First principles studies on boron sites in zeolites

A systematic computational investigation on protonated and nonprotonated boron-containing zeolites (boralites), performed by using different periodic density functional theory approximations, is presented. Both minimum energy structures and finite temperature behavior of model boron sodalites were analyzed. All of the adopted computational schemes agree in predicting an acid site composed of a silanol Si-OH group loosely linked to a planar BO(3) structure in the protonated system and a BO(4) tetrahedral site in the sodium-containing zeolite. Calculated structural and vibrational properties are in line with experimental data. Comparisons of the protonated boralite site with Al and Ga zeolitic acid sites are discussed as well. Results indicate that this class of mild acid catalysts is characterized by significant framework flexibility and pronounced thermal effects due to the loosely bound acid site.     

Effects of pressure on ion-molecule reactions in the chemical ionization mass spectrometry of carboxylic acids

The water elimination caused by bifunctional interaction in protonated dicarboxylic acids diminishes as sample pressure increases. This appears to be the result of stabilization of the protonated dixarboxylic acid by reversible formation of a protonted dimmer. The effect reaches a minimum for dicarboxylic acid with interfunctional chain length of 6–9 carbons where the free energy of activation probably also reaches a minimum. Self-acetylation by water elimination from protonated dimers was observed for the monocarboxylic acids only.     

Reaction competition in the fragmentation of protonated dipeptides

A major low-energy fragmentation reaction of many protonated dipeptides involves cleavage of the amide bond resulting in formation of either the y(1)" ion or the a(1) ion. For a series of protonated dipeptides H-Val-Xxx-OH it is observed that log(y(1)"/a(1)) is a linear function of the proton affinity of the variable C-terminal amino acid. For the series of protonated dipeptides H-Xxx-Phe-OH log(a(1)/y(1)") gives a poor correlation with the proton affinity or gas-phase basicity of H-Xxx-OH. However, a good limited correlation of log(a(1)/y(1)") with the Taft-Topsom sigma(alpha) for the alkyl group is observed when Xxx is an aliphatic amino acid. It is proposed that fragmentation occurs by initial formation of a proton-bound complex of an aziridinone and an amino acid which may fragment to form either a protonated amino acid (y(1)") or an N-protonated aziridinone with the corresponding neutrals being an aziridinone and an amino acid. Ab initio calculations show that the N-protonated aziridinone is unstable and fragments by loss of CO to form the a(1) immonium ion. However, the proton-bound complex of an aziridinone and an amine base is a stable species which exists in a potential well. Copyright 2000 John Wiley & Sons, Ltd.     

Collision‐induced dissociation processes of protonated benzoic acid and related compounds: competitive generation of protonated carbon dioxide or protonated benzene

Upon activation in the gas phase, protonated benzoic acid (m/z 123) undergoes fragmentation by several mechanisms. In addition to the predictable water loss followed by a CO loss, the m/z 123 ion more intriguingly eliminates a molecule of benzene to generate protonated carbon dioxide (H ‐ O⁺ ═ C ≡ O , m/z 45), or a molecule of carbon dioxide to yield protonated benzene (m/z 79). Experimental evidence shows that the incipient proton ambulates during the fragmentation processes. For the CO₂ or benzene loss, protonated benzoic acid transfers the charge‐imparting proton initially to the ortho position and then to the ipso position to generate a transient species which dissociates to form an ion‐neutral complex between benzene and protonated CO₂. The formation of the m/z 45 ion is not a phenomenon unique to benzoic acid: spectra from protonated isophthalic acid, terephthalic acid, trans‐cinnamic acid and some aliphatic acids also displayed a peak for m/z 45. However, the m/z 45 peak is structurally diagnostic only for certain benzene polycarboxylic acids because the spectra of compounds with two carboxyl groups on adjacent ring carbons do not produce a peak at m/z 45. For the m/z 79 ion to be formed, an intramolecular reaction should take place in which protonated CO₂ within the ion‐neutral complex acts as the attacking electrophile to transfer a proton to benzene. Copyright © 2017 John Wiley & Sons, Ltd.     

Facile synthesis of α-hydroxy carboxylic acids from the corresponding α-amino acids

An effective and improved procedure is developed for the synthesis of α-hydroxy carboxylic acids by treatment of the corresponding protonated α-amino acid with tert-butyl nitrite in 1,4-dioxane–water. The amino moiety must be protonated and located α to a carboxylic acid function in order to undergo initial diazotization and successive hydroxylation, since neither β-amino acids nor acid derivatives such as esters and amides undergo hydroxylations. The method is successfully applied for the synthesis of 18 proteinogenic amino acids.     

Complexation of Amino Acid Methylesters and Amino Alcohols by 18-Crown-6 and Benzo-18-crown-6 in Methanol

The complexation of protonated amino acid methylesters and amino alcohols bythe ligands 18-crown-6 (18C6) and benzo-18-crown-6 (B18C6) has been studiedin methanol using calorimetric titrations. No influence of the anions upon thestability constants and thermodynamic data for the reaction of protonated aminoacid methylesters with both ligands has been noticed, which indicates the completedissociation of the salts employed. A similar effect has been observed for thecomplexation of protonated and unprotonated amino alcohols with 18C6 andB18C6. The values obtained of the reaction enthalpies for the complexation ofprotonated amino acid methylesters with 18C6 are larger than those correspondingto the complexation with B18C6. The results demonstrate that the complex formationof unprotonated amino alcohols is favored by entropic contributions, while thecomplexation of protonated amino alcohols is favored by enthalpic contributionswith both ligands. The influence of various substituents on the complexation behaviorof amino acid and amino alcohol has also been investigated.     

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.     

Secondary processes in atmospheric pressure chemical ionization–ion trap mass spectrometry: a case study of orotic acid

Atmospheric pressure chemical ionization is known for producing unusual artifacts of the ionization process in some cases. In this work, processes occuring in atmospheric pressure chemical ionization/MS of orotic acid that afforded ions accompanying protonated and deprotonated orotic acid molecules in the spectra were studied. Two processes ran in parallel in the ion source: decarboxylation of neutral orotic acid and collision‐induced dissociation of its protonated or deprotonated form. A procedure discerning pre‐ionization decomposition and post‐ionization dissociation by manipulating ion source parameters was proposed. Experiments with isotopically labeled solvents confirmed ion–molecule reactions of the product of collision‐induced dissociation of protonated orotic acid with solvent molecules in the ion source and even under vacuum in the ion trap. Copyright © 2012 John Wiley & Sons, Ltd.     

A New Protonated form of Porphyrins in Solutions

The H-associate as a new protonated form of metalloporphyrins in strong acid media has been obtained and a qualitative reaction for its determination has been found; the properties and structure of a protonated form have been analyzed by spectral methods and quantum-chemical calculations.     

Effects of single amino acid substitution on the dissociation of multiply charged multiprotein complexes in the gas phase

The effects of amino acid substitutions on the product ion charge distributions for protonated and deprotonated homogeneous and heterogeneous multiprotein complexes in the gas phase are studied using Fourier-transform mass spectrometry and the blackbody infrared radiative dissociation technique. Notably, it is shown that a single amino acid substitution in the leaving subunit can cause a small but measurable change in product ion charge distribution. Evidence that the degree of charge enrichment of the leaving subunit is influenced by the number of strongly basic or acidic residues within the subunit for the protonated and deprotonated complexes, respectively, is reported.     

A computer program (COMPOST) for predicting mass spectrometric information from known amino acid sequences

A computer program (COMPOST) is described that carries out predictive computations on known amino acid sequences. The program is designed to be of use to mass spectrometrists with an interest in protein and peptide sequencing. Mass values (monoisotopic and average) for protonated peptide and protein molecules and elemental compositions are calculated. COMPOST also calculates mass to charge ratio values for protonated peptides expected from specified digests, locates specified amino acid subsequences or peptides of a specifIed molecular weight within a longer sequence, and predicts mass to charge ratio values for fragment ions from high-energy collision-induced dissociation of protonated peptides.     

ESR Spectra of radicals produced by reduction of pyridine and pyrazine

Radicals produced by reaction of e^?_aq with pyridine, pyrazine, and pyrazinedicarboxylic acid have been studied by electron spin resonance using the in situ radiolysis steady-state ESR technique. The radical anions initially produced have been found to undergo rapid protonation on nitrogen to form pyridinyl and pyrazinyl radicals. The NH proton of pyridinyl radical does not dissociate even at pH 13.7. The radical from pyrazine has been observed only in the doubly protonated positively charged form in acid and neutral solutions, but no spectrum was observed in alkaline media. With 2,3-pyrazinedicarboxylic acid the doubly protonated radical has been observed at pH 4–8 and the singly protonated one at pH 11–12. The pK for this dissociation is 9.2. The hyperfine constants of the pyridinyl radical are compared with those obtained from INDO molecular orbital calculations.     

Fine tuning of the catalytic effect of a metal-free porphyrin on the homogeneous oxygen reduction

The catalytic effect of tetraphenylporphyrin on the oxygen reduction with ferrocene in 1,2-dichloroethane can be finely tuned by varying the molar ratio of the acid to the catalyst present in the solution. The mechanism involves binding of molecular oxygen to the protonated free porphyrin base, in competition with ion pairing between the protonated base and the acid anion present.     

Noncovalent binding between fullerenes and protonated porphyrins in the gas phase

Noncovalent interactions between protonated porphyrin and fullerenes (C?? and C??) were studied with five different meso-substituted porphyrins in the gas phase. The protonated porphyrin-fullerene complexes were generated by electrospray ionization of the porphyrin-fullerene mixture in 3:1 dichloromethane/methanol containing formic acid. All singly protonated porphyrins formed the 1:1 complexes, whereas porphyrins doubly protonated on the porphine center yielded no complexes. The complex ion was mass-selected and then characterized by collision-induced dissociation with Xe. Collisional activation exclusively led to a loss of neutral fullerene, indicating noncovalent binding of fullerene to protonated porphyrin. In addition, the dissociation yield was measured as a function of collision energy, and the energy inducing 50% dissociation was determined as a measure of binding energy. Experimental results show that C?? binds to the protonated porphyrins more strongly than C??, and electron-donating substituents at the meso positions increase the fullerene binding energy, whereas electron-withdrawing substituents decrease it. To gain insight into π-π interactions between protonated porphyrin and fullerene, we calculated the proton affinity and HOMO and LUMO energies of porphyrin using Hartree-Fock and configuration interaction singles theory and obtained the binding energy of the protonated porphyrin-fullerene complex using density functional theory. Theory suggests that the protonated porphyrin-fullerene complex is stabilized by π-π interactions where the protonated porphyrin accepts π-electrons from fullerene, and porphyrins carrying bulky substituents prefer the end-on binding of C?? due to the steric hindrance, whereas those carrying less-bulky substituents favor the side-on binding of C??.     

Sequencing of sulfonic acid derivatized peptides by electrospray mass spectrometry

We report the application of nanoelectrospray ionization tandem mass spectrometry (nES-MS/MS) and capillary LC/microelectrospray MS/MS (cLC/&mgr;ES-MS/MS) for sequencing sulfonic acid derivatized tryptic peptides. These derivatives were specifically prepared to facilitate low-energy charge-site-initiated fragmentation of C-terminal arginine-containing peptides, and to enhance the selective detection of a single series of y-type fragment ions. Both singly and doubly protonated peptides were analyzed by MS/MS and the results were compared with those from their derivatized counterparts. Model peptides and peptides from tryptic digests of gel-isolated proteins were analyzed. Derivatized singly protonated peptides fragment in the same way by nES-MS/MS as they do by post-source decay matrix-assisted laser desorption/ionization mass spectrometry (PSD-MALDI-MS). They produce fragment ion spectra dominated by y-ions, and the simplified spectra are readily interpreted de novo. Doubly protonated peptides fragment in much the same way as their non-derivatized doubly protonated counterparts. The fragmentation of doubly protonated derivatives is especially useful for sequencing peptides that possess a proline residue near the N-terminus of the molecule. The singly protonated forms of these proline-containing derivatives often show enhanced fragmentation on the N-terminal side of the proline and considerably reduced fragmentation on the C-terminal side. In addition, sulfonic acid derivatization increases the in-source fragmentation of arginine-containing peptides. This could be useful for sequence verification and sequence tagging for use in single stage mass spectrometry. Copyright 2000 John Wiley & Sons, Ltd.     

Thermal Behaviour of Poly(propylene) Layered Silicate Nanocomposites

The thermal degradation behaviour of nanocomposites based upon poly(propylene)/organoclay, modified with protonated octadecyl amine (C18) in comparison to that of non‐exfoliated microcomposites based upon organoclay, modified with protonated butyl amine (C4), was studied by thermogravimetry. In the case of the nanocomposite, the temperature at which volatilisation occurs increases as compared of the microcomposite. Moreover, the thermal oxidation process of the polymer is strongly slowed down in the nanocomposite with high char yield both by a physical barrier effect, enhanced by ablative reassembling of the silicate, and by a chemical catalytic action due to the silicate and to the strongly acid sites created by thermal decomposition of the protonated amine silicate modifier.     

Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: Evidence for intraionic interactions

Oxidation of cysteine residues to cysteic acids in C-terminal arginine-eontaining peptides (such as those derived by tryptic digestion of proteins) strongly promotes the formation of multiple members of the Y? series of fragment ions following low energy collision-activated decomposition (CAD) of the protonated peptides, Removal of the arginine residue abolishes the effect, which is also attenuated by conversion of the arginine to dimethylpyrim-idylornithine. The data indicate the importance of an intraionic interaction between the cysteic acid and arginine side-chains. Low energy CAD of peptides which include cysteic acid and histidine residues, also provides evidence for intraionic interactions. It is proposed that these findings are consistent with the general hypothesis that an increased heterogeneity (with respect to location of charge) of the protonated peptide precursor ion population is beneficial to the generation of a high yield of product ions via several charge-directed, low energy fragmentation pathways. Furthermore, these data emphasize the significance of gas-phase conformations of protonated peptides in determining fragmentation pathways.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

Effects of Gas-Phase Basicity on the Proton Transfer between Organic Bases and Trifluoroacetic Acid in the Gas Phase: Energetics of Charge Solvation and Salt Bridges

The unimolecular dissociation pathways and kinetics of a series of protonated trimer ions consisting of two organic bases and trifluoroacetic acid were investigated using blackbody infrared radiative dissociation. Five bases with gas-phase basicities (GB) ranging from 238.4 to 246.2 kcal/mol were used. Both the dissociation pathways and the threshold dissociation energies depend on the GB of the base. Trimers consisting of the two most basic molecules dissociate to form protonated base monomers with an E(0) ~ 1.4 eV. Trimers consisting of the two least basic molecules dissociate to form protonated base dimers with an E(0) ~ 1.1-1.2 eV. These results indicate that the structures of the trimers change as a function of the GB of the basic molecule. The predominant structure of the protonated trimers consisting of the two most basic molecules is consistent with a salt bridge in which both of the basic molecules are protonated, and the trifluoroacetic acid molecule is deprotonated, whereas the predominant structure of the protonated trimers consisting of the two least basic molecules are consistent with charge-solvated complexes in which the proton is shared. The structure of the trimer consisting of the base of intermediate basicity is less clear; it dissociates to form primarily protonated base dimer, but has an E(0) ~ 1.2 eV. These results are consistent with the structure of this trimer as a salt bridge, but the resulting dissociation A(-). BH(+) product does not appear to be stable as an ion pair in the dissociative transition state.     

Dissociative electron-ion recombination of the interstellar species protonated glycolaldehyde, acetic acid, and methyl formate

Recently, methyl formate, glycolaldehyde, and acetic acid have been detected in the Interstellar Medium, ISM. The rate constants, α(e), for dissociative electron-ion recombination of protonated gycolaldehyde, (HOCH(2)CHO)H(+), and protonated methyl formate, (HCOOCH(3))H(+), have been determined at 300 K in a variable temperature flowing afterglow using a Langmuir probe to obtain the electron density. The recombination rate constants at 300 K are 3.2 × 10(-7) cm(3) s(-1) for protonated methyl formate and 7.5 × 10(-7) cm(3) s(-1) for protonated glycolaldehyde. The recombination rate constant of protonated acetic acid could not be directly measured, but it appears to have a rate constant, α(e), on the 10(-7) cm(3) s(-1) scale. Several high- and low-temperature measurements for protonated methyl formate were made. In addition, an α(e) measurement at 220 K for protonated glycolaldehyde was performed. The astrochemical implications of the rates of recombination, α(e), and protonation routes are discussed.