Gas-phase fragmentation of the Ag+-phenylalanine complex: cation-pi interactions and radical cation formation

Polystyrene Chain Geometry Probed by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulations

Polystyrene (PS) is a thermoplastic polymer commonly used in various applications due to its bulk properties. Designing functional polystyrenes with well-defined structures for targeted applications is of significant interest due to the rigid and apolar nature of the polymer chain. Progress is hindered to date by the limitations of current analytical methods in defining the atomistic-level folding of the polymer chain. The integration of ion mobility spectrometry and molecular dynamics simulations is beneficial in addressing these challenges. However, data on gas-phase polystyrene ions are rarely reported in the literature. We herein investigate the gas phase structure of polystyrene ions with different end groups to establish how the nature and the rigidity of the monomer unit affect the charge stabilization. We find that, in contrast to polar polymers in which the charges are located deep in the ionic globules, the charges in the PS ions are rather located at the periphery of the polymer backbone, leading to singly and doubly charged PS ions adopting dense elliptic-shaped structures. Molecular dynamics (MD) simulations indicate that the folding of the PS rigid chain is controlled by phenyl ring interactions with the charge ultimately remaining excluded from the core of the globular ions, whereas the folding of polyether ions is initiated by the folding of the flexible polyether chain around the sodium ion that remains deeply enclosed in the core of the ions.

Identification and Imaging of Prostaglandin Isomers Utilizing MS3 Product Ions and Silver Cationization

Prostaglandins (PGs) are important lipid mediators involved in physiological processes, such as inflammation and pregnancy. The pleiotropic effects of the PG isomers and their differential expression from cell types impose the necessity for studying individual isomers locally in tissue to understand the molecular mechanisms. Currently, mass spectrometry (MS)-based analytical workflows for determining the PG isomers typically require homogenization of the sample and a separation method, which results in a loss of spatial information. Here, we describe a method exploiting the cationization of PGs with silver ions for enhanced sensitivity and tandem MS to distinguish the biologically relevant PG isomers PGE2, PGD2, and Δ12-PGD2. The developed method utilizes characteristic product ions in MS3 for training prediction models and is compatible with direct infusion approaches. We discuss insights into the fragmentation pathways of Ag+ cationized PGs during collision-induced dissociation and demonstrate the high accuracy and robustness of the model to predict isomeric compositions of PGs. The developed method is applied to mass spectrometry imaging (MSI) of mouse uterus implantation sites using silver-doped pneumatically assisted nanospray desorption electrospray ionization and indicates localization to the antimesometrial pole and the luminal epithelium of all isomers with different abundances. Overall, we demonstrate, for the first time, isomeric imaging of major PG isomers with a simple method that is compatible with liquid-based extraction MSI methods.

CIPDB: A biological structure databank for studying cation and π interactions

As major forces for modulating protein folding and molecular recognition, cation and π interactions are extensively identified in protein structures. They are even more competitive than hydrogen bonds in molecular recognition, thus, are vital in numerous biological processes. In this review, we introduce the methods for the identification and quantification of cation and π interactions, provide insights into the characteristics of cation and π interactions in the natural state, and reveal their biological function together with our developed database (Cation and π Interaction in Protein Data Bank; CIPDB; http://chemyang.ccnu.edu.cn/ccb/database/CIPDB). This review lays the foundation for the in-depth study of cation and π interactions and will guide the use of molecular design for drug discovery.

Hydroxyl transfer versus cyclization reaction in the gas phase: Sequential loss of NH3 and CH2CO from protonated phenylalanine derivatives

Collisional activation of protonated phenylalanine derivatives deamination products leads to hydroxyl skeletal rearrangement versus cyclization reaction, and to form hydroxylbenzyl cation via elimination of CH₂CO. To better clarify this unusual fragmentation reaction, accurate mass measurements experiments, native isotope experiments, multiple-stage mass spectrometry experiments, different substituents experiments, and density functional theory (DFT) calculations were carried out to investigate the dissociation mechanistic pathways of protonated phenylalanine derivatives deamination products. In route 1, a three-membered ring-opening reaction and a 1,3-hydroxyl transfer (from the carbonyl carbon atom to the interposition carbon atom of carbonyl) occurs to form 3-hydroxy-1-oxo-3-phenylpropan-1-ylium, followed by dissociation to lose CH₂CO to give hydroxy (phenyl)methylium. In route 2, a successive cyclization rearrangement reaction and proton transfer occur to form a 2-hydroxylphenylpropionyl cation or protonated 2-hydroxy-4H-benzopyran, followed by dissociation to lose CH₂CO or CH≡COH to give 2-hydroxylbenzyl cation. In route 3, a successive hydroxyl transfer (from the carbonyl carbon atom to the ortho carbon atom on benzene) and two stepwise proton transfer (1,2-proton transfer to the ipso-carbon atom of the phenyl ring followed by 1,3-proton transfer to the ortho carbon atom of carbonyl) occurs to form a 2-hydroxylphenylpropionyl cation, which subsequently dissociates to form 2-hydroxylbenzyl cation by elimination of CH₂CO. DFT calculations suggested that route 1 was more favorable than route 2 and route 3 from a thermodynamic point of view.

Quantitative determination of sn-positional phospholipid isomers in MSn using silver cationization

Glycerophospholipids are one of the fundamental building blocks for life. The acyl chain connectivity to the glycerol backbone constitutes different sn-positional isomers, which have great diversity and importance for biological function. However, to fully realize their impact on function, analytical techniques that can identify and quantify sn-positional isomers in chemically complex biological samples are needed. Here, we utilize silver ion cationization in combination with tandem mass spectrometry (MSn) to identify sn-positional isomers of phosphatidylcholine (PC) species. In particular, a labile carbocation is generated through a neutral loss (NL) of AgH, the dissociation of which provides diagnostic product ions that correspond to acyl chains at the sn-1 or sn-2 position. The method is comparable to currently available methods, has a sensitivity in the nM-µM range, and is compatible with quantitative imaging using mass spectrometry in MS4. The results reveal a large difference in isomer concentrations and the ion images show that the sn-positional isomers PC 18:1_18:0 are homogeneously distributed, whereas PC 18:1_16:0 and PC 20:1_16:0 show distinct localizations to sub-hippocampal structures.

Analysis of the Fragmentation Pathways for the Collision-Induced Dissociation of Protonated Cyclophosphamide: A Mass Spectrometry and Quantum Mechanical Study

Cyclophosphamide is a well-known anticancer agent acting by means of DNA alkylation. Associated with its tumor selectivity, it also possesses a wide spectrum of toxicities. As the requirement of metabolic activation before cyclophosphamide exerts either its therapeutic or toxic effects is well recognized, research aiming at elucidating the pathways that lead to the activation of this drug is of key importance. This has created the necessity for developing an effective analytical method for detecting cyclophosphamide and its breakdown products. In this paper, an Acquity TQ tandem quadrupole mass spectrometer equipped with electrospray ionization in positive-ion mode was employed for detecting cyclophosphamide in its protonated form. The full-scan mass spectrum of cyclophosphamide shows two ion clusters displaying the characteristic isotopic pattern of two chlorine atoms and assigned as sodiated cyclophosphamide, [CP + Na]⁺, and protonated cyclophosphamide, [CP + H]⁺ or PCP. With the aid of quantum mechanical DFT calculation, free energy differences in the gas phase among PCP protomers were computed with respect to the most stable protomer being protonated on the 2-oxide oxygen of the 1,3,2-oxazaphosphorine-2-oxide ring. In addition, the interconversion mechanisms among the different protomers were also proposed by intercepting the corresponding transition states in the gas phase. Collision-induced dissociation (CID) of PCP generated six characteristic product ions. Fragmentation mechanisms were proposed and supported by computation. The calculated energy barriers for all of the located transition states were found to be accessible under the reported experimental conditions.

Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry

Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]⁺) and methionine enkephalin ([MetEnk+H]⁺) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur-aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]⁺. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]⁺.

A computational and experimental study of the fragmentation of l-leucine, l-isoleucine and l-allo-isoleucine under collision-induced dissociation tandem mass spectrometry

The isomeric amino acids l-leucine, l-isoleucine and l-allo-isoleucine, are essential to many vital biological processes and are therefore of interest to the fields of metabolomics and proteomics. Their discrimination can be problematic however due to their isomeric natue. This study demonstrates a systematic investigation of the fragmentations of l-leucine, l-isoleucine and l-allo-isoleucine in combination with a thorough theoretical rationalisation. Collision induced dissociation (CID) tandem mass spectra (MS/MS) of all three amino acids were collected under a range of different collision energies to identify spontaneous and sequential fragmentation processes. We demonstrate that the three structural isomers can be distinguished by their CID MS/MS spectra, and additional computational modelling is used to rationalise these differences.

Electrospray mass spectrometry and molecular modeling study of formation and stability of silver complexes with diazaperylene and bisisoquinoline

The complex formation of the following diazaperylene ligands (L) 1,12-diazaperylene 1, 1,1'-bisisoquinoline 2, 2,11-disubstituted 1,12-diazaperylenes (alkyl = methyl, ethyl, isopropyl, 3, 5, 7), 3,3'-disubstituted 1,1'-bisisoquinoline (alkyl = methyl, ethyl, isopropyl, 4, 6, 8 and with R = phenyl, 11 and with pyridine 12), and the 5,8-dimethoxy-substituted diazaperylene 9, 6,6'-dimethoxy-substituted bisisoquinoline 10 with AgBF4 was investigated. Collision-induced dissociation measurements were used to evaluate the relative stabilities of the ligands themselves and for the [1:1]⁺ complexes as well as for the homoleptic and heteroleptic silver [1:2]⁺ complexes in the gas phase. This method is very useful in rapid screening of the stabilities of new complexes in the gas phase. The influence of the spatial arrangement of the ligands and the type of substituents employed for the complexation were examined. The effect of the preorganization of the diazaperylene on the threshold activation voltages and thus of the relative binding energies of the different complexes are discussed. Density functional theory calculations were used to calculate the optimized structures of the silver complexes and compared with the stabilities of the complexes in the gas phase for the first time.

Collision-induced dissociation of phenethylamides: role of ion-neutral complexes

RATIONALE

Phenethylamides are a large group of naturally occurring molecules found both in the plant and animal kingdoms. In addition, they are used as intermediates for the synthesis of pharmaceutically important dihydro- and tetrahydroisoquinolines. To enable efficient characterization of this class of molecules, a detailed mass spectrometric fragmentation study of a broad series of analogs was carried out.

METHODS

The test compounds were synthesized using standard methods for amide bond formation. Low-energy high-resolution tandem mass spectra were acquired on a hybrid quadrupole/time-of-flight mass spectrometer using positive ion electrospray ionization.

RESULTS

A total of 26 analogs were investigated in the study. Fragmentation of phenethylamides was found to proceed via intermediate ion-neutral complexes. The complexes can break down via multiple pathways including dissociation, proton transfer, Friedel-Crafts acylation, and single electron transfer. The relative contribution of each of these pathways strongly depends on the structure of the coupling amine and acid.

CONCLUSIONS

A general scheme for the fragmentation of phenethylamides was developed. This study further extends the knowledge base of the ion-neutral complex by discovering Friedel-Crafts acylation as a novel reaction. The strong influence of minor structural modifications on the fragmentation patterns highlights the importance of testing many analogs in order to fully predict a fragmentation pattern of a particular class of molecules.

Chiral recognition of phenylglycinol enantiomers based on N-acetyl-l-cysteine capped CdTe quantum dots in the presence of Ag. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017;183:23-29. [PMID: 28432917 DOI: 10.1016/j.saa.2017.04.014]

In this study, a novel method for chiral recognition of phenylglycinol (PG) enantiomers was proposed. Firstly, water-soluble N-acetyl-l-cysteine (NALC)-capped CdTe quantum dots (QDs) were synthesized and experiment showed that the fluorescence intensity of the reaction system slightly enhancement when added PG enantiomers to NALC-capped CdTe quantum dots (QDs), but the R-PG and S-PG could not be distinguished. Secondly, when there was Ag⁺ presence in the reaction system, the experiment result was extremely interesting, the PG enantiomers cloud make NALC-capped CdTe QDs produce different fluorescence signal, in which the fluorescence of S-PG+Ag⁺+NALC-CdTe system was significantly enhanced, and the fluorescence of R-PG+Ag⁺+NALC-CdTe system was markedly decreased. Thirdly, all the enhanced and decreased of the fluorescence intensity were directly proportional to the concentration of R-PG and S-PG in the linearly range 10^-5-10^-7mol·L^-1, respectively. So, the new method for simultaneous determination of the PG enantiomers was built too. The experiment result of the method was satisfactory with the detection limit of PG can reached 10^-7mol·L^-1 and the related coefficient of S-PG and R-PG are 0.995 and 0.980, respectively. The method was highly sensitive, selective and had wider detection range compared with other methods.

Isomerization versus dissociation of phenylalanylglycyltryptophan radical cations

Four isomers of the radical cation of tripeptide phenylalanylglycyltryptophan, in which the initial location of the radical center is well defined, have been isolated and their collision-induced dissociation (CID) spectra examined. These ions, the π-centered [FGW_π˙]⁺, α-carbon- [FG_α˙W]⁺, N-centered [FGW_N˙]⁺ and ζ-carbon- [F_ζ˙GW]⁺ radical cations, were generated via collision-induced dissociation (CID) of transition metal-ligand-peptide complexes, side chain fragmentation of a π-centered radical cation, homolytic cleavage of a labile nitrogen-nitrogen single bond, and laser induced dissociation of an iodinated peptide, respectively. The π-centered and tryptophan N-centered peptide radical cations produced almost identical CID spectra, despite the different locations of their initial radical sites, which indicated that interconversion between the π-centered and tryptophan N-centered radical cations is facile. By contrast, the α-carbon-glycyl radical [FG_α˙W]⁺, and ζ-phenyl radical [F_ζ˙GW]⁺, featured different dissociation product ions, suggesting that the interconversions among α-carbon, π-centered (or tryptophan N-centered) and ζ-carbon-radical cations have higher barriers than those to dissociation. Density functional theory calculations have been used to perform systematic mechanistic investigations on the interconversions between these isomers and to study selected fragmentation pathways for these isomeric peptide radical cations. The results showed that the energy barrier for interconversion between [FGW_π˙]⁺ and [FGW_N˙]⁺ is only 31.1 kcal mol^-1, much lower than the barriers to their dissociation (40.3 kcal mol^-1). For the [FGW_π˙]⁺, [FG_α˙W]⁺, and [F_ζ˙GW]⁺, the barriers to interconversion are higher than those to dissociation, suggesting that interconversions among these isomers are not competitive with dissociations. The [z₃ - H]˙⁺ ions isolated from [FG_α˙W]⁺ and [F_ζ˙GW]⁺ show distinctly different fragmentation patterns, indicating that the structures of these ions are different and this result is supported by the DFT calculations.

Structural Characterization of Anticancer Drug Paclitaxel and Its Metabolites Using Ion Mobility Mass Spectrometry and Tandem Mass Spectrometry

Paclitaxel (PTX) is a popular anticancer drug used in the treatment of various types of cancers. PTX is metabolized in the human liver by cytochrome P450 to two structural isomers, 3′-p-hydroxypaclitaxel (3p-OHP) and 6α-hydroxypaclitaxel (6α-OHP). Analyzing PTX and its two metabolites, 3p-OHP and 6α-OHP, is crucial for understanding general pharmacokinetics, drug activity, and drug resistance. In this study, electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) and collision induced dissociation (CID) are utilized for the identification and characterization of PTX and its metabolites. Ion mobility distributions of 3p-OHP and 6α-OHP indicate that hydroxylation of PTX at different sites yields distinct gas phase structures. Addition of monovalent alkali metal and silver metal cations enhances the distinct dissociation patterns of these structural isomers. The differences observed in the CID patterns of metalated PTX and its two metabolites are investigated further by evaluating their gas-phase structures. Density functional theory calculations suggest that the observed structural changes and dissociation pathways are the result of the interactions between the metal cation and the hydroxyl substituents in PTX metabolites.

Collision-induced dissociation products of the protonated dipeptide carnosine: structural elucidation, fragmentation pathways and potential energy surface analysis

Collision-induced dissociation (CID) experiments on protonated carnosine, [carnosine + H](+), with several collision energies were shown to yield eleven different fragment ions with the generation of product ions [carnosine-H2O + H](+) and [carnosine-NH3 + H](+) being the lowest energy processes. Energy-resolved CID showed that at slightly higher collision energies the ions [histidine + H](+) and [histidine-H2O-CO + H](+) are formed. At even higher energies four other product ions were observed, however, attained relatively lower abundances. Quantum chemistry calculations, carried out at different levels of theory, were employed to probe fragmentation mechanisms that account for all the experimental data. All the adopted computational protocols give similar energetic trends, and the range of the calculated free energy barrier values for the generation of all the observed product ions is in agreement with the fragmentation mechanisms offered here.

Gas-phase intramolecular cyclization of argentinated N-allylbenzamides

The fragmentations of argentinated N-allylbenzamides have been exhaustively studied through collision-induced dissociation and through deuterium labeling. The intriguing elimination of AgOH is certified as the consequence of intramolecular cyclization between terminal olefin and carbonyl carbon following proton transfer to carbonyl oxygen, rather than simple enolization of amide. Linear free energy correlations and density functional theory (DFT) calculations were performed to understand the competitive relationship between AgOH loss and AgH loss, which results from the 1,2-elimination of α-hydrogen (to the amido nitrogen) with the silver.

Gas phase chemistry of N-benzylbenzamides with silver(i) cations: characterization of benzylsilver cation

Benzylsilver cations are synthesized in the gas phase from the collisional dissociation of argentinated N-benzylbenzamides, when the carbonyl oxygen nucleophilically attacks an α-hydrogen.

Gas-phase arylmethyl transfer and cyclodeamination of argentinated N-arylmethyl-pyridin-2-ylmethanimine

In collisional activation of argentinated N-arylmethyl-pyridin-2-ylmethanimine, a neutral molecule of AgNH2 is eliminated, carrying one hydrogen from the methylene and the other one from the ortho position (relative to the ipso carbon) of the aryl ring. Taking argentinated N-benzyl-pyridin-2-ylmethanimine for example, the proposition that the AgNH2 loss results from intramolecular arylmethyl transfer combined with cyclodeamination is rationalized by deuterium labeling experiments, blocking experiments, and theoretical calculations. The structure of the final product ion from loss of AgNH2 was confirmed further by multistage mass spectrometry.

Formation, isomerization, and dissociation of ε- and α-carbon-centered tyrosylglycylglycine radical cations

The CID spectra of [Y^ε˙GG]⁺ and [YGG^α˙]⁺ are identical, showing that interconversion occurs prior to dissociation. For [Y^ε˙GG]⁺, [Y^π˙GG]⁺ and [YG^α˙G]⁺, the dissociation products are all distinctly different, indicating that dissociation occurs more readily than isomerization.

Dissociations of complexes between monovalent metal ions and aromatic amino acid or histidine

The fragmentations of [AA + M](+) complexes, where AA = Phe, Tyr, Trp, or His, and M is a monovalent metal (Li, Na, or Ag), have been exhaustively studied through collision-induced dissociation (CID) and through deuterium labeling. Dissociations of the Li- and Ag-containing complexes gave a large number of fragment ions; by contrast, the sodium/amino acid complexes have lower binding energies, and dissociation resulted in much simpler spectra, with loss of the entire ligand dominating. Unambiguous assignments of these fragment ions were made and formation mechanisms are proposed. Of particular interest are fragmentations in which the charge was retained on the organic fragment and the metal was lost, either as a metal hydride (AgH) or hydroxide (LiOH) or as the silver atom (Ag(•)).

Characterization of [peptide+(Ag)n]+ complexes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Silver ion complexes of peptides [M + (Ag)(n) ](+) , M = angiotensin I or substance P where n = 1-8 and 17-23 for angiotensin I and n = 1-5 for substance P, are identified and characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The Ag(+) coordination number exceeds the number of available amino acid residues in angiotensin I whereas the number of observed complexes in substance P is less than the number of amino acid residues in it. The larger coordination number of angiotensin I with Ag(+) indicates the simultaneous binding of several Ag(+) ions to the amino acid residue present in it. The lower number of observed complexes in substance P suggests the binding of two or more residues to one Ag(+) ion. The presence of trifluoroacetic acid in the peptide samples reduces the Ag(+) coordination ability in both the peptides which indicates that the basic residues in it are already protonated and do not participate in the Ag(+) -binding process. The Ag(+) ion also forms a complex with the α-cyano-4-hydroxycinnamic acid (CHCA) matrix and is observed in the MALDI mass spectra and the formation of [CHCA + Ag](+) , [CHCA + AgNO(3) ](+) and [(CHCA)(2)  + Ag](+) ions is due to the high binding affinity of Ag(+) to the CN group of CHCA.

Isomer differentiation via collision-induced dissociation: the case of protonated alpha-, beta2- and beta3-phenylalanines and their derivatives

A combination of electrospray ionisation (ESI), multistage and high-resolution mass spectrometry experiments is used to examine the gas-phase fragmentation reactions of the three isomeric phenylalanine derivatives, alpha-phenylalanine, beta(2)-phenylalanine and beta(3)-phenylalanine. Under collision-induced dissociation (CID) conditions, each of the protonated phenylalanine isomers fragmented differently, allowing for differentiation. For example, protonated beta(3)-phenylalanine fragments almost exclusively via the loss of NH(3), only beta(2)-phenylalanine via the loss of H(2)O, while alpha- and beta(2)-phenylalanine fragment mainly via the combined losses of H(2)O + CO. Density functional theory (DFT) calculations were performed to examine the competition between NH(3) loss and the combined losses of H(2)O and CO for each of the protonated phenylalanine isomers. Three potential NH(3) loss pathways were studied: (i) an aryl-assisted neighbouring group; (ii) 1,2 hydride migration; and (iii) neighbouring group participation by the carboxyl group. Finally, we have shown that isomer differentiation is also possible when CID is performed on the protonated methyl ester and methyl amide derivatives of alpha-, beta(2)- and beta(3)-phenylalanines.

Collision-induced loss of AgH from Ag+ adducts of alkylamines, aminocarboxylic acids and alkyl benzyl ethers leads exclusively to thermodynamically favored product ions

The loss of AgH from [M+Ag]+ precursor ions of tertiary amines, aminocarboxylic acids and aryl alkyl ethers is examined by deuterium labeling combined with collision activation (CA) dissociation experiments. It was possible to demonstrate that the AgH loss process is highly selective toward the hydride abstraction. For tertiary amines and aminocarboxylic acids, hydrogen originates from the alpha-methylene group carrying the nitrogen function (formation of an immonium ion). In all cases examined, the most stable, i.e. the thermodynamically favored product ion is formed. In the AgH loss process, a large isotope effect operates discriminating against the loss of D. The [M+Ag]+ ion of benzyl methyl ether loses a hydride ion exclusively from the benzylic methylene group supporting the experimental finding that the AgH loss reaction selectively cleaves the weakest C-H bond available.

Dissociations of copper(II)-containing complexes of aromatic amino acids: radical cations of tryptophan, tyrosine, and phenylalanine

The dissociations of two types of copper(II)-containing complexes of tryptophan (Trp), tyrosine (Tyr), or phenylalanine (Phe) are described. The first type is the bis-amino acid complex, [Cu(II)(M)(2)].(2+), where M = Trp, Tyr, or Phe; the second [Cu(II)(4Cl-tpy)(M)].(2+), where 4Cl-tpy is the tridendate ligand 4'-chloro-2,2':6',2''-terpyridine. Dissociations of the Cu(ii) bis-amino acid complexes produce abundant radical cation of the amino acid, M.(+), and/or its secondary products. By contrast, dissociations of the 4Cl-tpy-bearing ternary complexes give abundant M.(+) only for Trp. Density functional theory (DFT) calculations show that for Tyr and Phe, amino-acid displacement reactions by H(2)O and CH(3)OH (giving [Cu(II)(4Cl-tpy)(H(2)O)].(2+) and [Cu(II)(4Cl-tpy)(CH(3)OH)].(2+)) are energetically more favorable than dissociative electron transfer (giving M.(+) and [Cu(I)(4Cl-tpy)](+)). The fragmentation pathway common to all these [Cu(II)(4Cl-tpy)(M)].(2+) ions is the loss of NH(3). DFT calculations show that the loss of NH(3) proceeds via a "phenonium-type" intermediate. Dissociative electron transfer in [Cu(II)(4Cl-tpy)(M-NH(3))].(2+) results in [M-NH(3)].(+). The [Phe-NH(3)] (+) ion dissociates facilely by eliminating CO(2) and giving a metastable phenonium-type ion that rearranges readily into the styrene radical cation.

Complexation of AlIII by Aromatic Amino Acids in the Gas Phase

The coordination properties of three natural aromatic amino acids (AAAs)-phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp)-to AlIII are studied in this work, devoting special attention to the role of the aromatic side chain. A comparison with aluminum(III)-alanine complexes is also presented. The polarizability arising from the ring has been seen to be a key factor in the stability of the complexes, with the order being Trp-AlIII > Tyr-AlIII > Phe-AlIII, starting from the most stable one. Cation-pi interactions between the metal and the aromatic ring are present in the lowest energy conformers, especially for Trp, which seems to be very well suited for these kinds of interactions, occurring with both the six- and five-membered rings of the indole side chain. The most stable coordination mode for the three AAAs is found to be tricoordinated with the N and O of the backbone chain and the aromatic ring, as was found theoretically and experimentally for other metals.

Silver complexation and tandem mass spectrometry for differentiation of isomeric flavonoid diglycosides

For detection and differentiation of isomeric flavonoids, electrospray ionization mass spectrometry is used to generate silver complexes of the type (Ag + flavonoid)+. Collisionally activated dissociation (CAD) of the resulting 1:1 silver/flavonoid complexes allows isomer differentiation of flavonoids. Eighteen flavonoid diglycosides constituting seven isomeric series are distinguishable from each other based on the CAD patterns of their silver complexes. Characteristic dissociation pathways allow identification of the site of glycosylation, the type of disaccharide (rutinose versus neohesperidose), and the type of aglycon (flavonol versus flavone versus flavanone). This silver complexation method is more universal than previous metal complexation methods, as intense silver complexes are observed even for flavonoids that lack the typical metal chelation sites. To demonstrate the feasibility of using silver complexation and tandem mass spectrometry to characterize flavonoids in complex mixtures, flavonoids extracted from grapefruit juice are separated by high-performance liquid chromatography and analyzed via a postcolumn complexation ESI-MS/MS strategy. Diagnostic fragmentation pathways of the silver complexes of the individual eluting flavonoids allow successful identification of the six flavonoids in the extract.

Cation−π Interactions and Oxidative Effects on Cu+ and Cu2+ Binding to Phe, Tyr, Trp, and His Amino Acids in the Gas Phase. Insights from First-Principles Calculations

The coordination properties of the four natural aromatic amino acids (AA(arom) = Phe, Tyr, Trp, and His) to Cu+ and Cu2+ have been exhaustively studied by means of ab initio calculations. For Cu+-Phe, Cu+-Tyr and Cu+-Trp, the two charge solvated tridentate N/O/ring and bidentate N/ring structures, with the metal cation interacting with the pi system of the ring, were found to be the lowest ones, relative DeltaG(298K) energies being less than 0.5 kcal/mol. The Cu+-His ground-state structure has the metal cation interacting with the NH2 group and the imidazole N. For these low-lying structures vibrational features are also discussed. Unlike Cu+ complexes, the ground-state structure of Cu2+-Phe, Cu2+-Tyr, and Cu2+-Trp does not present cation-pi interactions due to the oxidation of the aromatic ring induced by the metal cation. The ground-state structure of Cu2+-His does not present oxidation of the amino acid, the coordination to Cu2+ being tridentate with the oxygen of the carbonyl group, the nitrogen of the amine, and the N of the imidazole. Other less stable isomers, however, show oxidation of His, particularly of the imidazole ring, which can induce spontaneous proton-transfer reactions from the NH of the imidazole to the NH2 of the backbone. Finally, the computed binding energies for Cu+-AA(arom) and Cu2+-AA(arom) systems have been computed, the order found for the single charged systems being Cu+-His > Cu+-Trp > Cu+-Tyr > Cu+-Phe, in very good agreement with the experimental data.

Comparison of metal–amino acid interaction in Phe–Ag and Tyr–Ag complexes by spectroscopic measurements

In this article, we have compared the metal-amino acid interactions in Tyr-Ag and Phe-Ag complexes through pH dependent SERS measurements. By analyzing the variation in relative intensities of SERS bands with the pH of the amino acid solution, we have obtained the orientation and conformation of the amino acid molecules on the Ag surface. The results obtained from our experimental studies are supported by the energy minimized structures and the observed charge distributions in different terminals of the molecules. This, in a way, shows that SERS measurements not only exhibit the interaction of the amino acid molecules with Ag clusters but also demonstrate their orientation around it. We have addressed a long standing query on whether the amine group is directly attached to the Ag surface along with the carboxylate group and pi-electrons in these systems. In addition, pH dependent optical absorption and transmission electron microscopy measurements have been performed to understand the required conditions for the appearance of the SERS spectra in the light of the aggregation of metal particles and the number of hot sites in the sol. Our results confirm that the formation of hot sites in the sol plays a direct role in forming a stable Ag-ligand complex. Furthermore, the interaction kinetics of metal-amino acid complexes have been analyzed via both Raman and absorption measurements.

Dissociation of Alkaliated Alanine in the Gas Phase: The Role of the Metal Cation

The dissociation of prototypical metal-cationized amino acid complexes, namely, alkaliated alanine ([Ala+M]+, M+ = Li+, Na+, K+), was studied by energy-resolved tandem mass spectrometry with an ion-trap mass analyzer and by density functional theory. Dissociation leads to formation of fragment ions arising from the loss of small neutrals, such as H2O, CO, NH3, (CO+NH3), and the formation of Na+/K+. The order of appearance threshold voltages for different dissociation pathways determined experimentally is consistent with the order of critical energies (energy barriers) obtained theoretically, and this provides the necessary confidence in both experimental and theoretical results. Although not explicitly involved in the reaction, the alkali metal cation plays novel and important roles in the dissociation of alkaliated alanine. The metal cation not only catalyzes the dissociation (via the formation of loosely bound ion-molecule complexes and by stabilizing the more polar intermediates and transition structures), but also affects the dissociation mechanisms, as the cation can alter the shape of the potential energy surfaces. This compression/expansion of the potential energy surface as a function of the alkali metal cation is discussed in detail, and how this affects the competitive loss of H2O versus CO/(CO+NH3) from [Ala+M]+ is illustrated. The present study provides new insights into the origin of the competition between various dissociation channels of alkaliated amino acid complexes.

Novel fragmentation pathway for CID of (b(n) - 1 + Cat)+ ions from model, metal cationized peptides

We report a new fragmentation pathway for the CID of (b3 - 1 + Cat)+ product ions derived from the model peptide AXAG, where X = beta-alanine, gamma-aminobutyric acid, epsilon-amino-n-caproic acid, or 4-aminomethylbenzoic acid. By changing the amino acid to the C-terminal side of the amino acid X, and incorporating 15N and 13C labeled residues at the same position, we conclude that the dissociation pathway most likely leads to a metal cationized nitrile. With respect to the various amino acids at position X, the putative nitrile product becomes more prominent, relative to the conventional (a3 - 1 + Cat)+ species, in the order beta-alanine < gamma-aminobutyric acid < epsilon-aminocaproic acid < 4-aminomethylbenzoic acid. The pathway is not observed for peptides with alpha-amino acids at position X. The product ion is observed most prominently during the CID of Li+ and Na+ cationized peptides, only to a small extent for Ag+ cationized peptides, and not at all from protonated analogues.

Gas phase synthesis and reactivity of Agn+ and Agn–1H+ cluster cations

Multi-stage mass spectrometry (MSn) on [(M + Ag - H)x + Ag]+ precursor ions (where M = an amino acid such as glycine or N,N-dimethylglycine) results in the formation of stable silver (Ag3+, Ag5+ and Ag7+) and silver hydride (Ag2H+, Ag4H+ and Ag6H+) cluster cations in the gas phase. Deuterium labelling studies reveal that the source of the hydride can be either from the alpha carbon or from one of the heteroatoms. When M = glycine, the silver cyanide clusters Ag4CN+ and Ag5(H,C,N)+ are also observed. Collision induced dissociation (CID) and DFT calculations were carried out on each of these clusters to shed some light on their possible structures. CID of the Agn+ and Ag(n-1)H+ clusters generally results in the formation of the same Ag(n-2)+ product ions via the loss of Ag2 and AgH respectively. DFT calculations also reveal that the Agn+ and Ag(n-1)H+ clusters have similar structural features and that the Ag(n-1)H+ clusters are only slightly less stable than their all silver counterparts. In addition, Agn+ and Ag(n-1)H+ clusters react with 2-propanol and 2-butylamine via similar pathways, with multiple ligand addition occurring and a coupled deamination-dehydration reaction occurring upon condensation of a third (for Ag2H+) or a fourth (for all other silver clusters) 2-butylamine molecule onto the clusters. Taken together, these results suggest that the Agn+ and Ag(n-1)H+ clusters are structurally related via the replacement of a silver atom with a hydrogen atom. This replacement does not dramatically alter the cluster stability or its unimolecular or bimolecular chemistry with the 2-propanol and 2-butylamine reagents.

Electrospray mass spectrometric and DFT study of substituent effects in Ag+ complexation to polycyclic aromatic hydrocarbons (PAHs)

Complexation of Ag(i) cation to a series of substituted anthracenes (AN), phenanthrenes (PH), pyrenes (PY) and cyclopenta[a]phenanthrenes (CPaPH) was studied in competitive experiments by allowing PAHs to react in pairs with AgOTf. The resulting complexes were examined by electrospray mass spectrometry (ES-MS) to determine relative abundances of the corresponding monomeric and dimeric complexes. Based on this data a sequence of complexation ability rankings was derived for each group. Among the substituents examined, a -COMe group when placed at the meso position in AN and PH, or at the C-1 in PY is most effective in Ag(+) complexation, whereas an -NO(2) group is least efficient. Methyl groups at the meso positions are better than in the terminal rings. For the CPaPH series, bay region substitution (methyl and alkoxy) have limited effect as does carbonyl substitution in the annelated CP ring. In the PY series, a -COPh or a -CH(Me)OH group at C-1 is as efficient as -COMe. Based on extensive potential energy searches, four types of complexation modes were identified by B3LYP/LANL2DZ calculations involving Ag(+) complexation to -NO(2) oxygens, to -COMe or to -OH and a peri-carbon, to just one ring carbon, or by bridging two ring carbons. Among these modes, the first two are most favorable. The energetic preferences were rationalized with charge decomposition analysis (CDA). Effect of Ag(+) complexation on relative aromaticity in various rings was examined by NICS (nucleus independent chemical shift) in two representative cases. Structures and energies of the acetyl pyrene-Ag(+)-pyrene hetero-dimer and acetyl pyrene-Ag(+)-acetyl pyrene homo-dimer complexes were determined with the same model. These complexes have sandwich structures.

Neighbouring group processes in the deamination of protonated phenylalanine derivatives

The gas-phase fragmentation of protonated phenylalanine and a series of its derivatives (tyrosine, 4-methylphenylalanine, 4-aminophenylalanine, 4-methoxyphenylalanine, 4-tert-butylphenylalanine, 4-fluorophenylalanine, 4-chlorophenylalanine, 4-bromophenylalanine, 4-iodophenylalanine, 4-cyanophenylalanine, 4-nitrophenylalanine, 3-fluorophenylalanine, and 3,4-dichlorophenylalanine) were examined using a combination of low energy CID in a quadrupole ion trap mass spectrometer as well as DFT calculations and RRKM modelling. In particular, the relationship between the electron-donating ability of the substituent and the competitive losses of H2O + CO and NH3 were explored through the application of the Hammett equation. It was found that electron-donating substituents promote the loss of NH3, while electron-withdrawing substituents suppress the loss of NH3 and favour the H2O + CO loss fragmentation channel instead. These observations are consistent with a neighbouring group pathway operating for the loss of NH3. Molecular orbital calculation (at the B3LYP/6-31+G(d,p) level of theory) were also performed for a range of derivatives to compare the relative transition state energy barriers for three competing mechanisms: (i) the combined loss of H2O + CO, which is triggered by an initial intramolecular proton transfer from the ammonium group to hydroxyl OH, followed by the combined loss of H2O and CO to form an immonium ion; (ii) loss of NH3 via an aryl assisted neighbouring group pathway to yield a phenonium ion; (iii) loss of NH3 via a 1,2-hydride migration process, which results in the formation of a benzyl cation. The relative energy barriers for H2O + CO loss remain nearly constant, while that for both NH3 pathways increase as the substituent moves from electron-donating to electron-withdrawing. The relative transition state energy for loss of NH3 via the aryl assisted neighbouring group pathway is always lower than that of the 1,2-hydride migration process. RRKM modelling of the DFT predicted barrier heights suggest that the rate constants for H2O + CO loss are insensitive to the substituent on the ring, while the NH3 loss channels are greatly affected by the substituent. These theoretical results are consistent with the experimental observation of the relative yields of the competing fragmentation channels. Finally, comparisons with published gas phase and condensed phase studies on related systems are made.

Gas-phase reactions of protonated tryptophan

The gas phase reactions of protonated tryptophan have been examined in a quadrupole ion trap using a combination of collision induced dissociation, hydrogen-deuterium exchange, regiospecific deuterium labeling and molecular orbital calculations (at the B3LYP/6-31G* level of theory). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M + H - NH(3)](+) ion by nucleophilic attack from the C3 position of the indole side chain. Hydrogen-deuterium exchange and regiospecific deuterium labeling reveals that scrambling of protons in the C2 and C4 positions of the indole ring, via intramolecular proton transfer from the thermodynamically preferred site of protonation at the amino nitrogen, precedes ammonia loss. Molecular orbital calculations have been employed to demonstrate that the activation barriers to intramolecular proton transfer are lower than that for NH(3) loss.

Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non-peptidic combinatorial compounds

Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation.