand in the middle, and a random coil on its N-terminus (the RGD replica region). Upon its binding to AuNRs, a small portion of the β-strand is converted into a random coil, thus having a longer segment of random coil than its free form. Moreover, the steady-state conformational change is accompanied by a significant change in ultrafast structural dynamics, as revealed by time-resolved 2D IR spectroscopy. In particular, the increased rigidity in both β-strand and β-turn, including the side chain of arginine residues, is found in AuNRs@RGD. These steady-state and dynamic features both suggest that once attached to the surface of Au nanorods, the RGD peptide could exhibit an increased bio-binding stability due to the overall increased rigidity of the peptide, including the backbone and alternatively located and positively (R) and negatively (D) charged side chains at the N-terminus. Our work provides an insight into the structural dynamics of the working mechanism of the RGD peptides

Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin

Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E–F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a 13C, 15N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the 13C, 15N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm–1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E–F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins