Since its discovery in 1912, the Mannich reaction has been widely utilized in organic chemistry to form C-C bonds. Reactivity of an enol with an imine allows for easy formation of a [beta]-aminoketone. Enamines have also been widely utilized as convenient nucleophiles. In our work, unexpected reactivity of the [gamma] position of [beta]-enamidoesters in a Brønsted acid environment and high enantioselectivity of a Mannich reaction were achieved through chiral phosphoramidic acid catalysis. A novel class of chiral phosphoramidic acids was designed, synthesized from the corresponding diamines, with several sulfonyl N-protecting groups, and characterized. Their unique properties arise from their Brønsted acid nature, atropisomerism and ability to form complexes via H-bond. Once prepared, such catalysts were successfully used as organocatalysts for the regio- and enantioselective Mannich reaction of [beta]-enamidoesters and imines. Their activity is described as a method to reverse the regioselectivity of the nucleophile while achieving high enantioselectivities in the formation of chiral benzhydrils. A diverse range of imines has been tested, obtaining yields of up to 93% and enantioselectivities of up to 99:1. A few substituted enamines were also tested to study the influence of substituents on the regioselectivity. A mechanism for this reaction is proposed and kinetic studies confirmed that the reaction is first order in catalyst. The ozonolysis of the product of this Mannich reaction was performed to prove the absolute stereochemistry of the product; and a new efficient methodology for the asymmetric preparation of aminoacid [beta]-phenyl-[beta]-alanine benzyl ester is described. The reduction of the enamide moiety of the Mannich product was attempted via asymmetric hydrogenation and via hydride reduction to diastereomerically obtain 1,3-diamines, which are compounds of major synthetic interest. Unfortunately our attempts in this direction were not successful. Finally, a multicomponent reaction between an aldehyde, a substituted phenol, and a styrylboronate was developed as an alternative method for the preparation of chiral benzhydrils. This process is also organocatalytic and the methodology was optimized in the presence of 3-3'-disubstituted BINOLs. Yields up to 71% and enantioselectivities up to 96:4 were achieved. A mechanism for this organocatalytic reaction is also proposed.

Although α-keto carbocations have been demonstrated to be viable intermediates in solvolysis reactions, their applications in synthesis are scarce. These species can be considered to be equivalent to “reversed polarity” enolates and, as such, could be useful for the asymmetric formation of carbon-carbon and carbon-heteroatom bonds. In principle, facial selectivity in additions to α-keto carbocations may be induced using easily removed ester, amide, or imide chiral auxiliaries. Efforts to achieve such diastereoselective SN1 reactions of α-keto carbocations are described herein.

Although α-keto carbocations have been demonstrated to be viable intermediates in solvolysis reactions, their applications in synthesis are scarce. These species can be considered to be equivalent to “reversed polarity” enolates and, as such, could be useful for the asymmetric formation of carbon-carbon and carbon-heteroatom bonds. In principle, facial selectivity in additions to α-keto carbocations may be induced using easily removed ester, amide, or imide chiral auxiliaries. Efforts to achieve such diastereoselective SN1 reactions of α-keto carbocations are described herein.

Knowledge of the dissociation constants of the ionizable protons of weak acids in aqueous media is of fundamental importance in many areas of chemistry and biochemistry. The pKa value, or equilibrium dissociation constant, of a molecule determines the relative concentration of its protonated and deprotonated forms at a specified pH and is therefore an important descriptor of its chemical reactivity. Considerable efforts have been devoted to the determination of pKa values by deferent experimental techniques. Although in most cases the determination of pKa values from experimental is straightforward, there are situations where interpretation is difficult and the results ambiguous. It is, therefore, not surprising that the capability to provide accurate estimates of the pKa value has been a central goal in theoretical chemistry and there has been a large effort in developing methodologies for predicting pKa values for a variety of chemical systems by differing quantum chemical techniques. A prediction accuracy within 0.5 pKa units of experiment is the desirable level of accuracy. This is a non-trivial exercise, for an error of 1 kcal/mol in estimates of the free energy value would result in an error of 0.74 pKa units. In this thesis ab initio Car-Parrinello molecular dynamics (CPMD) has been used for investigating the Brϕnsted acid-base chemistry of weak acids in aqueous solution. A key issue in any dissociation event is how the solvating water molecules arrange themselves spatially and dynamically around the neutral and dissociated acid molecule. Ab initio methods have the advantage that all solvent water molecules can, in principle, be con- sidered explicitly. One of the factors that has inhibited the widespread use of ab initio MD methods to study the dissociation reaction is that dissociation of weak acids are rare events that require extremely long simulation times before one is observed. The metady- namics formalism provides a solution to this conundrum by preventing the system from revisiting regions of configuration space where it has been in the past. The formalism allows the system to escape the free-energy minima by biasing the dynamics with a history dependent potential (or force) that acts on select degrees of freedom, referred to as collective variables. The bias potentials, modeled by repulsive inverted Gaussians that are dropped during propagation, drive the system out of any free-energy minima and allow it to explore the configuration space by a relatively quick and efficient sampling. The the- sis deals with a detailed investigation of the Brϕnsted acid-base chemistry of weak acids in aqueous solutions by the CPMD-metadynamics procedure. In Chapter 1, current approaches for the theoretical estimation of pKa values are summarized while in Chapter 2 the simulation methodology and the metadynamics sampling techniques used in thisstudy are described. The potential of the CPMD-metadynamics procedure to provide estimates of the acid dissociation constant (pKa) is explored in Chapter 3, using acetic acid as a test sys- tem. Using the bond-distance dependent coordination number of protons bound to the dissociating carboxylic groups as the collective variable, the free-energy profile for the dissociation reaction of acetic acid in water was computed. Convergence of the free-energy profiles and barriers for the simulations parameters is demonstrated. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid and the deference in their values provides the estimate for pKa. The estimated value of pKa for acetic acid from the simulations, 4.80, is in good agreement with the experiment at value of 4.76. It is shown that the good agreement with experiment is a consequence of the cancellation of errors, as the pKa values are computed as the difference in the free energy values at the minima corresponding to the neutral and dissociated state. The chapter further explores the critical factors required for obtaining accurate estimates of the pKa values by the CPMD-metadynamics procedure. It is shown that having water molecules sufficient to complete three hydration shells as well as maintaining water density in the simulation cell as close to unity is important. In Chapter 4, the CPMD-metadynamics procedure described in Chapter-3 has been used to investigate the dissociation of a series of weak organic acids in aqueous solutions. The acids studied were chosen to highlight some of the major factors that influence the dissociation constant. These include the influence of the inductive effect, the stabilization of the dissociated anion by H-bonding as well as the presence of multiple ionizable groups. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cid and trans-butenedioic, the isomers of hydroxybenzoic acid and phthalic acids and its isomers. It was found that in each of these examples the CPMD-metadynamics procedure correctly estimates the pKa values, indicating that the formulism is capable of capturing these influences and equally importantly indicating that the cancellation of errors is indeed universal. Further, it is shown that the procedure can provide accurate estimates of the successive pKa values of polypro tic acids as well as the subtle deference in their values for deterrent isomers of the acid molecule. Changes in protonation-deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. It is shown that CPMD simulations in conjunction with metadynamics calculations of the free energy profile of the protonation- deprotonation reaction can provide estimates of the multiple pKa values of the 20 canonical α-amino acids in aqueous solutions in good agreement with experiment (Chapter 5). The distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic and the amine groups is used as the collective variable to explore the free energy profiles of the Brϕnsted acid-base chemistry of amino acids in aqueous solutions. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule were included explicitly in the computation procedure. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error with respect to experimental results, of 0.2 pKa units. The tripeptide Glutathione (GSH) is one of the most abundant peptides and the major repository for non-protein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thioldisulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influences the redox couple and hence the pKa value of the cysteine residue of GSH is critical to its functioning. In Chapter 6, it has been reported that ab initio Car-Parrinello Molecular Dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. It is shown that the free-energy landscape for the protonation - deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared to the isolated cysteine amino acid. The dissociation constants of weak acids are commonly determined from pH-titration curves. For simple acids the determination of the pKa from the titration curves using the Henderson-Hasselbalch equation is relatively straightforward. There are situations, however, especially in polypro tic acids with closely spaced dissociation constants, where titration curves do not exhibit clear inflexion and equivalence stages and consequently the estimation of multiple pKa values from a single titration curve is no longer straightfor- ward resulting in uncertainties in the determined pKa values. In Chapter 7, the multiple dissociation constant of the hexapeptide glutathione disulfide (GSSG) with six ionizable groups and six associated dissociation constants has been investigated. The six pKa values of GSSG were estimated using the CPMD-metadynamics procedure from the free-energy profiles for each dissociation reaction computed using the appropriate collective variable. The six pKa values of GSSG were estimated and the theoretical pH-titration curve was then compared with the experimentally measured pH-titration curve and found to be in excellent agreement. The object of the exercise was to establish whether interpretation of pH-titration curves of complex molecules with multiple ionizable groups could be facilitated using results of ab initio molecular dynamics simulations.

<p> Dimethylgermylene (GeMe2) has been generated by laser flash photolysis of 1,1dimethyl-3-phenylgermacyclopent-3-ene (23) and 1,1,3-trimethyl-4phenylgermacyclopent-3-ene (24) in hexanes at 25°C and its absorption maximum (λmax) has been unambiguously established to be 470 nm. GeMe2 decays with second-order kinetics under these conditions (2k/ε. = (10 ± 2) x 10^7 cm s^(-1)) to give Ge2Me4 (λmax = 370 nm). Kinetic studies of the reactions of GeMe2 and Ge2Me4 with typical germylene/digermene scavengers such as 1,3-dienes, olefins, alkynes, alkyl halides, group 14 metal hydrides, carboxylic acids, and amines have been carried out. </p> <p> GeMe2 reacts reversibly with MeOH, t-BuOH and THF to form Lewis acid-base complexes which exhibit relatively strong absorption bands that are blue-shifted with respect to GeMe2 (λmax ~ 295-310 nm). The decay of the Me2Ge-MeOH complex is accelerated in the presence of a Brnnsted acid (acetic acid or methanesulfonic acid) or base (MeONa). The reactions of the Me2Ge-THF complex with sodium methoxide, methanesulfonic acid, 4,4-dimethyl-1-pentene, 2,3-dimethyl-1-butadiene, acetic acid and CC4 have also been studied in THF. </p> <p> The photochemistry of two well-known precursors to GeMe2, namely dodecamethylcyclohexagermane (14) and dimethylphenyl(trimethylsilyl)germane (18) was reinvestigated. Laser flash photolysis of 14 in hexanes led to the formation of two transients, one with λmax= 490 nm (τ < & = 10 ns) and the second with λmax= 470 nm. The latter decays with second-order kinetics with concomitant formation of a new transient with λmax= 370 nm. The transient at 470 nm is assigned to GeMe2 and that at 370 nm to Ge2Me4, based on comparisons to the results obtained from laser flash photolysis of 23 and 24. Laser flash photolysis of 18-in hexane gives rise to two absorption bands centered at λmax = 300 nm and λmax = 430 nm, which are assigned to the dimethylphenylgerrnyl radical and the conjugated gerrnene derivative 38, respectively. GeMe2 cannot be detected in laser flash photolysis experiments with this compound. </p> / Thesis / Doctor of Philosophy (PhD)