Different chemical dynamics for different conformers of biological molecules: photoionization of glycine

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Longitudinal Relaxation Enhancement in 1H NMR Spectroscopy of Tissue Metabolites via Spectrally Selective Excitation

Nuclear magnetic resonance spectroscopy is governed by longitudinal (T₁) relaxation. For protein and nucleic acid experiments in solutions, it is well established that apparent T₁ values can be enhanced by selective excitation of targeted resonances. The present study explores such longitudinal relaxation enhancement (LRE) effects for molecules residing in biological tissues. The longitudinal relaxation recovery of tissue resonances positioned both down‐ and upfield of the water peak were measured by spectrally selective excitation/refocusing pulses, and compared with conventional water‐suppressed, broadband‐excited counterparts at 9.4 T. Marked LRE effects with up to threefold reductions in apparent T₁ values were observed as expected for resonances in the 6–9 ppm region; remarkably, statistically significant LRE effects were also found for several non‐exchanging metabolite resonances in the 1–4 ppm region, encompassing 30–50 % decreases in apparent T₁ values. These LRE effects suggest a novel means of increasing the sensitivity of tissue‐oriented experiments, and open new vistas to investigate the nature of interactions among metabolites, water and macromolecules at a molecular level.     

Improved depiction of small anatomic structures in MR images using Gaussian-weighted spirals and zero-filled interpolation

Partial-volume artifacts reduce the contrast and continuity of small structures in magnetic resonance images. Zero-filled interpolation (ZFI) has been known for some time as a useful technique to reduce partial-volume artifacts and improve the appearance of small structures and edges. However, its use is limited by the fact that ZFI can exacerbate image artifacts. For example, it can exacerbate Gibbs ringing, also known as the truncation artifact, which manifests itself as spurious ringing around sharp edges. Currently, the most common technique to address this problem is post-acquisition filtering, which causes blurring in the image. Using ZFI in conjunction with a variable-density sampling method designed to reduce ringing is proposed as a possible solution to this problem. This approach is demonstrated with a Gaussian-weighted spiral and is compared to conventional spiral sampling both with and without the application of a filter used to reduce ringing. The two spiral sampling techniques are compared using simulations, phantom images, and in vivo brain images. The Gaussian-weighted spiral demonstrates reduced ringing without the loss of spatial resolution commonly associated with post-acquisition filtering. Additionally, this sampling technique is shown to work well in conjunction with ZFI to reduce partial-volume artifacts without the apparent increase in Gibbs ringing usually associated with zero-filled reconstruction. This approach will be most useful for imaging techniques such as MR angiography which are known to be sensitive to partial-volume effects, as well as when imaging anatomic regions associated with more severe Gibbs ringing.     

Overcoming apparent susceptibility-induced anisotropy (aSIA) by bipolar double-pulsed-field-gradient NMR

Double-Pulsed-Field-Gradient (d-PFG) MR is emerging as a powerful new means for obtaining unique microstructural information in opaque porous systems that cannot be obtained by conventional single-PFG (s-PFG) methods. The angular d-PFG MR methodology is particularly important since it can utilize the effects of microscopic anisotropy (μA) and compartment shape anisotropy (csA) in the E(ψ) profile at the different t_m regimes to provide detailed information on compartment size and eccentricity. An underlying assumption is that the PFGs that are imparted to weigh diffusion are the only gradients present; however, in realistic systems and especially where there are randomly oriented anisotropic pores, susceptibility effects may induce strong internal gradients. In this study, the effects of such internal gradients on E(ψ) plots obtained from angular d-PFG MR and on microstructural information that can be obtained from s-PFG and d-PFG MR were investigated. First, it was found that internal gradients induce a bias in the s-PFG MR results, thus creating an anisotropy that is not related to microstructure, termed apparent-Susceptibility-Induced-Anisotropy (aSIA). We then show that aSIA effects are also manifest in different ways in the angular d-PFG MR experiment in controlled phantoms and in realistic systems such as quartz sand, emulsions, and biological systems. The effects of aSIA in some cases completely masked the effects of μA and csA; however, we subsequently show that by introducing bipolar gradients to the d-PFG MR (bp-d-PFG), the effects of aSIA can be largely suppressed, restoring the E(ψ) plots that are expected from the theory along with the microstructural information that it conveys. We conclude that when specimens are characterized by strong internal gradients, the novel information on μA and csA that is manifest in the E(ψ) plots can indeed be inferred when bp-d-PFG MR is used, i.e. when bipolar gradients are applied.     

Whole‐Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample

Metagenomic studies suggest that only a small fraction of the viruses that exist in nature have been identified and studied. Characterization of unknown viral genomes is hindered by the many genomes populating any virus sample. A new method is reported that integrates drop‐based microfluidics and computational analysis to enable the purification of any single viral species from a complex mixed virus sample and the retrieval of complete genome sequences. By using this platform, the genome sequence of a 5243 bp dsDNA virus that was spiked into wastewater was retrieved with greater than 96 % sequence coverage and more than 99.8 % sequence identity. This method holds great potential for virus discovery since it allows enrichment and sequencing of previously undescribed viruses as well as known viruses.     

Antibacterial and antifungal LDPE films for active packaging

Active antimicrobial packaging is a promising form of active packaging that can kill or inhibit microorganism growth in order to maintain product quality and safety. One of the most common approaches is based on the release of volatile antimicrobial agents from the packaging material such as essential oils. Due to their highly volatile nature, the challenge is to preserve the essential oils during the high‐temperature melt processing of the polymer, while maintaining high antimicrobial activity for a desired shelf life. This study suggests a new approach in order to achieve this goal. Antimicrobial active films are developed based on low‐density polyethylene (LDPE), organo‐modified montmorillonite clays (MMT) and carvacrol (used as an essential oil model). In order to minimize carvacrol loss throughout the polymer compounding, a pre‐compounding step is developed in which clay/carvacrol hybrids are produced. The hybrids exhibit a significant increase in the d‐spacing of clay and enhanced thermal stability. The resulting LDPE/(clay/carvacrol) films exhibit superior and prolonged antibacterial activity against Escherichia coli and Listeria innocua, while polymer compounded with pure carvacrol loses the antibacterial properties within days. The films also present an excellent antifungal activity against Alternaria alternata, used as a model plant pathogenic fungus. Furthermore, infrared spectroscopy analysis of the LDPE/(clay/carvacrol) system displayed significantly higher carvacrol content in the film as well as a slower out‐diffusion of the carvacrol molecules in comparison to LDPE/carvacrol films. Thus, these new films have a high potential for antimicrobial food packaging applications due to their long‐lasting and broad‐spectrum antimicrobial efficacy. Copyright © 2014 John Wiley & Sons, Ltd.     

Autoinductive exponential signal amplification: a diagnostic probe for direct detection of fluoride

A new example of an exponential signal amplification strategy for the direct detection of fluoride is demonstrated. The amplification occurred through reaction of fluoride with a responsive chromogenic probe. The probe activity is based on a unique dendritic chain reaction that generates a fluoride anion, which is the analyte of interest, during the disassembly pathway of the dendritic probe. This autoinductive amplification mechanism may be applied for detection of other analytes by coupling activity of a modified probe with that of the fluoride amplifier.     

X-Band Pulsed ENDOR Study ofFe-Substituted Sodalite— The Effect of the Zero-Field Splitting

X-band (∼9.3 GHz) pulsed ENDOR measurements were carried out on⁵⁷Fe-substituted sodalite (FeSOD) which contains only one type of Fe(III) (S=) located at a framework site. The ENDOR spectrum recorded atg= 2 shows three doublets corresponding to the sixM_Smanifolds. The assignment of these signals was confirmed by hyperfine-selective and triple ENDOR experiments. The components of each of the doublets had different intensities, reflecting the different populations of the EPR energy levels at the measurement temperature, 1.8 K. ENDOR spectra were recorded at magnetic fields within the EPR powder pattern, and the field dependence observed showed an anisotropic behavior, unexpected from the isotropic character of the⁵⁷Fe(III) hyperfine coupling. This dependence was attributed to the high-order effects of the zero-field splitting (ZFS) interaction on the ENDOR frequencies. Three different theoretical approaches were used to account for the dependence of the ENDOR spectrum on the ZFS interaction. The first involves the exact diagonalization of the total spin Hamiltonian, the second uses third-order perturbation approximations, and the third employs an effective nuclear Hamiltonian for each of theM_Smanifolds. The simulations showed that the ENDOR signals of theM_S= ±5/2 (ν_±5/2) manifold are the least sensitive to the magnitude of the ZFS parameterDand are therefore the most appropriate for the determination ofa_iso. It is shown that at X band anda_isovalues of about 30 MHz, the perturbation approach is valid up toDvalues of 500 MHz if all three doublets are concerned. However, if only the ν_±5/2doublet is considered, then this approach is valid forD< 1000 MHz. The third approach was found inappropriate fora_isovalues of ∼30 MHz. Using the method of exact diagonalization together with orientation selectivity, the trends observed in the experimental spectra could be reproduced. The ENDOR spectra of the⁵⁷Fe-substituted zeolites ZSM5, L, and mazzite showed broad and ill-defined peaks since the ZFS of Fe(III) in these zeolites is significantly larger than that of FeSOD. Because this broadening is a high-order effect, it can be significantly reduced at higher spectrometer frequencies.     

Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(1 0 0)-2 × 1 surface

The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 0 0)-2 × 1.

The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and “phonon” (cluster) modes.

Implications of the results for surface vibrational spectroscopy are discussed.