New method for direct linear-scaling calculation of electron density of proteins

A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate.     

Modular domain structure: a biomimetic strategy for advanced polymeric materials

A long lasting challenge in polymer science is to design polymers that combine desired mechanical properties such as tensile strength, fracture toughness, and elasticity into one structure. A novel biomimetic modular polymer design is reported here to address this challenge. Following the molecular mechanism used in nature, modular polymers containing multiple loops were constructed by using precise and strong hydrogen bonding units. Single-molecule force-extension experiments revealed the sequential unfolding of loops as a chain is stretched. The excellent correlation between the single-molecule and the bulk properties successfully demonstrates our biomimetic concept of using modular domain structure to achieve advanced polymer properties.     

Thermochemistry of 1,3-dithiacyclohexane 1-oxide (1,3-dithiane sulfoxide): calorimetric and computational study

The enthalpies of combustion and sublimation of 1,3-dithiacyclohexane 1-oxide (1,3-dithiane sulfoxide, 2) were measured by a rotating-bomb combustion calorimeter and the Knudsen effusion technique, and the gas-phase enthalpy of formation was determined, DeltafH degrees m(g) = -98.0 +/- 1.9 kJ mol(-1). This value is not as large (negative) as could have been expected from comparison with thermochemical data available for the thiane/thiane oxide reference system. High-level ab initio molecular orbital calculations at the MP2(FULL)/6-31G(3df,2p) level were performed, and the optimized molecular and electronic structures of 2 afforded valuable information on (1) the relative conformational energies of 2-axial and 2-equatorial--the latter being 7.1 kJ mol(-1) more stable than 2-axial, (2) the possible involvement of nS --> sigma*(C-S(O)) hyperconjugation in 2-equatorial, (3) the lack of computational evidence for sigma(S-C) --> sigma*(S-O) stereoelectronic interaction in 2-equatorial, and (4) the relevance of a repulsive electrostatic interaction between sulfur atoms in 1,3-dithiane sulfoxide, which apparently counterbalances any nS --> sigma*(C-S(O)) stabilizing hyperconjugative interaction and accounts for the lower than expected enthalpy of formation for sulfoxide 2.     

Synthesis and biological evaluation of 2-(3-fluoro-4-nitro phenoxy)-n-phenylacetamide derivatives as novel potential affordable antitubercular agents

A novel series of 2-(3-fluoro-4-nitrophenoxy)-N-phenylacetamide compounds were designed, synthesized and in vitro assessed for their antitubercular activities by a microdilution method. All the novel derivatives exerted potent or moderate active against M. tuberculosis H??Rv, with MIC values ranging from 4 to 64 μg/mL. The most potent derivative 3m showed an identical MIC value of 4 μg/mL for both M. tuberculosis H??Rv and rifampin-resistant M. tuberculosis 261. It demonstrated no inhibitory effects against six different tumor cell lines by a MTT assay and had a good safety profile in a vero cell line, providing a good lead for subsequent optimization in search of novel affordable antitubercular agents.     

Monodisperse REPO4 (RE = Yb, Gd, Y) hollow microspheres covered with nanothorns as affinity probes for selectively capturing and labeling phosphopeptides

Rare-earth phosphate microspheres with unique structures were developed as affinity probes for the selective capture and tagging of phosphopeptides. Prickly REPO(4) (RE = Yb, Gd, Y) monodisperse microspheres, that have hollow structures, low densities, high specific surface areas, and large adsorptive capacities were prepared by an ion-exchange method. The elemental compositions and crystal structures of these affinity probes were confirmed by energy-dispersive spectroscopy (EDS), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The morphologies of these compounds were investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and nitrogen-adsorption isotherms. The potential ability of these microspheres for selectively capturing and labeling target biological molecules was evaluated by using protein-digestion analysis and a real sample as well as by comparison with the widely used TiO(2) affinity microspheres. These results show that these porous rare-earth phosphate microspheres are highly promising probes for the rapid purification and recognition of phosphopeptides.     

Lanthanum silicate coated magnetic microspheres as a promising affinity material for phosphopeptide enrichment and identification

Novel Fe(3)O(4)@La(x)Si(y)O(5) affinity microspheres consisting of a superparamagnetic Fe(3)O(4) core and an amorphous lanthanum silicate shell have been synthesized. The core-shell-structured Fe(3)O(4)@La(x)Si(y)O(5) microspheres, with a mean size of ca. 480 nm, had rough lanthanum silicate surfaces and displayed relatively strong magnetism (47.2 emu g(-1)). This novel affinity material can be used for selective capture, rapid magnetic separation, and part dephosphorylation (which plays an important role in identifying phosphopeptides in MS) of the phosphopeptides in a peptide mixture. Its ability to selectively trap and magnetically isolate as well as label the phosphopeptides was evaluated using a standard phosphorylated protein (β-casein) and a real sample (human serum). Phosphopeptides and their corresponding label ions were detected for concentrations of β-casein as low as 1 × 10(-9) M and in mixtures of β-casein and BSA with molar ratios as low as 1:50. In addition, this affinity material, with its labeling properties, is superior to commercial TiO(2) beads in terms of interference from non-phosphopeptide molecules. These results reveal that the lanthanum silicate coated magnetic microspheres represent a promising affinity material for the rapid purification and recognition of phosphopeptides.     

Electrospray ionization mass spectra of amino acid phosphoramidates of adenosine

Amino acid phosphoramidates of adenosine were synthesized and determined by positive and negative ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). The fragmentation pathways were investigated. In the positive ion mass spectra abundant characteristic fragment ions appeared, and many complementary ions were found. In the negative ion mass spectra only a few fragment ions were observed, and most of them contained phosphoryl groups. The results show that ESI-MS is a useful tool for structural determination of amino acid phosphoramidates of nucleosides.     

Trapping an elusive intermediate in manganese-oxo cubane chemistry

A new member of the Mn-oxo cubane core complex family [Mn2III,2IV4O4L6] (1), where L = (p-MeOPh)2PO2-, has been synthesized and characterized. Compound 1 possesses structurally inequivalent MnIII and MnIV with clear valence electron localization in the crystal phase, quite unlike the structurally equivalent sites, tetrahedral core symmetry, and delocalized valence of its analogue where L = Ph2PO2-. Compound 1 exhibits appreciable positive shifts (0.1-0.3 V) of both the oxidation and reduction electrochemical potentials, attributable to the remote electron donating p-MeO groups. Reduction of 1 by methanol yields a novel core complex [MnIII4O2(OMe)2(MeOH)[(p-MeOPh)2PO2]6] (2). Each MnIII of 2 is tetragonally distorted due to the Jahn-Teller effect with elongated Mn-O bonds that are directed at the two micro3-MeO bridges and neither of the two micro3-oxos. These electronically driven distortions provide a structural rationale for the greater basicity of the former sites and explain why 2 of the 4 corner oxos are preferentially reduced to water molecules.     

The investigation of spin-orbit effect for the F((2)P)+HD reaction

In this paper, we employ the time-dependent quantum wave packet method to study the reaction of F((2)P(3/2), (2)P(1/2)) with HD on the Alexander-Stark-Werner potential energy surface. The reaction probabilities and total integral cross sections of the spin-orbit ground and excited states for the two possible products of the system are calculated. Because the reaction channel of the excited spin-orbit state is closed at the resonance energy, the resonance feature does not appear in the reaction probabilities and cross section for the F((2)P(1/2))+HD(v=j=0)-->HF+D reaction, in contrast with that found for the ground spin--orbit state. We also compare the average cross sections of the two possible products with the experimental measurement. The resonance peak in the present average cross section for the HF+D product is slightly larger than the experimental result, but much smaller than that of the single-state calculations on the potential energy surface of Stark and Werner. It seems that the spin--orbit coupling would play a relatively important role in this reaction. Moreover, the isotope effects of the ground and excited spin--orbit states and the reactivity of the two product channels from the excited spin--orbit state are presented.     

Effects of chromophore orientation and molecule conformation on surface-enhanced Raman scattering studied with alkanoic acids and colloidal silver nanoparticles

Experimental studies have been carried out to gain a better understanding of the effects of chromophore orientation and molecular conformation on surface-enhanced Raman scattering (SERS) based on metal nanostructures. A series of alkanoic acids that contain a phenyl ring separated by methylene groups from the carboxylic acid, including phenylacetic acid, 3-phenylpropionic acid, 4-phenylbutyric acid, 5-phenylvaleric acid, and 6-phenylhexanoic acid, was investigated as model molecules with colloidal silver nanoparticles as SERS substrates. As the number of methylene groups increases, the molecules display an interesting zigzag intensity pattern of the phenyl ring bending mode around 1000 cm(-1) as well as a trend of appearance and disappearance of either the degenerate ring breathing mode or C[Double Bond]O vibrational mode near 1585 and 1630 cm(-1), respectively. Molecules containing an odd number of methylene units display a higher ring bending intensity and degenerate ring breathing mode and are suggested to have a trans conformation on the particle surface. Molecules with an even number of methylene units show a C[Double Bond]O vibrational mode and weaker ring bending in their SERS spectra and are suggested to have a gauche conformation on the silver nanoparticle surface. The different conformation is attributed to the varying interactions of the carboxylic group or the phenyl ring pi electrons with the silver surface. The SERS intensity was found to change little as the length between the phenyl ring and the carboxylic group was increased by adding CH(2) spacers. This is possibly because the effective distance between the phenyl ring and the silver surface does not change much with increasing number of CH(2) spacers as a result of changes in molecular conformation and variations in the phenyl ring orientation with CH(2) addition. The insight gained from this study is important for understanding SERS of complex molecules for which chromophore orientation and molecular conformation must be taken into careful consideration.