Influence of Linkage Stereochemistry and Protecting Groups on Glycosidic Bond Stability of Sodium Cationized Glycosyl Phosphates

Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations

A detailed understanding of the reaction mechanism(s) leading to stereoselective product formation is crucial to understanding and predicting product formation and driving the development of new synthetic methodology. One way to improve our understanding of reaction mechanisms is to characterize the reaction intermediates involved in product formation. Because these intermediates are reactive, they are often unstable and therefore difficult to characterize using experimental techniques. For example, glycosylation reactions are critical steps in the chemical synthesis of oligosaccharides and need to be stereoselective to provide the desired α- or β-diastereomer. It remains challenging to predict and control the stereochemical outcome of glycosylation reactions, and their reaction mechanisms remain a hotly debated topic. In most cases, glycosylation reactions take place via reaction mechanisms in the continuum between S_N1- and S_N2-like pathways. S_N2-like pathways proceeding via the displacement of a contact ion pair are relatively well understood because the reaction intermediates involved can be characterized by low-temperature NMR spectroscopy. In contrast, the S_N1-like pathways proceeding via the solvent-separated ion pair, also known as the glycosyl cation, are poorly understood. S_N1-like pathways are more challenging to investigate because the glycosyl cation intermediates involved are highly reactive. The highly reactive nature of glycosyl cations complicates their characterization because they have a short lifetime and rapidly equilibrate with the corresponding contact ion pair. To overcome this hurdle and enable the study of glycosyl cation stability and structure, they can be generated in a mass spectrometer in the absence of a solvent and counterion in the gas phase. The ease of formation, stability, and fragmentation of glycosyl cations have been studied using mass spectrometry (MS). However, MS alone provides little information about the structure of glycosyl cations. By combining mass spectrometry (MS) with infrared ion spectroscopy (IRIS), the determination of the gas-phase structures of glycosyl cations has been achieved. IRIS enables the recording of gas-phase infrared spectra of glycosyl cations, which can be assigned by matching to reference spectra predicted from quantum chemically calculated vibrational spectra. Here, we review the experimental setups that enable IRIS of glycosyl cations and discuss the various glycosyl cations that have been characterized to date. The structure of glycosyl cations depends on the relative configuration and structure of the monosaccharide substituents, which can influence the structure through both steric and electronic effects. The scope and relevance of gas-phase glycosyl cation structures in relation to their corresponding condensed-phase structures are also discussed. We expect that the workflow reviewed here to study glycosyl cation structure and reactivity can be extended to many other reaction types involving difficult-to-characterize ionic intermediates.

Advancing Solutions to the Carbohydrate Sequencing Challenge

Carbohydrates possess a variety of distinct features with stereochemistry playing a particularly important role in distinguishing their structure and function. Monosaccharide building blocks are defined by a high density of chiral centers. Additionally, the anomericity and regiochemistry of the glycosidic linkages carry important biological information. Any carbohydrate-sequencing method needs to be precise in determining all aspects of this stereodiversity. Recently, several advances have been made in developing fast and precise analytical techniques that have the potential to address the stereochemical complexity of carbohydrates. This perspective seeks to provide an overview of some of these emerging techniques, focusing on those that are based on NMR and MS-hybridized technologies including ion mobility spectrometry and IR spectroscopy.

Structures and Relative Glycosidic Bond Stabilities of Protonated 2'-Fluoro-Substituted Purine Nucleosides

The 2'-substituent is the primary distinguishing feature between DNA and RNA nucleosides. Modifications to this critical position, both naturally occurring and synthetic, can produce biologically valuable nucleoside analogues. The unique properties of fluorine make it particularly interesting and medically useful as a synthetic nucleoside modification. In this work, the effects of 2'-fluoro modification on the protonated gas-phase purine nucleosides are examined using complementary tandem mass spectrometry and computational methods. Direct comparisons are made with previous studies on related nucleosides. Infrared multiple photon dissociation action spectroscopy performed in both the fingerprint and hydrogen-stretching regions allows for the determination of the experimentally populated conformations. The populated conformers of protonated 2'-fluoro-2'-deoxyadenosine, [Adofl+H]⁺, and 2'-fluoro-2'-deoxyguanosine, [Guofl+H]⁺, are highly parallel to their respective canonical DNA and RNA counterparts. Both N3 and N1 protonation sites are accessed by [Adofl+H]⁺, stabilizing syn and anti nucleobase orientations, respectively. N7 protonation and anti nucleobase orientation dominates in [Guofl+H]⁺. Spectroscopically observable intramolecular hydrogen-bonding interactions with fluorine allow more definitive sugar puckering determinations than possible for the canonical systems. [Adofl+H]⁺ adopts C2'-endo sugar puckering, whereas [Guofl+H]⁺ adopts both C2'-endo and C3'-endo sugar puckering. Energy-resolved collision-induced dissociation experiments with survival yield analyses provide relative glycosidic bond stabilities. The N-glycosidic bond stabilities of the protonated 2'-fluoro-substituted purine nucleosides are found to exceed those of their canonical analogues. Further, the N-glycosidic bond stability is found to increase with increasing electronegativity of the 2'-substituent, i.e., H < OH < F. The N-glycosidic bond stability is also greater for the adenine nucleoside analogues than the guanine nucleoside analogues.

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

Abstract

Nucleobases serve as ideal targets where drugs bind and exert their anticancer activities. Cisplatin (cisPt) preferentially coordinates to 2′-deoxyguanosine (dGuo) residues within DNA. The dGuo adducts that are formed alter the DNA structure, contributing to inhibition of function and ultimately cancer cell death. Despite its success as an anticancer drug, cisPt has a number of drawbacks that reduce its efficacy, including repair of adducts and drug resistance. Some approaches to overcome this problem involve development of compounds that coordinate to other purine nucleobases, including those found in RNA. In this work, amino acid-linked platinum(II) (AAPt) compounds of alanine and ornithine (AlaPt and OrnPt, respectively) were studied. Their reactivity preferences for DNA and RNA purine nucleosides (i.e., 2′-deoxyadenosine (dAdo), adenosine (Ado), dGuo, and guanosine (Guo)) were determined. The chosen compounds form predominantly monofunctional adducts by reacting at the N1, N3, or N7 positions of purine nucleobases. In addition, features of AAPt compounds that impact the glycosidic bond stability of Ado residues were explored. The glycosidic bond cleavage is activated differentially for AlaPt-Ado and OrnPt-Ado isomers. Formation of unique adducts at non-canonical residues and subsequent destabilization of the glycosidic bonds are important features that could circumvent platinum-based drug resistance.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-019-01693-y) contains supplementary material, which is available to authorized users.

Interrogating Proton Affinities of Organophosphonate Species Via Atmospheric Flow Tube Mass Spectrometry and Computational Methods

Within trace vapor analysis in environmental monitoring, defense, and industry, atmospheric flow tube mass spectrometry (AFT-MS) can fill a role that incorporates non-contact vapor analysis with the selectivity and low detection limits of mass spectrometry. AFT-MS has been applied to quantitating certain explosives by selective clustering with nitrate and more recently applied to detecting tributyl phosphate and dimethyl methylphosphonate as protonated species. Developing AFT-MS methods for organophosphorus species is appealing, given that this class of compounds includes a range of pollutants, chemical warfare agent (CWA) simulants, and CWA degradation products. A key aspect of targeting organophosphorus analytes has included the use of dopant ion chemistry to form adducts that impart additional analytical selectivity. The assessment of potential dopant molecules suited to enhance detection of these compounds is hindered by few published ion thermochemical properties for organophosphorus species, such as proton affinity, which can be used for approximating proton-bound dimer bond strength. As a preliminary investigation for the progression of sensing methods involving AFT-MS, we have applied both the extended kinetic method and computational approaches to eight organophosphorus CWA simulants to determine their respective gas-phase proton affinities. Notable observed trends, supported by computational efforts, include an increase in proton affinity as the alkyl chain lengths on the phosphonates increased. Graphical Abstract .

Ambient vapor sampling and selective cluster formation for the trace detection of tributyl phosphate via atmospheric flow tube mass spectrometry

In addition to serving as an f-element ligand and rare-earth method complexing agent, tributyl phosphate is a compound containing core functional groups that mimic those routinely found in degradation products from industrial processes. Because detection of trace quantities of tributyl phosphate can provide insight into the routes of contamination and degradation in the environment, there is a need to develop methods capable of detecting trace quantities of tributyl phosphate. Vapor detection at atmospheric pressure is one approach that is both sensitive and rapid. We present here the use of atmospheric flow tube mass spectrometry for the ambient vapor sampling of tributyl phosphate from headspace of ppb-level solutions in methanol. Gas phase clustering reactions were to enhance detection levels via the addition of small quantities of the dopants diethylamine, triethylamine, and pinacolyl methylphosphonate in the vapor stream. Detection of the tributyl phosphate vapor emanating from these solutions demonstrated a linear range for the protonated tributyl phosphate species of 1-1000 ppb from solution. The clusters of tributyl phosphate with diethylamine, triethylamine, and pinacolyl phosphonate each yielded linear ranges of 1-250 ppb for tributyl phosphate in solution. Despite smaller linear ranges, the addition of these dopant species added a layer of analytical selectivity and reduced variability in signals from quality control samples. These data were obtained using an atmospheric flow tube source coupled to a linear ion trap mass spectrometer, which demonstrates the applicability of trapping systems to the atmospheric flow tube ionization technique while monitoring positive ions.

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.

Direct Experimental Characterization of Glycosyl Cations by Infrared Ion Spectroscopy

Glycosyl cations are crucial intermediates formed during enzymatic and chemical glycosylation. The intrinsic high reactivity and short lifetime of these reaction intermediates make them very challenging to characterize using spectroscopic techniques. Herein, we report the use of collision induced dissociation tandem mass spectrometry to generate glycosyl cations in the gas phase followed by infrared ion spectroscopy using the FELIX infrared free electron laser. The experimentally observed IR spectra were compared to DFT calculated spectra enabling the detailed structural elucidation of elusive glycosyl oxocarbenium and dioxolenium ions.