Milena Petković

O–H Stretch in Phenol and Its Hydrogen-Bonded Complexes: Band Position and Relaxation Pathways

Anharmonic force fields are a suitable means for identification of vibrational degrees of freedom responsible for the peculiar shape of molecular spectra and the existence of diverse relaxation pathways. In this contribution, we investigated interactions that govern the position of the O-H stretching band in phenol and its dimers with water and ammonia. Dominant couplings are identified, and the nature of relaxation channels is analyzed. The effect of hydrogen bonding on O-H stretching motion and vibrational energy redistribution time through intra- and intermolecular interactions is studied, and possible vibrational predissociation upon O-H stretch excitation is addressed. The results based on computed anharmonic force constants are in accord with the available experimental findings.

Intramolecular OHO bonding in dibenzoylmethane: symmetry and spectral manifestations

Although both experimentalists and theoreticians agree that dibenzoylmethane exists in the enol form, there are different opinions concerning symmetry of the OHO fragment. Consequently, assignment of its vibrational spectra has been incomplete. In this contribution we computed Gibbs free energies with the G4MP2 method. Multi-dimensional potential energy surfaces obtained at M06-2X/cc-pVTZ level enabled vibrational analysis and comparison with available experimental data. Our results revealed presence of two conformers in the gas phase at room temperature, the asymmetric structure (with O–H stretching frequency around 2400 cm−1 and very low infrared intensity), and the symmetric conformer (with O⋯H⋯O asymmetric stretching band located around 500 cm−1). Characterization of hydrogen bonds was performed with quantum theory of atoms in molecules (QTAIM), which showed that O–H⋯O group represents a typical hydrogen bond, whereas hydrogen bonds in the O⋯H⋯O fragment have substantial covalent character.

Electron-Vibrational Coupling and Fluorescence Spectra of Tetra-, Penta-, and Hexacoordinated Chlorophylls c1 and c2.

Chlorophylls (Chls) are a group of pigments related to light absorption, excitation energy, and electron transfer in photosynthetic complexes. Given the importance of intramolecular nuclear motion for these electronic processes, many experimental studies were performed in order to relate its coupling to electronic coordinates of these pigments, but a detailed analysis is still lacking for isolated Chls c1 and c2. To gain insight into the intramolecular motion and fluoroscence spectra of these two pigments in tetra-, penta-, and hexacoodinated states, we performed a quantum chemical study based on density functional theory and multimode harmonic approximation with displaced, distorted, and rotated normal modes. In order to benchmark the employed methods, we simulated the high-resolution fluorescence spectra of tetracoodinated Chls a, b, and d and compared them with available experimental spectra obtained with fluorescence line-narrowing techniques. Although the experimental spectra were obtained for ligand coordinated Chls, qualitatively good agreement was found between the simulated and experimental spectra. Almost all resonances were reproduced in the spectroscopically interesting region from 200 to 1700 cm(-1). The significance of mode distortion and rotation for the simulated spectra is discussed. The fluorescence spectra of Chls c1 and c2 consist of a group of peaks in the 200-450 cm(-1) spectral range, a group of weak peaks from 700 to 1000 cm(-1), and a large group of strong peaks from 1100 to 1600 cm(-1). Ligand effects are also addressed, and a mode is identified as a sensitive probe for the coordination state of Chls c1 and c2.

E–H (E = B, Si, C) Bond Activation by Tuning Structural and Electronic Properties of Phosphenium Cations

In this work, strategic enhancement of electrophilicity of phosphenium cations for the purpose of small-molecule activation was described. Our synthetic methodology for generation of novel two-coordinate phosphorus(III)-based compounds [{C6H4(MeN)2C}2C·PR]2+ ([2a]2+, R = NiPr2; [2b]2+, R = Ph) was based on the exceptional electron-donating properties of the carbodicarbene ligand (CDC). The effects of P-centered substituent exchange and increase in the overall positive charge on small substrate activation were comparatively determined by incorporating the bis(amino)phosphenium ion [(iPr2N)2P]+ ([1]+) in this study. Implemented structural and electronic modifications of phosphenium salts were computationally verified and subsequently confirmed by isolation and characterization of the corresponding E-H (E = B, Si, C) bond activation products. While both phosphenium mono- and dications oxidatively inserted/cleaved the B-H bond of Lewis base stabilized boranes, the increased electrophilicity of doubly charged species also afforded the activation of significantly less hydridic Si-H and C-H bonds. The preference of [2a]2+ and [2b]2+ to abstract the hydride rather than to insert into the corresponding bond of silanes, as well as the formation of the carbodicarbene-stabilized parent phosphenium ion [{C6H4(MeN)2C}2C·PH2]+ ([2·PH2]+) were experimentally validated.

New Insight into Uracil Stacking in Water from Ab Initio Molecular Dynamics

Nucleobases spontaneously aggregate in water by forming stacked dimers and multimers. It is assumed that the main contributions to the aggregation stem from hydrophobic and base-base dispersion interactions. By studying the uracil monomer and dimer in bulk water with the first principle molecular dynamics, we discuss dimer structure and provide evidence that stacking increases the uracil-water hydrogen bonding strength and alters the hydration structure of uracil. These changes have a significant influence on the intensity and shift of the carbonyl stretching band as revealed by simulated infrared absorption spectra of the monomer and dimer and available experimental spectra. The contributions of dipole-dipole, dispersion, and water mediated forces to the stacking are discussed. The reported findings are valuable for understanding the microscopic mechanism of heteroaromatic association in water which is relevant to a large range of chemical and biological systems.

TiO2 nanocrystals – assisted laser desorption and ionization time-of-flight mass spectrometric analysis of steroid hormones, amino acids and saccharides. Validation and comparison of methods

In the present study, the possibility for the application of TiO2 nanocrystals of various shapes and sizes, for substrate-assisted laser desorption and ionization time-of-flight mass spectrometric (SALDI TOF MS) quantitative analysis of small molecules (steroid hormones, amino acids and saccharides) was investigated. Parameters, such as homogeneity of the substrate/analyte distribution, reproducibility of the measurements, within-day, and day-to-day repeatability, were determined. The homogeneity of different nanocrystal/analyte combinations on the target plate were compared based on the signal-to-noise values of several analyte signals. Obtained results show that all TiO2 nanocrystals, regardless of their shape, have great potential for the detection and determination of steroid hormones, amino acids and saccharides with good analytical parameters and detection limits. On the other hand, the reproducibility of the S/N ratio and detectability of the analytes recorded in various modes differ depending on the substrate. All examined molecules were detectable in negative ion mode with TiO2 NTs, in contrast to all other organic matrices and substrates, and the best reproducibility was obtained with the larger nanocrystals, TiO2 PNSs and TiO2 NTs, making them good candidates for the quantitative determination of small molecules.

Oxidation of a P-C bond under mild conditions

The reactivity of phosphenium dication [(Ph3P)2C-P-NiPr2](2+), 1(2+), towards pyridine N-oxide (O-py) has been investigated. The resulting oxophosphonium dication [(Ph3P)2C(NiPr2)P(O)(O-py)](2+), 2(2+), was surprisingly stabilized by a less nucleophilic O-py ligand instead of pyridine (py). This compound was then identified as an analogue of the elusive Criegee intermediate as it underwent oxygen insertion into the P-C bond through a mechanism usually observed for Baeyer-Villiger oxidations. This oxygen insertion appears to be the first example of a Baeyer-Villiger oxidation involving O-py.

Vibrational spectroscopy: can density functional theory cope with highly electronegative atoms?

Vibrational properties of molecules composed solely of highly electronegative atoms are studied by means of density functional methods. Performance of different combinations of exchange and correlation functionals is tested. It is demonstrated that certain functionals can successfully simulate infrared spectra of systems containing only fluorine, oxygen and nitrogen.

When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms

Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra‐atomic and inter‐atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra‐atomic and inter‐atomic terms that involve hydroquinones oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radicals oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange‐correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange‐correlation term dominates interaction between methoxy radicals methyl group and hydroquinones aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points.

Site-Specific Deuteration of Polyunsaturated Alkenes

Selective deuteration of drugs and biologically relevant molecules is becoming increasingly important in the pharmaceutical industry. Site-selective isotopic reinforcement of polyunsaturated fatty acids (PUFAs) at their bis-allylic sites has been identified as a unique approach in preventing oxidative damage in these molecules, which had been linked to neuronal and retinal diseases, atherosclerosis, and aging. Typical methods for preparation of site-selectively deuterated PUFAs require rather long, laborious, and expensive syntheses. In this report, we disclose a very efficient catalytic protocol for site-specific deuteration of PUFAs and analogous poly-alkenes under exceptional kinetic control. Deuterium oxide (D2O) has been identified not only as a deuterium source but also as a crucial component in the overall reaction mechanism responsible for averting the formation of thermodynamically favored side-products.