An Efficient and Accurate Formalism for the Treatment of Large Amplitude Intramolecular Motion

We propose a general approach to describe large amplitude motions (LAM) with multiple degrees of freedom (DOF) in molecules or reaction intermediates, which is useful for the computation of thermochemical or kinetic data. The kinetic part of the LAM Lagrangian is derived using a Z-matrix internal coordinate representation within a new numerical procedure. This derivation is exact for a classical system, and the uncertainties on the prediction of observable quantities largely arise from uncertainties on the LAM potential energy surface (PES) itself. In order to rigorously account for these uncertainties, we present an approach based on Bayesian theory to infer a parametrized physical model of the PES using ab initio calculations. This framework allows for quantification of uncertainties associated with a PES model as well as the forward propagation of these uncertainties to the quantity of interest. A selection and generalization of some treatments accounting for the coupling of the LAM with other internal or external DOF are also presented. Finally, we discuss and validate the approach with two applications: the calculation of the partition function of 1,3-butadiene and the calculation of the high-pressure reaction rate of the CH(3) + H → CH(4) recombination.     

Low-temperature combustion chemistry of biofuels: pathways in the initial low-temperature (550 K-750 K) oxidation chemistry of isopentanol

The branched C(5) alcohol isopentanol (3-methylbutan-1-ol) has shown promise as a potential biofuel both because of new advanced biochemical routes for its production and because of its combustion characteristics, in particular as a fuel for homogeneous-charge compression ignition (HCCI) or related strategies. In the present work, the fundamental autoignition chemistry of isopentanol is investigated by using the technique of pulsed-photolytic Cl-initiated oxidation and by analyzing the reacting mixture by time-resolved tunable synchrotron photoionization mass spectrometry in low-pressure (8 Torr) experiments in the 550-750 K temperature range. The mass-spectrometric experiments reveal a rich chemistry for the initial steps of isopentanol oxidation and give new insight into the low-temperature oxidation mechanism of medium-chain alcohols. Formation of isopentanal (3-methylbutanal) and unsaturated alcohols (including enols) associated with HO(2) production was observed. Cyclic ether channels are not observed, although such channels dominate OH formation in alkane oxidation. Rather, products are observed that correspond to formation of OH viaβ-C-C bond fission pathways of QOOH species derived from β- and γ-hydroxyisopentylperoxy (RO(2)) radicals. In these pathways, internal hydrogen abstraction in the RO(2)? QOOH isomerization reaction takes place from either the -OH group or the C-H bond in α-position to the -OH group. These pathways should be broadly characteristic for longer-chain alcohol oxidation. Isomer-resolved branching ratios are deduced, showing evolution of the main products from 550 to 750 K, which can be qualitatively explained by the dominance of RO(2) chemistry at lower temperature and hydroxyisopentyl decomposition at higher temperature.     

Charge Transport within a Three-Dimensional DNA Nanostructure Framework

Three-dimensional (3D) DNA nanostructures have shown great promise for various applications including molecular sensing and therapeutics. Here we report kinetic studies of DNA-mediated charge transport (CT) within a 3D DNA nanostructure framework. A tetrahedral DNA nanostructure was used to investigate the through-duplex and through-space CT of small redox molecules (methylene blue (MB) and ferrocene (Fc)) that were bound to specific positions above the surface of the gold electrode. CT rate measurements provide unambiguous evidence that the intercalative MB probe undergoes efficient mediated CT over longer distances along the duplex, whereas the nonintercalative Fc probe tunnels electrons through the space. This study sheds new light on DNA-based molecular electronics and on designing high-performance biosensor devices.     

Capillary size exclusion chromatography with picogram sensitivity for analysis of monoclonal antibodies purified from harvested cell culture fluid

Size exclusion chromatography (SEC) is widely used in the characterization and quality control of therapeutic proteins to detect aggregates. Aggregation is a carefully monitored quality attribute from the earliest stages of clinical development owing to the possibility of eliciting an immunogenic response in the patient. During early stage molecule assessment for cell culture production, small-scale screening experiments are performed to permit rapid turn-around of results so as to not delay timelines. We report the development of a capillary SEC methodology for preliminary molecule assessment to support the evaluation of therapeutic candidates at an early stage of development. By making several key modifications to a commercially available liquid chromatography system, we demonstrate a platform process to perform capillary SEC with excellent precision, picogram sensitivity and good ruggedness. The limit of quantitation was determined to be approximately 15 pg; picogram sensitivity for SEC analysis of monoclonal antibodies had not been achieved prior to this work. In addition, we have developed a method to capture low levels of antibody (1 μg/mL) from harvested cell culture fluid (HCCF) for capillary SEC analysis. Up to 40% recovery efficiency was achieved using this micro-recovery method on 3 mL HCCF samples. Using early stage cell culture transient transfection samples, which typically have much lower titers than stable cell line samples, we demonstrate a consistent method for analyzing aggregates in low protein concentration HCCF samples for molecule assessment and early stage candidate screening.     

Microstructure determination of AOT + phenol organogels utilizing small-angle X-ray scattering and atomic force microscopy.

Dry reverse micelles of the anionic twin-tailed surfactant bis(2-ethylhexyl) sulfosuccinate (AOT) dissolved in nonpolar solvents spontaneously form an organogel when p-chlorophenol is added in a 1:1 AOT:phenol molar ratio. The solvents used were benzene, toluene, m-xylene, 2,2,4-trimethylpentane (isooctane), decane, dodecane, tetradecane, hexadecane, and 2,6,10,14-tetramethylpentadecane (TMPD). The proposed microstructure of the gel is based on strands of stacked phenols linked to AOT through hydrogen bonding. Small-angle X-ray scattering (SAXS) spectra of the organogels suggest a characteristic length scale for these phenol-AOT strands that is independent of concentration but dependent on the chemical nature of the nonpolar solvent used. Correlation lengths determined from the SAXS spectra indicate that the strands self-assemble into fibers. Direct visualization of the gel in its native state is accomplished by using tapping mode atomic force microscopy (AFM). It is shown that these organogels consist of fiber bundle assemblies. The SAXS and AFM data reinforce the theory of a molecular architecture consisting of three length scales-AOT/phenolic strands (ca. 2 nm in diameter) that self-assemble into fibers (ca. 10 nm in diameter), which then aggregate into fiber bundles (ca. 20-100 nm in diameter) and form the organogel.     

Analysis of fluorescently labeled substance P analogs: binding, imaging and receptor activation

Background  

Substance P (SP) is a peptide neurotransmitter found in central and peripheral nerves. SP is involved in the control of smooth muscle, inflammation and nociception. The amino acid sequence of SP is Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH₂. Five different forms of fluorescently labeled SP have recently been synthesized, in which Alexa 488, BODIPY Fl, fluorescein, Oregon Green 488 or tetramethylrhodamine has been covalently linked to SP at Lys³. Here, these novel analogs are characterized as to their ligand binding, receptor activation and fluorescence labeling properties.     

Phase Transfer Catalysis Preparation of Arvl,Thiocyanates

Phase transfer catalvsis, PTC, has become a common preparative method in organic chemistry. Numerous aliphatic substitution reactions have been performed yielding cvanides,¹ azides,² thiocyanates,³ ethers,⁴ and many other types of substitution products.¹     

Phase Transfer Catalysis Preparation of Acyl Isothiocyanates

The use of phase transfer catalysis, PTC, for nucleophillic substitution reactions is well documented.^1,2 Included among these reactions is the preparation of both alkyl³ and aryl⁴ thiocyanates. However, PTC reactions at an acyl carbon are much less common. Brándstróm⁵ has reported the preparation of acyl azides and Weber⁶ has used PTC to prepare benzoyl cyanide. Recently Illi⁷ has used PTC to acylate sterically crowded phenols.     

A Mössbauer spectroscopy and neutron diffraction study of magnetostrictive,melt-spun Fe–Ga alloy ribbons

Ribbons of Fe_100−xGa_x (x=15, 17.5, 19.5 and 22.5) were prepared by rapid solidification from the melt. ⁵⁷Fe Mössbauer spectroscopy and high resolution neutron diffraction have revealed that Fe_100−xGa_x alloys with x=15 and 17.5 have the disordered bcc (A2) structure even after annealing, but the alloy with x=19.5 developed the short-range ordered D0₃ phase when annealed. The x=22.5 alloys showed mainly D0₃ phase with a fraction of bcc phase. A fraction of the bcc phase transformed into D0₃ phase and the long-range ordering of D0₃ phase was improved after annealing. ⁵⁷Fe Mössbauer spectra showed no observable L1₂ phase in any samples even though less than 1% volume of L1₂ phases has been found in the annealed samples by neutron diffraction. The additional absorption at hyperfine field of 25 T in x=22.5 samples was regarded as a result of imperfect D0₃ structure, rather than L1₂ phase.