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Chemical Physics | 1995

CASSCF, CASPT2, and MRCI investigations of formyloxyl radical (HCOO.)

Arvi Rauk; Dake Yu; Piotr Borowski; Björn O. Roos

Abstract The structures of the electronic states of HCOO . were optimized at CASSCF and CASPT2 levels of theory with generally contracted basis sets of atomic natural orbital type: [8s4p]/[3s2p] for hydrogen and [14s9p4d]/[4s3p2d] for carbon and oxygen atoms. Vibrational frequencies were calculated to verify the characteristics for some of the optimized stationary points. MRCI calculations were carried out for the σ radicals at the CASPT2 optimized geometries to provide a test on the higher-order correlation effects. At the CASPT2 level, the lowest electronic state of HCOO . is the 2 A 1 state. The electronic energy of the 2 B 2 state is 6 kJ/mol above. The broken symmetry 2 A′ state is predicted to lie 25k J/mol above the 2 A 1 state and to be a transition structure for rearrangement to HOCO . . Single-point MRCI calculations yield the reverse order for the C 2v symmetric states, 2 A 1 state being predicted to be 9.5 kJ/mol above the 2 B 2 state. The 2 A′ state is nearly degenerate with the 2 A 1 state. Relative energies predicted at the (unoptimized) MRCI level are almost identical to those found by single-reference CI calculations.


Journal of The Chemical Society-perkin Transactions 1 | 1994

RADICALS AND IONS OF FORMIC AND ACETIC ACIDS : AN AB INITIO STUDY OF THE STRUCTURES AND GAS AND SOLUTION PHASE THERMOCHEMISTRY

Dake Yu; Arvi Rauk; David A. Armstrong

The structures of HCOO˙, COOH˙, HCOO–, HCOOH˙+, HCOOH, CH2COO˙–, CH3COO˙, CH2COOH˙, CH3COO–, CH3COOH˙+ and CH3COOH were optimized at HF/6-31G(D) and MP2/6-31G(D) levels. The vibrational frequencies were calculated at the HF/6-31G(D) level and the total energies of these molecules were evaluated at the G2(MP2) level. Gas phase thermodynamic properties, Cp, S, H–H0, ΔfH and ΔfG were calculated as functions of temperature using standard statistical thermodynamic methods. For HCOO˙, COOH˙, CH3COO˙ and CH2COOH˙, the method of isodesmic reaction was used. The following are recommended values of ΔfH at 298 K in kJ mol–1: COOH˙–193, CH2COOH˙–243. CH2COO˙–322, HCOO˙–127, CH3COO˙–190, all with an uncertainty of ±7 kJ mol–1. Heats of formation of the RCOO–, and RCOOH˙+ ions were in excellent agreement with those in ref.1.On the basis of the structural information from the ab initio calculations and an analysis of the solution free energies of the parent compounds, aqueous solution free energies and free energies of formation in solution were calculated for the radicals. The values of E(RCOO˙/RCOO–) and other calculated reduction potentials for formate and acetate were shown to be in accord with rates of known redox reactions. Also the RCOO˙ radicals were predicted to have abnormally low (actually negative) pkas for the loss of C–H protons.


Journal of The Chemical Society-perkin Transactions 1 | 1995

Solution thermochemistry of the radicals of glycine

David A. Armstrong; Arvi Rauk; Dake Yu

Using gas phase thermochemical data, the following Gibbs energies of formation in aqueous solution (in kJ mol–1) have been estimated for radicals of glycine: H3N+CH2CO2˙– 93, H2N˙+CH2CO2H –163, H3N+CH˙CO2H –198, H2NCH˙C(OH)2+–268, H3N+CH2CO2––371, H2NCH2CO2˙–95, H2N˙+CH2CO2––158, HN˙CH2CO2H –148, H2NCH˙CO2H –246, HN˙CH2CO2––147 and H2NCH˙CO2––208. The uncertainty in these values is estimated to be ±20 kJ mol–1.In accord with earlier EPR studies, the H2NCH˙CO2H and H2NCH˙CO2– radicals are predicted to be the most stable. Non-equivalence of the NH protons of the latter can be rationalized by a strong internal H ⋯–OCO bond. Formation of the H3N+CH2CO2˙ and H2NCH2CO2˙ acyloxyl species is expected to require very strong oxidants (E° > 3 V). Production of H2N˙+CH2CO2H and H2N˙+CH2CO2– is proposed as a better explanation of H2NCH2˙ formation in SO4˙– oxidations. The H2N˙+CH2CO2– radical, which is also susceptible to loss of CO2, would lie above H2NCH2CO2˙ in the gas phase, but its Gibbs energy of formation in aqueous solution will be ca. 0.65 V less than that of H2NCH2CO2˙. E°(H2N˙+CH2CO2–/H2NCH2CO2–) is estimated to be near 1.6 V. This is in keeping with observed one electron oxidations of H2NCH2CO2– by triplet states of organic molecules with reduction potentials in the region of 1.5–1.8 V.


Journal of Chemical Physics | 1992

The transition probability of electron loss from anions in the gas phase: The lifetime of O2 ⋅−

Dake Yu; David A. Armstrong; Arvi Rauk

The unimolecular primary chemical process, A−→A+e−, is investigated from a theoretical and computational point of view. A ‘‘standard’’ procedure for calculating the lifetime of A− directly is proposed based on the quantum mechanical transition probability. Specific application of the standard procedure is made to electron loss from O ⋅−2. The lifetime of O ⋅−2(ν’=4) calculated with the proposed method is 36×10−12 s, in good agreement with experimental data. An improvement to the standard procedure yields the best theoretical estimate for the lifetime, 125×10−12 s. The lifetimes of O ⋅−2 at higher vibrationally excited states are also calculated and agree well with those of previous calculations. The dependence of the calculated lifetime on the geometric and vibrational parameters of O2 and O ⋅−2 is discussed.


Chemical Physics | 1996

The structures and relative energies of formamide (H2NCHO) and radical ions H2NCHO·+, H2NCOH·+ and H3NCO·+

Dake Yu; David A. Armstrong; Arvi Rauk

Abstract The structures of the electronic states of H2NCHO·+, its parent molecule H2NCHO and the isomers H2NCOH·+ and H3NCO·+ were optimized at the HF, MP2 and DFT levels with the 6-31G(D) basis sets, and at the CASSCF level with generally contracted basis sets of atomic natural orbital type: [8s4p]/[3s2p] for hydrogen atoms and [14s9p4d]/[4s3p2d] for carbon, nitrogen and oxygen atoms. Vibrational frequencies were calculated at the HF and hybrid HF-DFT levels to verify the characteristics of the optimized stationary points, and to provide an estimate of the vibrational zero-point energies. The energies of these species were calculated at high levels of theory including QCISD(T), G2(MP2) and CASPT2. The calculated ionization potential for H2NCHO is in reasonable agreement with the experimental value. The lowest electronic state of structure H2NCHO·+ is a σ radical (2A′) with the unpaired spin primarily centered on the oxygen atom. The electronic energy of the lowest π state of H2NCOH·+ (2A″) is 37.6 kJ/mol above as evaluated at the G2(MP2) level. The two tautomeric forms, H2NCOH·+ and H3NCO·+, are more stable than H2NCHO·+ at all correlated levels. At the G2(MP2) level, the relative stabilities in kJ/mol are: H2NCHO·+, 0.0; H2NCOH·+, −22; H3NCO·+, −14.


Journal of the American Chemical Society | 1995

Radicals and Ions of Glycine: An ab Initio Study of the Structures and Gas-Phase Thermochemistry

Dake Yu; Arvi Rauk; David A. Armstrong


Journal of the American Chemical Society | 1998

Oxidative Damage to and by Cysteine in Proteins: An ab Initio Study of the Radical Structures, C−H, S−H, and C−C Bond Dissociation Energies, and Transition Structures for H Abstraction by Thiyl Radicals

Arvi Rauk; Dake Yu; David A. Armstrong


Canadian Journal of Chemistry | 1992

Hydrogen bonding and internal rotation barriers of glycine and its zwitterions (hypothetical) in the gas phase

Dake Yu; David A. Armstrong; Arvi Rauk


Journal of the American Chemical Society | 1997

C−H Bond Dissociation Energies of Alkyl Amines: Radical Structures and Stabilization Energies§

Danial D. M. Wayner; K. B. Clark; Arvi Rauk; Dake Yu; David A. Armstrong


Canadian Journal of Chemistry | 1996

Oxidative damage to the glycyl α-carbon site in proteins: an ab initio study of the C—H bond dissociation energy and the reduction potential of the C-centered radical

David A. Armstrong; Dake Yu; Arvi Rauk

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Arvi Rauk

University of Calgary

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Mats Jonsson

Royal Institute of Technology

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