Acid dissociation constants (pKa’s) are key physicochemical properties that are needed to understand the structure and reactivity of molecules in solution. Theoretical pKa’s have been calculated for a set of 72 organic compounds with −OH and −OOH groups (48 with known experimental pKa’s). This test set includes 17 aliphatic alcohols, 25 substituted phenols, and 30 hydroperoxides. Calculations in aqueous medium have been carried out with SMD implicit solvation and three hybrid DFT functionals (B3LYP, ωB97XD, and M06-2X) with two basis sets (6-31+G(d,p) and 6-311++G(d,p)). The effect of explicit water molecules on calculated pKa’s was assessed by including up to three water molecules. pKa’s calculated with only SMD implicit solvation are found to have average errors greater than 6 pKa units. Including one explicit water reduces the error by about 3 pKa units, but the error is still far from chemical accuracy. With B3LYP/6-311++G(d,p) and three explicit water molecules in SMD solvation, the mean signed error and standard deviation are only −0.02 ± 0.55; a linear fit with zero intercept has a slope of 1.005 and R2 = 0.97. Thus, this level of theory can be used to calculate pKa’s directly without the need for linear correlations or thermodynamic cycles. Estimated pKa values are reported for 24 hydroperoxides that have not yet been determined experimentally.

The angular dependence of ionization by linear and circularly polarized light has been examined for N2, NH3, H2O, CO2, CH2O, pyrazine, methyloxirane, and vinyloxirane. Time-dependent configuration interaction with single excitations and a complex absorbing potential was used to simulate ionization by a seven cycle 800 nm cosine squared pulse with intensities ranging from 0.56 × 1014 to 5.05 × 1014 W cm–2. The shapes of the ionization yield for linearly polarized light can be understood primarily in terms of the nodal structure of the highest occupied orbitals. Depending on the orbital energies, ionization from lower-lying orbitals may also make significant contributions to the shapes. The shapes of the ionization yield for circularly polarized light can be readily explained in terms of the shapes for linearly polarized light. Averaging the results for linear polarization over orientations perpendicular to the direction of propagation yields shapes that are in very good agreement with direct calculations of the ionization yield by circularly polarized light.

Ascorbic acid is a well-known antioxidant and radical scavenger. It can be oxidized by losing two protons and two electrons, but normally loses only one electron at a time. The reactivity of the ascorbate radical is unusual, in that it can either disproportionate or react with other radicals, but it reacts poorly with non-radical species. To explore the oxidation mechanism of ascorbic acid, the pKa's and reduction potentials have been calculated using the B3LYP/6-31+G(d,p) and CBS-QB3 levels of theory with the SMD implicit solvent model and explicit waters. Calculations show that the most stable form of dehydroascorbic acid in water is the bicyclic hydrated structure, in agreement with NMR studies. The possible oxidation reactions at different pH conditions can be understood by constructing a potential-pH (Pourbaix) diagram from the calculated pKa's and standard reduction potentials. At physiological pH disproportionation of the intermediate radical is thermodynamically favored. The calculations show that disproportionation proceeds via dimerization of ascorbate radical and internal electron transfer, as suggested by Bielski. In the dimer, one of the ascorbate units cyclizes. Then protonation and dissociation yields the fully reduced and bicyclic fully oxidized structures. Calculations show that this mechanism also explains the reaction of the ascorbic acid radical with other radical species such as superoxide. Ascorbate radical combines with the radical, and intramolecular electron transfer followed by cyclization and hydrolysis yields dehydroascorbic acid and converts the radical to its reduced form.

Metal to ligand charge-transfer (MLCT) excited state emission quantum yields, ϕem, are reported in 77 K glasses for a series of pentaammine and tetraammine ruthenium(II) complexes with monodentate aromatic acceptor ligands (Ru-MDA) such as pyridine and pyrazine. These quantum yields are only about 0.2–1% of those found for their Ru-bpy (bpy = 2,2′-bipyridine) analogs in similar excited state energy ranges (hνem). The excited state energy dependencies of the emission intensity are characterized by mean radiative decay rate constants, kRAD, resolved from ϕem/τobs = kRAD (τobs = the observed emission decay lifetime; τobs–1 = kRAD + kNRD; kNRD = nonradiative decay rate constant). Except for the Ru-pz chromophores in alcohol glasses, the values of kNRD for the Ru-MDA chromophores are slightly smaller, and their dependences on excited state energies are very similar to those of related Ru-bpy chromophores. In principle, one expects kRAD to be proportional to the product of (hνem)3 and the square of the transition dipole moment (Me,g).2 However, from experimental studies of Ru-bpy chromophores, an additional hνem dependence has been found that originates in an intensity stealing from a higher energy excited state with a much larger value of Me,g. This additional hνem dependence is not present in the kRAD energy dependence for Ru-MDA chromophores in the same energy regime. Intensity stealing in the phosphorescence of these complexes is necessary since the triplet-to-singlet transition is only allowed through spin–orbit coupling and since the density functional theory modeling implicates configurational mixing between states in the triplet spin manifold; this is treated by setting Me,g equal to the product of a mixing coefficient and the difference between the molecular dipole moments of the states involved, which implicates an experimental first order dependence of kRAD on hνem. The failure to observe intensity stealing for the Ru-MDA complexes suggests that their weak emissions are more typical of “pure” (or unmixed) 3MLCT excited states.

The cyclopentane core is ubiquitous among a large number of biologically relevant natural products. Cyclopentenones have been shown to be versatile intermediates for the stereoselective preparation of highly substituted cyclopentane derivatives. Allene oxides are oxygenated fatty acids which are involved in the pathways of cyclopentenone biosynthesis in plants and marine invertebrates; however, their cyclization behavior is not well understood. Recent work by Brash and co-workers (J. Biol. Chem., 2013, 288, 20797) revealed an unusual cyclization property of the 9(S)-HPODE-derived allene oxides: the previously unreported 10Z-isomer cyclizes to a cis-dialkylcyclopentenone in hexane/isopropyl alcohol (100:3, v/v), but the known 10E-isomer does not yield cis-cyclopentenone under the same conditions. The mechanism for cyclization has been investigated for unsubstituted and methyl substituted vinyl allene oxide using a variety of methods including CASSCF, ωB97xD, and CCSD(T) and basis sets up to cc-pVTZ. The lowest energy pathway proceeds via homolytic cleavage of the epoxide ring, formation of an oxyallyl diradical, which closes readily to a cyclopropanone intermediate. The cyclopropanone opens to the requisite oxyallyl which closes to the experimentally observed product, cis-cyclopentenone. The calculations show that the open shell, diradical pathway is lower in energy than the closed shell reactions of allene oxide to cyclopropanone, and cyclopropanone to cyclopentenone.

The oxidation of guanine by triplet benzophenone in the presence of lysine has been shown to produce mono- and dilysine-substituted spiroiminodihydantion products, 8-Lys-Sp and 5,8-diLys-Sp. The potential energy surfaces for C8, C5, and C4 nucleophilic addition have been mapped out using the B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) level of density functional theory with the SMD solvation model and employing methylamine as a model for the side chain of lysine. Enthalpies, barrier heights, pKa’s, and reduction potentials were calculated for intermediates to find the lowest energy paths. For neutral methylamine plus guanine radical and neutral methylamine radical plus guanine, the barrier for addition at C8 is ca. 10 kcal/mol lower than that for addition at C5 and C4. The barriers for water addition at C8, C5, and C4 of guanine radical are 13–20 kcal/mol higher than that for methylamine addition at C8. Further oxidation and loss of a proton leads to 8-methylaminoguanine, the methylamino analogue of 8-oxo-7,8-dihydroguanine (8-oxoG). The barrier for the addition of a second methylamine at C5 of 8-methylaminoguanine is 4.5 kcal/mol lower than that for the corresponding addition of water. Nevertheless, if the concentration of methylamine (or lysine) is very low, water addition could be competitive with methylamine addition. This would lead to comparable fractions of 8-monosubstituted-Sp and 5–8-disubstituted-Sp, in agreement with the experimental observations.

The pKa’s of substituted thiols are important for understanding their properties and reactivities in applications in chemistry, biochemistry, and material chemistry. For a collection of 175 different density functionals and the SMD implicit solvation model, the average errors in the calculated pKa’s of methanethiol and ethanethiol are almost 10 pKa units higher than for imidazole. A test set of 45 substituted thiols with pKa’s ranging from 4 to 12 has been used to assess the performance of 8 functionals with 3 different basis sets. As expected, the basis set needs to include polarization functions on the hydrogens and diffuse functions on the heavy atoms. Solvent cavity scaling was ineffective in correcting the errors in the calculated pKa’s. Inclusion of an explicit water molecule that is hydrogen bonded with the H of the thiol group (in neutral) or S– (in thiolates) lowers error by an average of 3.5 pKa units. With one explicit water and the SMD solvation model, pKa’s calculated with the M06-2X, PBEPBE, BP86, and LC-BLYP functionals are found to deviate from the experimental values by about 1.5–2.0 pKa units whereas pKa’s with the B3LYP, ωB97XD and PBEVWN5 functionals are still in error by more than 3 pKa units. The inclusion of three explicit water molecules lowers the calculated pKa further by about 4.5 pKa units. With the B3LYP and ωB97XD functionals, the calculated pKa’s are within one unit of the experimental values whereas most other functionals used in this study underestimate the pKa’s. This study shows that the ωB97XD functional with the 6-31+G(d,p) and 6-311++G(d,p) basis sets, and the SMD solvation model with three explicit water molecules hydrogen bonded to the sulfur produces the best result for the test set (average error −0.11 ± 0.50 and +0.15 ± 0.58, respectively). The B3LYP functional also performs well (average error −1.11 ± 0.82 and −0.78 ± 0.79, respectively).

A practical method for calculating the pKa’s of selenols in aqueous solution has been developed by using density functional theory with the SMD solvation model and up to three explicit water molecules. The pKa’s of 30 different organoselenols, 16 with known experimental pKa’s, have been calculated by using three different functionals (ωB97XD, B3LYP, and M06-2X) and two basis sets (6-31+G(d,p) and 6-311++G(d,p)). Calculations using ωB97XD and B3LYP with SMD solvation without explicit waters are found to have errors of 3–6 pKa units; the errors with M06-2X are somewhat smaller. One explicit water interacting with the selenium reduces the calculated pKa’s by 1–2 pKa units along with improving the slope and intercept of the fit of the calculated pKa’s to experiment. The best results for SMD/M06-2X/6-31+G(d,p) are with one explicit water (MSE = −0.08 ± 0.37 and MUE = 0.32 ± 0.37) whereas ωB97XD and B3LYP still have errors larger than 2 pKa units. The best results for ωB97XD and B3LYP with 6-31+G(d,p) are obtained by using three explicit waters (MSE = 0.36 ± 0.24 and 0.34 ± 0.25, respectively) and a fit to experiment yields a slope of 1.06 with a zero intercept. The errors for M06-2X/6-31+G(d,p) with three explicit waters are significantly larger (−3.59 ± 0.45) because it overstabilizes the anions. On the basis of the molecules studied here, M06-2X/6-31+G(d,p) with one explicit water and ωB97XD/6-31+G(d,p) and B3LYP/6-31+G(d,p) with three explicit waters and the SMD solvation model can produce reliable pKa’s for the substituted selenols.

The redox stability of gold halide complexes in aqueous solution has been examined quantum-chemically by a systematic comparison of scalar- and nonrelativistic pseudopotential calculations, using both COSMO and D-COSMO-RS solvent models for water. After a computational benchmarking of density-functional methods against CCSD(T) results for the gas phase decomposition AuX4– → AuX2– + X2, B3LYP calculations have been used to establish solvent contributions. While relativity clearly enhances the stability of AuX4– (X = F, Cl, Br, I) complexes against X2 elimination, solvation favors the lower oxidation state. Solvation and relativity are nonadditive, due to the relativistic reduction of bond polarity. At scalar relativistic D-COSMO-RS level, the reaction AuX4– ⇌ AuX2– + X2 is computed to be endergonic, except for X = I, where it is slightly exergonic. Under the chosen conditions, partial hydrolysis of AuCl4– to AuCl3OH– is exergonic. The latter complex in turn is stable against Cl2 elimination. The disproportionation 3 AuCl2– ⇌ AuCl4– + 2 Au(s) + 2 Cl– is clearly exergonic. All of the computed reaction energies at scalar relativistic D-COSMO-RS level agree well with the observed speciation in dilute pH-neutral solutions at ambient temperatures.

Metal complexes that release ligands upon photoexcitation are important tools for biological research and show great potential as highly specific therapeutics. Upon excitation with visible light, [Ru(TQA)(MeCN)2]2+ [TQA = tris(2-quinolinylmethyl)amine] exchanges one of the two acetonitriles (MeCNs), whereas [Ru(DPAbpy)MeCN]2+ [DPAbpy = N-(2,2′-bipyridin-6-yl)-N,N-bis(pyridin-2-ylmethyl)amine] does not release MeCN. Furthermore, [Ru(TQA)(MeCN)2]2+ is highly selective for release of the MeCN that is perpendicular to the plane of the two axial quinolines. Density functional theory calculations provide a clear explanation for the photodissociation behavior of these two complexes. Excitation by visible light and intersystem crossing leads to a six-coordinate 3MLCT state. Dissociation of acetonitrile can occur after internal conversion to a dissociative 3MC state, which has an occupied dσ* orbital that interacts in an antibonding fashion with acetonitrile. For [Ru(TQA)(MeCN)2]2+, the dissociative 3MC state is lower than the 3MLCT state. In contrast, the 3MC state of [Ru(DPAbpy)MeCN]2+ that releases acetonitrile has an energy higher than that of the 3MLCT state, indicating dissociation is unfavorable. These results are consistent with the experimental observations that efficient photodissociation of acetonitrile occurs for [Ru(TQA)(MeCN)2]2+ but not for [Ru(DPAbpy)MeCN]2+. For the release of the MeCN ligand in [Ru(TQA)(MeCN)2]2+ that is perpendicular to the axial quinoline rings, the 3MLCT state has an occupied quinoline π* orbital that can interact with a dσ* Ru–NCCH3 antibonding orbital as the Ru–NCCH3 bond is stretched and the quinolines bend toward the departing acetonitrile. This reduces the barrier for the formation of the dissociative 3MC state, leading to the selective photodissociation of this acetonitrile. By contrast, when the acetonitrile is in the plane of the quinolines or bpy, no interaction occurs between the ligand π* orbital and the dσ* Ru–NCCH3 orbital, resulting in high barriers for conversion to the corresponding 3MC structures and no release of acetonitrile.

This is the first report of the 77 K triplet metal-to-ligand charge-transfer (3MLCT) emission spectra of pentaammine–MDA–ruthenium(II) ([Ru(NH3)5(MDA)]2+) complexes, where MDA is a monodentate aromatic ligand. The emission spectra of these complexes and of the related trans-[Ru(NH3)4(MDA) (MDA’)]2+ complexes are closely related, and their emission intensities are very weak. Density functional theory (DFT) calculations indicate that the energies of the lowest 3MLCT excited states of Ru–MDA complexes are either similar to or lower than those of the lowest energy metal-centered excited states (3MCX(Y)), that the barrier to internal conversion at 77 K is large compared to kBT, and that the 3MCX(Y) excited states are weakly bound. The [Ru(NH3)5py]2+ complex is an exception to the general pattern: emission has been observed for the [Ru(ND3)5(d5-py)]2+ complex, but its lifetime is apparently very short. DFT modeling indicates that the excited state distortions of the different 3MC excited states are very large and are in both Ru–ligand bonds along a single Cartesian axis for each different 3MC excited state, nominally resulting in 3MCX(Y), 3MC(X)Y, and 3MCZ lowest energy metal-centered states. The 3MCX(Y) and 3MC(X)Y states appear to be the pseudo-Jahn–Teller distorted components of a 3MC(XY) state. The 3MCX(Y) states are distorted up to 0.5 Å in each H3N–Ru–NH3 bond along a single Cartesian axis in the pentaammine and trans-tetraammine complexes, whereas the 3MCZ states are found to be dissociative. DFT modeling of the 3MLCT excited state of [Ru(NH3)5(py)]2+ indicates that the Ru center has a spin density of 1.24 at the 3MLCT energy minimum and that the 3MLCT → 3MCZ crossing is smooth with a very small barrier (<0.5 kcal/mol) along the D3N–Ru–py distortion coordinate, implying strong 3MLCT/3MC excited state configurational mixing. Furthermore, the DFT modeling indicates that the long-lived intermediate observed in earlier flash photolysis studies of [Ru(NH3)5py]2+ is a RuII-(η2(C═C)-py) species.

The angle-dependence of strong field ionization of O2, N2, CO2, and CH2O has been studied theoretically using a time-dependent configuration interaction approach with a complex absorbing potential (TDCIS-CAP). Calculation of the ionization yields as a function of the direction of polarization of the laser pulse produces three-dimensional surfaces of the angle-dependent ionization probability. These three-dimensional shapes and their variation with laser intensity can be interpreted in terms of ionization from the highest occupied molecular orbital (HOMO) and lower lying orbitals, and the Dyson orbitals for the ground and excited states of the cations.

The angle dependence of strong-field ionization was studied for a set of second period hydrides (BH3, CH4, NH3, H2O, and HF) and third period hydrides (AlH3, SiH4, PH3, H2S, and HCl). Time-dependent configuration interaction with a complex absorbing potential was used to model ionization by a seven cycle 800 nm cosine squared pulse. The ionization yields were calculated as a function of the laser polarization and plotted as three-dimensional surfaces. The general shapes of angular dependence can be understood in terms of ionization from the highest occupied orbitals. Variations in the shapes with laser intensity indicate that ionization occurs not just from the highest occupied orbitals, but also from lower-lying orbitals. These deductions are supported by variations in the population analysis with the intensity of the laser field and the direction of polarization.

Fragmentation and isomerization of methylamine (CH3NH2+), methanol (CH3OH+), and methyl fluoride (CH3F+) cations by short, intense laser pulses have been studied by ab initio classical trajectory calculations. Born–Oppenheimer molecular dynamics (BOMD) on the ground-state potential energy surface were calculated with the CAM-B3LYP/6-31G(d,p) level of theory for the cations in a four-cycle laser pulse with a wavelengths of 7 μm and intensities of 0.88 × 1014 and 1.7 × 1014 W/cm2. The most abundant reaction path was CH2X+ + H (63–100%), with the second most favorable path being HCX+ + H2 (0–33%), followed by isomerization to CH2XH+ (0–8%). C–X cleavage after isomerization was observed only in methyl fluoride. Compared to random orientation, CH3X+ with the C–X aligned with the laser polarization gained energy nearly twice as much from laser fields. The percentage of CH3+ + X dissociation increased when the C–X bond was aligned with the laser field. Alignment also increased the branching ratio for H2 elimination in CH3NH2+ and CH3OH+ and for isomerization in CH3OH+.

The heretofore unknown emission properties of the metal-to-ligand charge-transfer (MLCT) excited states of several complexes with (ruthenium)(monodentate aromatic ligand, MDA) chromophores are given. Emission spectra and lifetimes in 77 K glasses are reported for several monometallic complexes of the type [Ru(NH3)5–n(L)n(MDA)]2+ and two bimetallic pyrazine (pz)-bridged [{Ru(NH3)4–n(L)n}2pz]4+ complexes (L = pz, pyridine, or a multipyridine ligand; MDA = pz or a substituted pyridine, Y-py). The emission maxima occur in the visible and near-IR spectral regions and have much more poorly resolved vibronic sidebands than do related complexes with Ru-bpy chromophores, and the excited-state lifetimes are characteristic of Ru-bpy MLCT excited states in this energy range. The emission yields of trans-[Ru(NH3)4(MDA)(pz)]2+ (MDA = py or pz) are less than 0.2%, and combined with the other observations, this implies that most of the excited-state quenching occurs in high-energy excited states whose population precedes that of the lowest-energy 3MLCT excited state. The pz-bridged, bimetallic complexes have mixed-valence excited states, and they absorb and emit at lower energies than their monometallic analogues do.

A new, more accurate Hessian-based predictor-corrector algorithm has been developed for simulating classical trajectories of molecules in intense laser fields. The first and second derivatives of the gradient with respect to the electric field are included in the both the predictor and the corrector steps for integrating trajectories. A Taylor expansion of the gradient is used as the surface for integrating the predictor step; a distance weighted interpolant of the gradient is employed for the corrector step. Test trajectories were calculated for HCO+ in a continuous 10 μm, 2.9 × 1014 W cm–2 laser field and triplet allene dication in a 10 μm, 5.7 × 1013 W cm–2 four cycle cosine pulse. The first derivative of the gradient with respect to the electric field makes a significant contribution, while the second derivative makes a smaller contribution and can be neglected. To reduce the cost, the Hessian can be updated for several steps before being recalculated. The calculations indicate that a step size of Δt = 0.25 fs and 20 updates is efficient and reliable for these test systems.

A computational approach for calculating the distortions in the lowest energy triplet metal to ligand charge-transfer (3MLCT = T0) excited states of ruthenium(II)–bipyridine (Ru–bpy) complexes is used to account for the patterns of large variations in vibronic sideband amplitudes found in the experimental 77 K emission spectra of complexes with different ancillary ligands (L). Monobipyridine, [Ru(L)4bpy]m+ complexes are targeted to simplify analysis. The range of known emission energies for this class of complexes is expanded with the 77 K spectra of the complexes with (L)4 = bis-acetonylacetonate (emission onset at about 12 000 cm–1) and 1,4,8,11-tetrathiacyclotetradecane and tetrakis-acetonitrile (emission onsets at about 21 000 cm–1); no vibronic sidebands are resolved for the first of these, but they dominate the spectra of the last two. The computational modeling of excited-state distortions within a Franck–Condon approximation indicates that there are more than a dozen important distortion modes including metal–ligand modes (low frequency; lf) as well as predominately bpy modes (medium frequency; mf), and it simulates the observed 77 K emission spectral band shapes of selected complexes very well. This modeling shows that the relative importance of the mf modes increases very strongly as the T0 energy increases. Furthermore, the calculated metal-centered SOMOs show a substantial bpy−π-orbital contribution for the complexes with the highest energy T0. These features are attributed to configurational mixing between the diabatic MLCT and the bpy 3ππ* excited states at the highest T0 energies.

The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid–base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3. Solvation free energies were computed at the SMD/B3LYP/6-31+G(d,p) level of theory. Compared to experimental results, calculations with the CBS-QB3 level of theory have a mean absolute error (MAE) of ca. 1 kcal/mol for the gas phase proton affinity/gas phase basicity and an MAE of ca. 0.04 eV for the adiabatic/vertical ionization potentials. The B3LYP calculations have a MAE of ∼2 kcal/mol for the proton affinity/gas phase basicity data but systematically underestimated ionization potentials by 0.14–0.21 eV. Solvent cavities for charged solute species were rescaled uniformly by fitting computed pKa data to experimentally measured pKa values. After solvent cavity scaling, the MAEs for computed pKa's compared to experimental results are 0.7 for B3LYP and 0.9 for CBS-QB3. In acetonitrile, the computed E°(XH+•/XH) redox potentials are systematically lower than experimentally measured potentials by 0.21 V for CBS-QB3 and 0.33 V for B3LYP. However, the redox potentials relative to adenine are in very good agreement with experimental results, with MAEs of 0.10 V for CBS-QB3 and 0.07 V for B3LYP. In aqueous solution, B3LYP and CBS-QB3 have MAEs of 0.21 and 0.19 V for E7(X•,H+/XH). Replacing the methyl substituent with ribose changes the calculated E7 potentials by 0.1–0.2 V. The calculated difference between the guanine and adenine oxidation potentials is too large compared to experimental results, but the calculated difference between guanine and 8-oxoguanine is in good agreement with the measured values.

Ionization of ethylene, butadiene, hexatriene, and octatetraene by short, intense laser pulses was simulated using the time-dependent single-excitation configuration-interaction (TD-CIS) method and Klamroth’s heuristic model for ionization (J. Chem. Phys.2009, 131, 114304). The calculations used the 6-31G(d,p) basis set augmented with up to three sets of diffuse sp functions on each heavy atom as well as the 6-311++G(2df,2pd) basis set. The simulations employed a seven-cycle cosine pulse (ω = 0.06 au, 760 nm) with intensities up to 3.5 × 1014 W cm–2 (Emax = 0.10 au) directed along the vector connecting the end carbons of the linear polyenes. TD-CIS simulations for ionization were carried out as a function of the escape distance parameter, the field strength, the number of states, and the basis set size. With a distance parameter of 1 bohr, calculations with Klamroth’s heuristic model reproduce the expected trend that the ionization rate increases as the molecular length increases. While the ionization rates are too high at low intensities, the ratios of ionization rates for ethylene, butadiene, hexatriene, and octatetraene are in good agreement with the ratios obtained from the ADK model. As compared to earlier work on the optical response of polyenes to intense laser pulses, ionization using Klamroth’s model is less sensitive to the number of diffuse functions in the basis set, and only a fraction of the total possible CIS states are needed to model the strong field ionizations.

A number of different levels of theory have been tested in TD-CI simulations of the response of butadiene interacting with very short, intense laser pulses. Excitation energies and transition dipoles were calculated with linear-response time-dependent Hartree−Fock (also known as the random phase approximation, RPA), configuration interaction in the space of single excitations (CIS), perturbative corrections to CIS involving double excitations [CIS(D)], and the equation-of-motion coupled-cluster (EOM-CC) method using the 6-31G(d,p) basis set augmented with n = 0−3 sets of diffuse sp functions on all carbons and only on the end carbons [6-31 n+ G(d,p) and 6-31(n+)G(d,p), respectively]. Diffuse functions are particularly important for transitions between the pseudocontinuum states above the ionization threshold. Simulations were carried out with a three-cycle Gaussian pulse (ω = 0.06 au, 760 nm) with intensities up to 1.26 × 1014 W cm−2 directed along the vector connecting the end carbons. Depending on the basis set, up to 500 excited states were needed for the simulations. Under the conditions selected, the response was too weak with the 6-31G(d,p) basis set, and the difference between levels of theory was more pronounced. When two or three set of diffuse functions were included on all of the carbons, the RPA, CIS, and EOM-CC results were comparable, but the CIS(D) response was too large compared to the more accurate EOM-CC calculations. Even though the frequency of the pulse is not resonant with any of the ground-to-excited transitions, excitations to valence and pseudocontinuum states occur readily above a threshold in the intensity.

Ab initio classical molecular dynamics calculations have been used to simulate the dissociation of H2NCH2+ in a strong laser field. The frequencies of the continuous oscillating electric field were chosen to be ω = 0.02, 0.06, and 0.18 au (2280, 760, and 253 nm, respectively). The field had a maximum strength of 0.03 au (3.2 × 1013 W cm–2) and was aligned with the CN bond. Trajectories were started with 100 kcal/mol of vibrational energy above zero point and were integrated for up to 600 fs at the B3LYP/6-311G(d,p) level of theory. A total of 200 trajectories were calculated for each of the three different frequencies and without a field. Two dissociation channels are observed: HNCH+ + H+ and H2NC+ + H+. About one-half to two-thirds of the H+ dissociations occurred directly, while the remaining indirect dissociations occurred at a slower rate with extensive migration of H+ between C and N. The laser field increased the initial dissociation rate by a factor of ca. 1.4 and decreased the half-life by a factor of ca. 0.75. The effects were similar at each of the three frequencies. The HNCH+ to H2NC+ branching ratio decreased from 10.6:1 in the absence of the field to an average of 8.4:1 in the laser field. The changes in the rates and branching ratios can be attributed to the laser field lowering the reaction barriers as a result of a difference in polarizability of the reactant and transition states.

Complexes of the form An2(C8H8)2 (An = Th, Pa, U, and Np) were investigated using density functional theory with scalar-relativistic effective core potentials. For uranium, a coaxial isomer with D8h symmetry is found to be more stable than a Cs isomer in which the dimetal unit is perpendicular to the C8 ring axis. Similar coaxial structures are predicted for Pa2(C8H8)2 and Np2(C8H8)2, while in Th2(C8H8)2, the C8H8 rings tilt away from the An−An axis. Going from Th2(C8H8)2 to Np2(C8H8)2, the An−An bond length decreases from 2.81 Å to 2.19 Å and the An−An stretching frequency increases from 249 to 354 cm−1. This is a result of electrons populating An−An 5f π- and δ-type bonding orbitals and ϕ nonbonding orbitals, thereby increasing in An−An bond order. U2(C8H8)2 is stable with respect to dissociation into U(C8H8) monomers. Disproportionation of U2(C8H8)2 into uranocene and the U atom is endothermic but is slightly exothermic for uranocene plus 1/2U2, suggesting that it might be possible to prepare double stuffed uranocene if suitable conditions can be found to avoid disproportionation.

The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high-level ab initio calculations along the reaction path and by using classical transition state theory, path-integral quantum transition state theory, and the quantum instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed.

SB-3CT, (4-phenoxyphenylsulfonyl)methylthiirane, is a potent, mechanism-based inhibitor of the gelatinase subclass of the matrix metalloproteinase (MMP) family of zinc proteases. The gelatinase MMPs are unusual in that there are several examples where both enantiomers of a racemic inhibitor have comparable inhibitory abilities. SB-3CT is one such example. Here, the inhibition mechanism of the MMP2 gelatinase by the (S)-SB-3CT enantiomer and its oxirane analogue is examined computationally and compared to the mechanism of (R)-SB-3CT. Inhibition of MMP2 by (R)-SB-3CT was shown previously to involve enzyme-catalyzed C−H deprotonation adjacent to the sulfone, with concomitant opening by β-elimination of the sulfur of the three-membered thiirane ring. Similarly to the R enantiomer, (S)-SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part (46 atoms) and the AMBER force field for the MM part were used to compare the reaction of (S)-SB-3CT and its oxirane analogue in the active site of MMP2 (9208 atoms). These calculations show that the barrier for the proton abstraction coupled ring-opening reaction of (S)-SB-3CT in the MMP2 active site is 4.4 kcal/mol lower than that of its oxirane analogue, and the ring-opening reaction energy of (S)-SB-3CT is only 1.6 kcal/mol less exothermic than that of its oxirane analogue. Calculations also show that the protonation of the ring-opened products by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane than for the thiolate obtained from the thiirane. In contrast to (R)-SB-3CT and the R-oxirane analogue, the double bonds of the ring-opened products of (S)-SB-3CT and its S-oxirane analogue have the cis configuration. Vibrational frequency and intrinsic reaction path calculations on a reduced size QM/MM model (2747 atoms) provide additional insight into the mechanism. These calculations yield 5.9 and 6.7 for the deuterium kinetic isotope effect for C−H bond cleavage in the transition state for the R and S enantiomers of SB-3CT, in good agreement with the experimental results.

The lowest energy metal to ligand charge transfer (MLCT) absorption bands found in ambient solutions of [Ru(NH3)4(Y-py)2]2+ and [Ru(L)2(bpy)2]+ complexes (Y-py a pyridine ligand and (L)n a substituted acetonylacetonate, halide, am(m)ine, etc.) consist of two partly resolved absorption envelopes, MLCTlo and MLCThi. The lower energy absorption envelope, MLCTlo, in these spectra has the larger amplitude for the bis-(Y-py) complexes, but the smaller amplitude for the bis-bpy the complexes. Time-dependent density functional theory (TD-DFT) approaches have been used to model 14 bis-bpy, three bis-(Y-py), and three mono-bpy complexes. The modeling indicates that the lowest unoccupied molecular orbital (LUMO) of each bis-(Y-py) complex corresponds to the antisymmetric combination of individual Y-py acceptor orbitals and that the transition involving the highest occupied molecular orbital (HOMO) and LUMO (HOMO→LUMO) is the dominant contribution to MLCTlo in this class of complexes. The LUMO of each bis-bpy complex that contains a C2 symmetry axis also corresponds largely to the antisymmetric combination of individual ligand acceptor orbitals, while the LUMOs are more complex when there is no C2 axis; furthermore, the energy difference between the HOMO→LUMO and HOMO→LUMO+1 transitions is too small (<1000 cm−1) to resolve in the spectra of the bis-bpy complexes in ambient solutions. Relatively weak MLCTlo absorption contributions are found for all of the [Ru(L)2(bpy)2]m+ complexes examined, but they are experimentally best defined in the spectra of the (L)2 = X-acac complexes. TD-DFT modeling of the HOMO→LUMO transition of [Ru(L)4bpy]m+ complexes indicates that it is too weak to be detected and occurs at significantly lower energy (about 3000−5000 cm−1) than the observed MLCT absorptions. Since the chemical properties of MLCT excited states are generally correlated with the HOMO and/or LUMO properties of the complexes, such very weak HOMO→LUMO transitions can complicate the use of spectroscopic information in their assessment. As an example, it is observed that the correlation lines between the absorption energy maxima and the differences in ground state oxidation and reduction potentials (ΔE1/2) have much smaller slopes for the bis-bpy than the mono-bpy complexes. However, the observed MLCTlo and the calculated HOMO→LUMO transitions of bis-bpy complexes correlate very similarly with ΔE1/2 and this indicates that it is the low energy and small amplitude component of the lowest energy MLCT absorption band that is most appropriately correlated with excited state chemistry, not the absorption maximum as is often assumed.

The three-dimensional structures of metal and non-metal enzymes that catalyze the same reaction are often quite different, a clear indication of convergent evolution. However, there are interesting cases in which the same scaffold supports both a metal and a non-metal catalyzed reaction. One of these is 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase (KDO8PS), a bacterial enzyme that catalyzes the synthesis of KDO8P and inorganic phosphate (Pi) from phosphoenolpyruvate (PEP), arabinose 5-phosphate (A5P), and water. This reaction is one of the key steps in the biosynthesis of bacterial endotoxins. The evolutionary tree of KDO8PS is evenly divided between metal and non-metal forms, both having essentially identical structures. Mutagenesis and crystallographic studies suggest that one or two residues at most determine whether or not KDO8PS requires a metal for function, a clear example of “minimalist evolution”. Quantum mechanical/molecular mechanical (QM/MM) simulations of both the enzymatic and non-enzymatic synthesis of KDO8P have revealed the mechanism underlying the switch between metal and non-metal dependent catalysis. The principle emerging from these studies is that this conversion is possible in KDO8PS because the metal is not involved in an activation process, but primarily contributes to orienting properly the reactants to lower the activation energy, an action easily mimicked by amino acid side-chains.Potential Energy Surface (PES) of the reaction of PEP and A5P in the presence of Zn2+ coordinated to the water that attacks PEP. The PES is defined by two reaction coordinates: formation of the bond between C3PEP and C1A5P, and formation of the bond between the oxygen of water and C2PEP. Distances are in Å, energies in kcal/mol. Colors on the PES reflect energy levels, as represented in the reference bar on the side.

The gas phase reaction of Th+ with H2O to produce HThO+ + H and ThO+ + H2 was investigated using density functional theory and coupled cluster methods. RRKM calculations of the branching ratio favor the H atomic elimination channel in disagreement with experiment. Ab initio classical trajectory calculations were carried out to obtain a better model of the molecular dynamics. The molecular dynamics simulations yield a branching ratio of ca. 80% for the H2 elimination channel to 20% for the H atomic elimination channel in qualitative agreement with the observed ratio of 65% to 35%.

(4-Phenoxyphenylsulfonyl)methylthiirane (SB-3CT) is the selective inhibitor of matrix metalloproteinase 2 (MMP2). The inhibition mechanism of MMP2 by SB-3CT involves C−H deprotonation with concomitant opening of the three-membered heterocycle. In this study, the energetics of the deprotonation-induced ring-opening of (4-phenoxyphenylsulfinyl)methylthiirane, the sulfoxide analogue of SB-3CT, are examined computationally using DFT and QM/MM calculations. A model system, 2-(methylsulfinylmethyl)thiirane, is used to study the stereoelectronic and conformational effects of reaction barriers in methanol. For the model system in methanol solution (using the polarizable continuum model), the reaction barriers range from 17 to 23 kcal/mol with significant stereoelectronic effects. However, the lowest barriers of the (R,R) and (S,R) diastereomers are similar. Two diastereomers of the sulfoxide analogue of SB-3CT are studied in the active site of MMP2 by QM/MM methods with an accurate partial charge fitting procedure. The ring-opening reactions of these two diastereomers have similar reaction energetics. Both are exothermic from the reactant to the ring-opening product (thiolate). The protonation of the thiolate by a water molecule is endothermic in both cases. However, the deprotonation/ring-opening barriers in the MMP2 active site using QM/MM methods for the (R,R) and (S,R) inhibitions are quite different (23.3 and 28.5 kcal/mol, respectively). The TSs identified in QM/MM calculations were confirmed by vibrational frequency analysis and following the reaction path. The (R,R) diastereomer has a hydrogen bond between the sulfoxide oxygen and the backbone NH of Leu191, while the (S,R) has a hydrogen bond between the sulfoxide oxygen and a water molecule. The dissimilar strengths of these hydrogen bonds as well as minor differences in the TS structures contribute to the difference between the barriers. Compared to SB-3CT, both diastereomers of the sulfoxide analogue have higher reaction barriers and have less exothermic reaction energies. This agrees well with the experiments, where SB-3CT is a more effective inhibitor of MMP2 than its sulfoxide analogue.

SB-3CT is a 2-[(arylsulfonyl)methyl]thiirane that achieves potent inhibition, by a thiirane-opening mechanism, of the MMP2 and MMP9 zinc metalloproteases. The deprotonation mechanism for thiirane opening of SB-3CT and for the opening of its oxirane analogue, both relevant to the inhibition of MMP2, was investigated computationally using the acetate anion as the Brønsted base and in methanol and acetonitrile as solvents. The activation barriers for the reaction show a significant stereoelectronic effect. The lowest energy paths have the breaking C−H bond gauche to both sulfone oxygens and with this C−H bond anti to the breaking C−S bond of the thiirane. The calculated primary isotope effect agrees with experimental data.

The experimental and computational results for the tautomerization reaction of 2-pyridone are reviewed. G3, G4, CBS-APNO, and W1 model chemistries are used to generate state-of-the-art reaction energetics for the tautomerization reaction with and without catalytic water molecules in both the gas and aqueous phases. Reactive, electronic potential energy surface surfaces for use in molecular dynamics simulations were generated for these reactions following a recently improved empirical valence bond formulation. The form of molecular mechanics potentials needed for a satisfactory fit is also discussed.

Experimentally, it was observed that the oxidized guanine lesion spiroiminodihydantoin (Sp) contained in highly purified oligodeoxynucleotides slowly converts to guanidinohydantoin (Gh). The reaction is accelerated in the presence of acid. The possible mechanisms of this transformation have been analyzed computationally. Specifically, the potential energy surface for formation of Gh from Sp has been mapped using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets, and the integral equation formalism for the polarizable continuum model (IEF-PCM) solvation model. The results favor a mechanism in which proton-assisted hydration of the C6 carbonyl group forming a gem-diol leads to ring opening of the iminohydantoin ring. The resulting species resembles a β-ketoacid in its ability to decarboxylate; tautomerization of the resulting enol forms Gh. The results of these studies indicate that incubation of nucleosides or oligonucleotides containing Sp should be avoided in acidic media when high purity or an accurate assessment of the amounts of hydantoin lesions is desired.

The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computationally. The inhibition mechanism involves C−H deprotonation with concomitant opening of the three-membered heterocycle. SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine the reaction of these two inhibitors in the active site of MMP2. The calculations show that the reaction barrier for transformation of SB-3CT is 1.6 kcal/mol lower than its oxirane analogue, and the ring-opening reaction energy of SB-3CT is 8.0 kcal/mol more exothermic than that of its oxirane analogue. Calculations also show that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane than for the thiolate obtained from the thiirane. A six-step partial charge fitting procedure is introduced for the QM/MM calculations to update atomic partial charges of the quantum mechanics region and to ensure consistent electrostatic energies for reactants, transition states, and products.

3-Deoxy-d-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P, a key precursor in the biosynthesis of the endotoxin of Gram-negative bacteria. Earlier studies have established that the condensation occurs with a syn addition of water to the si side of C2PEP and of C3PEP to the re side of C1A5P. Two stepwise mechanisms have been proposed for this reaction. One involves a transient carbanion intermediate, formed by attack of water or a hydroxide ion on C2PEP. The other involves a transient oxocarbenium zwitterionic intermediate, formed by direct attack of C3PEP onto C1A5P, followed by reaction of water at C2. In both cases, the transient intermediates are expected to converge to a more stable tetrahedral intermediate, which decays into KDO8P and inorganic phosphate. In this study we calculated the potential energy surfaces (PESs) associated with all possible reaction paths in the active site of KDO8PS: the path involving a syn addition of water to the si side of C2PEP and of C3PEP to the re side of C1A5P, with the PEP phosphate group deprotonated, has the lowest energy barrier (∼14 kcal/mol) and is strongly exoergonic (reaction energy of −38 kcal/mol). Consistent with the experimental observations, other potential reaction paths, like an anti addition of water to the re side of C2PEP or addition of C3PEP to the si side of C1A5P, are associated with much higher barriers. An important new finding of this study is that the lowest energy reaction path does not correspond to either one of the pure stepwise mechanisms proposed formerly but can be described instead as a partially concerted reaction between PEP, A5P, and water. The success in using PESs to reproduce established features of the reaction and to discriminate between different mechanisms suggests that this approach may be of general utility in the study of other enzymatic reactions.

The dissociation of pentane-2,4-dione radical cation has been studied by ab initio direct classical trajectory calculations at the MP2/6-31G(d) level of theory. A bond additivity correction has been used to improve the MP2 potential energy surface (BAC-MP2). A microcanonical ensemble was constructed using quasiclassical normal-mode sampling by distributing 10 kcal/mol of excess energy above ZPE for the transition state for the tautomerization of the enol with a terminal double bond, 4-hydroxypent-4-en-2-one radical cation, to the diketo form. A total of 244 trajectories were run starting from this transition state, yielding pentane-2,4-dione radical cation and depositing energy in the terminal CC bond. As a result, the branching ratio for dissociation of the terminal CC bond versus the interior CC bonds is significantly larger than expected from RRKM theory. The branching ratio for the dissociation of the two interior CC bonds is ∼20:1, with the one closest to the activated methyl breaking more often. Since the two interior bonds are equivalent and should dissociate with equal probability, this branching ratio represents a very large deviation from statistical behavior. A simple kinetic scheme has been constructed to model the dissociation rates. The nonstatistical behavior is seen because the rate of energy flow within the molecule is comparable to or less than the rates of dissociation for the activated system. In addition to the expected dissociation products, some of the trajectories also lead to the formation of an ester-like product, prop-1-en-2-yl acetate radical cation.

An efficient computational method has been identified that uses B3LYP density functional theory, IEF-PCM solvation modeling with a modified UFF cavity, and Boltzmann weighting of tautomers to predict the site-specific and global pKa of DNA nucleobases and their oxidation products. The method has been used to evaluate the acidity of guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), two highly mutagenic guanine oxidation products. The trend observed for the pKa values of Gh (9.64 and 8.15) is consistent with the experimentally observed values for guanidine cation (13.7) and hydantoin (9.16). The pKa1(calc) value for deprotonation of Sp cation (Sp+ → Sp) is very close to the experimentally observed pKa1 for 8-oxoG and is consistent with the similarity in their structures. The data suggest that the imide (N7) proton in Sp is considerably more acidic than that in Gh, possibly due to the presence of the through-space electronic effects of the carbonyl group located at C6. This difference in the acidity of Gh and Sp may be an indication of their potential toxicity and mutagenicity in vivo and remains a fertile area for experimental study.

The potential energy surface for protonated acetylene has been re-examined with large basis sets and highly correlated methods. The energy difference of 3.6–3.8 kcal/mol between the classical structure and non-classical (bridged) structure computed with CCSD (T)/cc-pVQZ, CCSD(T)/6-311+G(3df,2pd), BD(T)/cc- pVQZ, BD(T)/6-311+G(3df,2pd) and CBS-APNO methods is in very good agreement with the best previous calculations, 3.7–4.0 kcal/mol. In contrast, BLYP, B3LYP, PW91, PBE and TPSS density functional methods do rather poorly, yielding −0.52. 0.29, 1.81, 2.16 and 0.62 kcal/mol, respectively, with the 6-311+G(3df,2pd) basis. MP2 calculations predict the classical structure to be a transition state; however, frequency calculations at the CCSD/6-311+G(3df,2pd) level of theory show that the classical structure is a local minimum. CCSD(T), BD(T) and CBS-APNO energy calculations along the MP2/6-311+G(3df,2pd) reaction path indicate that the classical structure is a shallow local minimum separated from the non-classical structure by a very small barrier of 0.11–0.13 kcal/mol. Because the barrier for proton exchange between the non-classical isomers via the classical structure is broad and nearly flat at the top, the tunneling splitting should be reduced, possibly accounting for the 15% difference between the calculated and experimental barrier heights.

Nitric oxide (NO) is a biologically active species and its carrier molecules RXNO (X = S, O, NH) have drawn significant attention recently. In the present work, the CBS-QB3 level of theory was used to study the transnitrosation and thiolation reaction between MeXNO (X = S, O, and NH) molecules and three reactive forms of the methanethiol: the neutral molecule, MeSH, the anion, MeS−, and the radical, MeS˙. The transnitrosation and thiolation reactions between MeXNO and MeSH have the highest barriers, both with and without a molecule of water assisting. Reactions with MeS− proceed with much lower barriers, while reactions with radical MeS˙ have the lowest barriers. Comparing the reactions of MeXNO (X = S, O, NH), both transnitrosation and thiolation are more favorable for X = S than X = O or NH.

Tris(8-hydroxyquinoline)aluminum(III), AlQ3, is used in organic light-emitting diodes (OLEDs) as an electron-transport material and emitting layer. The reaction of AlQ3 with trace H2O has been implicated as a major failure pathway for AlQ3-based OLEDs. Hybrid density functional calculations have been carried out to characterize the hydrolysis of AlQ3. The thermochemical and atomistic details for this important reaction are reported for both the neutral and oxidized AlQ3/AlQ3+ systems. In support of experimental conclusions, the neutral hydrolysis reaction pathway is found to be a thermally activated process, having a classical barrier height of 24.2 kcal mol−1. First-principles infrared and electronic absorption spectra are compared to further characterize AlQ3 and the hydrolysis pathway product, AlQ2OH. The activation energy for the cationic AlQ3 hydrolysis pathway is found to be 8.5 kcal mol−1 lower than for the neutral reaction, which is significant since it suggests a role for charge imbalance in promoting chemical failure modes in OLED devices.

The geometry optimization using direct inversion in the iterative subspace (GDIIS) has been implemented in a number of computer programs and is found to be quite efficient in the quadratic vicinity of a minimum. However, far from a minimum, the original method may fail in three typical ways: (a) convergence to a nearby critical point of higher order (e.g. transition structure), (b) oscillation around an inflection point on the potential energy surface, (c) numerical instability problems in determining the GDIIS coefficients. An improved algorithm is presented that overcomes these difficulties. The modifications include: (a) a series of tests to control the construction of an acceptable GDIIS step, (b) use of a full Hessian update rather than a fixed Hessian, (c) a more stable method for calculating the DIIS coefficients. For a set of small molecules used to test geometry optimization algorithms, the controlled GDIIS method overcomes all of the problems of the original GDIIS method, and performs as well as a quasi-Newton RFO (rational function optimization) method. For larger molecules and very tight convergence, the controlled GDIIS method shows some improvement over an RFO method. With a properly chosen Hessian update method, the present algorithm can also be used in the same form to optimize higher order critical points.

Organic light-emitting diodes (OLEDs) are currently under intense investigation for use in next-generation display technologies. Research into the fundamental properties of the materials used in OLEDs, such as structure and vibrational modes, will help provide experimental probes which are required to gain insight into the processes leading to device degradation and failure. Calculations using the hybrid B3LYP functional and the split-valence polarized 6-31G(d) basis set have been carried out to assign the IR bands of the OLED hole transport material N,N′-diphenyl-N,N′-bis(1-naphthyl)-1,1′-biphenyl-4,4″-diamine (NPB). Excellent agreement was found between the computed and experimental wavenumbers allowing the reliable assignment of major IR bands. Comparison of the reflection absorption IR (RAIRS) spectra obtained from room temperature and thermally annealed NPB thin films indicates that, upon annealing, structural changes occur and the average orientation of the NPB naphthyl groups become predominately flat with respect to the surface.

The cyclopentane core is ubiquitous among a large number of biologically relevant natural products. Cyclopentenones have been shown to be versatile intermediates for the stereoselective preparation of highly substituted cyclopentane derivatives. Allene oxides are oxygenated fatty acids which are involved in the pathways of cyclopentenone biosynthesis in plants and marine invertebrates; however, their cyclization behavior is not well understood. Recent work by Brash and co-workers (J. Biol. Chem., 2013, 288, 20797) revealed an unusual cyclization property of the 9(S)-HPODE-derived allene oxides: the previously unreported 10Z-isomer cyclizes to a cis-dialkylcyclopentenone in hexane/isopropyl alcohol (100:3, v/v), but the known 10E-isomer does not yield cis-cyclopentenone under the same conditions. The mechanism for cyclization has been investigated for unsubstituted and methyl substituted vinyl allene oxide using a variety of methods including CASSCF, ωB97xD, and CCSD(T) and basis sets up to cc-pVTZ. The lowest energy pathway proceeds via homolytic cleavage of the epoxide ring, formation of an oxyallyl diradical, which closes readily to a cyclopropanone intermediate. The cyclopropanone opens to the requisite oxyallyl which closes to the experimentally observed product, cis-cyclopentenone. The calculations show that the open shell, diradical pathway is lower in energy than the closed shell reactions of allene oxide to cyclopropanone, and cyclopropanone to cyclopentenone.

Ascorbic acid is a well-known antioxidant and radical scavenger. It can be oxidized by losing two protons and two electrons, but normally loses only one electron at a time. The reactivity of the ascorbate radical is unusual, in that it can either disproportionate or react with other radicals, but it reacts poorly with non-radical species. To explore the oxidation mechanism of ascorbic acid, the pKa's and reduction potentials have been calculated using the B3LYP/6-31+G(d,p) and CBS-QB3 levels of theory with the SMD implicit solvent model and explicit waters. Calculations show that the most stable form of dehydroascorbic acid in water is the bicyclic hydrated structure, in agreement with NMR studies. The possible oxidation reactions at different pH conditions can be understood by constructing a potential-pH (Pourbaix) diagram from the calculated pKa's and standard reduction potentials. At physiological pH disproportionation of the intermediate radical is thermodynamically favored. The calculations show that disproportionation proceeds via dimerization of ascorbate radical and internal electron transfer, as suggested by Bielski. In the dimer, one of the ascorbate units cyclizes. Then protonation and dissociation yields the fully reduced and bicyclic fully oxidized structures. Calculations show that this mechanism also explains the reaction of the ascorbic acid radical with other radical species such as superoxide. Ascorbate radical combines with the radical, and intramolecular electron transfer followed by cyclization and hydrolysis yields dehydroascorbic acid and converts the radical to its reduced form.