Mechanism of the Sharpless Epoxidation Reaction: A DFT Study.

The Sharpless reaction is an enantioselective epoxidation of prochiral allylic alcohols that employs a Ti(IV) catalyst formed from titanium tetra(isopropoxide), Ti(O-i-Pr)4, diethyl tartrate (DET), and the oxidizing agent tert-butyl hydroperoxide. The M06-2X DFT functional with the 6-311+G(d,p) basis set has been employed to model the structures and energetics of the Sharpless epoxidation reaction. The monomeric tetracoordinate titanium(IV) diethyltartrate is thermodynamically strongly favored to dimerize, producing a pentacoordinate catalyst, [Ti(DET)(O-i-Pr)2]2, that is a more reactive chiral epoxidation catalyst. The rapid ligand exchange reactions needed to generate the "loaded" catalyst and to repeat the overall catalytic cycle have been examined and are found to have activation energies that are much lower than the epoxidation barriers. The transition structures and activation energies for the enantioselective epoxidation of allyl alcohol, trans-methyl-allyl alcohol and trans-tert-butyl-allyl alcohol with the "loaded" Sharpless catalyst, [Ti2(DET)2(O-i-Pr)2-(OAllyl)-(OOt-Bu)], are presented. The effect of the C═O···Ti interactions on the activation energies and the significance of the O-C-C═C dihedral angle on the enantioselectivity of the epoxidation reaction are discussed.

Rare Events Sampling Methods for Quantum and Classical Ab Initio Molecular Dynamics.

We provide an approach to sample rare events during classical ab initio molecular dynamics and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of freedom are introduced that may harmonically interact with the electronic and nuclear degrees of freedom to steer the dynamics in a conservative fashion toward energetically forbidden regions. A similar approach when introduced for quantum wavepacket dynamics has the effect of biasing the trajectory of the wavepacket centroid toward the regions of the potential surface that are difficult to sample. The approach is demonstrated for a phenol-amine system, which is a prototypical problem for condensed phase-proton transfer, and for model potentials undergoing wavepacket dynamics. In all cases, the approach yields trajectories that conserve energy while sampling rare events.

Scope and Mechanistic Probe into Asymmetric Synthesis of α-Trisubstituted-α-Tertiary Amines by Rhodium Catalysis.

Asymmetric reactions that convert racemic mixtures into enantioenriched amines are of significant importance due to the prevalence of amines in pharmaceuticals, with about 60% of drug candidates containing tertiary amines. Although transition-metal catalyzed allylic substitution processes have been developed to provide access to enantioenriched α-disubstituted allylic amines, enantioselective synthesis of sterically demanding α-tertiary amines with a tetrasubstituted carbon stereocenter remains a major challenge. Herein, we report a chiral diene-ligated rhodium-catalyzed asymmetric substitution of racemic tertiary allylic trichloroacetimidates with aliphatic secondary amines to afford α-trisubstituted-α-tertiary amines. Mechanistic investigation is conducted using synergistic experimental and computational studies. Density functional theory calculations show that the chiral diene-ligated rhodium promotes the ionization of tertiary allylic substrates to form both anti and syn π-allyl intermediates. The anti π-allyl pathway proceeds through a higher energy than the syn π-allyl pathway. The rate of conversion of the less reactive π-allyl intermediate to the more reactive isomer via π-σ-π interconversion was faster than the rate of nucleophilic attack onto the more reactive intermediate. These data imply that the Curtin-Hammett conditions are met in the amination reaction, leading to dynamic kinetic asymmetric transformation. Computational studies also show that hydrogen bonding interactions between ß-oxygen of allylic substrate and amine-NH greatly assist the delivery of amine nucleophile onto more hindered internal carbon of the π-allyl intermediate. The synthetic utility of the current methodology is showcased by efficient preparation of α-trisubstituted-α-tertiary amines featuring pharmaceutically relevant secondary amine cores with good yields and excellent selectivities (branched-linear >99:1, up to 99% enantiomeric excess).

Attosecond Imaging of Electronic Wave Packets.

An electronic wave packet has significant spatial evolution besides its temporal evolution, due to the delocalized nature of composing electronic states. The spatial evolution was not previously accessible to experimental investigations at the attosecond timescale. A phase-resolved two-electron-angular-streaking method is developed to image the shape of the hole density of an ultrafast spin-orbit wave packet in the krypton cation. Furthermore, the motion of an even faster wave packet in the xenon cation is captured for the first time: An electronic hole is refilled 1.2 fs after it is produced, and the hole filling is observed on the opposite side where the hole is born.

Charge Migration in HCCI Cations Probed by Strong Field Ionization: Time-Dependent Configuration Interaction and Vibrational Wavepacket Simulations.

Strong field ionization of neutral iodoacetylene (HCCI) can produce a coherent superposition of the X and A cations and results in charge migration between the CC π orbital and the iodine π-type lone pair. This charge migration causes oscillations in the rate of strong field ionization of the cation to the dication that can be monitored using intense few-cycle probe pulses. The dynamics and strong field ionization of the coherent superposition the X and A states of HCCI+ have been modeled by time-dependent configuration interaction (TDCI) simulations. When the nuclei are allowed to move, the electronic wavefunctions need to be multiplied by vibrational wavefunctions. Nuclear motion has been modeled by vibrational packets moving on quadratic approximations to the potential energy surfaces for the X and A states of the cation. The overlap of the vibrational wavepackets decays in about 10-15 fs. Consequently, the oscillations in the strong field ionization decay on the same time scale. A revival of the vibrational overlap and in the oscillations of the strong field ionization is seen at 60-110 fs. TDCI simulations show that the decay and revival of the charge migration can be monitored by strong field ionization with intense 2- and 4-cycle linearly polarized 800 nm pulses. The revival is also seen with 7-cycle pulses.

Calculated pKa Values for a Series of Aza- and Deaza-Modified Nucleobases.

A variety of synthetic modified nucleobases have been used to investigate the structure and function of RNA and DNA or act as enzyme inhibitors. A set of these modifications involves the addition or removal of a nitrogen atom in the ring. These aza and deaza modifications have garnered interest as useful biochemical tools, but information on some of their physical characteristics is lacking. In this study, the B3LYP density functional with the 6-31+G(d,p) basis set and an implicit-explicit solvent model was used to perform ab initio quantum mechanical studies to estimate pKa values of aza- and deaza-modified nucleobases. A comparison between theoretical and known experimental pKa values was carried out, and adjustment factors were applied to 57 pKa values in the purine and pyrimidine data sets.

Carrier-Envelope Phase Controlling of Ion Momentum Distributions in Strong Field Double Ionization of Methyl Iodide.

In strong field ionization of methyl iodide initiated by elliptically polarized few-cycle pulses, a significant correlation was observed between the carrier-envelope phases (CEPs) of the laser and the preferred ejection direction of methyl cation arising from dissociative double ionization. This was attributed to the carrier-envelope phase dependent double ionization yields of methyl iodide. This observation provides a new way for monitoring the absolute CEPs of few-cycle pulses by observing the ion momentum distributions.

Stereoselective 1,2-cis Furanosylations Catalyzed by Phenanthroline.

Stereoselective formation of the 1,2-cis furanosidic linkage, a motif of many biologically relevant oligosaccharides and polysaccharides, remains an important synthetic challenge. We herein report a new stereoselective 1,2-cis furanosylation method promoted by phenanthroline catalysts under mild and operationally simple conditions. NMR experiments and density functional theory calculations support an associative mechanism in which the rate-determining step occurs from an inverted displacement of the faster-reacting phenanthrolinium ion intermediate with an alcohol nucleophile. The phenanthroline catalysis system is applicable to a number of furanosyl bromide donors to provide the challenging 1,2-cis substitution products in good yield with high anomeric selectivities. While arabinofuranosyl bromide provides ß-1,2-cis products, xylo- and ribofuranosyl bromides favor α-1,2-cis products.

Ab Initio Direct Dynamics.

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this "on-the-fly" approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. This approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH2O → H2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

Distinct Bimetallic Cooperativity Among Water Reduction Catalysts Containing [CoIII CoIII ], [NiII NiII ], and [ZnII ZnII ] Cores.

Three binuclear species [LCoIII 2 (µ-Pz)2 ](ClO4 )3 (1), [LNiII 2 (CH3 OH)2 Cl2 ]ClO4 (2), and [LZnII 2 Cl2 ]PF6 (3) supported by the deprotonated form of the ligand 2,6-bis[bis(2-pyridylmethyl) amino-methyl]-4-methylphenol were synthesized, structurally characterized as solids and in solution, and had their electrochemical and spectroscopic behavior established. Species 1-3 had their water reduction ability studied aiming to interrogate the possible cooperative catalytic activity between two neighboring metal centers. Species 1 and 2 reduced H2 O to H2 effectively at an applied potential of -1.6 VAg/AgCl , yielding turnover numbers of 2,820 and 2,290, respectively, after 30 minutes. Species 3 lacked activity and was used as a negative control to eliminate the possibility of ligand-based catalysis. Pre- and post-catalytic data gave evidence of the molecular nature of the process within the timeframe of the experiments. Species 1 showed structural, rather than electronic cooperativity, while species 2 displayed no obvious cooperativity. DFT methods complemented the experimental results determining plausible mechanisms.

Properties of Amine-Containing Ligands That Are Necessary for Visible-Light-Promoted Catalysis with Divalent Europium.

We describe a study of the influence of amine-containing ligands on the photoredox-relevant properties of EuII toward the rational design of EuII-containing catalysts for visible-light-promoted photoredox reactions. We report our observations of the effects of the degree of functionalization of amines, denticity, and macrocylic ligands on the absorbance of EuII. Ligands that contain secondary amines bathochromically shift the absorbance of EuCl2 relative to ligands that contain primary or tertiary amines. Similarly, ligands of larger denticity have a larger bathochromic shift of the absorbance than ligands of smaller denticity. We observed that macrocyclic ligands have a larger effect on the absorbance of EuCl2 than nonmacrocyclic ligands. Also, we report the photoredox reactivity of four new EuII-containing complexes. These observations are potentially influential in understanding the ligand properties that promote the use of EuII in visible-light-promoted photoredox catalysis.

Calculations of pKa Values for a Series of Naturally Occurring Modified Nucleobases.

Modified nucleobases are found in functionally important regions of RNA and are often responsible for essential structural roles. Many of these nucleobase modifications are dynamically regulated in nature, with each modification having a different biological role in RNA. Despite the high abundance of modifications, many of their characteristics are still poorly understood. One important property of a nucleobase is its pKa value, which has been widely studied for unmodified nucleobases, but not for the modified versions. In this study, the pKa values of modified nucleobases were determined by performing ab initio quantum mechanical calculations using a B3LYP density functional with the 6-31+G(d,p) basis set and a combination of implicit-explicit solvation systems. This method, which was previously employed to determine the pKa values of unmodified nucleobases, is applicable to a variety of modified nucleobases. Comparisons of the pKa values of modified nucleobases give insight into their structural and energetic impacts within nucleic acids.

Alkyl Radical-Free Cu(I) Photocatalytic Cross-Coupling: A Theoretical Study of Anomerically Specific Photocatalyzed Glycosylation of Pyranosyl Bromide.

Previously, we reported a visible light-activated Cu(I) photocatalyst capable of facilitating C-O bond formation of glycosyl bromides and aliphatic alcohols with a high degree of diastereoselectivity. This catalyst functions equally well in the presence of radical traps, suggesting an entirely inner sphere mechanism atypical for heteroleptic Cu photocatalysis. Further, experimental estimates put the chromophore reducing power at -1.30 V vs Ag/AgCl. This is much more positive than the ∼-2.0 V vs Ag/AgCl onset observed for irreversible reduction of glycosyl bromides in our experiments. Theoretical investigations were undertaken to explain the function of the catalyst. Outer sphere electron transfer from a chromophore to substrate was discounted based on thermodynamics and electron transfer barriers determined by Marcus theory and non-equilibrium solvation calculations. Unactivated and activated chromophores were found to disproportionate to Cu(0) and Cu(II) species. The resulting Cu(0) species undergoes oxidative addition with a glycosyl bromide generating a Cu(II) species. Addition of a nucleophilic alcohol and oxidation of the Cu(II) species to Cu(III) result in rapid reductive elimination forming products and resetting the catalytic cycle.

Ellipticity controlled dissociative double ionization of ethane by strong fields.

The yields of all dissociation channels of ethane dications produced by strong field double ionization were measured. It was found that the branching ratios can be controlled by varying the ellipticity of laser pulses. The CH3+ formation and H+ formation channels show a clear competition, producing the highest and lowest branching ratios at ellipticity of ∼0.6, respectively. With the help of theoretical calculations, such a control was attributed to the ellipticity dependent yields of different sequential ionization pathways.

The Bond Dissociation Energy of the N-O Bond.

Bond dissociation energy (BDE) has been calculated for a series of compounds that contain N-O bonds. These structures encompass model N,N,O-trisubstituted hydroxylamines that include O-methoxy, O-acyl, and O-phenyl hydroxylamines. The calculations used three accurate composite methods, CBS-QB3, CBS-APNO, and G4 methods and the computationally more affordable M06-2X/6-311+G(3df,2p) density functional theory (DFT) functional. The calculated N-O single-bond BDEs are 5-15 kcal/mol higher than a generic N-O BDE of 48 kcal/mol quoted in the literature and in textbooks. The M06-2X DFT functional provides BDEs that are in excellent agreement with the higher-level composite methods. We also provided a comparison of the N-O BDE for pyridine-N-oxide to simple trialkylamine oxides. Based on an experimental BDE of 63.3 ± 0.5 kcal/mol for pyridine-N-oxide, our best estimate gives 56.7 ± 0.9 kcal/mol N-O BDE for trimethylamine-N-oxide and 59.0 ± 0.8 kcal/mol for triethylamine-N-oxide.

Mechanism of Orbital Interactions in the Sharpless Epoxidation with Ti(IV) Peroxides: A DFT Study.

The M06-2X DFT functional has been employed to examine monomeric titanium(IV) hydroperoxo catalysts that model the individual steps in the dimeric titanium(IV)-catalyzed Sharpless reaction. This is the first example of a transition structure for titanium(IV) tert-butyl hydroperoxide-catalyzed epoxidation that describes the molecular motion required for oxygen atom transfer. These epoxidation catalysts have been examined for both bimolecular reactions with E-2-butene and the intramolecular epoxidation of allyl alcohol. The transition structure for the bimolecular peroxyacetic acid epoxidation of E-2-butene has been shown to be spiro in nature, and likewise, the intramolecular epoxidation of allyl alcohol is also nearly spiro. The significance of the O-C-C═C dihedral angle of allyl alcohol is examined for the Ti(IV) tert-butyl hydroperoxide epoxidation mechanism. Evidence is presented that supports a hexacoordinate titanium peroxo environment that exists in the dimeric form of the Sharpless catalyst. The mechanism for a 1,3-rearrangement of the alkoxide ligand in a titanium hydroperoxide to the Ti center in concert with oxygen atom transfer of the proximal oxygen to the C═C bond of the substrate is presented. The dimerization of Ti(IV)-(R,R)-diethyl tartrate-diisopropoxide and its hydrolysis have been calculated. The mechanism for rapid ligand exchange with alkyl hydroperoxides involving the Ti(O-i-Pr)4 precursor is examined to show how the active epoxidation catalyst is produced.

Sequential double ionization of molecules by strong laser fields simulated with time-dependent configuration interaction.

A new time-dependent configuration interaction method has been developed for simulating strong field sequential double ionization of molecular systems. Ionization of the neutral is simulated by time-dependent configuration interaction with single excitations (TD-CIS) and an absorbing boundary. At each time step, the ionized part of the wavefunction from the TD-CIS calculation is transferred to a second time-dependent configuration interaction simulation for ionization of the cation to the dication. The second simulation uses a CISD-IP wavefunction that consists of singly ionized configurations and singly excited, singly ionized configurations (TD-CISD-IP). The transfer between the TD-CIS and TD-CISD-IP simulations is accomplished by partitioning the first ionization rate into contributions from individual orbitals or by singular value decomposition of the absorbed wavefunction. Sequential double ionization simulations have been carried out for HBr in five cycle 800 nm linearly polarized pulses and HI (with spin-orbit coupling) in four cycle 800 nm circularly polarized pulses, with intensities chosen so that the population of the neutral was depleted by the mid-pulse. The singular value decomposition of the cation produced by the first ionization is dominated by a single component for the two orientations considered. The population of the cation rises and then falls as it is ionized to the dication. Depending on the pulse shape and field strength, the ionization of the cation to the dication can continue for several half cycles. For HI with circularly polarized light, the rates for both the first and second ionization peak when the electric field is aligned with the pπ orbital.

Computational Investigation into the Oxidation of Guanine to Form Imidazolone (Iz) and Related Degradation Products.

Imidazolone (Iz) is one of the many products resulting from oxidative damage to DNA. Three pathways for the formation of Iz and related degradation products have been studied by density functional theory using the ωB97XD functional with the 6-31+G(d,p) basis set and SMD implicit water solvation plus a small number of explicit water molecules positioned to help stabilize charged species and facilitate reaction steps. The first pathway starts with guanine radical and the addition of superoxide at C5. Endoperoxide formation was calculated to have slightly lower barriers than diol formation. The next steps are pyrimidine ring opening and decarboxylation. Ring migration then proceeds via an acyclic intermediate rather than a bicyclic intermediate and is followed by formamide loss to yield Iz. The second pathway starts with 8oxoG and proceeds via C5 superoxide addition and diol formation to a relatively stable intermediate, oxidized guanidinohydantoin (Ghox). The barriers for hydroxide ion addition to Ghox are much lower than for water addition and should yield more Iz and parabanic acid at higher pH. The third pathway starts with 8-hydroxy guanine radical formed by hydroxyl radical addition to C8 of guanine or water addition to C8 of guanine radical. Superoxide addition at C5 is followed by diol formation, ring opening and decarboxylation similar to pathways 1 and 2, subsequently leading to Iz formation. The calculated pathways are in good agreement with experimental observations.

Bond Dissociation Energy of Peroxides Revisited.

When dealing with organic peroxides in both laboratory and industrial applications, the relative strengths of the O-O bond are of vital importance, both from a safety and mechanistic perspective. Although it is well known that such oxidizing agents are highly reactive, reliable O-O bond dissociation energies (BDEs) have only recently been established. In an earlier report, we suggested a median O-O BDE value of ca. 45 kcal/mol for a variety of well-known peroxides based upon G2 ab initio calculations. In the present report, we have calculated the O-O BDE of twenty peroxides of varying structures at a more accurate CBS-APNO level. We have also compared these bond energies to the corresponding BDEs calculated with several DFT functionals and shown that the M06-2X functional produces O-O bond energies that compare very favorably with G4 and CBS-APNO values.

Angular Dependence of Strong Field Ionization of 2-Phenylethyl-N,N-dimethylamine (PENNA) Using Time-Dependent Configuration Interaction with an Absorbing Potential.

Ionization of 2-phenylethyl-N,N-dimethylamine (PENNA) may lead to charge migration between the amine group and the phenyl group. The angular dependence of strong field ionization of PENNA has been modeled by time-dependent configuration interaction with an absorbing potential. The total ionization rate can be partitioned into contributions from the amine group and the phenyl group, and these components have very distinct shapes. Ionization from the amine is primarily from the side opposite to the lone pair and is dominated by the CH2 and CH3 groups. Similarly, trimethylamine (N(CH3)3), dimethyl ether (CH3OCH3), and methyl fluoride (CH3F) are also found to ionize primarily from the methyl groups. The predominance of ionization from the methyl groups can be attributed to the fact that the orbital energies of individual lone pairs of N, O, and F are lower than the CH3 groups. Because the angular dependence of ionization of the two groups is quite different, alignment of PENNA could be used to control the ratio of the amine and phenyl cations and potentially probe charge migration in PENNA cation.