Structures, energetics and vibrational frequency shifts of hydrated pyrimidine

Raman Spectroscopic and Quantum Chemical Investigation of the Pyridine-Borane Complex and the Effects of Dative Bonding on the Normal Modes of Pyridine

The pyridine-borane (PyBH₃) complex was analyzed by Raman vibrational spectroscopy and density functional theory to elucidate its structural and vibrational properties and to compare these with those for neat pyridine (Py). The borane-nitrogen (BN) bond length, the BN dative bond stretching frequency, and the effects of dative-bonded complex formation on Py are presented. Rather than having a single isolated stretching motion, the complex exhibits multiple BN dative bond stretches that are coupled to Py's vibrations. These modes exhibit large shifts that are higher in energy relative to neat Py, similar to previous observations of Py/water mixtures. However, significantly higher charge transfer was observed in the dative-bonded complex when compared to the hydrogen-bonded complex with water. A linear relationship between charge transfer and shifts to higher frequencies of pyridine's vibrational modes agrees well with earlier observations. The present work is of interest to those seeking a stronger relationship between charge-transfer events and concomitant changes in molecular properties.

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.

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.

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.

Competition between Hydrophilic and Argyrophilic Interactions in Surface Enhanced Raman Spectroscopy

The competition for binding and charge-transfer (CT) from the nitrogen containing heterocycle pyrimidine to either silver or to water in surface enhanced Raman spectroscopy (SERS) is discussed. The correlation between the shifting observed for vibrational normal modes and CT is analyzed both experimentally using Raman spectroscopy and theoretically using electronic structure theory. Discrete features in the Raman spectrum correspond to the binding of either water or silver to each of pyrimidine's nitrogen atoms with comparable frequency shifts. Natural bond orbital (NBO) calculations in each chemical environment reveal that the magnitude of charge transfer from pyrimidine to adjacent silver atoms is only about twice that for water alone. These results suggest that the choice of solvent plays a role in determining the vibrational frequencies of nitrogen containing molecules in SERS experiments.

The onset of electron-induced proton-transfer in hydrated azabenzene cluster anions

The prospect that protons from water may be transferred to N-heterocyclic molecules due to the presence of an excess electron is studied in hydrated azabenzene cluster anions using spectroscopy and computational chemistry.

Photoelectron spectroscopic and computational study of hydrated pyrimidine anions

The stabilization of the pyrimidine anion by the addition of water molecules is studied experimentally using photoelectron spectroscopy of mass-selected hydrated pyrimidine clusters and computationally using quantum-mechanical electronic structure theory. Although the pyrimidine molecular anion is not observed experimentally, the addition of a single water molecule is sufficient to impart a positive electron affinity. The sequential hydration data have been used to extrapolate to -0.22 eV for the electron affinity of neutral pyrimidine, which agrees very well with previous observations. These results for pyrimidine are consistent with previous studies of the hydrated cluster anions of uridine, cytidine, thymine, adenine, uracil, and naphthalene. This commonality suggests a universal effect of sequential hydration on the electron affinity of similar molecules.

Effect of protonation and hydrogen bonding on 2, 4, 6-substituted pyrimidine and its salt complex-experimental and theoretical evidence

Quantum molecular simulations of chemical systems can provide detailed information that is often inaccessible to direct experimental measurement. Pyrimidine is an interesting π-electron heterocyclic aromatic system which acts as the building block of many nucleic acid bases. The hydrogen bonds associated with the 2, 4, and 6-substituted pyrimidine and its hydrogen sulfate anion are considered for this current work. The experimental and computational evidence for the strength of these intra and intermolecular hydrogen are determined using vibrational spectra and quantum chemical calculations. Thus the effect of hydrogen bonding on the title compound is studied using its geometrical parameters, interaction energies, and vibrational spectra. Aromaticity and charge transfer studies have been performed to ascertain the aromatic behavior of the molecule. The PES scan studies have been done by varying the bond length to ascertain the protonation process of the compound. The IR spectral red shift (∼100 cm⁻¹), blue shift (∼97 cm⁻¹) and broadening of the polar stretching peaks shows the inter and intramolecular hydrogen bonding strength. Bond length alternation of proton donors along with the enormous interaction energies (∼0.5-150 kJ mol⁻¹) between the lone pair and proton donors provides clear evidence for this hydrogen bonding. The charge transfer due to the methyl substitutions which enhances the possibility of hydrogen bonding has been discussed. The main scope of this work is to study the protonation and hydrogen bonding associated with charge transfer which has great effect on the 2-amino-4, 6-dimethyl pyrimidinium hydrogen sulfate (ADHS) molecule.

Charge transfer and blue shifting of vibrational frequencies in a hydrogen bond acceptor

A comprehensive Raman spectroscopic/electronic structure study of hydrogen bonding by pyrimidine with eight different polar solvents is presented. Raman spectra of binary mixtures of pyrimidine with methanol and ethylene glycol are reported, and shifts in ν1, ν3, ν6a, ν6b, ν8a, ν8b, ν9a, ν15, ν16a, and ν16b are compared to earlier results obtained for water. Large shifts to higher vibrational energy, often referred to as blue shifts, are observed for ν1, ν6b, and ν8b (by as much as 14 cm(-1)). While gradual blue shifts with increasing hydrogen bond donor concentration are observed for ν6b and ν8b, ν1 exhibits three distinct spectral components whose relative intensities vary with concentration. The blue shift of ν1 is further examined in binary mixtures of pyrimidine with acetic acid, thioglycol, phenylmethanol, hexylamine, and acetonitrile. Electronic structure computations for more than 100 microsolvated structures reveal a significant dependence of the magnitude of the ν1 blue shift on the local microsolvation geometry. Results from natural bond orbital (NBO) calculations also reveal a strong correlation between charge transfer and blue shifting of pyrimidine's normal modes. Although charge transfer has previously been linked to blue shifting of the X-H stretching frequency in hydrogen bond donors, here, a similar trend in a hydrogen bond acceptor is demonstrated.