Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

Rapid biomass analysis

New, rapid, and inexpensive methods that monitor the chemical composition of corn stover and corn stover-derived samples are a key element to enabling the commercialization of processes that convert stover to fuels and chemicals. These new techniques combine near infrared (NIR) spectroscopy and projection to latent structures (PLS) multivariate analysis to allow the compositional analysis of hundreds of samples in 1 d at a cost of about $10 each. The new NIR/PLS rapid analysis methods can also be used to support a variety of research projects that would have been too costly to pursue by traditional methods.     

Ethanol/water pulp enzymatic pretreatment: Chemical and FTIR-PCA analyses

Pulps obtained from ethanol/water cooking of sugarcane bagasse were treated at different times using xylanase enzyme obtained from Thermomyces lanuginosus IOC-4145 or commercially (Cartazyme HS, Sandoz Products Ltd.). The enzyme dosage was 18 IU per g of dry pulp and the time varied from 4 h to 12 h. When xylanase from T. lanuginosus was used, the kappa number and viscosity improved independently of the processing time used (4 h, 8 h, and 12 h). After chemical evaluation, the obtained pulps were classified using Fourier Transformed Infra-Red Spectroscopy and Principal Component Analysis. The results showed that the first three principal components explained more than 90 % of the total variance of the pulp spectra.     

DNA-mediated coordinative assembly of upconversion hetero-nanostructures for targeted dual-modality imaging of cancer cells

We reported a simple and universal strategy for DNA-mediated assembly of CdTe quantum dots (QDs) and lanthanide-doped upconversion nanoparticles (UCNPs). Such DNA-QD/UCNPs heterostructures not only maintains both fluorescent properties of QDs and upconversion luminescence behaviors of UCNPs, but also offers a polyvalent DNA surface, allowing for targeted dual-modality imaging of cancer cells using an aptamer     

Infrared Evidence for Hoffman Reaction During Calcination of Surfactant-Templated Silica Films and Analysis of the Resulting Surface Sites

Fourier Transform Infrared transmission spectroscopy is used to characterize surfactant-templated silica films on glass. The calcination process is followed in situ and evidence for the removal of the surfactant along the Hoffman reaction is given. Once calcined, the surface of the pores of the mesoporous films is proven by deuteration experiment to be hydroxylated. Bands are attributed to isolated and hydrogen-bonded silanols. Silylation reaction with hexamethyldisilazane only occurs with isolated silanol groups.     

Occurrence and distribution of metals and porphyrins in Nigerian coal minerals

The metal contents of Nigerian coal minerals were analyzed using an atomic absorption spectrophotometer. Calcium, Na, and Fe occurred as the major elements with concentrations ranging from 9 782 μg/g for Ca to 432 μg/g for Na whereas K, Mg, Mn, Ni, Cr, Zn, Pb, and Cu, which occurred at trace levels ranged from 673.73 μg/g for Mg to 2.97 μg/g for Mn. The results of the quantitative analysis of porphyrins extracted from the coal minerals showed that Onyeama coal has the highest amount of porphyrins (ca～0.96 μg/g) while Okpara has the lowest (ca～0.30 μg/g). The porphyrins were qualitatively characterized by a combination of thin layer chromatography (TLC), infrared, and ultraviolet-visible spectrophotometers. The results of the mid infrared analysis (MIR) showed the presence of absorption bands at 3 440 cm～1～3 450 cm-1 and 1 640 cm-1～1 680 cm-1 , which are owing to the stretching vibrations of N - H and C = C of aromatics, with C- H out of plane (oop) bending vibrations at wavenumbers less than 900 cm-1, all of which are characteristic absorptions of porphyrin free base. The ultraviolet-visible data showed prominent peaks at ～400 nm(Soret band) and at wavelength ranges of 535 nm～550 nm(β-band) and 565 nm～ 600 nm (α-band) for the coal porphyrins analyzed. The geochemical significance of the metals and porphyrins in coal minerals are discussed.     

Electronic spectral and photophysical properties of some p-phenylenevinylene oligomers in solution and thin films

A comprehensive photophysical and spectroscopic study of a new class of p-phenylenevinylene oligomers (PPV-trimers) possessing different alkyl and alkyloxy sidechain substituents and different end groups (aldehyde, CC, phenylene and anthracene units) was undertaken in solution at room temperature (293 K), low temperature (77 K) and in thin films. The study comprises absorption, emission and triplet–triplet absorption spectra, together with quantitative measurements of quantum yields (fluorescence, intersystem crossing, internal conversion and singlet oxygen formation) and lifetimes. The data allow the determination of rate constants for all decay processes. From these, several conclusions could be drawn. Changing from alkyl to alkyloxy substituents does not change fluorescence and internal conversion yields but decreases the (already small) intersystem crossing yield. The introduction of anthracene at the terminal ends of the PPV-trimers leads to the lowest fluorescence yield reported in this study. Of particular importance is the fact that the fluorescence quantum yields in films are of the same order of magnitude as those in solution, which suggests the potential for use of these oligomers for light-emitting device applications. With one of the alkyloxy derivatives, a more detailed study of the early part of the fluorescence decay was made, and it was found that upon excitation a fast conformational relaxation process of the initially excited oligomer occurs, leading to a more planar conjugation segment.     

中药配方颗粒红外光谱法的快速鉴别

采用红外光谱法对中药配方颗粒及其辅料进行了鉴别研究。结果表明：不同生产厂商的配方颗粒中所添加的辅料类型及用量有较大差别；不同种的配方颗粒在辅料含量较低的情况下有较明显的指纹性，而辅料含量较高时，采用差谱技术可以提高谱图的指纹性，达到中药配方颗粒--鉴别的目的。该法简便、快速、可靠，是中药配方颗粒宏观质控的一个强有力的手段。     

Structural Analysis of Ti And Pb Citrate Using NMR and FT-Raman Signals and Quantum Mechanics Simulations

Titanium citrate and lead and titanium citrate were prepared by polymeric precursor method in aqueous solution. This citrate was analyzed by ¹H, ¹³C NMR and gHMBC–NMR (Hetero-nuclear multiple-bond correlation) to investigate the formation of the citrate complexs and influence of the Pb²⁺ ion in this complex. These complexs were characterized by interaction between Ti⁴⁺ ion and citric acid carboxyls. Quantum mechanic simulations in level ab initio were used to study the electronic structure and natural charges (NBO) to both the complexs. Such techniques indicated the formation of an octahedral complex with an arrangement similar to Ti atom in the crystalline structure of the PbTiO₃. A study using the technique FT-Raman made possible the confirmation of the interaction among the Ti⁴⁺ and Pb²⁺ ions with the citric acid carboxyls.     

Classification of cultivation area of ginseng by near infrared spectroscopy and ICP-AES

A rapid and nondestructive near infrared (NIR) method using soft independent modeling of class analogy (SIMCA) for the classification of cultivation area (Korea and China) was evaluated and confirmed. Raw, first, and second derivative NIR spectra were compared to develop a robust classification rule. The chemical properties of ginseng samples were also investigated to find out the differences between Korean samples and Chinese samples. These differences make NIR spectroscopic method viable. The average value of each Korean and Chinese ginseng sample for crude fiber, crude protein, starch, and 10 inorganic constituents were measured and compared with F-test and t-test. The inorganic constituents were also measured by induced coupled plasma-atomic emission spectroscopy (ICP-AES). It could be found that the amount of starch and ten inorganic elements for example Na, Mg, P, K, Ca, Mn, Fe, Ni, Cu and Zn in ginseng samples are considerably different based on cultivation area. SIMCA has been applied to the inorganic data to investigate the possibility of ICP-AES as classification tool. However, it was observed that the result was not equal to than NIR spectra data. The overall results showed the availability of NIR method using SIMCA would be adequate for classification of cultivation of ginseng, since NIR spectra includes useful and various information on chemical properties in spite of broad and overlapped bands.