Theoretical Studies on the Isomerization Kinetics of Low-Lying Isomers of the SiC4H2 System.

The low-lying isomers of SiC4H2 are investigated to understand the kinetics of isomerization pathways using density functional theory. In our earlier work, we studied the various possible isomers (J. Phys. Chem. A, 2020, 124, 987-1002) and the chemical bonding of low-lying isomers of SiC4H2 (J. Phys. Chem. A, 2022, 126, 9366-9374). Among them, four isomers, 1-ethynyl-3-silacycloprop-1-en-3-ylidene (1), 3-silapent-1,4-diyn-3-ylidene (2), 1-silapent-1,2,3,4-tetraen-1-ylidene (4), and 1-silapent-2,4-diyn-1-ylidene (5) have already been identified in the laboratory. The previously known theoretical isomer 2-methylene-1-silabicyclo[1.1.0]but-1(3)-en-4-ylidene (3) and the newly identified unknown isomer through the present kinetic studies 5-silabicyclo[2.1.0]pent-1(4),2-dien-5-ylidene (N6) remain elusive in the laboratory to date. The isomerization pathways of the low-lying isomers of SiC4H2 are predicted through the transition state structures. Intrinsic reaction coordinate analysis identifies the minimum energy reaction pathways connecting the transition state from one isomer to another of the investigated system. The present kinetic data reveal the isomerization of global minimum energy isomer 1 to thermodynamically stable low-lying isomers, 2 and 5. Interestingly, isomer 3 interconverts to the experimentally known low-energy isomer 4, the second most thermodynamically stable isomer among them. The thermodynamic and kinetic parameters of the low-lying isomers of SiC4H2 are also documented in this work. The rate coefficient and equilibrium constant for isomerization reactions are calculated using the Rice-Ramsperger-Kassel-Marcus theory. The equilibrium constant delineates the difficulties in forming N6 and 3 through the isomerization pathways. Furthermore, ab initio molecular dynamics studies dictate the stability of low-lying isomers of SiC4H2 within the time scale of the simulation.

Shock Processing of Amino Acids Leading to Complex Structures-Implications to the Origin of Life.

The building blocks of life, amino acids, are believed to have been synthesized in the extreme conditions that prevail in space, starting from simple molecules containing hydrogen, carbon, oxygen and nitrogen. However, the fate and role of amino acids when they are subjected to similar processes largely remain unexplored. Here we report, for the first time, that shock processed amino acids tend to form complex agglomerate structures. Such structures are formed on timescales of about 2 ms due to impact induced shock heating and subsequent cooling. This discovery suggests that the building blocks of life could have self-assembled not just on Earth but on other planetary bodies as a result of impact events. Our study also provides further experimental evidence for the 'threads' observed in meteorites being due to assemblages of (bio)molecules arising from impact-induced shocks.

Discovery of carbon nanotubes in sixth century BC potteries from Keeladi, India.

Unique black coatings were observed in the inner wall of pottery shreds excavated from Keeladi, Tamilnadu, India. Raman spectroscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy were used to understand the nature of the coating. The analysis revealed the presence of single, multi-walled carbon nanotubes and layered sheets in the coating. The average diameter of single-walled carbon nanotube found to be about 0.6 ± 0.05 nm. This is the lowest among the single-walled carbon nanotubes reported from artefacts so far and close to the theoretically predicted value (0.4 nm). These nanomaterials were coated in the pottery's that date backs to sixth century BC, and still retain its stability and adhesion. The findings of nano materials in the pre-historic artifacts, its significance and impact are discussed in this article.

Near-Threshold Photodetachment Cross Section of (SF6)(n)(-) Cluster Anions: The Ion Core Structure.

Photodetachment cross sections as a function of photon energy are measured for cold (SF6)n(-) cluster anions stored in an electrostatic ion beam trap. Absolute photodetachment cross sections near the adiabatic limit are reported. The strong dependence of the SF6(-) absolute photodetachment cross section on the anion equilibrium bond length leads to the conclusion that the excess charge is localized on a SF6(-) ion core that is only subtly perturbed by the neighboring cluster units.

Synthesis of Bifunctional Azobenzene Glycoconjugates for Cysteine-Based Photosensitive Cross-Linking with Bioactive Peptides.

Azobenzene linker molecules can be utilized to control peptide/protein function when they are ligated to appropriately spaced amino acid side chains of the peptide. This is because the photochemical E/Z isomerization of the azobenzene N=N double bond allows to switch peptide conformation between folded and unfolded. In this context, we have introduced carbohydrate-functionalized azobenzene derivatives in order to advance the biocompatible properties of azobenzene peptide linkers. Chloroacetamide-functionalized and O-allylated carbohydrate derivatives were synthesized and conjugated with azobenzene to achieve new bifunctional cross-linkers, in order to allow ligation to cysteine side chains by nucleophilic substitution or thiol-ene reaction, respectively. The photochromic properties of the new linker glycoconjugates were determined and first ligation reactions performed.

Switching of bacterial adhesion to a glycosylated surface by reversible reorientation of the carbohydrate ligand.

The surface recognition in many biological systems is guided by the interaction of carbohydrate-specific proteins (lectins) with carbohydrate epitopes (ligands) located within the unordered glycoconjugate layer (glycocalyx) of cells. Thus, for recognition, the respective ligand has to reorient for a successful matching event. Herein, we present for the first time a model system, in which only the orientation of the ligand is altered in a controlled manner without changing the recognition quality of the ligand itself. The key for this orientational control is the embedding into an interfacial system and the use of a photoswitchable mechanical joint, such as azobenzene.

Synthesis and photochromic properties of configurationally varied azobenzene glycosides.

Spatial orientation of carbohydrates is a meaningful parameter in carbohydrate recognition processes. To vary orientation of sugars with temporal and spatial resolution, photosensitive glycoconjugates with favorable photochromic properties appear to be opportune. Here, a series of azobenzene glycosides were synthesized, employing glycoside synthesis and Mills reaction, to allow "switching" of carbohydrate orientation by reversible E/Z isomerization of the azobenzene N=N double bond. Their photochromic properties were tested and effects of azobenzene substitution as well as the effect of anomeric configuration and the orientation of the sugars 2-hydroxy group were evaluated.

Synthesis and surface-spectroscopic characterization of photoisomerizable glyco-SAMs on Au(111).

Photoisomerizable glyco-SAMs (self-assembled monolayers), utilizing synthetic azobenzene glycoside derivatives were fabricated. The ultimate goal of this project is to assay the influence of the 3D arrangement of sugar ligands on cell adhesion, and eventually make cell adhesion photoswitchable. However, it is a prerequisite for any biological study on the spatial conditions of carbohydrate recognition, that photoisomerization of the surface molecules can be verified. Here, we employed IRRAS and XPS to spectroscopically characterize glyco-SAMs. In particular and unprecedented to date, we prove reversible E→Z→E isomerization of azobenzene glycoside-terminated SAMs.

Neutrophil uptake of nitrogen-bisphosphonates leads to the suppression of human peripheral blood γδ T cells.

Nitrogen-bisphosphonates (n-BP), such as zoledronate, are the main class of drugs used for the prevention of osteoporotic fractures and the management of cancer-associated bone disease. However, long-term or high-dose use has been associated with certain adverse drug effects, such as osteonecrosis of the jaw and the loss of peripheral of blood Vγ9Vδ2 T cells, which appear to be linked to drug-induced immune dysfunction. In this report we show that neutrophils present in human peripheral blood readily take up zoledronate, and this phenomenon is associated with the potent immune suppression of human peripheral blood Vγ9Vδ2 T cells. Furthermore, we found this zoledronate-mediated inhibition by neutrophils could be overcome to fully reconstitute Vγ9Vδ2 T cell proliferation by concomitantly targeting neutrophil-derived hydrogen peroxide, serine proteases, and arginase I activity. These findings will enable the development of targeted strategies to mitigate some of the adverse effects of n-BP treatment on immune homeostasis and to improve the success of immunotherapy trials based on harnessing the anticancer potential of peripheral blood γδ T cells in the context of n-BP treatment.

Synthesis and testing of the first azobenzene mannobioside as photoswitchable ligand for the bacterial lectin FimH.

In order to allow spatial and temporal control of carbohydrate-specific bacterial adhesion, it has become our goal to synthesise azobenzene mannosides as photoswitchable inhibitors of type 1 fimbriae-mediated adhesion of E. coli. An azobenzene mannobioside 2 was prepared and its photochromic properties were investigated. The E→Z isomerisation was found to be highly effective, yielding a long-lived (Z)-isomer. Both isomers, E and Z, show excellent water solubility and were tested as inhibitors of mannoside-specific bacterial adhesion in solution. Their inhibitory potency was found to be equal and almost two orders of magnitude higher than that of the standard inhibitor methyl mannoside. These findings could be rationalised on the basis of computer-aided docking studies. The properties of the new azobenzene mannobioside have qualified this glycoside to be eventually employed on solid support, in order to fabricate photoswitchable adhesive surfaces.

Inhibition of bacterial adhesion to live human cells: activity and cytotoxicity of synthetic mannosides.

Bacterial adhesion to glycosylated surfaces is a key issue in human health and disease. Inhibition of bacterial adhesion by suitable carbohydrates could lead to an anti-adhesion therapy as a novel approach against bacterial infections. A selection of five α-mannosides has been evaluated as inhibitors of bacterial adhesion to the polysaccharide mannan, as well as to the surface of live human HT-29 cells. Cell toxicity studies were performed to identify the therapeutic window for a potential in vivo-application of the tested carbohydrates. A previously published mannosidic squaric acid diamide was shown to be exceptionally effective as inhibitor of the bacterial lectin FimH.

Sweet switches: azobenzene glycoconjugates synthesized by click chemistry.

Azobenzene glycoconjugates can be switched between two isomeric states, E and Z, to change the spatial orientation of the conjugated carbohydrate ligands. Mono-, di- and trivalent azobenzene glycoconjugates were synthesized using click chemistry and their photochromic properties determined. Multivalency effects were observed in photoisomerisation.

Direct infrared absorption spectroscopy of benzene dimer.

The direct infrared (IR) absorption spectrum of benzene dimer formed in a free-jet expansion was recorded in the 3.3 µm region for the first time. This has led to the observation of the C-H stretching fundamental mode ν(13) (B(1u)), which is both IR and Raman forbidden in the monomer. Moreover, the IR forbidden and Raman allowed ν(7) (E(2g)) mode has been observed as well. These two modes were found to be red-shifted along with the IR allowed ν(20) (E(1u)) mode, as previously reported by Erlekam et al. [Erlekam; Frankowski; Meijer; Gert von Helden J. Chem. Phys.2006, 124, 171101], using ion-dip spectroscopy, contrary to the blue-shift predicted earlier by theoretical studies. The observation of the ν(13) band indicates that the symmetry is reduced in the dimer, confirming the T-shaped structure observed by Erlekam et al. Our experimental results have not provided any direct evidence for the presence of the parallel displaced geometry, the main objective of the present work, as predicted by theoretical calculations.