Zlatko Meić

VIBRATIONAL ANALYSIS OF STILBENE AND ITS ISOTOPOMERS ON THE GROUND STATE POTENTIAL ENERGY SURFACE

Abstract Optimized geometries and vibrational frequencies of trans- and cis-stilbene in the S0 state are calculated by the semiempirical RHF/AM1 method and by means of ab initio RHF method using the 6-31G(d) basis set. Fully optimized geometry and vibrational frequencies of the perpendicular stilbene are calculated by means of the UHF function of the two MO methods. With only one imaginary frequency, the perpendicular configuration is a transition state on the ground-state potential energy surface. The three stilbene isomers possess C2 symmetry. The reaction coordinate leading either to trans or cis isomer is not only the rotation around the central bond but also includes significant changes in bond lengths and angles of the ethylenic moiety. A high value of the secondary kinetic isotope effect for thermal isomerization of cis-stilbene and α,α′-D2-cis-stilbene calculated using the ab initio frequencies agrees very well with the recent experimental result. Infrared and Raman spectra for the ground state cis-stilbene and eleven of its deuterated isotopomers (D0-, 4-D1-, 4,4′-D2-, 2,3,4,5,6-D5- (D5-cS), 2,3,4,5,6,4′-D6- and 2,3,4,5,6,2′,3′,4′,5′,6′-D10-cS (D10-cS) in group I, α-D1-, 4,α′-D2-, 2,3,4,5,6, α-D6-, and D11-cS in group II, and α,α′-D2- and D12-cS in group III) have been recorded. The vibrational assignments for both stilbene isomers were deduced to the largest possible extent on the basis of band intensities in solution and solid phases, isotopic frequency shifts and phenyl characteristic frequencies. The experimental frequencies of three isotopomers (D0, α,α′-D2 and D10) were used simultaneously to obtain the scaled quantum chemical force fields for the trans and cis isomer separately, i.e. no scaling factor was given an arbitary value. The semiempirical force field after scaling reproduces the experimental frequencies with an average error of 13 cm−1 which is twice as large as the error of the scaled ab initio force field. The possibility of using the same set of scaling factors for different isomers is considered. The eight modes (5A+3B) involved in the low-frequency region are thoroughly analyzed and reasons are given why the phenyl torsions of trans-stilbene can only be properly explained by a non-planar ground-state structure. The AM1 barrier hindering the thermal transition between the chiral ground-state cis-stilbene of C2 symmetry to its enantiomer is rather low (1.3 kcal mol−1) and comparable to that of trans-stilbene (1.7 kcal mol−1). It accounts for the large bandwidths of some composite low-frequency Raman bands (below 400 cm−1).

Investigation of hydrogen bond structure in benzoic acid solutions

Abstract Significant changes in 13 C chemical shifts of benzoic acid (BA) were observed for the carboxyl and quarternary carbon atoms on going from non-polar benzene to solvents with different hydrogen bond donor or acceptor abilities. Shielding effects of 6.145 and 5.413 ppm at the carboxyl carbon in dimethyl sulfoxide (DMSO) and acetone, respectively, are due to the redistribution of electron density upon the formation of new intermolecular hydrogen bonds with solvent molecules. 1 H NMR upfield shifts of the carboxyl proton in DMSO and chloroform solutions in comparison with benzene solution, and shifts in the CO stretching frequency, ν CO , observed in infrared spectra of BA complexes are consistent with these results. Structural parameters and interaction energies of the hydrogen-bonded complexes determined by quantum-chemical calculations substantiate the experimental observations. Using the semiempirical PM3 hamiltonian, hydrogen bonding was treated as the donor-acceptor mechanism within the natural bond orbital (NBO) formalism. Two correlations, which reflect hydrogen bonding in different solvents, are proposed: one between the 13 C chemical shifts and the change in p-character of the carboxyl carbon atom and the other between the carboxyl CO stretching frequency and the calculated interaction energy of the hydrogen-bonded complexes.

Infrared and Raman spectra of cis-stilbene and its deuterated isotopomers

Abstract The vibrational analysis of cis -stilbene in the ground electronic state based on the infrared and Raman spectra of a series of its isotopomers and scaled semiempirical AM1 calculations is reported. The C α C α stretching, all the four C α H deformations and the C α C α torsion are described. A comparison with trans -stilbene shows a much lesser degree of couplings between olefinic and phenyl vibrations in cis -stilbene.

Vibrational spectra and DFT calculations of PPV-oligomers

Abstract The first two members of the p -phenylenevinylene-oligomer family (i.e. 1,4-distyrylbenzene and 4,4′-distyrylstilbene) were synthesized and their infrared and Raman spectra recorded and empirically assigned. Molecular geometries were optimized for the planar point group ( C 2 h ) by the density functional theory (DFT) method using the B3LYP functional and 6-31G* basis set. Calculations of vibrational spectra, including intensities, were carried out subsequently using the DFT method with the same basis set and linear scaling was applied. Calculated vibrational wavenumbers are in a fair agreement with our own experimental spectra. In order to explore changes in vibrational dynamics that are obtained with the extension of the chain, differences in potential energy distribution of normal modes are investigated and discussed. It was shown that B3LYP functional well describes the mentioned differences in infrared and Raman spectra and presents a sound basis for a more thorough research. The results are compared with those of trans -stilbene, a molecule structurally most closely related to the members of the p -phenylenevinylenes family.

Vibrational coupling in trans-azobenzene and its isotopomers

Abstract Infrared (4000−400 cm−1) and Raman spectra (4000−100 cm−1) of six trans-azobenzene isotopomers, including the parent one, were recorded. Using mono and double 15N-labelled isotopomers, the assignment of the NN stretching was confirmed at 1439 cm−1 in the parent isotopomer. This vibration is strongly coupled with the phenyl mode 19b. In isotopomers with one and two perdeuterium-labelled phenyl groups the NN stretching shifts to higher wavenumbers, since this coupling is no longer effective.

Recognition of homo-polynucleotides containing adenine by a phenanthridinium bis-uracil conjugate in aqueous media

Among novel bis-nucleobase-phenanthridinium conjugates bis-uracil analogue stabilized significantly more effective poly-dA-poly-dT and poly-AH(+)-poly-AH(+) than adenine analogue and reference compound . For the alternating poly-dAdT-poly-dAdT however, the binding preference is lost, pointing to the importance of specific interactions of uracils of with homopolynucleotides containing consecutive adenines.

Near-infrared Fourier transform Raman spectra of protonated and deuterated trans-azobenzene isotopomers

Abstract Near-infrared Fourier transform (NIR FT) Raman spectra of five trans -azobenzene isotopomers and their protonated and deuterated forms were recorded. Trifluoroacetic acid was found to be a good protonation agent for measuring Raman spectra of protonated azobenzene. An assignment of the most relevant vibrational modes (NN stretching and N  H N  2 H in-plane bending) of the protonated and deuterated species is proposed. The NN stretching band in trans -azobenzene isotopomers decreases by about 40 cm −1 upon protonation, while it varies within ± 10 cm −1 upon deuteration with respect to the unprotonated (undeuterated) form. A comparison is made with the protonated form of the isoelectronic trans - N -benzylideneaniline.

Force fields for neutral and protonated Schiff bases

Abstract In order to analyse the vibrational dynamics of the imino group in its neutral and protonated forms, a normal coordinate analysis of the model aromatic Schiff base trans-N -benzylideneaniline (tBA) was undertaken. The results of the valence force field calculations for neutral tBA, based on the experimental geometry and the vibrational spectra of a series of tBA isotopomers, display a considerable mixing of imino coordinates. For the protonated species a different conformation was found by optimising the geometry using the AM1 method; in this conformation both dihedral angles are less than in the neutral tBA molecule. Although an increase in the CN stretching frequency by 45 cm 1 was observed, a decrease in the CN stretching force constant was found. The results of the calculations showed a decrease in the NPh stretching, but an increase in the imino CH and CPh stretching, as well as the imino CH in-plane deformation constants. No change in the CH out-of-plane deformation constant was found, but some interaction force constants changed their values. Protonation of tBA brings about many changes in the vibrational spectra, probably owing to the change in hybridisation and mass distribution around the nitrogen atom and to the different conformation, rather than to changes in bond lengths or counter ion effects.

Isotope effects in 13C NMR spectra of monodeuteriated trans-N-bezylideneanilines

Abstract Deuterium isotope effects on 13 C chemical shifts have been determined in a series of monodeuteriated trans -N-benzylideneanilines. The effects over two bonds ( 2 Δ) observed at C-1 and over three bonds ( 3 Δ) observed at C-2,6 are sensitive to steric interactions involving nitrogen lone-pair electrons and C-Ph ortho -protons. Like in similar π-electron systems, the effect over six bonds ( 6 Δ) is related to molecular conformation.

Interactions of phenanthridinium–nucleobase conjugates with polynucleotides in aqueous media. Recognition of poly U

Adenine containing conjugates 4 and 5 exhibit specific spectroscopic changes and two orders of magnitude higher affinity toward poly U than uracil conjugates 2 and 3 and the reference compound 1 due to the existence of specific interactions between adenine and uracil, possibly Watson-Crick hydrogen bonding between the bases stacked on the phenanthridinium moiety.