Biomedical subjects

Joanna E Rode

Publications and source records attributed to Joanna E Rode.

5 recordsLinked to original sources

PubMed2006

An ab initio study on the allene-isocyanic acid and ketene-vinylimine [2 + 2] cycloaddition reaction paths.

The reaction paths of [2 + 2] cycloadditions of allene (H2C=C=CH2) to isocyanic acid (HN=C=O) and ketene (H2C=C=O) to vinylimine (H2C=C=NH), leading to all the possible 14 four-membered ring molecules, were investigated by the MP2/aug-cc-pVDZ method. In the two considered reactions, the 2-azetidinone (beta-lactam) ring compounds were predicted to be the most stable thermodynamically in the absence of an environment. Although 4-methylene-2-azetidinone is the most stable product of the ketene-vinylimine cycloaddition, its activation barrier is higher than that for 4-methylene-2-iminooxetane by ca. 6 kcal/mol. Therefore, the latter product can be obtained owing to kinetic control. The activation barriers in the allene-isocyanic acid reactions are quite high, 50-70 kcal/mol, whereas in the course of the ketene-vinylimine cycloaddition they are equal to ca. 30-55 kcal/mol. All the reactions studied were found to be concerted and mostly asynchronous. Simulation of the solvent environment (toluene, tetrahydrofuran, acetonitrile, and water) by using Tomasi's polarized continuum model with the integral equation formalism (IEF-PCM) method showed the allene-isocyanic reactions remained concerted, yet the activation barriers were somewhat higher than those in the gas phase, whereas the ketene-vinylimine reactions became stepwise. The larger the solvent dielectric constant, the lower the activation barriers found. The lowest-energy pathways in the gas phase and in solvent were confirmed by intrinsic reaction coordinate (IRC) calculations. The atoms in molecules (AIM) analysis of the electron density distribution in the transition-state (TS) structures allowed us to distinguish pericyclic from pseudopericyclic from nonplanar-pseudopericyclic types of reactions.

Alkadienes↗

PubMed2006

Reaction paths of the [2+2] cycloaddition of X=C=Y molecules (X, Y=S or O or CH2). Ab initio study.

The reaction paths of [2+2] cycloaddition of the X=C=Y cumulenes were modeled at the MP2/aug-cc-pVDZ level. Cycloadditions of allene and CO2, CS2, or OCS lead in part to the same four-membered products as dimerizations of either ketene or thioketene or addition of ketene and thioketene, respectively. All the reactions studied are concerted and mostly asynchronous. The majority of the allene cycloadditions studied are endoergic and proceed with much higher activation barriers than do the alternative (thio)ketene additions. In comparison with the energy of the substrates, the four-membered cycles incorporating S-atoms are stabilized more than the analogous structures with O-atoms built into the rings. There are also some products that are thermodynamically disfavored, yet seem to be obtainable thanks to a relatively low barrier of the reaction. The AIM analysis of the electron density distribution in the transition state structures allowed distinguishing pericyclic from pseudopericyclic and nonplanar-pseudopericyclic types of reaction.

Alkadienes↗

PubMed2005

Interactions in open-shell clusters: ab initio study of pre-reactive complex O(3P) + HCl.

Van der Waals interactions between the ground-state triplet O(3P) atom and the closed-shell HCl molecule are investigated in the pre-reactive region. Three adiabatic (two of A'' symmetry and one of A' symmetry) and four non-relativistic diabatic potential energy surfaces are obtained by combining a restricted open-shell coupled cluster approach with the multireference configuration interaction method. The lower A'' adiabatic potential surface has a single minimum (D(e) = 589 cm(-1)) for a linear O...HCl configuration. The upper A'' potential has a weak (D(e) = 65 cm(-1)) minimum for a linear HCl...O configuration. The A' adiabatic potential has a weak (124 cm(-1)) T-shaped minimum. Adiabatic potentials intersect once in the O...HCl linear configuration and twice in the linear HCl...O geometry. The role of electrostatic interactions in shaping these potentials is discussed. The effects of spin-orbit coupling on this interaction are also investigated assuming a constant value of the SO parameter.

Journal Article↗

PubMed2005

DFT study of vibrational circular dichroism spectra of D-lactic acid-water complexes.

This paper presents a discussion of the interaction energies, conformations, vibrational absorption (VA, harmonic and anharmonic) and vibrational circular dichroism (VCD) spectra for conformers of monomeric chiral d(-)-lactic acid and their complexes with water at the DFT(B3LYP)/aug-cc-pVDZ and DFT(B3LYP)/aug-cc-pVTZ levels. A detailed analysis has been performed principally for the two most stable complexes with water, differing by lactic acid conformation. The VCD spectra were found to be sensitive to conformational changes of both free and complexed molecules, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Using the theoretical prediction, we demonstrate that the VCD technique can be used as a powerful tool for structural investigation of intermolecular interactions of chiral molecules and can yield information complementary to data obtained through other molecular spectroscopy methods.

Circular Dichroism↗

PubMed2005

Ar-matrix IR spectra of 5-halouracils interpreted by means of DFT calculations.

The infrared low-temperature Ar-matrix spectra of 5-halouracils and unsubstituted uracil were measured and interpreted in terms of the spectra calculated at the DFT/B3PW91/6-311G level followed by a potential energy distribution (PED) analysis. For the PED analysis, the sets of halouracil mode definitions were constructed so that dissimilarities in the interpretations of the different spectra were minimized. Anharmonic frequency calculations enabled more light to be shed on the Fermi resonance (FR) phenomena occurring in the nu(C=O) stretching vibrations region. For each halouracil vibrational spectrum, several FRs manifest themselves in the nu(C=O) stretching vibrations region. We show that the most frequent components participating in these resonances are the nu(C(4)=O(10)) frequency, a beta(N-H) mode frequency, and a beta(C=O) mode frequency. The experimental nu(N-H) frequencies are reproduced by the calculated anharmonic frequencies better than by the scaled harmonic ones, and the nu(C=O) frequencies respond in the opposite manner. The experimental frequencies located below 1500 cm(-1) are reproduced equally well by the two kinds of calculations.

Journal Article↗