Mode recognition in UV resonance Raman spectra of imidazole: histidine monitoring in proteins

Toward the improvement of vibronic spectra and non-radiative rate constants using the vertical Hessian method

For the computation of vibrationally resolved electronic spectra, various approaches can be employed. Adiabatic approaches simulate vibronic transitions using harmonic potentials of the initial and final states, while vertical approaches extrapolate the final state potential from the gradients and Hessian at the Franck-Condon point, avoiding a full exploration of the potential energy surface of the final state. Our implementation of the vertical Hessian (VH) method has been validated with a benchmark set of four small molecules, each presenting unique challenges, such as complex topologies, problematic low-frequency vibrations, or significant geometrical changes upon electronic excitation. We assess the quality of both adiabatic and vertical approaches for simulating vibronic transitions. For two types of donor-acceptor compounds with promising thermally activated delayed fluorescence properties, our computations confirm that the vertical approaches outperform the adiabatic ones. The VH method significantly reduces computational costs and yields meaningful emission spectra, where adiabatic models fail. More importantly, we pioneer the use of the VH method for the computation of rate constants for non-radiative processes, such as intersystem crossing and reverse intersystem crossing along a relaxed interpolated pathway of a donor-acceptor compound. This study highlights the potential of the VH method to advance computational vibronic spectroscopy by providing meaningful simulations of intricate decay pathway mechanisms in complex molecular systems.

Electrochemical Shell-Isolated Nanoparticle-Enhanced Raman Spectroscopy of Imidazole Ring Functionalized Monolayer on Smooth Gold Electrode

The imidazole ring (Im) of histidine side chains plays a unique role in the function of proteins through covalent bonding with metal ions and hydrogen bonding interactions with adjusted biomolecules and water. At biological interfaces, these interactions are modified because of the presence of an electric field. Self-assembled monolayers (SAMs) with the functional Im group mimic the histidine side chain at electrified interfaces. In this study, we applied in-situ shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) to probe the structure and hydrogen bonding of Im-functionalized SAM on smooth Au at the electrochemical interface. The self-assembly of molecules on the Au induced the proton shift from N1 atom (Tautomer-I), which is the dominant form of Im in the bulk sample, to N3 atom (Tautomer-II). The impact of electrode potential on the hydrogen bonding interaction strength of the Im ring was identified by SHINERS. Temperature-Raman measurements and density functional theory (DFT) analysis revealed the spectral marker for Im ring packing (mode near 1496-1480 cm^-1) that allowed us to associate the confined and strongly hydrogen bonded interfacial Im groups with electrode polarization at -0.8 V. Reflection adsorption IR (RAIR) spectra of SAMs with and without Im revealed that the bulky ring prevented the formation of a strongly hydrogen bonded amide group network.

Coordination of Quantum Dots in a Polar Solvent by Small-Molecule Imidazole Ligands

Colloidal quantum dots (QDs) are attractive fluorophores for bioimaging and biomedical applications because of their favorable and tunable optoelectronic properties. In this study, the native hydrophobic ligand environment of oleate-capped sphalerite CdSe/ZnS core/shell QDs was quantitatively exchanged with a set of imidazole-bearing small-molecule ligands. Inductively coupled plasma-optical emission spectroscopy and ¹H NMR were used to identify and quantify three different ligand exchange processes: Z-type dissociation of the Zn(oleate)₂, L-type association of the imidazole, and X-type anionic exchange of oleate with Cl^-, all of which contributed to the overall ligand exchange.

Mononuclear manganese(iii) complexes with reduced imino nitroxide radicals by single-electron transfer and intermolecular hydrogen bonds as an intramolecular structural driving force

One-electron transfer from Mn(ii) ions to an imino nitroxide radical gives mononuclear Mn(iii) complexes of the reduced amino imine-oxide form for which crystal structures evidence hydrogen bonds networks acting as a stabilizing driving-force.

X-ray Raman scattering: a new in situ probe of molecular structure during nucleation and crystallization from liquid solutions

X-ray Raman scattering (XRS) has been used for in situ probing of solute molecule speciation in solution during cooling crystallization.

General formulation of vibronic spectroscopy in internal coordinates

Our general platform integrating time-independent and time-dependent evaluations of vibronic effects at the harmonic level for different kinds of absorption and emission one-photon, conventional and chiral spectroscopies has been extended to support various sets of internal coordinates. Thanks to the implementation of analytical first and second derivatives of different internal coordinates with respect to cartesian ones, both vertical and adiabatic models are available, with the inclusion of mode mixing and, possibly, Herzberg-Teller contributions. Furthermore, all supported non-redundant sets of coordinates are built from a fully automatized algorithm using only a primitive redundant set derived from a bond order-based molecular topology. Together with conventional stretching, bending, and torsion coordinates, the availability of additional coordinates (including linear and out-of-plane bendings) allows a proper treatment of specific systems, including, for instance, inter-molecular hydrogen bridges. A number of case studies are analysed, showing that cartesian and internal coordinates are nearly equivalent for semi-rigid systems not experiencing significant geometry distortions between initial and final electronic states. At variance, delocalized (possibly weighted) internal coordinates become much more effective than their cartesian counterparts for flexible systems and/or in the presence of significant geometry distortions accompanying electronic transitions.

Highly selective ratiometric fluorescent recognition of histidine by tetraphenylethene–terpyridine–Zn(ii) complexes

Fluorescent detection of histidine is achieved with distinctive color change from yellow to blue by using the Zn(ii) complexes of the terpyridine–tetraphenylethene conjugates.

A robust and effective time-independent route to the calculation of Resonance Raman spectra of large molecules in condensed phases with the inclusion of Duschinsky, Herzberg-Teller, anharmonic, and environmental effects

We present an effective time-independent implementation to model vibrational resonance Raman (RR) spectra of medium-large molecular systems with the inclusion of Franck-Condon (FC) and Herzberg-Teller (HT) effects and a full account of the possible differences between the harmonic potential energy surfaces of the ground and resonant electronic states. Thanks to a number of algorithmic improvements and very effective parallelization, the full computations of fundamentals, overtones, and combination bands can be routinely performed for large systems possibly involving more than two electronic states. In order to improve the accuracy of the results, an effective inclusion of the leading anharmonic effects is also possible, together with environmental contributions under different solvation regimes. Reduced-dimensionality approaches can further enlarge the range of applications of this new tool. Applications to imidazole, pyrene, and chlorophyll a1 in solution are reported, as well as comparisons with available experimental data.

His26 protonation in cytochrome c triggers microsecond β-sheet formation and heme exposure: implications for apoptosis

Cytochrome c unfolds locally and reversibly upon heating at pH 3. UV resonance Raman (UVRR) spectra reveal that instead of producing unordered structure, unfolding converts turns and some helical elements to β-sheet. It also disrupts the Met80-heme bond, and has been previously shown to induce peroxidase activity. Aromatic residues that are H-bonded to a heme propionate (Trp59 and Tyr48) alter their orientation, indicating heme displacement. T-jump/UVRR measurements give time constants of 0.2, 3.9, and 67 μs for successive phases of β-sheet formation and concomitant reorientation of Trp59. UVRR spectra reveal protonation of histidines, and specifically of His26, whose H-bond to Pro44 anchors the 40s Ω loop; this loop is known to be the least stable 'foldon' in the protein. His26 protonation is proposed to disrupt its H-bond with Pro44, triggering the extension of a short β-sheet segment at the 'neck' of the 40s Ω loop into the loop itself and back into the 60s and 70s helices. The secondary structure change displaces the heme via H-bonds from residues in the growing β-sheet, thereby exposing it to exogenous ligands, and inducing peroxidase activity. This unfolding mechanism may play a role in cardiolipin peroxidation by cyt c during apoptosis.