Surface-enhanced Raman spectral measurements of 5-fluorouracil in saliva

The ability of surface-enhanced Raman spectroscopy (SERS) to measure 5-fluorouracil (5-FU) in saliva is presented. The approach is based on the capacity of Raman spectroscopy to provide a unique spectral signature for virtually every chemical, and the ability of SERS to provide microg/mL sensitivity. A simple sampling method, that employed 1-mm glass capillaries filled with silver-doped sol-gels, was developed to isolate 5-FU from potential interfering chemical components of saliva and simultaneously provide SERSactivity. The method involved treating a 1 mL saliva sample with 1 mL of acetic acid, drawing 10 microL of sample into a SERS-active capillary by syringe, and then measuring the SER spectrum. Quality SER spectra were obtained for samples containing as little as 2 microg of 5-FU in 1 mL saliva. The entire process, the acid pretreatment, extraction and spectral measurement, took less than 5 minutes. The SERS of 5-fluorouridine and 5-fluoro-2'-deoxyuridine, two major metabolites of 5-FU, were also measured and shown to have unique spectral peaks. These measurements suggest that disposable SERS-active capillaries could be used to measure 5-FU and metabolite concentrations in chemotherapy patient saliva, thereby providing metabolic data that would allow regulating dosage. Tentative vibrational mode assignments for 5-FU and its metabolites are also given.     

Contribution of charged groups to the enthalpic stabilization of the folded states of globular proteins

In this paper we use the results from all-atom molecular dynamics (MD) simulations of proteins and peptides to assess the individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the "unfolded state") and charged amino acids in globular proteins (the "folded state"). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO(-)) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while N(+)(3) groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously.     

Optimized quantum mechanics/molecular mechanics strategies for nitrile vibrational probes: acetonitrile and para-tolunitrile in water and tetrahydrofuran

The nitrile (Ctriple bondN) group is a powerful probe of structure and dynamics because its vibrational frequency is extraordinarily sensitive to the electrostatic and chemical characteristics of its local environment. For example, site-specific nitrile labels are useful indicators of protein structure because their infrared (IR) absorption spectra can clearly distinguish between solvent-exposed residues and residues buried in the hydrophobic core of a protein. In this work, three variants of the optimized quantum mechanics/molecular mechanics (OQM/MM) technique for computing Ctriple bondN vibrational frequencies were developed and assessed for acetonitrile in water. For the most robust variant, the transferability of the OQM/MM methodology to different solutes and solvents was evaluated by simulating the IR absorption spectra of para-tolunitrile in water and tetrahydrofuran and comparing to experiment and density functional theory (DFT) calculations. The OQM/MM frequencies compared favorably to DFT for para-tolunitrile/water, and the calculated IR absorption spectra are in qualitative agreement with experiment. This suggests that a single parametrization of the OQM/MM technique is reasonable for the calculation of nitrile line shapes when the probe is attached to different chemical moieties and when the label experiences local environments of different polarity.     

Stability of polydimethylsiloxane-magnetite nanoparticle dispersions against flocculation: interparticle interactions of polydisperse materials

The colloidal stability of dispersions comprised of magnetite nanoparticles coated with polydimethylsiloxane (PDMS) oligomers was investigated theoretically and experimentally. Particle-particle interaction potentials in a theta solvent and in a good solvent for the PDMS were predicted by calculating van der Waals, electrostatic, steric, and magnetic forces as functions of interparticle separation distances. A variety of nanoparticle sizes and size distributions were considered. Calculations of the interparticle potential in dilute suspensions indicated that flocculation was likely for the largest 1% of the population of particles. Finally, the rheology of these complexes over time in the absence of a solvent was measured to probe their stabilities against flocculation as neat fluids. An increase in viscosity was observed upon aging, suggesting that some agglomeration occurs with time. However, the effects of aging could be removed by exposing the sample to high shear, indicating that the magnetic fluids were not irreversibly flocculated.     

Infrared-vacuum ultraviolet-pulsed field ionization-photoelectron study of CH(3)I(+) using a high-resolution infrared laser

By using a high-resolution single mode infrared-optical parametric oscillator laser to prepare CH(3)I in single (J,K) rotational levels of the nu(1) (symmetric C-H stretching) =1 vibrational state, we have obtained rovibrationally resolved infrared-vacuum ultraviolet-pulsed field ionization-photoelectron (IR-VUV-PFI-PE) spectra of the CH(3)I(+)(X(2)E(32);nu(1)(+)=1;J(+),P(+)) band, where (J,K) and (J(+),P(+)) represent the respective rotational quantum numbers of CH(3)I and CH(3)I(+). The IR-VUV-PFI-PE spectra observed for K=0 and 1 are found to have nearly identical structures. The IR-VUV-PFI-PE spectra for (J,K)=(5,0) and (7, 0) are also consistent with the previous J-selected IR-VUV-PFI-PE measurements. The analysis of these spectra indicates that the photoionization cross section of CH(3)I depends strongly on DeltaJ(+)=J(+)-J: but not on J and K. This observation lends strong support for the major assumption adopted for the semiempirical simulation scheme, which has been used for the simulation of the origin bands observed in VUV-PFI-PE study of polyatomic molecules. Using the state-to-state photoionization cross sections determined in this IR-VUV study, we have obtained excellent simulation of the VUV-PFI-PE origin band of CH(3)I(+)(X (2)E(32)), yielding more precise IE(CH(3)I)=76 930.7+/-0.5 cm(-1) and nu(1) (+)=2937.8+/-0.2 cm(-1).     

Cationic photopolymerizations of thick polymer systems: Active center lifetime and mobility

Cationic photopolymerizations are essentially non-terminating and the long-lived active centers may lead to “dark cure” long after the illumination has ceased. In this contribution, it is shown that long cationic active center lifetimes known to be responsible for dark cure can also lead to “shadow cure” of unilluminated regions of thick systems. “Shadow cure” occurs when the active centers migrate out of the illuminated region, leading to polymerization of unexposed monomer. Photopolymerizations of a cycloaliphatic diepoxide monomer were performed in which active centers were produced in the first 0.7 mm of a thick system by illuminating one end of the sample, and the shadow cure was monitored up to 8 h. A polymerization front (with a highly crosslinked polymer matrix on one side and unreacted monomer on the other) was observed to move from the illuminated region into the shadow region at a rate proportional to the square root of time. The effective shadow cure diffusion coefficient at 50 °C was found to be 1 × 10⁻⁵ cm²/s, and the temperature dependence of the diffusion coefficient was well described by the Arrhenius relationship with an activation energy of 89 kJ/mol. Studies based upon photoinitiator counter-ions of differing size revealed that the system with the larger counter-ion (and therefore a correspondingly higher propagation rate constant) exhibited a significantly higher effective shadow cure diffusion coefficient. All of the experimental observations are consistent with the hypothesis that the active center mobility responsible for shadow cure arises largely from reactive diffusion.     

Quenching mechanism of Zn(salicylaldimine) by nitroaromatics

Nitroaromatics and nitroalkanes quench the fluorescence of Zn(Salophen) (H2Salophen = N,N'-phenylene-bis-(3,5-di- tert-butylsalicylideneimine); ZnL(R)) complexes. A structurally related family of ZnL(R) complexes (R = OMe, di-tBu, tBu, Cl, NO2) were prepared, and the mechanisms of fluorescence quenching by nitroaromatics were studied by a combined kinetics and spectroscopic approach. The fluorescent quantum yields for ZnL(R) were generally high (Phi approximately 0.3) with sub-nanosecond fluorescence lifetimes. The fluorescence of ZnL(R) was quenched by nitroaromatic compounds by a mixture of static and dynamic pathways, reflecting the ZnL(R) ligand bulk and reduction potential. Steady-state Stern-Volmer plots were curved for ZnL(R) with less-bulky substituents (R = OMe, NO2), suggesting that both static and dynamic pathways were important for quenching. Transient Stern-Volmer data indicated that the dynamic pathway dominated quenching for ZnL(R) with bulky substituents (R = tBu, DtBu). The quenching rate constants with varied nitroaromatics (ArNO2) followed the driving force dependence predicted for bimolecular electron transfer: ZnL* + ArNO2 --> ZnL(+) + ArNO2(-). A treatment of the diffusion-corrected quenching rates with Marcus theory yielded a modest reorganization energy (lambda = 25 kcal/mol), and a small self-exchange reorganization energy for ZnL*/ZnL(+) (ca. 20 kcal/mol) was estimated from the Marcus cross-relation, suggesting that metal phenoxyls may be robust biological redox cofactors. Electronic structure calculations indicated very small changes in bond distances for the ZnL --> ZnL(+) oxidation, suggesting that solvation was the dominant contributor to the observed reorganization energy. These mechanistic insights provide information that will be helpful to further develop ZnL(R) as sensors, as well as for potential photoinduced charge transfer chemistry.