Genetic, genomic and physiological state studies on single-needle bio-electrosprayed human cells

Bio-electrospraying, a non-contact jet-based direct cell engineering approach, was recently pioneered and demonstrated for handling a wide range of primary living cells. In those studies, post-treated cells were biologically assessed in comparison to several controls by way of flow cytometry. Although flow cytometry accurately assesses those viable populations of cells, subtle effects at a sub-cellular level could have been missed. Therefore, in the present study we demonstrate metaphase chromosome breakage studies carried out on single-needle bio-electrosprayed human T-lymphocytes, which are compared with several controls. The results indicate that post-treated T-lymphocytes do not demonstrate any increase in chromosome damage in comparison to control cells. These studies further validate bio-electrospraying as a technique with potential for clinical utility.     

Structural isomerism of mono- and sesquiterpenoid skeletons

A generator of chemical structures (CONGEN) has been utilized to investigate two aspects of the structural isomerism of mono- and sesquiterpenoid skeletons: (1) the scope of possible isomers under various structural constraints; and (2) the scope of possible isomers based on a mechanistic model which allows interactive exploration of reactions of formation and interconversion. The possibilities, even under severe constraints, are many more than the structural types commonly encountered in natural. These results indicate the potential danger of structural assignment based in part on biogenic grounds.     

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

Background

Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding.

Results

We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.

Conclusion

Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.     

Intramolecular carbozincation of unactivated alkenes occurs through a zinc radical transfer mechanism

The cyclizations of a number of terminally unsaturated alkenyl zinc iodides to cyclopentylmethylzinc iodides, formerly believed to be nonradical in nature, have been revealed as radical chain cyclizations initiated by adventitious oxygen. Five cases are presented in which the published carbozincation cis/trans selectivities are essentially the same as those found for the cyclizations of the unsaturated alkyl iodide precursors of the alkylzinc iodides by the iodine atom transfer method at approximately the same temperatures. In addition, it has been found that one of the organozinc cyclizations does not occur in a system in which oxygen has been rigorously excluded. The combined findings strongly suggest that these organozinc cyclizations occur by a zinc radical transfer mechanism rather than by a conventional carbometallation that is thought to occur with the analogous organolithium and organomagnesium cyclizations.     

Products and mechanism of acene dimerization. A computational study

The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso-carbon atoms of the central ring of acene blocks the reactivity of this ring but does not efficiently prevent dimerization through other rings.     

The spin-orbit and rotational constants for the N2 C" 5Pi(ui) (v = 3) state

The spin-orbit (A = -16.4 cm(-1)) and rotational (B = 1.017 cm(-1)) constants for the N2 C" 5Pi(ui)(v = 3) level are determined by a fit to rotational lines in the C" 5Pi(u)-A' 5Sigma(g)+(3-1) band that terminate in J'Omega' = 3(3), 4(3), 3(2), and 4(2) levels of the C" state. The C"-state spin-orbit constant is consistent with semi-empirical estimates, based on spin-orbit constants observed in several other electronic states of N2 and the atomic spin-orbit coupling constant, zeta(N 2p). The C"-A' bands exhibit the unusual feature of oppositely degraded sub-band heads, Omega' = 3 (red) and Omega' = 1, 0, and -1 (blue). The unusually wide range of B(Omega)eff values, from 0.85 cm(-1) (Omega = 3) to 1.28 cm(-1) (Omega = -1) for C" 5Pi(v = 3) should be diagnostically useful for Omega'-assignments. The C" 5Pi(v = 3) level lies 14257.17 and 90599 cm(-1) above A' 5Sigma(g)+(v = 1) and X 1Sigma(g)+(v = 0), respectively, and Re(C" 5Pi) = 1.50 A.     

Deconvolution filters to enhance resolution of dense time-of-flight survey spectra in the time-lag optimization range

By applying time-domain filters to time-of-flight (TOF) mass spectrometry signals, we have simultaneously smoothed and narrowed spectra resulting in improved resolution and increased signal-to-noise ratios. This filtering procedure has an advantage over detailed curve fitting of spectra in the case of large dense spectra, when neither the location nor the number of mass peaks is known a priori. This time series method is directly applicable in the time lag optimization range, where point density per peak is constant. We present a systematic methodology to optimize the filters according to any desired figure of merit, illustrating the procedure by optimizing the signal-to-noise per unit bandwidth of matrix-assisted laser desorption/ionization (MALDI) data. We also introduce a nonlinear filter that reduces the spurious structure that often accompanies deconvolution filters. The net result of the application of these filters is that we can identify new structures in dense MALDI-TOF data, clearly showing small adducts to heavy biomolecules.     

Modulation gap detection: effects of modulation rate, carrier separation, and mode of presentation.

Modulation gap detection (MGD) is a procedure that measures the sensitivity to an interruption in the modulation pattern imposed upon one or more carrier frequencies. The MGD task was developed to test conditions where a temporal event traverses frequency, but without a concomitant interruption in the spectral continuity of the stimulus. This contrasts with across-frequency gap detection where there is an inherent spectral discontinuity associated with the temporal gap, and where there is a marked decline in performance when the markers of the temporal gap are widely separated in frequency. The purpose of this study was to test the hypothesis that a wideband temporal analysis will be facilitated if there exists a spectral continuity throughout the temporal event. Experiment 1 established the procedure of MGD and indicated that a modulation rate of 8 Hz was optimal for the task. Experiment 2 showed that performance declined markedly when the carrier frequencies of the modulation markers were widely separated in frequency. This finding indicates that spectral continuity across the temporal event is not a sufficient prerequisite for the auditory system to undertake a wideband temporal analysis. Experiment 3 revealed that dichotic MGD also results in poor performance, similar to that seen for widely separated carrier frequencies in the monaural case. This supports the hypothesis that the "channels" across which temporal events are poorly processed do not necessarily correspond to peripheral frequency channels.     

Correlation of the rates of solvolysis of benzoyl fluoride and a consideration of leaving-group effects

The specific rates of solvolysis of benzoyl fluoride have been determined at 25.0 degrees C in 37 pure and binary solvents. Together with seven values from the literature, these give a satisfactory correlation over the full range of solvents when the extended Grunwald-Winstein equation is applied. The sensitivities to changes in solvent nucleophilicity and solvent ionizing power are very similar to those for octyl fluoroformate, suggesting that the addition step of an addition-elimination mechanism is rate determining. In the solvent-composition region where benzoyl chloride also shows bimolecular solvolysis, the appreciable k(Cl)/k(F) values are proposed as being primarily due to a more efficient ground-state stabilization for the fluoride.     

Internal rotation and pyramidal inversion in triacylphosphines

MO calculations predict a P-C rotation barrier in triformylphosphine of less than 6 kcal/mol, and an inversion barrier of ca 14 kcal/mol.