Ab Initio Study of Peroxyacetic Nitric Anhydride and Peroxyacetyl Radical: Characteristic Infrared Band of Peroxyacetyl Radical

Vibalizer: A free, web-based tool for rapid, quantitative comparison and analysis of calculated vibrational modes

This report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web-based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first-approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www.compchem.org, and it is also available as a locally-installable package that will run on a Linux-based web server.

A simple rule for classification of polychlorinated dibenzo-p-dioxin congeners on the basis of IR frequency patterns

The IR spectra of 76 dioxin congeners with zero to eight chlorines have been calculated by the DFT (B3LYP) method. Close inspection of the calculated spectra provides a simple rule for IR spectral analysis in polychlorinated dibenzo-p-dioxins (PCDDs). All congeners with a common structural motif of chlorine substitution in either of two benzene rings share the same main IR frequency, and the chlorination of one ring has little influence on the vibrational frequencies of the other ring. As a result, the main ring vibrational frequencies of all dioxin congeners could be classified into 10 groups according to the chlorine substitution pattern. This simplifies the complex IR spectral analysis of PCDDs to identifying two main peaks in essence, each of which corresponds to either of two chlorinated benzene rings. The systematic trend originates from the mass effect of the substituted chlorines. The C-H bending (in plane) character in the ring skeleton vibration mode is affected in quite different ways, depending on whether the chlorine is substituted on longitudinal or lateral positions. In particular, when all the lateral positions (2, 3, 7, 8) are chlorinated in PCDDs, the vibrational frequency of a b(1u) mode (or its analogues in other symmetry) gives a characteristic IR peak around 1392 cm(-1). This peak is unique to all toxic congeners and could be used as an indicator for them.

Gas-phase structures of acetyl peroxynitrate and trifluoroacetyl peroxynitrate

The molecular structures and conformational properties of acetyl peroxynitrate (PAN, CH3C(O)OONO2) and trifluoroacetyl peroxynitrate (FPAN, CF3C(O)OONO2) were investigated in the gas phase by electron diffraction (GED), microwave spectroscopy (MW), and quantum chemical methods (HF/3-21G, HF/6-31G*, MP2/6-31G*, B3PW91/6-31G*, and B3PW91/6-311+G*). All experimental and theoretical methods show the syn conformer (C=O bond of acetyl group syn to O-O bond) to be strongly predominant relative to the anti conformer. The O-NO2 bonds are extremely long, 1.492(7) A in PAN and 1.526(10) A in FPAN, which correlates with their low bond energy and the easy formation of CX3C(O)OO* and *NO2 radicals in the atmosphere. The O-O bonds (1.418(12) A in PAN and 1.408(8) A in FPAN) are shorter than that in hydrogen peroxide (1.464 A). In both compounds the C-O-O-N dihedral angle is close to 85 degrees.

Proton affinity of peroxyacetyl nitrate. A computational study of topical proton affinities

The structure and energetics of the peroxyacetyl nitrate conformers syn- and anti-PAN and several cations formed by PAN protonation were investigated by a combination of density functional theory and ab initio calculations. syn-PAN is the more stable conformer that is predicted to predominate in gas-phase equilibria. The acetyl carbonyl oxygen was found to be the most basic site in PAN, the oxygen atoms of the peroxide and NO(2) groups being less basic. The 298 K proton affinity of syn-PAN was calculated as 759-763 kJ mol(-1) by effective QCISD(T)/6-311 + G(3df,2p) and 771-773 kJ mol(-1) by B3-MP2/6-311 + G(3df,2p). The calculated values are 25-39 kJ mol(-1) lower than the previous estimate by Srinivasan et al. (Rapid Commun. Mass Spectrom. 1998; 12: 328) that was based on competitive dissociations of proton-bound dimers (the kinetic method). The calculated threshold dissociation energies predicted the formation of CH(3)CO(+) + syn - HOONO(2) and CH(3)COOOH + NO(2)(+) to be the most favorable fragmentations of protonated PAN that required 83 and 89 kJ mol(-1) at the respective thermochemical thresholds at 298 K. The previously observed dissociation to CH(3)COOH + NO(3)(+) was calculated by effective QCISD(T)/6-311 + G(3df,2p) to require 320 kJ mol(-1). The disagreement between the experimental data and calculated energetics is discussed.