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Determining structure of highly flexible protein with multiple conformations can be challenging. This paper aims to combine molecular dynamics (MD) and small angle X-ray diffraction (SAX) techniques as a solution to overcome issues related to protein conformation in hardly crystallized protein. Based on prior studies, a cold-active lipase AMS8 was simulated in solvents showing stability in its N-terminal and high flexibility in its C-terminal. However, MD in its own algorithm could not explain the basis of macromolecule conformational transitions or changes related to protein through folding. Hence, by combining SAXS with MD, it is possible to understand the structure of flexible AMS8 lipase in natural space. Based on the findings, SAXS ab-initio model of AMS8 lipase was identified as a monomeric protein in which the optimized model of cold-active lipase AMS8 derived from SAXS data was found to be aligned with AMS8 homology model under series of MD timeframe.

Herein, optimization of zeolite NaA/NaX synthesis conditions in order to obtain the final product with high surface area and pore volume was investigated. An optimal synthesis condition was 5 days aging time and crystallization time of 9 h with the co-addition of cetyltrimethylammonium bromide (CTAB) and heptane. All those optimal synthesis conditions provided mixed phase between zeolite NaA and NaX, and addition of those organic phases improved the surface area and pore volume of the final synthesized zeolite. The role of CTAB and heptane on increasing the surface area of zeolite was studied by in situ small-angle X-ray scattering (SAXS). The SAXS results evidenced that small nucleation precursor was formed upon the addition of organic phase, and this nucleation precursor can provide zeolite with high-characteristic XRD signals of mixed phase of zeolite A and X after the crystallization process. The synthesized zeolite obtained from optimal synthesis condition with high surface area was further used as a catalyst support by impregnating with 5, 10, 15, and 20wt%Ni for catalyzing CO2 methanation reaction. The results found that 15wt%Ni/zeolite expressed the highest catalytic activity with high CH4 selectivity and stability. This was due to high dispersion of Ni species on catalyst surface and high metal-support interaction between Ni and zeolite. These results indicated that the mixed phase zeolite support can be a potential catalyst support for this reaction.

Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible “flap motif” whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (K(i) of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.

In this work, two pairs of silicon and aluminium sources (sodium silicate solution + Al(OH)3 and sodium silicate powder + sodium aluminate) were used for synthesizing zeolites which were labeled as Z1 and Z2, respectively. The results from XRD, BET and surface analysis indicated that sodium silicate and sodium aluminate sources yielded zeolite with high surface area and pore volume. Cetyltrimethylammonium bromide (CTAB) and heptane were used to modify the CO2 adsorption capacity and selectivity of zeolite NaX. The surface area and pore volume of zeolite products increased due to smaller crystalline size and then resulted in significant enhancement of CO2 uptake of the synthesized zeolite NaX. The role of additives on zeolite formation was to increase the nuclei formation rate and number which gave rise to smaller zeolite crystals. The best adsorbent exhibited high CO2 adsorption capacity (5.08 mmol g−1 at 303 K) and relatively high CO2 selectivity over N2 (116) which indicated the potential of adsorbent to separate CO2 from flue gas application.

Biomaterial-based hydrogels incorporating antibacterial agents may provide sustainable solutions to biomedical device failures and the prevention of infections. Herein we report guar gum hydrogels, cross-linked with borax and loaded with silver nanoparticles, that are injectable, exhibit rapid self-healing, and show antibacterial properties towards both gram-positive and gram-negative bacteria. The hydrogels are fully characterized by infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, and rheological measurements. An important focus was to minimize borax content, thus reducing the toxicity of the gels greatly, whilst retaining their favorable viscoelastic properties. When the low borax-content hydrogels are composited with curcumin-stabilized silver nanoparticles, the hydrogels show activity against Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), and Staphylococcus aureus (S. aureus).

The first step in the degradation of p-hydroxyphenylacetic acid (HPA) is catalyzed by the two-component enzyme p-hydroxyphenylacetate 3-hydroxylase (HPAH). The two components of Acinetobacter baumannii HPAH are known as C1 and C2, respectively. C1 is a flavin reductase that uses NADH to generate reduced flavin mononucleotide (FMNH-), which is used by C2 in the hydroxylation of HPA. Interestingly, although HPA is not directly involved in the reaction catalyzed by C1, the presence of HPA dramatically increases the FMN reduction rate. Amino acid sequence analysis revealed that C1 contains two domains: an N-terminal flavin reductase domain, and a C-terminal MarR domain. Although MarR proteins typically function as transcription regulators, the MarR domain of C1 was found to play an auto-inhibitory role. Here, we report a crystal structure of C1 and small-angle X-ray scattering (SAXS) studies that revealed that C1 undergoes a substantial conformational change in the presence of HPA, concomitant with the increase in the rate of flavin reduction. Amino acid residues that are important for HPA binding and regulation of C1 activity were identified by site-directed mutagenesis. Amino acid sequence similarity analysis revealed several as yet uncharacterized flavin reductases with N- or C-terminal fusions.

Coarse-grained simulation models are developed to study both template-bound and free porphyrin nanoring systems. Key interactions are modeled with relatively simple (and physically motivated) energy functions which allow for relatively facile transfer both between different ring sizes and between the template-bound and free nanoring systems. The effects of varying the model parameters on the respective radii of gyration are determined. The effects of including different templates on the ring structure are investigated both in terms of the detailed geometry of the template and the interaction strength between the template and the metal centers in the nanorings. The role of the template-nanoring interaction strength in controlling potential "caterpillar track" rotational motion is discussed. The relationship of the model to experimental small-angle X-ray, exchange spectroscopy, and electron spin resonance results is discussed.

Three different types of template-directed syntheses of linear porphyrin oligomers are presented. In the classical approach the product has the same number of binding sites as the template, whereas in Vernier reactions the product has the lowest common multiple of the numbers of binding sites in the template and the building block. Mutual Vernier templating is like Vernier templating except that both strands of the Vernier complex undergo coupling simultaneously, so that it becomes impossible to say which is the 'template' and which is the 'building block'. The template-directed synthesis of monodisperse linear oligomers is more difficult than that of cyclic oligomers, because the products of linear templating have reactive ends. All three types of templating are demonstrated here, and used to prepare a nickel(ii) porphyrin dodecamer with 4-pyridyl substituents on all twelve porphyrin units. The stabilities and cooperativities of the double-strand complexes involved in these reactions were investigated by UV-vis-NIR titration. The four-rung ladder duplex has a stability constant of about 2 × 10(18) M(-1) in dichloromethane at 298 K.

For more than half of humanity, rice is life. Rice is a grain which has shaped the history, culture, diet and economy of billions of people in Asia. In Thailand, it is the essence of life. Archaeological evidence revealed that rice had been planted in northeastern area of Thailand more than 5,500 years ago which is earlier than in China and India. The ancient rice grains were found in various archaeological sites in Thailand such as Nakhon Nayok, Suphan Buri and Prachin Buri Provinces. In this work, the ancient black rice from Nakhon Nayok Province was elementally analyzed using scanning electron microscope coupled with energy dispersive X-ray fluorescence spectroscopy, proton induced X-ray emission spectroscopy and micro-beam energy dispersive X-ray fluorescence spectroscopy. Infrared (IR) spectroscopy was also used to study the chemical composition and bio-molecular structure. The grains were oblique in shape with a rough surface. Three major elements (Si, Ca and Al) and other trace elements were detected. The IR spectra provided some information about the presence of molecular bonds.

Supramolecular antenna-ring complexes are of great interest due to their presence in natural light-harvesting complexes. While such systems are known to provide benefits through robust and efficient energy funneling, the relationship between molecular structure, strain (governed by nuclear coordinates and motion), and energy dynamics (arising from electronic behavior) is highly complex. We present a synthetic antenna-nanoring system based on a series of conjugated porphyrin chromophores ideally suited to explore such effects. By systematically varying the size of the acceptor nanoring, we reveal the interplay between antenna-nanoring binding, local strain, and energy dynamics on the picosecond time scale. Binding of the antenna unit creates a local strain in the nanoring, and this strain was measured as a function of the size of the nanoring, by UV–vis-NIR titration, providing information on the conformational flexibility of the system. Strikingly, the energy-transfer rate is independent of nanoring size, indicating the existence of strain-localized acceptor states, spread over about six porphyrin units, arising from the noncovalent antenna-nanoring association.

The first microbeam synchrotron X-ray fluorescence (µ-SXRF) beamline using continuous synchrotron radiation from Siam Photon Source has been constructed and commissioned as of August 2011. Utilizing an X-ray capillary half-lens allows synchrotron radiation from a 1.4 T bending magnet of the 1.2 GeV electron storage ring to be focused from a few millimeters-sized beam to a micrometer-sized beam. This beamline was originally designed for deep X-ray lithography (DXL) and was one of the first two operational beamlines at this facility. A modification has been carried out to the beamline in order to additionally enable µ-SXRF and synchrotron X-ray powder diffraction (SXPD). Modifications included the installation of a new chamber housing a Si(111) crystal to extract 8 keV synchrotron radiation from the white X-ray beam (for SXPD), a fixed aperture and three gate valves. Two end-stations incorporating optics and detectors for µ-SXRF and SXPD have then been installed immediately upstream of the DXL station, with the three techniques sharing available beam time. The µ-SXRF station utilizes a polycapillary half-lens for X-ray focusing. This optic focuses X-ray white beam from 5 mm × 2 mm (H × V) at the entrance of the lens down to a diameter of 100 µm FWHM measured at a sample position 22 mm (lens focal point) downstream of the lens exit. The end-station also incorporates an XYZ motorized sample holder with 25 mm travel per axis, a 5× ZEISS microscope objective with 5 mm × 5 mm field of view coupled to a CCD camera looking to the sample, and an AMPTEK single-element Si (PIN) solid-state detector for fluorescence detection. A graphic user interface data acquisition program using the LabVIEW platform has also been developed in-house to generate a series of single-column data which are compatible with available XRF data-processing software. Finally, to test the performance of the µ-SXRF beamline, an elemental surface profile has been obtained for a piece of ancient pottery from the Ban Chiang archaeological site, a UNESCO heritage site. It was found that the newly constructed µ-SXRF technique was able to clearly distinguish the distribution of different elements on the specimen.

We report the synthesis of LH2-like supramolecular double- and triple-stranded complexes based upon porphyrin nanorings. Energy transfer from the antenna dimers to the $\pi$-conjugated nanoring occurs on a subpicosecond time scale, rivaling transfer rates in natural light-harvesting systems. The presence of a second nanoring acceptor doubles the transfer rate, providing strong evidence for multidirectional energy funneling. The behavior of these systems is particularly intriguing because the local nature of the interaction may allow energy transfer into states that are, for cyclic nanorings, symmetry-forbidden in the far field. These complexes are versatile synthetic models for natural light-harvesting systems.

Photoemission electron microscopy end station is installed at Beamline 3.2b of Siam Photon Laboratory of the Synchrotron Light Research Institute in Thailand. The system has been tested for sample imaging using synchrotron, a UV lamp and an electron gun as sources with successful results. Multi-disciplinary research at the PEEM end station is reported in this paper. Arc discharge problem which have been found during the experiments is also discussed.