Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

Extrusion processing for ammonia fiber explosion (AFEX)

The ammonia fiber explosion (AFEX) process, previously run only in a batch reactor, has been adapted to run on a twin-screw extruder. The sugar yield of AFEX material after enzymatic hydrolysis has been increased up to 3.5 times over that of completely untreated material. The ruminant digestibility of corn fodder has been increased up to 32% (from 54–71%) over completely untreated material, and 23% (from 63–77%) over material extruded with no ammonia. Extrusion-treated material proved more digestible by the ruminant at 48 h than material treated in the batch reactor.     

A data mining and ab initio study of the interaction between the aromatic and backbone amide groups in proteins

Interactions between aromatic groups and backbone amide groups in protein environments are characterized both through data mining analyses of X‐ray protein structures and through ab initio molecular orbital calculations on a model complex. The data mining analyses of 1029 X‐ray protein structures elucidate the configurational characteristics of the interaction as well as the positions of the interacting moieties involved. On a statistical average, more than seven such interactions occur in a typical protein structure. The configurations of these interactions are restricted with the face‐to‐face orientation as the preferred arrangement. The interaction occurs mainly within a single peptide chain. Both α‐helix and β‐strand secondary structures provide an almost equal number of backbone amides to participate within this interaction. The interaction energy was evaluated with the supermolecular ab initio method at the MP2 level. It is shown that aromatic–amide(backbone) interactions identified in proteins can achieve a stabilization energy of 3.3 kcal/mol. The interaction involves the entirety of the backbone amide rather than only its amine portion. This study concludes that the interaction between aromatic and backbone amide groups is of general significance to protein structure due to its strength and common occurrence. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 44–60, 2000     

Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0

Three genetic algorithm programs, GAP 1.0, 2.0, and 3.0, were used in conjunction with the ECEPP/2 force field to search the conformation space of [Met]-enkephalin. Each program was proficient at quickly finding many diverse low-energy conformers. Conformer populations displayed a variety of secondary structure motifs including those likely to bind to the μ-opioid receptor. Limitations in the program's sampling behavior are discussed and method improvements are suggested. Although still in a developmental stage, the GAP programs represent a useful addition to conformational search techniques when no a priori structural information is available. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1329–1342, 1999     

Mechanism of PdO thin film formation during the oxidation of Pd(1 1 1)

We investigated the mechanism by which a surface oxide layer on Pd(1 1 1) transforms to a PdO(1 0 1) thin film during oxidation with gaseous oxygen atoms in ultrahigh vacuum. Our results provide evidence that the precursor to bulk PdO formation is a distinct oxide phase that forms as small particles, referred to as PdO seeds, after the surface oxide saturates. With increasing oxygen coverage, the PdO seeds grow in size and eventually transform to more stable particles that agglomerate to yield a PdO film. Oxidation effectively ceases when the surface oxide layer is completely replaced by the bulk PdO film, demonstrating that the surface oxide is needed for PdO formation at the conditions studied. Both the kinetics of PdO formation and the final thickness of the PdO thin film depend strongly on the thermal stability of the PdO seeds. Below the decomposition temperature of the seeds (600 K), oxidation follows kinetics similar to Langmuirian adsorption and appears to be limited only by the rate of oxygen adsorption onto the surface oxide. In contrast, PdO formation above 600 K initially exhibits acceleratory kinetics, with the rates starting low but increasing steadily during the initial growth of PdO. We also observe a significant decrease in PdO(1 0 1) film thickness and improved crystallinity when oxidation is conducted below 600 K. We show that the trends observed in the oxidation kinetics and film thickness can be qualitatively explained within the context of a model in which the thermodynamic stability of PdO particles increases with increasing particle size and PdO seeds/particles coexist with a two-dimensional (2D) gas of oxygen atoms adsorbed on the surface oxide layer. This model suggests that the PdO particle-2D gas coexistence relation gives rise to three distinct growth regimes, namely, stable seed nucleation, metastable seed nucleation and oxygen dissolution into the subsurface where the latter is established at 2D gas coverages below the stability limit of a flat PdO surface.     

Excited-state mixed-valence distortions in a diisopropyl diphenyl hydrazine cation

Excited-state mixed valence (ESMV) occurs in the 1,2-diphenyl-1,2-diisopropyl hydrazine radical cation, a molecule in which the ground state has a symmetrical charge distribution localized primarily on the hydrazine, but the phenyl to hydrazine charge-transfer excited state has two interchangeably equivalent phenyl groups that have different formal oxidation states. Electronic absorption and resonance Raman spectra are presented. The neighboring orbital model is employed to interpret the absorption spectrum and coupling. Resonance Raman spectroscopy is used to determine the excited-state distortions. The frequencies of the enhanced modes from the resonance Raman spectra are used together with the time-dependent theory of spectroscopy to fit the two observed absorption bands that have resolved vibronic structure. The origins of the vibronic structure and relationships with the neighboring orbital model are discussed.     

Advantages of deuterium-labelled mixed triacylglycerol in studies of intraluminal fat digestion

The (13)C-mixed triacylglcerol (MTG, 1,3-distearyl, 2-[1-(13)C]octanoyl glycerol) breath test is a non-invasive measure of intraluminal fat digestion. Recovery of (13)C in breath CO(2) is incomplete (<50%) owing to sequestration of (13)C into organic molecules via the tricarboxylic acid (TCA) cycle. In addition lack of knowledge of CO(2) production rate (VCO(2)) during the test leads to errors in the calculated percentage dose recovered (PDR). (2)H sequestration into organic molecules is low ( approximately 4%) and is not influenced by factors that affect VCO(2) such as food intake or physical activity. After oxidation of (2)H-labelled macromolecules, the label appears in body water, which can be sampled non-invasively in urine or saliva. After an overnight fast, two healthy adults consumed [(2)H]MTG (1,3-distearyl, 2-[(2)H(15)]octanoyl glycerol) and [(13)C]MTG (1,3 distearyl, 2-[1-(13)C]octanoyl glycerol) simultaneously. Total body water (TBW) was measured by (18)O dilution and also estimated from height and weight. Urine and saliva were sampled at baseline and for 10 h after consumption of the test meal. The abundance of (2)HOH and H(2) (18)O in urine and saliva was measured by continuous-flow isotope-ratio mass spectrometry. Cumulative PDR of (2)H and (18)O was calculated from the plateau enrichment, which was reached by 6 h in both saliva and urine. Recovery of (2)H calculated using measured TBW was compared with that using an estimated value of TBW. Mean recovery of (2)H in saliva was 99.3% and in urine was 96.4%. Errors introduced by estimating TBW were <5%. [(2)H]MTG could provide a simpler, more robust, indirect test of intraluminal fat digestion compared with the (13)C-breath test. Further studies are required in pancreatic insufficient patients.     

Effect of block length, polydispersity, and salt concentration on PEO-PDEAMA block copolymer structures in dilute solution

A series of poly(ethylene oxide)-block-poly(N,N-diethylaminoethyl methacrylate) (PEO-PDEAMA) block copolymers with relatively high polydispersity (1.36 < PDI < 1.96) have been prepared to determine the effect that polydispersity has on the self-assembly of amphiphilic block copolymers in dilute solution. Because monodisperse macroinitiators were used for the ATRP reactions, the polydispersity resides within the hydrophobic block. By adjusting the relative block lengths, spherical micelles, wormlike micelles, vesicles, or a precipitate is formed. Here, we show that relatively high polydispersity in the block copolymer does not preclude efficient self-assembly. We also discuss the effect of increasing the concentration of NaCl in the systems and show that this can result in a shift from one morphology to another. These shifts are reversible in some cases, but for PEO12-PDEAMA39, this method allows access to giant vesicles of between 500 nm and 1 microm in diameter.     

Anticipating colloidal instabilities in cationic vesicle dispersions by measuring collective motions with dynamic light scattering

Vesicle dispersions are useful for many applications from medicinal to consumer products. However, using these dispersions requires some knowledge of and control over their colloidal properties. Measuring interparticle interactions between vesicles should allow framing the problem in terms of Smoluchowski kinetic models and consequently anticipating time-dependent aggregation and coalescence for the dispersions. However, this can be a difficult task for many complex mixtures. A primary goal of this paper is to show that it is possible to measure interparticle potential between small vesicles by measuring the concentration-dependent collective motion using dynamic light scattering. These measurements allow determination of the second virial coefficient for the dispersion, providing a convenient platform for summing all contributions to the interaction potential over all vesicle conformations, thus making the analysis of complex mixtures more tractable. As a verification of the approach, a comparison is made to dispersions in which the stability is governed solely by electrostatics, using existing techniques to anticipate instabilities. A second goal of this paper is to build a simple potential model in which the Smoluchowski model can be used to quantitatively anticipate the aggregation behavior of the small vesicle dispersion. Together, these observations constitute a convenient approach to anticipating the behavior of vesicle (and other) dispersions in complex mixtures.     

Optical spectra of protected diamine 10-bond-bridged intervalence radical cations related to N,N,N'N'-tetraalkylbenzidine

The optical absorption spectra of the delocalized intervalence radical cations of seven o,o'-linked benzidine derivatives that have the nitrogens protected as 9-(9-aza-bicyclo[3.3.1]nonan-3-one) derivatives are discussed and compared with that of the p-phenylene radical cation. The linking units are CH2, CH2CH2, NMe, S, SO2, and C=O, and we also studied H,H (the unlinked benzidine). The lowest-energy absorption band is assigned as the transition from the antibonding combination of symmetrical N and aromatic orbitals to the antibonding combination of the antisymmetric N and aromatic orbitals using TD-DFT calculations, and a good correlation between the observed transition energies and those calculated using the simple Koopmans theorem-based "neutral in-cation geometry" calculations on the UB3LYP/6-31G* structures is found. The use of the two-state model that equates the electronic interaction through the bridge between the amino groups with half of the lowest transition energy is seriously incorrect for these and other delocalized intervalence compounds. The problem of extracting the electronic interactions that actually are involved from calculated transition energies is discussed.