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.

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.

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).

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.

Stereoselective glycosylation reactions with 2-deoxyglucose: a computational study of some catalysts.

2-Deoxy glycosides are important components of many oligosaccharides with antibiotic and anti-cancer activity, but their synthesis can be very challenging. Phenanthrolines and substituted pyridines promote stereoselective glycosylation of 1-bromo sugars via a double SN2 mechanism. Pyridine reacting with α-bromo, 2-deoxyglucose was chosen to model this reaction. The first step involves displacement of bromide by pyridine which can be rate limiting because bromide ion is poorly solvated in the non-polar solvents used for these reactions. We examined a series of small molecules to bind bromide and stabilize this transition state. Geometry optimization and vibrational frequencies were calculated using M06-2X/6-31+G(d,p) and SMD implicit solvation for diethyl ether. More accurate energies were obtained with M06-2X/aug-cc-pVTZ and implicit solvation. Urea, thiourea, guanidine and cyanoguanidine bind bromide more strongly than alkylamines, (NH2CH2CH2)nNH3-n. Compared to the uncatalyzed reaction, urea, thiourea and cyanoguanidine lower the free energy of the transition state by 3 kcal/mol while guanidine lowers the barrier by 2 kcal/mol.

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.

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.

A bioinspired cobalt catalyst based on a tripodal imidazole/pyridine platform capable of water reduction and oxidation.

The prototypical drug carrier [CoII(L1)Cl]PF6 (1), where L1 is a tripodal amine bound to pyridine and methyl-imidazoles, had its electrocatalytic water splitting activity studied under different pH conditions. This species contains a high-spin 3d7 CoII metal center, and is capable of generating both H2 from water reduction and O2 from water oxidation. Turnover numbers reach 390 after 3 h for water reduction. Initial water oxidation activity is molecular, with TONs of 71 at pH 7 and 103 at pH 11.5. The results reveal that species 1 can undergo several redox transformations, including reduction to the 3d8 CoI species that precedes a LS3d6 hydride for water reduction, as well as nominal CoIVO and CoIII-OOH species required for water oxidation. Post-catalytic analyses confirm the molecular nature of reduction and support initial molecular activity for oxidation.

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.

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.

Ionization of HCCI Neutral and Cations by Strong Laser Fields Simulated With Time Dependent Configuration Interaction.

Strong field ionization of neutral iodoacetylene (HCCI) can produce a coherent superposition of the X and A cations. This superposition results in charge migration between the CC π orbital and the iodine π-type lone pair which can be monitored by strong field ionization with short, intense probe pulses. Strong field ionization of the X and A states of HCCI cation was simulated with time-dependent configuration interaction using singly ionized configurations and singly excited, singly ionized configurations (TD-CISD-IP) and an absorbing boundary. Studies with static fields were used to obtain the 3-dimensional angular dependence of instantaneous ionization rates by strong fields and the orbitals involved in producing the cations and dications. The frequency of charge oscillation is determined by the energy separation of the X and A states; this separation can change depending on the direction and strength of the field. Furthermore, fields along the molecular axis can cause extensive mixing between the field-free X and A configurations. For coherent superpositions of the X and A states, the charge oscillations are characterized by two frequencies-the driving frequency of the laser field of the probe pulse and the intrinsic frequency due to the energy separation between the X and A states. For linear and circularly polarized pulses, the ionization rates show marked differences that depend on the polarization direction of the pulse, the carrier envelope phase and initial phase of the superposition. Varying the initial phase of the superposition at the beginning of the probe pulse is analogous to changing the delay between the pump and probe pulses. The charge oscillation in the coherent superposition of the X and A states results in maxima and minima in the ionization yield as a function of the superposition phase.

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.

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.

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.

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.

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.

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.

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.

Phenanthroline-Catalyzed Stereoselective Formation of α-1,2-cis 2-Deoxy-2-Fluoro Glycosides.

Phenanthroline is a heterocyclic aromatic organic compound and commonly used in coordination chemistry acting as a bidentate ligand. The C4 and C7 positions of phenanthroline can often be substituted to change the binding capabilities of the ligand. Recently, there has been a push in the field of chemistry to create environmental-friendly chemical methodologies by utilizing catalysts and minimizing solvent. Herein, we have illustrated how, at high concentrations with minimal use of solvent, the C4 and C7 positions of phenanthroline can be tuned to develop an efficient and stereoselective catalyst for the formation of α-1,2-cis-fluorinated glycosides. By activating 2-deoxy-2-fluoro glycosyl halides with phenanthroline-based catalysts, we have been able to achieve glycosylations with high levels of α-selectivities and moderate to high yields. The catalytic system has been applied to several glycosyl halide electrophiles with a range of glycosyl nucleophilic acceptors. The proposed mechanism for this catalytic glycosylation system has been investigated by density functional theory calculations, indicating that the double SN2 displacement pathways with phenanthroline catalysts have lower barriers and ensure stereoselective formation of α-1,2-cis-2-fluoro glycosides.