Mass spectrometry in organic and bio-organic catalysis: Using thermochemical properties to lend insight into mechanism.

In this review, we discuss gas phase experimentation centered on the measurement of acidity and proton affinity of substrates that are useful for understanding catalytic mechanisms. The review is divided into two parts. The first covers examples of organocatalysis, while the second focuses on biological catalysis. The utility of gas phase acidity and basicity values for lending insight into mechanisms of catalysis is highlighted.

Gas Phase Experimental and Computational Studies of AlkB Substrates: Intrinsic Properties and Biological Implications.

The gas phase acidity and proton affinity of nucleobases that are substrates for the DNA repair enzyme AlkB have been examined using both computational and experimental methods. These thermochemical values have not heretofore been measured and provide experimental data that help benchmark the theoretical results. We also use our gas phase results to lend insight into the AlkB mechanism, particularly in terms of the role AlkB plays in DNA repair, versus its complementary enzyme AlkA.

Gas-Phase Studies of Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase (HG(X)PRT) Substrates.

The gas-phase acidity and proton affinity of nucleobases that are substrates for the enzyme Plasmodium falciparum hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (Pf HG(X)PRT) have been examined using both computational and experimental methods. These thermochemical values have not heretofore been measured and provide experimental data to benchmark the theoretical results. Pf HG(X)PRT is a target of interest in the development of antimalarials. We use our gas-phase results to lend insight into the Pf HG(X)PRT mechanism, and also propose kinetic isotope studies that could potentially differentiate between possible mechanisms.

NEIL1 Recoding due to RNA Editing Impacts Lesion-Specific Recognition and Excision.

A-to-I RNA editing is widespread in human cells but is uncommon in the coding regions of proteins outside the nervous system. An unusual target for recoding by the adenosine deaminase ADAR1 is the pre-mRNA of the base excision DNA repair enzyme NEIL1 that results in the conversion of a lysine (K) to arginine (R) within the lesion recognition loop and alters substrate specificity. Differences in base removal by unedited (UE, K242) vs edited (Ed, R242) NEIL1 were evaluated using a series of oxidatively modified DNA bases to provide insight into the chemical and structural features of the lesion base that impact isoform-specific repair. We find that UE NEIL1 exhibits higher activity than Ed NEIL1 toward the removal of oxidized pyrimidines, such as thymine glycol, uracil glycol, 5-hydroxyuracil, and 5-hydroxymethyluracil. Gas-phase calculations indicate that the relative rates in excision track with the more stable lactim tautomer and the proton affinity of N3 of the base lesion. These trends support the contribution of tautomerization and N3 protonation in NEIL1 excision catalysis of these pyrimidine base lesions. Structurally similar but distinct substrate lesions, 5-hydroxycytosine and guanidinohydantoin, are more efficiently removed by the Ed NEIL1 isoform, consistent with the inherent differences in tautomerization, proton affinities, and lability. We also observed biphasic kinetic profiles and lack of complete base removal with specific combinations of the lesion and NEIL1 isoform, suggestive of multiple lesion binding modes. The complexity of NEIL1 isoform activity implies multiple roles for NEIL1 in safeguarding accurate repair and as an epigenetic regulator.

Nucleophilicity and Electrophilicity in the Gas Phase: Silane Hydricity.

Hydricity is of great import as hydride transfer reactions are prominent in many processes, including organic synthesis, photoelectrocatalysis, and hydrogen activation. Herein, the kinetic hydricity of a series of silanes is examined in the gas phase. Most of these reactions have not heretofore been studied in vacuo and provide valuable data that can be compared to condensed-phase hydricity, to reveal the effects of solvent. Both experiments and computations are used to gain insight into mechanism and reactivity. In a broader sense, these studies also represent a first step toward systematically understanding nucleophilicity and electrophilicity in the absence of a solvent.

The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA.

The chemical nature of the 5' end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency, and has been proposed to provide a layer of 'epitranscriptomic' gene regulation. Recently it has been shown that some bacterial RNA species carry a 5'-end structure reminiscent of the 5' 7-methylguanylate 'cap' in eukaryotic RNA. In particular, RNA species containing a 5'-end nicotinamide adenine dinucleotide (NAD+) or 3'-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated 'ab initio capping' may occur in all organisms.

Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications.

The gas-phase acidity and proton affinity (PA) of 5-halouracils (5-fluorouracil, 5-chlorouracil, 5-bromouracil, and 5-iodouracil) have been examined using both theoretical and experimental methods. This work represents a comprehensive study of the thermochemical properties of these nucleobases. Other than 5-fluorouracil acidity, the intrinsic acidity and PA of these halouracils have not been heretofore measured; these new experimental data provide a benchmark for the computational values. Furthermore, we examine these 5-halouracils in the context of the enzyme thymine DNA glycosylase (TDG), which is an enzyme that protects the genome by cleaving these substrates from DNA. Our gas-phase results are compared and contrasted to TDG excision rates to afford insights into the TDG mechanism.

Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY.

The DNA glycosylase MutY prevents deleterious mutations resulting from guanine oxidation by recognition and removal of adenine (A) misincorporated opposite 8-oxo-7,8-dihydroguanine (OG). Correct identification of OG:A is crucial to prevent improper and detrimental MutY-mediatedadenine excision from G:A or T:A base pairs. Here we present a structure-activity relationship (SAR) study using analogues of A to probe the basis for OG:A specificity of MutY. We correlate observed in vitro MutY activity on A analogue substrates with their experimental and calculated acidities to provide mechanistic insight into the factors influencing MutY base excision efficiency. These data show that H-bonding and electrostatic interactions of the base within the MutY active site modulate the lability of the N-glycosidic bond. A analogues that were not excised from duplex DNA as efficiently as predicted by calculations provided insight into other required structural features, such as steric fit and H-bonding within the active site for proper alignment with MutY catalytic residues. We also determined MutY-mediated repair of A analogues paired with OG within the context of a DNA plasmid in bacteria. Remarkably, the magnitudes of decreased in vitro MutY excision rates with different A analogue duplexes do not correlate with the impact on overall MutY-mediated repair. The feature that most strongly correlated with facile cellular repair was the ability of the A analogues to H-bond with the Hoogsteen face of OG. Notably, base pairing of A with OG uniquely positions the 2-amino group of OG in the major groove and provides a means to indirectly select only these inappropriately placed adenines for excision. This highlights the importance of OG lesion detection for efficient MutY-mediated cellular repair. The A analogue SARs also highlight the types of modifications tolerated by MutY and will guide the development of specific probes and inhibitors of MutY.

Gas-Phase and Ionic Liquid Experimental and Computational Studies of Imidazole Acidity and Carbon Dioxide Capture.

The capture and storage of carbon dioxide are pressing environmental concerns. Nucleophilic capture by anions in ionic liquids, such as imidazolates, is a promising strategy. Herein, the gas-phase acidity of a series of imidazoles is examined both experimentally and computationally. The intrinsic acidity of these imidazoles has not heretofore been measured; these experimental data provide a benchmark for the computational values. The relationship between imidazole acidity and carbon dioxide capture is explored computationally, both in the gas phase and in ionic liquid. The improved understanding of imidazolate properties provided herein is important for the design and development of improved systems for carbon dioxide capture.

Gas-Phase Deprotonation of Benzhydryl Cations: Carbene Basicity, Multiplicity, and Rearrangements.

Many fundamental properties of carbenes, particularly basicity, remain poorly understood. Herein, an experimental and computational examination of the deprotonation of a series of benzhydryl cations has been undertaken. These studies represent the first attempt at providing experimental values for diarylcarbene basicities. Pathways to deprotonation, including whether the singlet or triplet carbene is formed, are probed. Because diarylcarbenes are expected to be among the strongest organic bases known, assessing the energetics of protonation of these species is of fundamental importance for a wide range of chemical processes.

The importance of N-heterocyclic carbene basicity in organocatalysis.

N-Heterocyclic carbenes (NHCs) are versatile species that figure prominently as catalysts. Despite their widespread use in organocatalysis, studies of the relationship between the basicity of NHCs and their catalytic ability are limited. Herein we review work on both the examination of NHC basicity as well as its impact on organocatalysis. The review is divided into three main parts: an overview of NHC basicity studies, both in solution and in the gas phase; the role of basicity in Umpolung-type catalysis; and the relationship between NHC basicity and its growing role as a Brønsted base catalyst. This review is not an exhaustive catalog of all NHC catalysis, but rather focuses on work that specifically examines and discusses the effect of NHC basicity on catalyst function.

Experimental and Computational Gas Phase Acidities of Conjugate Acids of Triazolylidene Carbenes: Rationalizing Subtle Electronic Effects.

In recent years, triazolylidene carbenes have come to the forefront as important organocatalysts for a wide range of reactions. The fundamental properties of these species, however, remain largely unknown. Herein, the gas phase acidities have been measured and calculated for a series of triazolium cations (the conjugate acids of the triazolylidene carbenes) that have not been heretofore examined in vacuo. The results are discussed in the context of these species as catalysts. We find correlations between the gas phase acidity and selectivity in two Umpolung reactions catalyzed by these species; such correlations are the first of their kind. We are able to use these linear correlations to improve reaction enantioselectivity. These results establish the possibility of using these thermochemical properties to predict reactivity in related transformations.

Gas-Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates.

Gas-phase thermochemical properties (tautomerism, acidity, and proton affinity) have been measured and calculated for a series of nucleobase derivatives that have not heretofore been examined under vacuum. The studied species are substrates for the enzyme formamidopyrimidine glycosylase (Fpg), which cleaves damaged nucleobases from DNA. The gas-phase results are compared and contrasted to solution-phase data, to afford insight into the Fpg mechanism. Calculations are also used to probe the energetics of various possible mechanisms and to predict isotope effects that could potentially allow for discrimination between different mechanisms. Specifically, (18) O substitution at the ribose O4' is predicted to result in a normal kinetic isotope effect (KIE) for a ring-opening "endocyclic" mechanism and an inverse KIE for a direct base excision "exocyclic" pathway.

Gas Phase Studies of N-Heterocyclic Carbene-Catalyzed Condensation Reactions.

N-Heterocyclic carbenes (NHCs) catalyze Umpolung condensation reactions of carbonyl compounds, including the Stetter reaction. These types of reactions have not heretofore been examined in the gas phase. Herein, we explore the feasibility of examining these reactions in the absence of solvent. A charge-tagged thiazolylidene catalyst is used to track the reactions by mass spectrometry. We find that the first Umpolung step, the addition of the NHC catalyst to a carbonyl compound to form the "Breslow intermediate", does not readily proceed in the gas phase, contrary to the case in solution. The use of acylsilanes in place of the carbonyl compounds appears to solve this issue, presumably because of a favorable Brook rearrangement. The second addition reaction, with enones, does not occur under our gas phase conditions. These reactions do occur in solution; the differential reactivity between the condensed and gas phases is discussed, and calculations are used to aid in the interpretation of the results.

An Isolable, Photoswitchable N-Heterocyclic Carbene: On-Demand Reversible Ammonia Activation.

The first isolable, photoswitchable N-heterocyclic carbene was synthesized and found to undergo reversible electrocyclic isomerization upon successive exposure to UV and visible radiation. The UV-induced ring closure afforded substantial changes to the electronic structure of the dithienylethene-based NHC, as evidenced by changes in the corresponding UV/Vis absorption and (13)C NMR spectra. Likewise, molecular orbital calculations revealed diminished electron density at the carbene nucleus upon photocyclization, consistent with the enhanced electrophilicity displayed by the ring-closed form. The photoswitchable NHC was successfully switched between its ring-opened and ring-closed states with high fidelity over multiple cycles. Furthermore, the ring-closed isomer was found to undergo facile N-H bond activation, allowing for the controlled capture and release of ammonia upon cycling between its isomeric states.

Computational studies of the gas-phase thermochemical properties of modified nucleobases.

In this Synopsis, we highlight some recent computational studies of the gas-phase thermochemical properties of modified nucleobases. Although this field is relatively nascent, we aim herein to show a few examples of insights that have already been gained by gas-phase calculations. We focus on modified nucleobases that are substrates for enzymes that excise damaged bases from DNA. Because these enzymes have hydrophobic active sites, calculations in the "ultimate" nonpolar environment of the gas phase prove to be particularly relevant, providing insight into enzyme mechanism.

Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA.

5-Methylcytosine (mC) is an epigenetic mark that impacts transcription, development, and genome stability, and aberrant DNA methylation contributes to aging and cancer. Active DNA demethylation involves stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), and potentially 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and restoration of cytosine via follow-on base excision repair. Here, we investigate the mechanism for TDG excision of fC and caC. We find that 5-carboxyl-2'-deoxycytidine ionizes with pK(a) values of 4.28 (N3) and 2.45 (carboxyl), confirming that caC exists as a monoanion at physiological pH. Calculations do not support the proposal that G·fC and G·caC base pairs adopt a wobble structure that is recognized by TDG. Previous studies show that N-glycosidic bond hydrolysis follows a stepwise (S(N)1) mechanism, and that TDG activity increases with pyrimidine N1 acidity, that is, leaving group quality of the target base. Calculations here show that fC and the neutral tautomers of caC are acidic relative to other TDG substrates, but the caC monoanion exhibits poor acidity and likely resists TDG excision. While fC activity is independent of pH, caC excision is acid-catalyzed, and the pH profile indicates that caC ionizes in the enzyme-substrate complex with an apparent pKa of 5.8, likely at N3. Mutational analysis reveals that Asn191 is essential for excision of caC but dispensable for fC activity, indicating that N191 may stabilize N3-protonated forms of caC to facilitate acid catalysis and suggesting that N191A-TDG could potentially be useful for studying DNA demethylation in cells.

1,2,3-triazoles: gas phase properties.

1,2,3-Triazoles have come to the forefront as compounds of import in a vast number of applications. The fundamental properties of these species, however, remain largely unknown. Herein, the gas phase properties of 4-phenyl-1,2,3-triazole, benzotriazole, and a series of 1-phenylbenzotriazoles are described. Proton affinity and acidity values are computed and measured. Furthermore, ion-molecule reactions and H/D exchange studies are used to ascertain tautomer prevalence for the 4-phenyl species.

Assessing the proton affinities of N,N'-diamidocarbenes.

The gas-phase proton affinities (PAs) of a series of novel diamidocarbenes (DACs) were assessed and compared to various imidazolylidene-based N-heterocyclic carbenes (NHCs) through experimental and computational methods. Apart from a perfluorinated-phenyl derivative (PA = 233 kcal/mol), the calculated and measured PAs for a range of DACs (256-261 kcal/mol) were comparable to those of the NHCs (260-266 kcal/mol). Proton transfer from the protonated carbene to various reference bases, as observed by mass spectrometry, was inhibited by steric bulk and precluded the direct measurement of the PA for the known DACs, N,N'-dimesityl-4,6-diketo-5,5-dimethylpyrimidin-2-ylidene and N,N'-diisopropylphenyl-4,6-diketo-5,5-dimethylpyrimidin-2-ylidene. However, DACs featuring less hindered N-aryl substituents facilitated proton transfer, and the measured PA values were found to be consistent with density functional theory calculations (B3LYP/6-31+G(d)). Notably, the PAs of the DACs studied were similar to those of the NHCs, indicating that the former retain many of the nucleophilic characteristics intrinsic to their parent diaminocarbenes and that the observed differences in chemical reactivity may be primarily attributed to an enhanced electrophilicity.

Gas-phase studies of purine 3-methyladenine DNA glycosylase II (AlkA) substrates.

3-Methyladenine DNA glycosylase II (AlkA) is an enzyme that cleaves a wide range of damaged bases from DNA. The gas-phase thermochemical properties (tautomerism, acidity, and proton affinity) have been measured and calculated for a series of AlkA purine substrates (7-methyladenine, 7-methylguanine, 3-methyladenine, 3-methylguanine, purine, 6-chloropurine, xanthine) that have not been heretofore examined. The damaged nucleobases are found to be more acidic than the normal nucleobases adenine and guanine. Because of this increased acidity, the damaged bases would be expected to be more easily cleaved from DNA by AlkA (their conjugate bases should be better leaving groups). We find that the gas-phase acidity correlates to the AlkA excision rates, which lends support to an AlkA mechanism wherein the enzyme provides a nonspecific active site, and nucleobase cleavage is dependent on the intrinsic N-glycosidic bond stability.