Biomedical subjects

Joseph S Francisco

Publications and source records attributed to Joseph S Francisco.

At least 19 recordsLinked to original sources

PubMed2006

Photodissociation dynamics of CBr4 at 267 nm by means of ion velocity imaging.

The photodissociation dynamics of CBr4 at 267 nm has been studied using time of flight (TOF) mass spectrometry and ion velocity imaging techniques. The photochemical products are detected with resonance enhanced multiphoton ionization (REMPI) as well as single-photon vacuum ultraviolet ionization at 118 nm. REMPI at 266.65 and 266.71 nm was used to detect the ground Br(2P32) and spin-orbit excited Br(2P12) atoms, respectively. The translational energy and angular distributions are consistent with direct dissociation from an excited triplet state and indirect dissociation from high vibrational levels on the singlet ground state surface. Br2+ ions are also observed in the TOF spectra with a focused 267 nm laser. The counter fragment, CBr2+, is observed when this photolysis laser is unfocused, and photons at 118 nm are used to ionize the radical products. The translational energy distributions of the CBr2+ and Br2+ products can be momentum matched, which indicates that molecular Br2 elimination is one of the primary dissociation channels.

Free Radicals↗

PubMed2006

Ground and electronically excited states of methyl hydroperoxide: comparison with hydrogen peroxide.

Equilibrium geometries of the ground states of hydrogen peroxide (H(2)O(2)) and methyl hydroperoxide (CH(3)OOH) have been obtained using quadratic configuration interaction methods with correlation-consistent basis sets. These results are compared with experiments and prior calculations. The dipole moments of the ground states of these two molecules have been calculated. The results illustrate the sensitivity of this quantity to molecular geometry. Several excited states of H(2)O(2) and CH(3)OOH were calculated using the equation-of-motion coupled-cluster singles-and-doubles method. Aside from vertical excitation energies, excited state energies along the O-O, O-H, and C-O dissociation pathways were calculated. The results are expected to be of assistance in resolving discrepancies in the experimental interpretation of the UV absorption spectrum and photodissociation of CH(3)OOH.

Journal Article↗

PubMed2006

An ab initio study of the low-lying electronic states of S3.

Accurate calculations of the low-lying singlet and triplet electronic states of thiozone, S(3), have been carried out using large multireference configuration interaction wave functions. Cuts of the full potential energy surfaces along the stretching and bending coordinates have been presented, together with the vertical excitation spectra. The strong experimentally observed absorption around 395 nm is assigned to the 1 (1)B(2) state, which correlates to ground state products. Absorption at wavelengths shorter than 260 nm is predicted to lead to singlet excited state products, S(2) (a (1)Delta(g))+S((1)D). The spectroscopic properties of the X (3)Sigma(g) (-), a (1)Delta(g), and b (1)Sigma(g) (+) electronic states of the S(2) radical have also been accurately characterized in this work. The investigations of the low-lying electronic states were accompanied by accurate ground state coupled cluster calculations of the thermochemistry of both S(2) and S(3) using large correlation consistent basis sets with corrections for core-valence correlation, scalar relativity, and atomic spin-orbit effects. Resulting values for D(0)(S(2)+S) and SigmaD(0) for S(3) are predicted to be 61.3 and 162.7 kcal/mol, respectively, with conservative uncertainties of +/-1 kcal/mol. Analogous calculations predict the C(2v)-D(3h) (open-cyclic) isomerization energy of S(3) to be 4.4+/-0.5 kcal/mol.

Journal Article↗

PubMed2006

The OH radical-H2O molecular interaction potential.

The OH radical is one of the most important oxidants in the atmosphere due to its high reactivity. The study of hydrogen-bonded complexes of OH with the water molecules is a topic of significant current interest. In this work, we present the development of a new analytical functional form for the interaction potential between the rigid OH radical and H(2)O molecules. To do this we fit a selected functional form to a set of high level ab initio data. Since there is a low-lying excited state for the H(2)O.OH complex, the impact of the excited state on the chemical behavior of the OH radical can be very important. We perform a potential energy surface scan using the CCSD(T)/aug-cc-pVTZ level of electronic structure theory for both excited and ground states. To model the physics of the unpaired electron in the OH radical, we develop a tensor polarizability generalization of the Thole-type all-atom polarizable rigid potential for the OH radical, which effectively describes the interaction of OH with H(2)O for both ground and excited states. The stationary points of (H(2)O)(n)OH clusters were identified as a benchmark of the potential.

Journal Article↗

PubMed2006

Experimental and ab initio study of the HO2.CH3OH complex: thermodynamics and kinetics of formation.

Near-infrared spectroscopy was used to monitor HO2 formed by pulsed laser photolysis of Cl2-O2-CH3OH-N2 mixtures. On the microsecond time scale, [HO2] exhibited a time dependence consistent with a mechanism in which [HO2] approached equilibrium via HO2 + HO2.CH3OH (3, -3). The equilibrium constant for reaction 3, K(p), was measured between 231 and 261 K at 50 and 100 Torr, leading to standard reaction enthalpy and entropy values (1 sigma) of delta(r) = -37.4 +/- 4.8 kJ mol(-1) and delta(r) = -100 +/- 19 J mol(-1) K(-1). The effective bimolecular rate constant, k3, for formation of the HO2.CH3OH complex is .10(-15).exp[(1800 +/- 500)/T] cm3 molecule(-1) s(-1) at 100 Torr (1 sigma). Ab initio calculations of the optimized structure and energetics of the HO2.CH3OH complex were performed at the CCSD(T)/6-311++G(3df,3pd)//MP2(full)/6-311++G(2df,2pd) level. The complex was found to have a strong hydrogen bond (D(e) = 43.9 kJ mol(-1)) with the hydrogen in HO2 binding to the oxygen in CH3OH. The calculated enthalpy for association is delta(r) = -36.8 kJ mol(-1). The potentials for the torsion about the O2-H bond and for the hydrogen-bond stretch were computed and 1D vibrational levels determined. After explicitly accounting for these degrees of freedom, the calculated Third Law entropy of association is delta(r) = -106 J mol(-1) K(-1). Both the calculated enthalpy and entropy of association are in reasonably good agreement with experiment. When combined with results from our previous study (Christensen et al. Geophys. Res. Lett. 2002, 29; doi:10.1029/2001GL014525), the rate coefficient for the reaction of HO2 with the complex, HO2 + HO2.CH3OH, is determined to be (2.1 +/- 0.7) x 10(-11) cm3 molecule(-1) s(-1). The results of the present work argue for a reinterpretation of the recent measurement of the HO2 self-reaction rate constant by Stone and Rowley (Phys. Chem. Chem. Phys. 2005, 7, 2156). Significant complex concentrations are present at the high methanol concentrations used in that work and lead to a nonlinear methanol dependence of the apparent rate constant. This nonlinearity introduces substantial uncertainty in the extrapolation to zero methanol.

Journal Article↗

PubMed2006

Atmospheric oxidation pathways of acetic acid.

One of the most abundant carboxylic acids measured in the atmosphere is acetic acid (CH(3)C(O)OH), present in rural, urban, and remote marine environments in the low-ppb range. Acetic acid concentrations are not well reproduced in global 3-D atmospheric models because of the poor inventory of sources and sinks to model its global distribution. To understand the complete oxidation of acetic acid in the atmosphere initiated by OH radicals, ab initio calculations are performed to describe in detail the energetics of the reaction potential energy surface (PES). The proposed reaction mechanism suggests that the CH(3)C(O)OH + OH reaction takes place via three pathways: the addition of OH to the central carbon, the abstraction of a methyl hydrogen, and the abstraction of an acidic hydrogen. The PES is characterized by prereactive H-complexes, transition states, and more interestingly unique radical-mediated isomerization reactions. From the analysis of the energetics, acetic acid atmospheric oxidation will proceed mainly via the abstraction of the acidic hydrogen, consistent with previous experimental and theoretical studies. The major byproducts from each pathway are identified. Glyoxylic acid is suggested to be a major byproduct of the atmospheric oxidation of acetic acid. The atmospheric fate of glyoxylic acid is discussed.

Journal Article↗

PubMed2006

Ab initio study of the structure, bonding, vibrational spectra, and energetics of XBS+ (where X=H, F, and Cl).

High level ab initio electronic structure calculations at the CCSD(T) level with augmented correlation-consistent basis set extrapolated to complete basis set limit have been performed on XBS and XBS+ for X=H, F, and Cl. The geometries have been optimized up through the aug-cc-pV5Z level and the vibrational frequencies have been calculated with the aug-cc-pVQZ basis sets. Analysis of the bonding in XBS and XBS+ using natural bond orbital analysis shows that the BS bond in XBS is a triple bond, while in XBS+ it is a double bond. The energetic properties of XBS cation and its first excited state are reported. The calculated adiabatic ionization potential is 11.11+/-0.01 eV as compared to the experimental value of 11.11+/-0.03 eV for HBS. The adiabatic ionization potentials for FBS and CIBS are 10.89+/-0.01 and 10.57+/-0.01 eV, respectively.

Journal Article↗

PubMed2006

Theoretical investigation of product channels in the CH3O2 + Br reaction.

Several reaction pathways on the potential energy surface (PES) for the reaction of CH3O2 radicals with Br atoms are examined using both ab initio and density functional methods. Analysis of the PES suggests the presence of the stable intermediates CH3OOBr and CH3OBrO. CH3OOBr is calculated to be more stable than CH3OBrO by 9.7 kcal mol(-1) with a significant barrier preventing formation of CH3OBrO via isomerization of CH3OOBr. The relative importance of bi- and termolecular product channels resulting from the initially formed CH3OOBr adduct are assessed based on calculated barriers to the formation of CH2OO + HBr, CH3O + BrO, CH3Br + O2, and CH2O + HOBr.

Journal Article↗

PubMed2006

Thermochemical properties of HxNO molecules and ions from ab initio electronic structure theory.

Coupled-cluster calculations through noniterative triple excitations were used to compute optimized structures, atomization energies at 0 K, and heats of formation at 0 and 298 K for NH2O, HNOH, NH2O-, NH2OH+, NH3OH+, HNO-, and HON. These molecules are important in the gas-phase oxidation of NH3, as well as its solution-phase chemistry. The O-H, N-H, and N-O bond energies of these molecules are given and compared. The N-H and O-H bond energies are quite low, and, for NH2OH, the O-H bond is weaker than the N-H bond (by 7.5 kcal/mol). The energetics for a variety of ionic chemical processes in the gas phase, including the electron affinities of NH2O and HNO, the proton affinities of NH2O and NH2OH, and the acidities of NH2OH and NH2O, are given. The compounds are weak bases and weak acids in the gas phase. Solvation effects were included at the PCM and COSMO levels. The COSMO model gave better values than the PCM model. The relative values for pKa for NH2O and NH2OH are in good agreement with the experimental values, showing both compounds to be very strong bases in aqueous solution with NH2OH being the stronger base by 1.8 pK units at the COSMO level, compared to the experimental pK difference of 1.1+/-0.3 pK units. We predict that NH2OH+ will not be formed in aqueous solution, because it is a very strong acid. Based on the known acidity of NH3OH+, we predict pKa(NH2OH+)=-5.4 at the COSMO level, which is in good agreement with the experimental estimate of pKa(NH2OH+)=-7+/-2.

Journal Article↗

PubMed2005

Graph theory for fused cubic clusters of water dodecamer.

The stable structures of the fused cubic water cluster (H2O)12 are examined using graph theoretical techniques and ab initio calculations. The calculations are obtained by scanning the symmetry of digraph structures of hydrogen-bond network spanning 12 oxygen atom vertexes. Using the Pólya theorem the cycle index expressions for 12 vertexes and 20 edges of a cuboid in point-group symmetry D(4h) are developed. A total of 91 energy-allowed fused cubic structures are obtained, which are classified by 8 point-group symmetries: 1 D(2h), 2 S4, 5 C4, 1 D2, 11 C2, 10 C(i), 1 C(s), and 60 C1. An energy level diagram of the structures reveals 14 bands that correspond to 14 unique two-colored graphs derived from the distributions of four free hydrogens of the cluster.

Macromolecular Substances↗

PubMed2005

Dimethyl ether oxidation at elevated temperatures (295-600 K).

Dimethyl ether (DME) has been proposed for use as an alternative fuel or additive in diesel engines and as a potential fuel in solid oxide fuel cells. The oxidation chemistry of DME is a key element in understanding its role in these applications. The reaction between methoxymethyl radicals and O(2) has been examined over the temperature range 295-600 K and at pressures of 20-200 Torr. This reaction has two product pathways. The first produces methoxymethyl peroxy radicals, while the second produces OH radicals and formaldehyde molecules. Real-time kinetic measurements are made by transient infrared spectroscopy to monitor the yield of three main products-formaldehyde, methyl formate, and formic acid-to determine the branching ratio for the CH(3)OCH(2) + O(2) reaction pathways. The temperature and pressure dependence of this reaction is described by a Lindemann and Arrhenius mechanism. The branching ratio is described by f = 1/(1 + A(T)[M]), where A(T) = (1.6(+2.4)(-1.0) x 10(-20)) exp((1800 +/- 400)/T) cm(3) molecule(-1). The temperature dependent rate constant of the methoxymethyl peroxy radical self-reaction is calculated from the kinetics of the formaldehyde and methyl formate product yields, k(4) = (3.0 +/- 2.1) x 10(-13) exp((700 +/- 250)/T) cm(3) molecule(-1) s(-1). The experimental and kinetics modeling results support a strong preference for the thermal decomposition of alkoxy radicals versus their reaction with O(2) under our laboratory conditions. These characteristics of DME oxidation with respect to temperature and pressure might provide insight into optimizing solid oxide fuel cell operating conditions with DME in the presence of O(2) to maximize power outputs.

Journal Article↗

PubMed2005

Spectroscopic evidence for the existence of the CF3OSO3 radical.

The first spectroscopic evidence for the existence of the CF(3)OSO(3) radical has been obtained from matrix isolation and FT-IR and UV spectroscopic studies. The vibrational frequencies measured are in reasonable agreement with predictions from density functional calculations. Upon visible and UV photolysis of the CF(3)OSO(3) radical, SO(3) is produced and provides experimental support for a new light-driven route for the oxidation of SO(2) to SO(3) assisted by CF(3)O radicals.

Journal Article↗

PubMed2005

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Journal Article↗

PubMed2005

The binding energy and bonding in dialane.

The binding energy of dialane, Al2H6, has been measured using mass spectrometric techniques to be 33 +/- 5 kcal/mol. This represents the first measurement of the thermochemical properties of dialane, which has only recently been observed in low-temperature matricies. High-level quantum mechanical calculations give a binding energy in agreement with the measured value. Experimental and quantum mechanical calculations show that dialane is chemically similar to diborane, B2H6, even though the bonding for these two systems shows significant differences.

Aluminum Compounds↗

PubMed2005

High-level ab initio studies of the structure, vibrational spectra, and energetics of S3.

Observation of mass-dependent and non-mass-dependent sulfur isotope fractionations in elemental sulfur is providing new insight into the nature of the sulfur cycle in the atmosphere. Interpretation of the experimental isotope data requires estimation of the energetics for the reaction S+S2-->S3 (isoelectronic with O+O2-->O3). Key molecular properties of the S3 potential-energy surface, such as vibrational frequencies and isotopic shifts, are presented that can be used to assess the mass-dependent fractionation effect. Ab initio results are compared to the available experimental results for S2 to evaluate the reliability of the computational results for S3. The S-S bond dissociation energy for S3 is determined to be 60.9+/-1 kcal mol(-1).

Journal Article↗

PubMed2005

Direct ab initio dynamics study of the OH + HOCO reaction.

The reaction between OH and HOCO has been examined using the coupled-cluster method to locate and optimize the critical points on the ground-state potential energy surface. The energetics are refined using the coupled-cluster method with basis set extrapolation to the complete basis set (CBS) limit. Results show that the OH + HOCO reaction produces H2O + CO2 as final products and the reaction passes through an HOC(O)OH intermediate. In addition, the OH + HOCO reaction has been studied using a direct dynamics method with a dual-level ab initio theory. Dynamics calculations show that hydrogen bonding plays an important role during the initial stages of the reaction. The thermal rate constant is estimated over the temperature range 250-800 K. The OH + HOCO reaction is found to be nearly temperature-independent at lower temperatures, and at 300 K, the thermal rate constant is predicted to be 1.03 x 10(-11) cm3 molecule(-1) s(-1). In addition, there may be an indication of a small peak in the rate constant at a temperature between 300 and 400 K.

Journal Article↗

PubMed2005

Unimolecular dissociation and thermochemistry of CH3OOH.

The unimolecular dissociation of CH3OOH is investigated by exciting the molecule in the region of its 5nu(OH) band and probing the resulting OH fragments using laser-induced fluorescence. The measured OH fragment rotational and translational energies are used to determine the CH3O-OH bond dissociation energy, which we estimate to be approximately 42.6+/-1 kcal/mol. Combining this value with the known heats of formation of the fragments also gives an estimate for the heat of formation of CH3OOH which at 0 K we determine to be deltaH(f)0=-27+/-1 kcal/mol. This experimental value is in good agreement with the results of ab initio calculations carried out at the CCSD(T)/complete basis set limit which finds the heat of formation of CH3OOH at 0 K to be deltaH(f)0=-27.3 kcal/mol.

Journal Article↗

PubMed2005

The importance of weak absorption features in promoting tropospheric radical production.

Atmospheric field measurement and modeling studies have long noted discrepancies between observation and predictions of OH and HO(2) concentrations in the atmosphere. Novel photochemical mechanisms have been proposed to explain these differences. Although inclusion of these additional sources improves agreement, they are unable to fully account for the observations. We report and demonstrate the importance of weak electronic absorption features, normally ignored or not measured, in contributing to significant OH radical production. Experiments on methyl hydroperoxide, a prototypical organic peroxide in large abundance in the troposphere, highlights how photochemistry in the neglected electronic absorption tail makes an important addition to the tropospheric OH budget. The present results underscore the need to measure absorption cross sections for atmospheric molecules over a wider dynamic range, especially over the wavelength regions where the solar flux is high, to fully quantitate their contributions to atmospheric photochemistry.

Journal Article↗