Competition between Hydrophilic and Argyrophilic Interactions in Surface Enhanced Raman Spectroscopy

Guest-Host Raman Under liquid Nitrogen Spectroscopy for the acquisition of improved vibrational spectra of solids

Guest-Host Raman under liquid nitrogen spectroscopy (GHRUNS) is introduced whereby solid state guest molecules are isolated inside cage-like host environments for the facile acquisition of their Raman spectra. This convenient method features reduced fluorescence, the analysis of populations in their ground states, and increased signal to noise ratios. Samples are also preserved through the reduction of thermal degradation and oxidation. To demonstrate the benefits of this new method, Raman spectra of the ubiquitous molecule C 60 inside a cage of water ice are presented. Using this technique, a new normal mode of C 60 is elucidated. The GHRUNS methodology is of interest to those seeking to acquire and characterize the vibrational spectra, structure, and properties of emissive, air-sensitive molecules.

Determination of vibrational band positions in the E-hook of β-tubulin

Raman spectral characterization of the β-TUBB2A E-hook hexapeptide, EGEDEA, is determined through experimental analysis combined with full geometry optimizations and corresponding harmonic vibrational frequency computations employing DFT methods. The hexapeptide is first broken down into di- and tetrapeptide fragments which are analyzed both quantum chemically and experimentally, and then combined to achieve an energetic minimum of the large EGEDEA hexapeptide. The Raman spectral characterization of EGEDEA band positions are then verified via the literature and comparison to the small fragment's similarly located band positions. The approach employed provides further evidence for the use of fragments as a helpful tool in characterization of the vibrational band positions of large peptides. STATEMENT OF SIGNIFICANCE: To investigate β-TUBB2A E-hook hexapeptide, a unique approach is employed whereby the hexapeptide is broken into fragments, EG, ED, EA, EGED, and EDEA and analyzed via experimental Raman spectroscopy of the crystalline solids. The experimentally observed vibrational band positions are compared to those computed using and scaled from DFT methods and Pople's 6-311+G(2df,2pd) basis set. The reported vibrational band positions are also confirmed by previously reported bands of similar peptides in the literature. This methodology facilitates differentiation between the behaviors of various side chains and their influence on the structure of the hexapeptide, providing insight into not only the nature of the peptide but also defining regions for potential protein and cytoplasmic interactions, without requiring excessive computing resources or overly-sensitive experimental methods.

The mutual noncovalent interactions based on metallophilic cluster and anions: A theoretical investigation of the molecular structure and spectroscopic properties of Host–Guest complexes

The d[Formula: see text] metallophilic host clusters [Au(NHC)2][Formula: see text] [M(CN)2][Formula: see text] [Au(NHC)2][Formula: see text](NHC [Formula: see text] N-heterocyclic carbene, [Formula: see text], Ag) with high phosphorescence are synthesized recently and their phosphorescent modulation by solvents is investigated in theory. In this paper, the guest anions (F−, Cl−, Br−, NO[Formula: see text], and BF[Formula: see text] are used to elucidate their effects on metallophilic interactions and phosphorescence of hosts, and also they served as the probes to study the recognition characters of metallophilic hosts. The calculation shows that the guest anions can mutually interact with the host clusters and further, which can modulate the metallophilic Au[Formula: see text]M distances and the phosphorescence spectra of the hosts.

A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C–H···O or C–H···N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly.

Theoretical Approaches for Modeling the Effect of the Electrode Potential in the SERS Vibrational Wavenumbers of Pyridine Adsorbed on a Charged Silver Surface

Vibrational wavenumbers of pyridine adsorbed on a silver electrode have been correlated to the calculated ones from different theoretical approaches based on DFT methods. The vibrational tuning caused by the electrode potential has been simulated by means of pyridine-silver clusters with different densities of charge or, alternatively, under applied external electric fields. Both methodologies predict correctly a qualitative red-shift of the vibrational wavenumbers at negative potentials. As a result, harmonic frequency calculations performed at the B3LYP/LanL2DZ level of theory by using a linear [Ag_nPy]^q complex model with different densities of charge (q_eff = q/n) have exhibited the best agreement with the experimental observations although the tuning amplitudes are overestimated. Electric fields calculations are unable to account for subtle details observed in the spectra related to the differentiated chemical nature of the metal-molecule bond at positive or negative potentials with respect to the potential of zero charge of the electrode.

Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions

This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.

Noncovalent Interactions between Trimethylamine N-Oxide (TMAO), Urea, and Water

Trimethylamine N-oxide (TMAO) and urea are two important osmolytes with their main significance to the biophysical field being in how they uniquely interact with proteins. Urea is a strong protein destabilizing agent, whereas TMAO is known to counteract urea's deleterious effects. The exact mechanisms by which TMAO stabilizes and urea destabilizes folded proteins continue to be debated in the literature. Although recent evidence has suggested that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored, it has also been suggested that urea acts indirectly to denature proteins by destabilizing the surrounding hydrogen bonding water networks. Here, we elucidate the molecular level mechanism of TMAO's unique ability to counteract urea's destabilizing nature by comparing Raman spectroscopic frequency shifts to the results of electronic structure calculations of microsolvated molecular clusters. Experimental and computational data suggest that the addition of TMAO into an aqueous solution of urea induces blue shifts in urea's H-N-H symmetric bending modes, which is evidence for direct interactions between the two cosolvents.

Phosphorescent Modulation of Metallophilic Clusters and Recognition of Solvents through a Flexible Host-Guest Assembly: A Theoretical Investigation

MP2 (Second order approximation of Møller–Plesset perturbation theory) and DFT/TD-DFT (Density functional theory/Time-dependent_density_functional_theory) investigations have been performed on metallophilic nanomaterials of host clusters [Au(NHC)₂]⁺⋅⋅⋅[M(CN)₂]⁻⋅⋅⋅[Au(NHC)₂]⁺ (NHC = N-heterocyclic carbene, M = Au, Ag) with high phosphorescence. The phosphorescence quantum yield order of clusters in the experiments was evidenced by their order of μ_S1/ΔE_S1−T1 values (μS1: S₀ → S₁ transition dipole, ∆ES1−T1: splitting energy between the lowest-lying singlet S₁ and the triplet excited state T₁ states). The systematic variation of the guest solvents (S1: CH₃OH, S2: CH₃CH₂OH, S3: H₂O) are employed not only to illuminate their effect on the metallophilic interaction and phosphorescence but also as the probes to investigate the recognized capacity of the hosts. The simulations revealed that the metallophilic interactions are mainly electrostatic and the guests can subtly modulate the geometries, especially metallophilic Au⋅⋅⋅M distances of the hosts through mutual hydrogen bond interactions. The phosphorescence spectra of hosts are predicted to be blue-shifted under polar solvent and the excitation from HOMO (highest occupied molecular orbital) to LUMO (lowest unoccupied molecular orbital) was found to be responsible for the ³MLCT (triplet metal-to-ligand charge transfer) characters in the hosts and host-guest complexes. The results of investigation can be introduced as the clues for the design of promising blue-emitting phosphorescent and functional materials.

Analysis of Serotonin Molecules on Silver Nanocolloids-A Raman Computational and Experimental Study

Combined theoretical and experimental analysis of serotonin by quantum chemical density functional calculations and surface-enhanced Raman spectroscopy, respectively, is presented in this work to better understand phenomena related to this neurotransmitter’s detection and monitoring at very low concentrations specific to physiological levels. In addition to the successful ultrasensitive analyte detection on silver nanoparticles for concentrations as low as 10⁻¹¹ molar, the relatively good agreement between the simulated and experimentally determined results indicates the presence of all serotonin molecular forms, such as neutral, ionic, and those oxidized through redox reactions. Obvious structural molecular deformations such as bending of lateral amino chains are observed for both ionic and oxidized forms. Not only does this combined approach reveal more probable adsorption of serotonin into the silver surface through hydroxyl/oxygen sites than through NH/nitrogen sites, but also that it does so predominantly in its neutral (reduced) form, somewhat less so in its ionic forms, and much less in its oxidized forms. If the development of opto-voltammetric biosensors and their effective implementation is envisioned for the future, this study provides some needed scientific background for comprehending changes in the vibrational signatures of this important neurotransmitter.

Quantifying the Effects of Halogen Bonding by Haloaromatic Donors on the Acceptor Pyrimidine

The effects of intermolecular interactions by a series of haloaromatic halogen bond donors on the normal modes and chemical shifts of the acceptor pyrimidine are investigated by Raman and NMR spectroscopies and electronic structure computations. Halogen-bond interactions with pyrimidine's nitrogen atoms shift normal modes to higher energy and upfield shift ¹ H and ¹³ C NMR peaks in adjacent nuclei. This perturbation of vibrational normal modes is reminiscent of the effects of hydrogen bonded networks of water, methanol, or silver on pyrimidine. The unexpected observation of vibrational red shifts and downfield ¹³ C NMR shifts in some complexes suggests that other intermolecular forces such as π interactions are competing with halogen bonding. Natural bond orbital analyses indicate a wide range of charge transfer is possible from pyrimidine to different haloaromatic donors and computed halogen bond binding energies can be larger than a typical hydrogen bond. These results emphasize the importance in strategic selection of substituents and electron withdrawing groups in developing supramolecular structures based on halogen bonding.