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.     

The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin

The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base in bR, the results show that Asp₈₅ and Asp₂₁₂, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced by the presence of the neighboring amino acids. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Ab initioMO investigation of the ethanolamine–formic acid complex

The title complex is considered a model for the interaction of catecholamine-type ligands with anionogenic sites of receptors. It is usually assumed that the ligands interact in the protonated form, but there is no direct evidence of this. Model computations of proton transfer processes should contribute to the elucidation of this important problem. As a first step in this direction we have made computations in the STO-4G base of the interaction energies, molecular electrostatic potentials, the proton potential curves, and the Mulliken population for three different arrangements of the acid and base molecules. Proton potential functions have also been computed for the complexes with two water molecules attached to the acid. The deeper potential well is nearer to the carboxylic oxygen in all cases examined.     

Interaction of chromophore, 11-<Emphasis Type="Italic">cis</Emphasis>-retinal,with amino acid residues of the visual pigment rhodopsin in the region of protonated Schiff base: A molecular dynamics study

A molecular dynamics study of the dark adapted visual pigment rhodopsin molecule was carried out. The interaction of the chromophore group, 11-cis-retinal, with the nearest amino acid residues in the chromophore center of the molecule, namely, in the region of the protonated Schiff base linkage, was analyzed. Most likely, the interaction of the CH=NH bond with the negatively charged amino acid residue Glu113 cannot be described as a simple electrostatic interaction of two oppositely charged groups. One can propose that not only Glu113 but also Glu181 and Ser186 are involved in stabilization of the protonated Schiff base linkage. Accord-ing to calculations, Glu181 interacts, as the counter-ion, with the Schiff base indirectly via Ser186. The intramolecular mechanisms of protonated Schiff base stabilization in rhodopsin are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 19–27, January, 2007.     

Reducing fragmentation observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of triacylglycerols in vegetable oils

Edible oils consist primarily of triacylglycerols (TAGs). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra of the oils are typically dominated by sodium adducts of these TAGs but also show prominent fragment ions (that do not contain sodium), which can interfere with analytical measurements of other components in oils. The fragments seemingly correspond to the loss of a fatty acid moiety from the sodiated TAGs as a sodium salt: RCOONa. However, a previous study suggested that the fragments actually arise from nearly complete fragmentation of unseen protonated TAGs. These authors suggested that the fragmentation occurs so rapidly and completely that protonated TAGs are not normally observed in the spectra of these oils. In this paper, we present evidence to support their theory and also demonstrate an approach to eliminate these interfering ions from the MALDI-TOF mass spectra via addition of a base to the matrix/sample mixture. The added base does not impede formation of the sodiated TAGs, but does significantly reduce the amount of fragments observed. We propose that this occurs by depleting the H+ ions from the matrix, thus preventing the formation of significant numbers of protonated TAGs in the first place. For measurements by MALDI-TOF, the relative abundances of the fragment ions are related to the strength of the base, and can be almost completely eliminated. However, in longer time-scale experiments such as in post-source decay and Fourier transform mass spectrometry, sodiated and non-sodiated diacylglycerol (DAG)-like fragments are present in spectra, regardless of whether or not a base is added to the sample.     

Intramolecular catalysis in the mass spectrometer: Mechanisms for loss of methanol from methyl esters upon electron-impact

A review of the literature indicates compelling evidence that: (1) loss of ROH from esters requires protonation of the alkoxy oxygen; (2) the (symmetry forbidden) [1,3] hydrogen migration from protonated carbonyl to alkoxy oxygen does not occur in the mass spectra of esters; (3) hydrogen abstraction in esters occurs almost exclusively to the carbonyl oxygen. Mechanisms are proposed which account for all examples of ROH loss from esters. Alkanol loss from molecular ions in esters requires the presence of a second functional group to act as an intramolecular catalyst, either as a general acid in transferring a proton to the alkoxy oxygen, or as a general base in assisting the [1,3] carbonyl oxygen to alkoxy oxygen proton transfer. Loss of ROH from fragment ions requires proton transfer from an atom α to the positive charge to the alkoxy oxygen. These mechanisms are generalized to include a wide class of bifunctional esters and a selection of natural products.     

A POSSIBLE MECHANISM FOR THE ROLE OF N-RETINYLIDENE PHOSPHATIDYL ETHANOLAMINE IN THE REGENERATION OF RHODOPSIN

Abstract— A series of molecular orbital calculations on a model Schiff base comparable to protonated N -retinylidene phosphatidyl ethanolamine isomers has been made. The effect of the charged oxygen atoms of the phosphate moiety on the distribution of positive charge along the polyene chain of these isomers has been calculated. The stabilizing coulombic energy of interaction of these opposite charges and the possibility of free rotation around carbonxarbon double bonds in the electronically excited state has led to the conclusion that an 11- cis Schiff base isomer is the most probable product of the photoisomerization of an all-trans Schiff base.
The formation of a stable unprotonated all-trans Schiff base in aqueous detergent dispersion and its subsequent conversion to the protonated form, both with absorption spectra in conformity with the literature, is demonstrated.     

Voltammetry of 2,5-diphenyloxazole in acetonitrile-fuming sulfuric acid mixtures

2,5-Diphenyloxazole is protonated by sulfuric acid in acetonitrile solvent. The existence of a simple acid base equilibrium is demonstrated by u.v.—visible spectroscopy. Polarographic and cyclic voltammetric data suggest that the protonated heteroaromatic is reduced in a diffusion-controlled step at potentials slightly less negative than the nonprotonated form.     

THE PHOTOSENSITIZERS BENZOPHENOXAZINE and THIAZINES: COMPREHENSIVE INVESTIGATION OF PHOTOPHYSICAL and PHOTOCHEMICAL PROPERTIES

Eight differently substituted title dye compounds have been investigated regarding intersystem crossing, triplet state, fluorescence and singlet excited state pKa properties. In general, non-halogenated oxazines and thiazines as well as a mono bromooxazine show very low triplet quantum yields, phi tau (less than 0.03) and relatively long triplet lifetimes (approximately 40 microseconds) in acidic methanol. The phi tau data correlate well with known singlet oxygen yields. In basic methanol no triplet transient is observed but a significant yield of a ground state transient protonated (base dye) form is produced with a short lifetime, approximately 400 ns. Fluorescence can be seen simultaneously from both the excited base and the protonated base dye forms in basic methanol. For iodinated oxazine or thiazines, the triplet yield increases and can be as high as 0.5 (diiodo case) in acidic methanol. The triplet lifetimes are further shortened to approximately 10 microseconds compared to the non-iodinated derivatives above. The triplet yields of the iodo compounds are higher or equal to known singlet oxygen yields. In basic methanol triplet yields up to 0.2 can be seen, the triplet lifetime are shortened still further to 1 microsecond but no observable protonated form is produced (in distinction to the non-iodinated cases). Consideration is given to the correlation of triplet and singlet oxygen yields, ground and excited pKa properties, spin-orbit coupling and internal conversion properties, solvent effects, and phototherapeutic activity of these dyes.     

Kinetics of Hydrolysis of Some Bifunctional Schiff Bases

Kinetics of hydrolysis of some bifunctional Schiff bases, bis(x-benzylidenes)-o-phenylenediamine, have been investigated in aqueous media containing 0.1 mole fraction of ethanol under base and acid conditions. Under base conditions the rate determining step is the hydroxide ion attack on the protonated substrate while under weak acid conditions the attack of water rather than hydroxide ion on the protonated substrate becomes the predominant reaction pathway. The bifunctional Schiff base molecular structure-base or acid hydrolysis reactivity relationship has been examined and discussed. Effect of medium (water content and nature of organic solvents) has been investigated and it is deduced that specific solute-solvent interactions, namely the proton-solvent, play a vital role on such hydrolysis reaction.     

Proton affinity of β-oxalylaminoalanine (BOAA): Incorporation of direct entropy correction into the single-reference kinetic method

A new version of the single-reference-extended kinetic method is presented in which direct entropy correction is incorporated. Results of calibration experiments with the monodentate base pyridine and the bidentate base ethylenediamine are presented for which the method provides proton affinities in excellent agreement with published values and reasonable predictions for the protonation entropies. The method is then used to determine the proton affinity and protonation entropy of the non-protein amino acid beta-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 +/- 7.8 kJ/mol and a prediction for the protonation entropy of -39 J mol(-1) K(-1) is also obtained, indicating a significant degree of intramolecular hydrogen bonding in the protonated form. These results are supported by hybrid density functional theory calculations at the B3LYP/6-311++G**//B3LYP/6-31+G* level. They indicate that the preferred site of protonation is the alpha-nitrogen atom (PA = 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the alpha-amino group and one of the carbonyl oxygen atoms on the side chain.     

Protonation Switching to the Least‐Basic Heteroatom of Carbamate through Cationic Hydrogen Bonding Promotes the Formation of Isocyanate Cations

We found that phenethylcarbamates that bear ortho‐salicylate as an ether group (carbamoyl salicylates) dramatically accelerate O?C bond dissociation in strong acid to facilitate generation of isocyanate cation (N‐protonated isocyanates), which undergo subsequent intramolecular aromatic electrophilic cyclization to give dihydroisoquinolones. To generate isocyanate cations from carbamates in acidic media as electrophiles for aromatic substitution, protonation at the ether oxygen, the least basic heteroatom, is essential to promote C?O bond cleavage. However, the carbonyl oxygen of carbamates, the most basic site, is protonated exclusively in strong acids. We found that the protonation site can be shifted to an alternative basic atom by linking methyl salicylate to the ether oxygen of carbamate. The methyl ester oxygen ortho to the phenolic (ether) oxygen of salicylate is as basic as the carbamate carbonyl oxygen, and we found that monoprotonation at the methyl ester oxygen in strong acid resulted in the formation of an intramolecular cationic hydrogen bond (>C?O⁺?H???O<) with the phenolic ether oxygen. This facilitates O?C bond dissociation of phenethylcarbamates, thereby promoting isocyanate cation formation. In contrast, superacid‐mediated diprotonation at the methyl ester oxygen of the salicylate and the carbonyl oxygen of the carbamate afforded a rather stable dication, which did not readily undergo C?O bond dissociation. This is an unprecedented and unknown case in which the monocation has greater reactivity than the dication.     

Theoretical investigation of the π -electronic structure and spectra of protonated aromatic carbonyl compounds

The π-electronic structure and spectra of the protonated aromatic carboxylic acids, aldehydes and ketones have been calculated by the Pariser–Parr–Pople method. An essential modification was that the positive charge has been considered as delocalized within the substituent group. The best agreement for the cation of benzoic acid was obtained using a symmetric carboxy model with equal charges on both oxygen atoms. This model gave equally good results for the protonated fluoro-, chloro- and methylbenzoic acids, as well. The delocalized charge model was successfully applied in the calculation of aromatic aldehydes and ketones. The methyl group was treated both as a one- and as a two-centre substituent.     

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.     

PHOTO-INDUCED ELECTRON TRANSFER FROM NUCLEOTIDES TO RUTHENIUM-TRIS-1,4,5,8TETRAAZAPHENANTHRENE: MODEL FOR PHOTOSENSITIZED DNA OXIDATION

The luminescence quenching of ruthenium-tris-1,4,5,8-tetraazaphenanthrene [Ru(tap)3(2+)] by nucleotides approaches the diffusion rate only with guanosine-5'-monophosphate (GMP), the most reducing nucleotide, and leads to an electron transfer with the production of the monoreduced complex and the oxidized base. The resulting deprotonated GMP(-H).radical recombines with the monoreduced complex according to a bimolecular equimolar process. The pH dependence of the decay of the transient reduced complex, in the presence of an oxidant (oxygen or benzoquinone) indicates the formation of Ru(tap)2(tapH)2+, i.e. the reduced protonated species, subsequent to the electron transfer, with a pKa of 7.6 as confirmed from pulse radiolysis experiments. As the non-protonated reduced complex, Ru(tap)2(tap-.)+, has a higher reducing power than the protonated one, oxygen is able to reoxidize only the non-protonated species, whereas benzoquinone reoxidizes both species but with different rate constants. The flash photolysis of Ru(tap)3(2+) in the presence of DNA and the effect of Mg2+ ions and GMP as supplementary additives also show the existence of a photo-induced electron transfer with the nucleic acid, which can be correlated to the photosensitized cleavage of DNA by this complex.     

PREPARATION AND PURIFICATION OF SCHIFF BASE AND PROTONATED SCHIFF BASE FROM 9-CIS-RETINAL

A modified method for preparation and purification of Schiff base and protonated Schiff base from 9-cis-retinal has been suggested. Reaction took place in chloroform phase and purification was conducted by using water to remove the excess solvent, base and acid.     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.     

The effect of electron-withdrawing properties of substituents on the hydrolysis of some Schiff bases

The dissociation kinetics of the Schiff bases investigated in the present paper [N,N-bis(X-benzylidenes)ethylenediamine], have been examined under basic and acidic conditions, in aqueous medium 25% acetone in water (wt-wt). The base hydrolysis reaction of these compounds was found to follow second-order kinetics, first-order with respect to each of the Schiff base and the hydroxide ions. The rate-determining step is suggested to be the hydroxide ions attack on the free base. The effect of acetone ratio, in hydrolysis medium, has been studied under alkaline conditions. It is deduced that both the hydrogen bonding formation and solvent-solvent interaction have a pronounced role in such hydrolysis reactions. The acid hydrolysis reaction is strictly second-order kinetics, first-order with respect to the Schiff base and also to the hydrogen ions, and the attack of water molecules on the protonated substrate becomes the rate-determining step. A slower rate of the base hydrolysis was observed through the Schiff base II (p-NO₂), on the other hand, a fast acid hydrolysis rate was detected in the case of compound III (p-COOH). Furthermore, from the effect of temperature on the reaction rate, the various thermodynamic parameters have been also calculated and discussed.     

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.     

Surface modification of aromatic polyamide film by oxygen plasma

The surface of poly(p-phenylene terephthalamide) (PPTA) films was modified by oxygen plasma, and the modified film surface was analyzed by an advancing contact meter and X-ray photoelectron spectroscopy (XPS). The advancing contact measurement showed that the oxygen plasma treatment made the surface of the PPTA film hydrophilic. The XPS analyses also showed the increase in the O/C and N/C atom ratio, especially the O/C atom ratio, at the PPTA film surface by the oxygen plasma treatment. A main oxygen functionality formed by the oxygen plasma treatment is a carboxylic acid group, and a main nitrogen functionality formed is a protonated amino group. The formation of the oxygen and nitrogen functionalities formed by the oxygen plasma treatment is not restricted to the surface of the PPTA film, but penetrates at least 35 Å deep from the film surface. The formation of these carboxylic acid and protonated amino groups is a result of the bond scission of the amide linkages in the PPTA film. Interactions of photons in the oxygen plasma rather than interactions of electrons and activated oxygen atoms contribute greatly to the bond scission. © 1995 John Wiley & Sons, Inc.