Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds

Hyperconjugation in diethyl ether cation versus diethyl sulfide cation

Electron donation from the CH bond to the single occupied orbital is observed through the large red shift in the CH stretching band for the diethyl ether cation.

UV-MALDI mass spectrometric quantitation of uracil based pesticides in fruit soft drinks along with matrix effects evaluation

This study focused on the development of the accurate and precise quantitative method for the determination of pesticides bromacil (1), terbacil (2), lenacil (3), butafenacil (4) and flupropacil (5) in fruit based soft drinks. Three different types of drinks are bought from market; huddled orange fruit drink (100%) (I), red-oranges (II) and multivitamin drink containing strawberry, orange, banana and maracuja (III). Samples were analyzed "with" and "without" pulp utilizing LC-ESI (or APCI) MS/MS, HPLC-ESI-(or APCI)-MS/MS and UV-MALDI-Orbitrap-MS methods. The effect of high complexity of the food matrix on the analysis was discussed. Study focuses on the advantages of the UV-MALDI-Orbitrap-MS method compared to the traditionally involved GC alone or hybrid methods such as GC-MS and LC-MS/MS for quantification of pesticides in water and soft drinks. The developed method included the techniques performed for validation, calibration and standardization. The target pesticides are widely used for the treatment of citrus fruits and pineapples, but for soft drink products, there are still no clear regulations on pesticide residues limits. The matrix effects in the analysis of fruit drinks required implementation of the exact standard reference material corresponds to the variety of food matrices. This paper contributed to the broad analytical implementation of the UV-MALDI-Orbitrap-MS method in the quality control and assessment programs for monitoring of pesticide contamination in fruit based sodas.

Isomer-selective infrared spectroscopy of the cationic trimethylamine dimer to reveal its charge sharing and enhanced acidity of the methyl groups

The isomer-selective infrared spectroscopy revealed the charge-shared (hemibond) and the C⋯HN hydrogen-bond structures of the trimethylamine dimer cation.

Communication: The ionization spectroscopy of mixed carboxylic acid dimers

We report mass analyzed threshold ionization spectroscopy of supersonically cooled gas phase carboxylic complexes with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. The vibrationally resolved cation spectrum for the 9HFCA complex with formic acid allows accurate determination of its ionization potential (IP), 64,374 ± 8 cm(-1). This is 545 cm(-1) smaller than the IP of 9HFCA monomer. The IPs of 9HFCA complexes with acetic acid and benzoic acid shift by -1133 cm(-1) and -1438 cm(-1), respectively. Density functional calculations confirm that Cs symmetry is maintained upon ionization of the 9HFCA monomer and its acid complexes, in contrast to the drastic geometric rearrangement attending ionization in complexes of 9-fluorene carboxylic acid. We suggest that the marginal geometry changes and small IP shifts are primarily due to the collective interactions among one intramolecular and two intermolecular hydrogen bonds in the dimer.

Voltage-gated proton channels: molecular biology, physiology, and pathophysiology of the H(V) family

Voltage-gated proton channels (H(V)) are unique, in part because the ion they conduct is unique. H(V) channels are perfectly selective for protons and have a very small unitary conductance, both arguably manifestations of the extremely low H(+) concentration in physiological solutions. They open with membrane depolarization, but their voltage dependence is strongly regulated by the pH gradient across the membrane (ΔpH), with the result that in most species they normally conduct only outward current. The H(V) channel protein is strikingly similar to the voltage-sensing domain (VSD, the first four membrane-spanning segments) of voltage-gated K(+) and Na(+) channels. In higher species, H(V) channels exist as dimers in which each protomer has its own conduction pathway, yet gating is cooperative. H(V) channels are phylogenetically diverse, distributed from humans to unicellular marine life, and perhaps even plants. Correspondingly, H(V) functions vary widely as well, from promoting calcification in coccolithophores and triggering bioluminescent flashes in dinoflagellates to facilitating killing bacteria, airway pH regulation, basophil histamine release, sperm maturation, and B lymphocyte responses in humans. Recent evidence that hH(V)1 may exacerbate breast cancer metastasis and cerebral damage from ischemic stroke highlights the rapidly expanding recognition of the clinical importance of hH(V)1.

A TDDFT study on the excited-state intramolecular proton transfer (ESIPT): excited-state equilibrium induced by electron density swing

One important issue of current interest is the excited-state equilibrium for some ESITP dyes. However, so far, the information about the driving forces for excited-state equilibrium is very limited. In this work, the time-dependent density functional theory (TDDFT) method was employed to investigate the nature of the excited-state intramolecular proton transfer (ESIPT). The geometric structures, vibrational frequencies, frontier molecular orbitals (MOs) and the potential-energy curves for 1-hydroxy-11H-benzo[b]fluoren-11-one (HHBF) in the ground and the first singlet excited state were calculated. Analysis of the results shows that the intramolecular hydrogen bond of HHBF is strengthened from E to E*. Moreover, it is found that electron density swing between the proton acceptor and donor provides the driving forces for the forward and backward ESIPT, enabling the excited-state equilibrium to be established. Furthermore, we proposed that the photoexcitation and the interchange of position for electron-donating and electron-withdrawing groups are the main reasons for the electron density swing. The potential-energy curves suggest that the forward ESIPT and backward ESIPT may happen on the similar timescale, which is faster than the fluorescence decay of both E* and K* forms.

Molecular beam mass spectrometry with tunable vacuum ultraviolet (VUV) synchrotron radiation

Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics(1-4). Fundamental studies of photoionization processes of biomolecules provide information about the electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water(1, 5-9). We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-dimethyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline(10) located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds(1). Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations(11, 12). By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species (1, 3).

Candida species: new insights into biofilm formation

Biofilms of Candida albicans, Candida parapsilosis, Candida glabrata and Candida tropicalis are associated with high indices of hospital morbidity and mortality. Major factors involved in the formation and growth of Candida biofilms are the chemical composition of the medical implant and the cell wall adhesins responsible for mediating Candida-Candida, Candida-human host cell and Candida-medical device adhesion. Strategies for elucidating the mechanisms that regulate the formation of Candida biofilms combine tools from biology, chemistry, nanoscience, material science and physics. This review proposes the use of new technologies, such as synchrotron radiation, to study the mechanisms of biofilm formation. In the future, this information is expected to facilitate the design of new materials and antifungal compounds that can eradicate nosocomial Candida infections due to biofilm formation on medical implants. This will reduce dissemination of candidiasis and hopefully improve the quality of life of patients.

Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer

Benchmark calculations of the lowest ionized state of the (A:T)2 (mixed adenine-thymine) cluster at the geometry taken from the DNA X-ray structure are presented. Vertical ionization energies (IEs) computed by the equation-of-motion coupled-cluster method with single and double substitutions are reported and analyzed. The shift in IE relative to the monomer (A) is -0.7 eV. The performance of the widely used B3LYP, ωB97X-D, and M06-2X functionals with respect to their ability to describe energetics and the character (localization versus delocalization) of the ionized states is also investigated. The shifts in IEs caused by H-bonding and stacking interactions are analyzed in terms of additive versus cooperative effects. It is found that the cooperative effect accounts for more than 20% of the shift in IE relative to the monomer. The cooperative effect and, consequently, the magnitude of the shift are well reproduced by the hybrid quantum mechanics/molecular mechanics scheme in which neutral thymine bases are represented by point charges.