Biomedical subjects

Andras Bodi

Publications and source records attributed to Andras Bodi.

5 recordsLinked to original sources

PubMed2007

Unexpected conformational properties of 1-trifluoromethyl-1-silacyclohexane, C5H10SiHCF3: gas electron diffraction, low-temperature NMR spectropic studies, and quantum chemical calculations.

The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol%/equatorial=42(12) mol%) at T=293 K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length Si--C 1.934(10) A. A low-temperature 19F NMR experiment results in an axial/equatorial ratio of 17(2) mol%:83(2) mol% at 113 K and a DeltaG (not equal) of 5.5(2) kcal mol-1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100-300 K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method.

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PubMed2006

Photoion photoelectron coincidence spectroscopy of primary amines RCH2NH2 (R = H, CH3, C2H5, C3H7, i-C3H7): alkylamine and alkyl radical heats of formation by isodesmic reaction networks.

Alkylamines (RCH(2)NH(2), R = H, CH(3), C(2)H(5), C(3)H(7), i-C(3)H(7)) have been investigated by dissociative photoionization by threshold photoelectron photoion coincidence spectroscopy (TPEPICO). The 0 K dissociation limits (9.754 +/- 0.008, 9.721 +/- 0.008, 9.702 +/- 0.012, and 9.668 +/- 0.012 eV for R = CH(3), C(2)H(5), C(3)H(7), i-C(3)H(7), respectively) have been determined by preparing energy-selected ions and collecting the fractional abundances of parent and daughter ions. All alkylamine cations produce the methylenimmonium ion, CH(2)NH(2)+, and the corresponding alkyl free radical. Two isodesmic reaction networks have also been constructed. The first one consists of the alkylamine parent molecules, and the other of the alkyl radical photofragments. Reaction heats within the isodesmic networks have been calculated at the CBS-APNO and W1U levels of theory. The two networks are connected by the TPEPICO dissociation energies. The heats of formation of the amines and the alkyl free radicals are then obtained by a modified least-squares fit to minimize the discrepancy between the TPEPICO and the ab initio values. The analysis of the fit reveals that the previous experimental heats of formation are largely accurate, but certain revisions are suggested. Thus, Delta(f)Ho(298K)[CH(3)NH(2)(g)] = -21.8 +/- 1.5 kJ mol-1, Delta(f)Ho(298K)[C(2)H(5)NH(2)(g)] = -50.1 +/- 1.5 kJ mol(-1), Delta(f)Ho(298K)[C(3)H(7)NH(2)(g)] = -70.8 +/- 1.5 kJ mol(-1), Delta(f)Ho(298K)[C(3)H(7)*] = 101.3 +/- 1 kJ mol(-1), and Delta(f)Ho(298K)[i-C(3)H(7)*] = 88.5 +/- 1 kJ mol(-1). The TPEPICO and the ab initio results for butylamine do not agree within 1 kJ mol-1; therefore, no new heat of formation is proposed for butylamine. It is nevertheless indicated that the previous experimental heats of formation of methylamine, propylamine, butylamine, and isobutylamine may have been systematically underestimated. On the other hand, the error in the ethyl radical heat of formation is found to be overestimated and can be decreased to +/- 1 kJ mol(-1); thus, Delta(f)Ho(298K)[C(2)H(5).] = 120.7 +/- 1 kJ mol(-1). On the basis of the data analysis, the heat of formation of the methylenimmonium ion is confirmed to be Delta(f)Ho(298K)[CH(2)NH(2)+] = 750.3 +/- 1 kJ mol(-1).

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PubMed2006

Adiabatic approximations to internal rotation.

A number of subtle and confusing issues are addressed concerning large amplitude motion (LAM) coordinates (chi) for internal molecular motions, using the methyl rotation in acetaldehyde (CH(3)CHO) as a model problem. If the LAM coordinate is chosen to be one of the H-C-C-O dihedral angles rho(1), rho(2), or rho(3), it lacks the required 2pi3 periodicity, and its use is thus undesirable. An excellent local internal coordinate for this model problem is tau(3)=13(rho(1)+rho(2)+rho(3)-2pi). A similarly good but nonlocal coordinate for the adiabatic approximation of internal rotation is provided by the intrinsic reaction coordinate s. Comparison of the mass-independent V(0)(tau(3)) and the mass-dependent V(0)(s) internal rotation curves shows that the two are virtually identical for the parent isotopolog of acetaldehyde. A unified internal coordinate projection scheme for determining complementary vibrational frequencies and subsequently V(ZPVE)(chi) along a path for LAM has been formulated, where V(ZPVE)(chi) is the zero-point vibrational energy correction to the internal rotation curve. In addition to its simplicity, the projection scheme developed for a distinguished reaction path generated by constrained optimizations is appealing because the vibrational frequencies along the LAM path are invariant to chemically meaningful choices of the internal coordinates for the complementary modes.

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PubMed2005

Dissociative photoionization of mono-, di- and trimethylamine studied by a combined threshold photoelectron photoion coincidence spectroscopy and computational approach.

Energy selected mono-, di- and trimethylamine ions were prepared by threshold photoelectron photoion coincidence spectroscopy (TPEPICO). Below 13 eV, the main dissociative photoionization path of these molecules is hydrogen atom loss. The ion time-of-flight (TOF) distributions and breakdown diagrams for H loss are analyzed in terms of the statistical RRKM theory, which includes tunneling. Experimental evidence, supported by quantum chemical calculations, indicates that the reverse barrier along the H loss potential energy curve for monomethylamine is 1.8 +/- 0.6 kJ mol(-1). Accurate dissociation onset energies are derived from the TOF simulation, and from this analysis we conclude that Delta(f)H degrees (298K)[CH(2)NH(2)(+)] = 750.4 +/- 1.3 kJ mol(-1) and Delta(f)H degrees (298K)[CH(2)NH(CH(3))(+)] = 710.9 +/- 2.8 kJ mol(-1). Quantum chemical calculations at the G3, G3B3, CBS-APNO and W1U levels are extensively used to support the experimental data. The comparison between experimental and ab initio isodesmic reaction heats also suggests that Delta(f)H degrees (298K)[N(CH(3))(3)] = -27.2 +/- 2 kJ mol(-1), and that the dimethylamine ionization energy is 8.32 +/- 0.03 eV, both of which are in slight disagreement with previous experimental values. Above 13 eV photon energy, additional dissociation channels appear besides the H atom loss, such as a sequential C(2)H(4) loss from trimethylamine for which a dissociation mechanism is proposed.

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PubMed2005

On the parallel mechanism of the dissociation of energy-selected P(CH3)3+ ions.

Energy selected trimethyl phosphine ions were prepared by threshold photoelectron photoion coincidence (TPEPICO) spectroscopy. This ion dissociates via H, CH(3), and CH(4) loss, the latter two involving hydrogen transfer steps. The ion time-of-flight distribution and the breakdown diagram are analyzed in terms of the statistical RRKM theory, which includes tunneling. Ab initio and DFT calculations provide the vibrational frequencies required for the RRKM modeling. CH(3) loss could produce both the P(CH(3))(2)(+) by a simple bond dissociation step, and the more stable HP(CH(2))CH(3)(+) ion by a hydrogen transfer step. Quantum chemical calculations are extensively used to uncover the reaction scheme, and they strongly suggest that the latter product is exclusively formed via an isomerization step in the energy range of the experiment. The data analysis, which includes modeling with the trimethyl phosphine thermal energy distribution, provides accurate onset energies for both H (E(0K) = 1024.1 +/- 3.5 kJ/mol) and CH(3) (E(0K) = 1024.8 +/- 3.5 kJ/mol) loss reactions. From this analysis, we conclude that the Delta(f)H(298K) degrees [HP(CH(2))(CH(3))(+)] = 783 +/- 8 kJ/mol and Delta(f)H(298K) degrees [P(CH(2))(CH(3))(2)(+)] = 711 +/- 8 kJ/mol.

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