Vasilios S. Melissas

A quantum mechanical study of the structure, vibrational spectra and relative energetics of XOOI, XIO2 and XOIO (X=Cl, Br, I) isomers

Abstract Two different effective-core-potential methodologies, augmented by extra polarization functions were used at the MP2 and CCSD(T) levels of theory to investigate a number of iodine containing isomers of the type XOOI, XIO2 and XOIO (X=Cl, Br, I). The procedures, successfully tested first on the well studied Cl2O2 system, produced results for XIO2 isomers analogous to the corresponding Cl and Br species. The relative energetics however, indicates competing stability depending on the method, between the peroxide XOOI and the Y-shaped XIO2 form for ClIO2 and BrIO2 and between IOOI and IOIO for the I2O2 family.

Ab initio calculations for (BrO)2 system and quasiclassical dynamics study of BrO self-reaction

Abstract Ab initio quantum mechanical studies for BrOOBr peroxide and its isomers were carried out at the MP2 level of theory using the 6-311+G(2d) basis set. Three minima were determined which are in good consistency with previous density functional theory calculations. On the basis of the ab initio results a simple analytical potential energy surface (PES) was constructed and quasiclassical trajectory calculations (QCT) for the self-reaction of BrO radical were performed. Reactive cross-sections, rate coefficients and branching ratios for the two reactive channels are calculated for a series of initial relative kinetic energies which compare favourably with the experimental trends. The quantum mechanical calculations and the analysis of the trajectory results support the experimental evidence that the reaction proceeds through an energetically enriched conformer of BrOOBr peroxide. In addition, the increasing collision lifetime with decreasing collision energy indicates a possible weak stabilization of a short-lived collision complex at lower temperatures which must be responsible for the increasing importance of the rate coefficient of the secondary channel as the temperature decreases, in consistency with the experimental evidence.

Quantum mechanical studies of methyl bromoperoxide isomers and the CH3O+BrO reaction

Ab initio quantum mechanical methods are employed to study methyl bromoperoxide and its isomers which are interesting intermediates in the reaction between methoxy radicals and bromine monoxide. Structural parameters, harmonic frequencies and relative energetics are calculated for all isomeric and conformeric forms. The CH3OOBr isomer is found to be the lowest energy structure followed by CH3OBrO while CH3BrO2 lies much higher in energy. The role of these isomers in the mechanism of the reaction CH3O + BrO is examined. Several transition state structures for the most important reaction channels are also investigated.

A two-dimensional magnetic hybrid material based on intercalation of a cationic Prussian blue analog in montmorillonite nanoclay

A highly ordered two-dimensional hybrid magnetic nanocomposite has been prepared by synthesizing and intercalating a new cationic aluminum-hydroxy ferric ferrocyanide compound into a cation-adsorbing nanoclay (montmorillonite). Chemical and structural properties were investigated by X-ray diffraction, transmission electron microscopy, thermogravimetric and differential thermal analyses, Fourier transform infrared, X-ray photoemission, and Mössbauer spectroscopies. Elemental analysis was based on proton-induced gamma ray emission and X-ray fluorescence spectroscopy data, N/C elemental ratios, and cation-exchange capacity measurements. Magnetic properties were studied by SQUID magnetometry. The results suggest: (i) that the cationic Prussian blue analog comprises Al-hydroxy cations embedded into a monolayer thick two-dimensional ferric ferrocyanide array; and (ii) that the clay-Prussian blue nanohybrid consists of such arrays stacked between the clay layers. The latter material orders ferromagnetically at approximately 5K showing a hundred times higher remanence than that of the starting material, soluble Prussian blue (ammonium ferric ferrocyanide).

Structural and relative stability studies of IOOX peroxides (X=Cl, Br, I) and their isomers

Abstract Two different effective-core-potential methodologies, augmented with extra polarization functions are used at the MP2 level of theory to investigate the isomers of I-containing peroxides of the type XOOI, XIO 2 , IXO 2 , XOIO and IOXO (X=Cl, Br, I). The reliability of the results is checked against the all-electron calculations of Misra and Marshall [J. Phys. Chem. A, 102 (1998) 9056] for the IOOI family. Contrary to what has been well established for the chlorine and bromine analogs, the present study confirms the interesting observation that the I-containing peroxide isomers, XOOI, are not the most stable structures in each subfamily.

A “hidden” role of amino and imino groups is unveiled during the micro-solvation study of three biomolecule groups in water

The 13C longitudinal relaxation times (T1) of three biomolecule groups of major significance to proteins and cells – protein amino acids (AAs), acetyl-amino acids (Ac-AAs) and betaines – and the 14N linewidths (Δν1/2) of Ac-AAs and betaines were measured in aqueous solutions at acidic and neutral pH, by NMR spectroscopy, to estimate the effect of the molecular weight (Mw) on 13C longitudinal relaxation times and 14N linewidths, respectively. 13C relaxation times indicate that AAs and Ac-AAs strongly interact with the same number of water molecules at acidic and neutral pH, respectively, whereas both 13C and 14N results indicate that their Mw values at acidic pH (protonated, positively charged AAs and zero-charged Ac-AAs) increase relatively to those at pH 6.0 (zwitterionic AAs and negatively charged Ac-AAs) that translates into their extra hydration with an excess of one water molecule. Both 13C and 14N relaxation times revealed that betaines retain their hydration grade in both their ionization states at two pH values, while exhibiting their hydration differences from AAs and Ac-AAs and pointing out the “controlling” role of the amino and imino groups in the extra hydration of protonated AAs and Ac-AAs, enlightening the so far unknown significant role of the N-terminus and the −NH near the C-terminus in peptide solvation. Moreover, DFT calculations of the interacting water molecules through hydrogen bonds with Ala, Ac-Ala and Ala betaine molecules in their protonated and neutral pH forms are in absolute agreement with NMR results. Finally, a fully promising method arises with a view on hydration–solvation studies of oligopeptides and other bio-organic molecules by 13C relaxation.

An experimental and theoretical study of the S1←S0 transition of p-ethynyltoluene

The one photon and the two photon S(1)<--S(0) spectra of jet-cooled p-ethynyltoluene have been measured for the first time, and a detailed vibronic analysis for both spectra has been attained. Mass analyzed resonance enhanced multiphoton ionization spectroscopy is the employed technique. In the one photon spectrum, the allowed component (origin and Franck-Condon bands) is much weaker than the forbidden component, and the same mechanisms as in the one photon spectrum of phenylacetylene are observed. The methyl torsional transitions are active. The 0(0) (0) band is at 35 483 cm(-1). The two photon spectrum is very strong and bears a resemblance to the two photon spectrum of phenylacetylene. The potential barrier of the methyl rotor in the S(1) state has been determined as V(6)=-12 cm(-1) with B(CH(3) )=5.55 cm(-1). Ab initio calculations, MP2(full)/cc-pVTZ and CAS/cc-pVTZ, have been implemented for the geometry optimization and the normal mode vibration computation in the S(0) and S(1) states.

CHAPTER 4:The Chemistry of Betaine

In this short overview, a summary and brief explanation of the most important biological functions of betaine is attempted, under the prism of its chemistry and physical properties behavior. Simply put, betaine is an organic molecule and its structure is that of the amino acid glycine, with the difference being that the amino group is trimethylated. Several plants have natural abundance of betaine, while humans either obtain betaine by food intake or synthesize it through choline oxidation. This molecule belongs to the general family of osmolytes, since it is found to play an osmoprotective role during osmotic stress environmental conditions in bacterial, plant and human cells. Moreover, betaine acts as a methyl donor during DNA methylation, resulting to a crucial organic molecule for biological processes of major importance for cells function. Betaine contributes to the stabilization of proteins as well as DNA structure, indirectly, namely through its direct interactions with water molecules close to the hydration shell of proteins and DNA. All the above-mentioned physicochemistry-related biological functions of betaine are briefly exhibited in this chapter.

A quantum mechanical study of IOX (X = Cl, Br, I) isomers

Two different effective-core-potential methodologies, augmented by extra polarization functions were used to investigate a number of iodine triatomics of the type XOI, XIO and IXO (X = Cl, Br, I). The procedures were tested first on the well-studied ClOCl, BrOBr, ClOBr and IOI systems and they were shown to reproduce the full-electron calculation results with reasonable consistency. The results exhibit the same tendencies as the corresponding Cl and Br analogues and produce the greater stability for the isomer with the least electronegative atom in the middle.

CHAPTER 8:Assays of Betaines using 1H NMR Spectroscopy

In this short review, an attempt is made to highlight the biological importance as well as the impact of glycine betaine and other N-methylated compounds, structurally similar to glycine betaine, revealed by 1H-NMR spectroscopy. Namely, glycine betaines, trimethylamines, trimethylamine-N-oxides, proline betaines, carnitines, cholines and trigonellines identification and quantification solely via 1H-NMR spectroscopy in complex biomixtures are pointed out through selected longitudinal research studies. Moreover, these indicative examples certify that these metabolites are not only essential for proper biological function of all kinds of living organisms but also their concentration-level variations establish them as nutritional and medicinal biomarkers. Simultaneously, 1H-NMR spectroscopy is proved to be a trustful, accurate, noninvasive analytical tool in modern biomedicine and pharmaceutical research fields.