Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.     

Dynamic 19F NMR studies The torsional barrier in pentafluorobenzaldehyde,its conjugate acid and protonated pentafluoroacetophenone

An upper limit of the barrier to internal rotation around the phenyl-carbonyl bond in pentalfluorobenzaldehyde dissolved in a freon mixture has been estimated from low temperature ₁₉F NMR study. Protonation of this compound increases drastically the free energy of activation ΔG≠. Complete lineshape analysis leads to ΔG≠ (273 K) = 60.4 kJ/mol, comparable to the value obtained for protonated benzaldehyde. This result, as well as those obtained by CNDO/2 calculations support the conclusions that protonated pentafluorobenzaldehyde is planar in the ground state. This is not the case for protonated pentafluoroacetophenone in which the lower barrier height when compared to protonated acetophenon has been related to the steric strain and dipole repulsion.     

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.     

Electrophoretic investigation of the boron cluster anion [7-(2'-pyridyl)-nido-7,8-dicarbaundecaborate]- and its protonated zwitterionic product

ACN is a better solvent than methanol for both [NMe(4)] [7-(2'-pyridyl)-nido-7,8-C(2)B(9)H(11)] and its protonated anion. The investigated laboratory preparations of the salt and of its protonated anion are electrophoretically pure solids stable for 2 months at 4 degrees C. At a longer storage, the solid salt is more stable than the solid protonated anion. In the 40:60 v/v water-methanol solvent, decomposition products of the salt anion are detectable after one-week storage of the salt solution at 4 degrees C. The protonated anion does not decompose for almost 1 year in water-organic solutions at 4 degrees C. The exchange of the proton between the protonated anion and the solution is reversible and fast at room temperature. The pH dependence of the mobility of the [7-(2(-pyridyl)-nido-7,8-C(2)B(9)H(11)](-) anion reveals that the basicity of the nitrogen atom in the pyridine ring is not significantly affected by the bonding of the pyridyl group to the nido-7,8-C(2)B(9)H(11) cluster in position 7 and that the proton from the solution is accepted by the nitrogen atom in the 2-pyridyl ring. The UV-spectra of the salt and of its protonated anion indicate that the accepted proton is probably slightly shifted to the open face of the nido-7,8-C(2)B(9)H(11) cluster. The [1](-) is chiral.     

Theoretical studies on the protonation behavior of tropone and its metal complexes

Density functional theory calculations were carried out to investigate structures and stabilities of tropone and troponeiron complexes, (tropone)Fe(CO)₃, (tropone)Fe(CO)₂(PH₃) and (tropone)Fe(PH₃)₃, and their protonated species. The results show that the oxygen-protonated tropone is more stable than the carbon-protonated tropone. On the contrary, in the troponeiron complexes, the carbon protonated species are more stable than the oxygen protonated species. In the neutral and oxygen-protonated complexes, the tropone and oxygen-protonated tropone ligands are η⁴-coordinated. In the carbon-protonated complexes, the carbon-protonated tropone ligand is η⁵-coordinated. The results also show that the metal shift for complexes containing phosphine ligands is more difficult than that for those containing carbonyl ligands. For the neutral methyl-substituted troponeiron complexes, steric effect was found to play a key role in determining the relative stability of the regioisomers. For their protonated species, the electron-donating properties of the methyl substituent(s) were found to be important in determining the relative stability among the different regioiosmers.     

Primaquine diphosphate and its cation radical: a spectrochemical investigation

Primaquine diphosphate (PQD) and its oxidation product have been studied by visible—UV, Raman and EPR spectroscopy as well as cyclic voltammetry. It is shown that the doubly protonated form of the drug is oxidized to a radical that absorbs strongly in the visible region (552 nm). Such a species is highly reactive, and its time-decay is mainly due to its interaction with the non-oxidized drug. Another radical can be generated at higher pH, possibly originating from the singly protonated form of the drug.     

Spectroscopic characterization of aminoacetonitrile,its ions and protonated aminoacetonitrile using quantum chemical methods

We present theoretical vibrational and absorption spectra of aminoacetonitrile, its cation, anion, cyanoprotonated, and aminoprotonated aminoacetonitrile. We used second‐order Moller–Plesset perturbation method (MP2) with TZVP basis set to obtain ground state geometries and vibrational spectra. Time dependent density functional theory method was used to obtain absorption spectra. Shifts in vibrational modes for aminoacetonitrile upon ionization and protonation are determined. The C≡N stretching mode which is the most important mode in detection of nitriles in space is more intense in aminoacetonitrile ions and its two protonated form and is less IR active for neutral aminoacetonitrile. The nature of electronic transition for these molecules is identified. All the electronic transitions for neutral aminoacetonitrile and its cation are the σ → σ* electronic transitions, whereas its anion and protonated aminoacetonitrile display the σ → σ* as well as π → π* transitions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Factors affecting relative stabilities and proton affinities of oxazolidinone and its N,C5-formyl derivatives

The proton affinities of all the potential sites of oxazolidinone (OXA) and formyl substituted OXA have been evaluated using ab initio and DFT methods. N4- and C5-formyl oxazolidinone isomers and their protonated structures have been analyzed for relative stabilities. The proton affinity (PA) of carbonyl oxygen of oxazolidinone is observed to be highest in un-substituted and formyl substituted OXA molecules. The PA values decrease for the potential sites in the range 0.5–15.51 kcal/mol as a result of the presence of the formyl substituent. Atomic charges and electron delocalization of neutral and protonated species have been analyzed with the application of NBO. The various factors such as variation in geometrical parameters, atomic charge redistribution, alterations in conjugative interactions, effect of formyl substituent, the presence of intramolecular hydrogen bonding and electronic effects have been explored to rationalize the relative stabilities and proton affinities of OXA and its N,C5 formyl derivatives.     

Interaction of guanine, its anions, and radicals with lysine in different charge states

Modification in DNA or protein structure can severely affect DNA-protein interactions and the functioning of biological systems. Some new insights into radiation-induced effects of guanine-lysine interactions have been obtained here by theoretical investigations. Geometries of zwitterionic and non-zwitterionic lysine in different charge states (neutral, radical cation, and protonated cation) were optimized employing the B3LYP/6-31G** and B3LYP/AUG-cc-pVDZ levels of hybrid density functional theory (DFT) and using the second-order M?ller-Plesset perturbation theory along with the 6-31G** basis set. In the case of neutral lysine in the gas phase, no zwitterionic structure was obtained. The non-zwitterionic structures of lysine in radical and protonated cationic forms are appreciably more stable than the corresponding zwitterionic structures in the gas phase as obtained at all levels of theory employed here. Binding of guanine and different dehydrogenated guanine radicals with lysine in different charge states was studied at the B3LYP/6-31G** level of DFT. When guanine makes a complex with the lysine radical cation, large amounts of spin and positive charge densities are transferred from the lysine radical cation to guanine and the guanine is thus converted from its normal form to the radical cationic form. Complexation of the lysine radical cation with the H1-hydrogen-abstracted guanine radical leads to CO2 liberation and proton transfer from lysine. These results are compared with the available experimental ones.     

Structure effects of the protonated lincomycin molecule on the mechanism of its complexation with organic compounds

The mechanism of complexation of the protonated lincomycin molecule with para-substituted nitrobenzenes in the gas phase is analyzed by quantum chemical methods. The regioselectivity of lincomycin protonation is treated in a B3LYP/6-31G(d′, p) approximation; the geometrical structure and conformation of the molecule are analyzed. The lincomycin molecule is protonated at the nitrogen atom of the pyrrolidine cycle. In stable conformers, a pseudovoid is formed and stabilized by intramolecular hydrogen bonding. The cross section of the pseudovoid (1.77–2.62 Å) is too small for the protonated lincomycin molecule to participate in host guest complexation with organic compounds. According to B3LYP/6-31G(d′, p) calculations, complexation of the protonated lincomycin molecule with nitrobenzenes occurs through hydrogen bonding.     

Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with ab initio theory

We have carried out extensive calculations for neutral, cationic protonated, anionic deprotonated phenol dimers. The structures and energetics of this system are determined by the delicate competition between H-bonding, H-π interaction and π-π interaction. Thus, the structures, binding energies and frequencies of the dimers are studied by using a variety of functionals of density functional theory (DFT) and M?ller-Plesset second order perturbation theory (MP2) with medium and extended basis sets. The binding energies are compared with those of highly reliable coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit. The neutral phenol dimer is unique in the sense that its experimental rotational constants have been measured. The geometry of the neutral phenol dimer is governed by the hydrogen bond formed by two hydroxyl groups and the H-π interaction between two aromatic rings, while the structure of the protonated/deprotonated phenol dimers is additionally governed by the electrostatic and induction effects due to the short strong hydrogen bond (SSHB) and the charges populated in the aromatic rings in the ionic systems. Our salient finding is the substantial differences in structure between neutral, protonated, and deprotonated phenol dimers. This is because the neutral dimer involves in both H(π)···O and H(π)···π interactions, the protonated dimer involves in H(π)···π interactions, and the deprotonated dimer involves in a strong H(π)···O interaction. It is important to compare the reliability of diverse computational approaches employed in quantum chemistry on the basis of the calculational results of this system. MP2 calculations using a small cc-pVDZ basis set give reasonable structures, but those using extended basis sets predict wrong π-stacked structures due to the overestimation of the dispersion energies of the π-π interactions. A few new DFT functionals with the empirical dispersion give reliable results consistent with the CCSD(T)/CBS results. The binding energies of the neutral, cationic protonated, and anionic deprotonated phenol dimers are estimated to be more than 28.5, 118.2, and 118.3 kJ mol(-1), respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.     

Raman, SERS and theoretical studies of papaverine hydrochloride and its neutral species

Density functional theory (DFT) calculations and an experimental vibrational characterization of papaverine hydrochloride were performed. The computed structural parameters agree very well with the experimental values of the related crystal structure. The pH dependent Raman and SERS spectra of papaverine hydrochloride were recorded and discussed with the assistance of our theoretical results (harmonical vibrational wavenumbers, Raman scattering activities, total electron density and Natural Population Analysis of the molecule) and the SERS surface selection rules. Two different adsorption geometries were found for the corresponding evidenced species of papaverine, protonated and neutral, respectively.     

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.     

High- and low-energy collisionally activated decompositions of octaethylporphyrin and its metal complexes

High-energy (HE) and low-energy (LE) collisionally activated decompositions of octaethylporphyrin (OEP) and its metal complexes (ZnOEP and CuOEP) depend on whether the precursor is produced by electrospray ionization as protonated molecules or by fast atom bombardment as radical cations or protonated molecules. LE activation leads to such simple product-ion spectra that a complete picture of fragmentation emerges only after nine stages of tandem mass spectrometry (MS⁹). HE activation, on the other hand, gives product-ion spectra that afford an integrated view of all the decomposition channels in a single MS/MS experiment. These results are the basis of a recommendation that OEP is an appropriate model compound for investigating energy effects in the collisional activation of organic and bioorganic molecule ions.     

Dissolution of copper phthalocyanine and fabrication of its nano-structure film

The mono-protonated and di-protonated forms of copper phthalocyanine (CuPc) were obtained by increasing concentrations of trifluoroacetic acid (TFA) solution to a fixed concentration of CuPc solutions. UV-Vis spectrum shows that the Q bands of these two derivatives split and shift to the red, which means successive protonation happened and caused the two derivatives to lose their symmetry. After the protonation step, the solubility of protonated CuPc in organic solvent increased 60 times. The CuPc film was fabricated by the electrophoretic deposition (EPD) method from the protonated CuPc dissolved in nitromethane containing TFA. Scanning electron microscopy (SEM) showed that the deposited CuPc film on the indium tin oxide (ITO) substrate is composed of thread-like nanobelts with diameters between 100 nm and 200 nm. Furthermore, the CuPc film is in α phase with stacking direction (b-axis) parallel to the substrate, which was detected by X-ray diffraction.     

Structural aspects of phencyclidines: crystal structure and quantum mechanical calculations for 1-[1-(2-thienyl)cyclohexyl] piperidine and its hydrochloride

Crystal structure determinations for neutral and protonated phencyclidine, 1-[1-(2-thienyl)cyclohexyl] piperidine, show that the piperidine-axial conformer on the cyclohexane ring is present in the neutral compound, and that the piperidine-equatorial conformer in the protonated species. Quantum mechanical calculations in vacuo using ab initio techniques also arrive at the same conclusion. A search of the crystallographic literature via the Cambridge structural database reveals that all protonated phencyclidines assume the piperidine-equatorial conformation, and most neutral phencyclidines assume the piperidine-axial conformation.     

Gas phase infrared multiple-photon dissociation spectra of methanol, ethanol and propanol proton-bound dimers, protonated propanol and the propanol/water proton-bound dimer

The infrared multiphoton dissociation (IRMPD) spectra of three homogenous proton-bound dimers are presented and the major features are assigned based on comparisons with the neutral alcohol and with density functional theory calculations. As well, the IRMPD spectra of protonated propanol and the propanol/water proton-bound dimer (or singly hydrated protonated propanol) are presented and analysed. Two primary IRMPD photoproducts were observed for each of the alcohol proton bound dimers and were found to vary with the frequency of the radiation impinging upon the ions. For example, when the proton-bound dimer absorbs weakly a larger amount of S(N)2 product, protonated ether and water, are observed. When the proton-bound dimer absorbs more strongly, an increase in the simple dissociation product, protonated alcohol and neutral alcohol, is observed. With the aid of RRKM calculations this frequency dependence of the branching ratio is explained by assuming that photon absorption is faster than dissociation for these species and that only a few photons extra are necessary to make the higher-energy dissociation channel (simple cleavage) competitive with the lower energy (S(N)2) reaction channel.     

Distribution mechanism of protonated l,10-phenanthroline between unbuffered aqueous and 1,2-dichloroethane phases

The faradaic ion transfer of protonated l.iO-phenanthroline [H(Phen)+] across the interface between unbuffered aqueous and 1,2-dichloroethane (DCE) solutions was investigated by means of current scan polarography at ascending aqueous electrolyte electrode, as well as chronopotentiometry. It follows from the splitting of the waves observed at the pH of aqueous phase (sodium sulfate solution) between 2.5–3.8 that neutral reagent (Phen) distributes into the aqueous phase, where it is protonated. The positive wave is associated with the mass transfer controlled by the H+influx, whereas the negative one is by the Phen influx. The reverse chronopotentiometry indicated that all the protonated transfer processes were reversible. A good agreement between experimental results and theoretical treatment was achieved. The aqueous acid dissociation constant of protonated Phen, K₂ can be evaluated from the dependence of the wave heights on the pH in the base of the equilibrium.     

A fragmentation study of podophyllotoxin and its 4'-demethyl-4beta-substituted derivatives by electrospray ionization ion-trap time-of-flight tandem mass spectrometry

High-resolution electrospray ionization multistage tandem mass spectrometry (MS(1-9)) was used to determine the accurate masses and the fragmentation pathways of protonated podophyllotoxin (1) and its corresponding 4'-demethyl-4beta-substituted derivatives (2-4). The protonated molecules, [M + H](+), of all the four compounds were observed in the conventional single-stage mass spectra. Two fragmentation pathways, that appear to be characteristic of the four compounds, are proposed on the basis of their multistage tandem mass spectrometric data. The characteristic elimination, from the precursor protonated ions, of the neutral groups 4-R(1)H, 1-ArH, CO, CH(2)O and C(4)H(4)O(2), in which R is located on C-4, is the common elimination, and the product ions at m/z 267, 239, 229, 181, 173, 153, 143 and 115 are the common diagnostic masses. The elimination of the R(1) group substituent located on the C-4 position of compounds 1-4 has a significant influence on the fragmentation pathway obtained in the conventional single-stage mass spectra. A large R(1) group would be unfavorable for this elimination, unless the collision energy is raised. Apart from the common fragmentations obtained for the protonated molecules 1-4, significant additional product ions were detected in the various multistage tandem mass spectrometric analyses, particularly in the case of the product ions derived initially from the phenolic hydroxyl group of 2-4, which are different from those of 1. Based on these additional formed product ions, several additional fragmentation pathways for 1 or 2-4 are also presented.