Spectroscopic study of a representative polar cap of buckminsterfullerene: Cyclopentacorannulene

The spectroscopic properties of corannulene and cyclopentacorannulene are examined by use of absorption and steady-state fluorescence measurements. A red shift in the emission maxima of cyclopentacorannulene is noted with respect to the emission maxima in the corannulene spectrum. Similar differences in the absorption spectra of both molecules are also observed. Reasons for the dissimilarities in the absorption and emission spectra of these molecules are discussed. The fluorescence quantum yields and lifetimes of the molecules measured in organic solvents are reported. The fluorescence quantum yield and lifetime of cyclopentacorannulene are lower than those of corannulene. This difference is attributed to the highly strained and nonplanar structure of cyclopentacorannulene. The effectiveness of nitromethane as a quencher of corannulene and cyclopentacorannulene fluorescence is examined. In contrast to previously reported results, the fluorescence of these molecules is quenched by nitromethane. Fluorescence quenching of the molecules has been attributed to complex formation in the ground state, i.e., static quenching.     

Using semiseparable matrices to compute the SVD of a general matrix product/quotient

In this work we reduce the computation of the singular values of a general product/quotient of matrices to the computation of the singular values of an upper triangular semiseparable matrix. Compared to the reduction into a bidiagonal matrix the reduction into semiseparable form exhibits a nested subspace iteration. Hence, when there are large gaps between the singular values, these gaps manifest themselves already during the reduction algorithm in contrast to the bidiagonal case.     

Compatible Structures on Lie Algebroids and Monge-Ampère Operators

We study pairs of structures, such as the Poisson-Nijenhuis structures, on the tangent bundle of a manifold or, more generally, on a Lie algebroid or a Courant algebroid. These composite structures are defined by two of the following, a closed 2-form, a Poisson bivector or a Nijenhuis tensor, with suitable compatibility assumptions. We establish the relationships between PN-, P Ω- and Ω N-structures. We then show that the non-degenerate Monge-Ampère structures on 2-dimensional manifolds satisfying an integrability condition provide numerous examples of such structures, while in the case of 3-dimensional manifolds, such Monge-Ampère operators give rise to generalized complex structures or generalized product structures on the cotangent bundle of the manifold.     

Interaction of self-assembled monolayers of DNA with electrons: HREELS and XPS studies

We present results from high-resolution electron energy loss spectroscopy (HREELS) and XPS studies of self-assembled monolayers of DNA. The monolayers are well-organized and display sharp vibrational peaks in the HREEL spectra. The electrons interact mainly with the backbone of the DNA. The XPS results indicate that, in most of the samples studied, the phosphates on the DNA are not charged.     

Torsional anharmonicity in the conformational analysis of tryptamine

In this paper we calculate the relative conformer populations of the tryptamine molecule. Our approach combines high level electronic structure conformer energies with harmonic frequencies and an anharmonic treatment of the torsional motions using the torsional path integral Monte Carlo method. We have developed a 3-D potential energy surface as a function of the torsional coordinates at the B3LYP/6-31+G(d) level using 2535 grid points. Eight conformers of tryptamine were found to be significantly populated at 430 K as opposed to the experimental observation of seven. This, along with further comparisons with various experimental data, leads us to suppose that conformer interconversion occurs during the cooling phases of many of the experiments. The ordering of the calculated populations fits well with available experimental data. Torsional anharmonicity is found to affect conformer populations more significantly at 430 K than at 100 K (although overall the effects are small), while quantum mechanical effects are not important at either temperature.     

Torsional anharmonicity in transition state theory calculations

We present a new application for the Torsional Path Integral Monte Carlo (TPIMC) method in which the TPI partition functions are introduced into the calculation of Transition State Theory (TST) rate constants. In this way, an explicit treatment of torsional anharmonicity is included in the TST calculations and the magnitude of these effects can be assessed. The new method is tested on the C(2)H(6) + H hydrogen abstraction reaction and concerted hydrogen transfer in the carbonic acid dimer, for which we have developed torsional potential energy surfaces. For the C(2)H(6) + H reaction the rate constants are halved at room temperature on including a treatment of torsional anharmonicity, while the effects are found to be much smaller for the hydrogen transfer reaction in the carbonic acid dimer.     

Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies

Whole genome amplification (wga) of DNA is being widely implemented in many laboratories to extend the life of samples only available in limited quantities for genetic analysis. We determined the reliability of wgaDNA genotypes in three sets of replicates from the same individuals: (i) 23 pairs of genomic DNA (gDNA), (ii) 43 pairs gDNA versus wgaDNA, and (iii) 29 pairs of independently amplified wgaDNA. Amplification was performed using multiple displacement amplification (MDA). Genotyping was successful for both DNA types for 1268 out of 1534 SNPs from 164 cardiovascular candidate genes assayed in a single Illumina panel. Amplified DNA failed for 77 SNPs (6%) that were genotyped successfully with genomic material. Percent of successful SNP calls, and concordance between pairs and kappa statistics (kappa) were determined. A total of 54 110 genotypes from gDNA-wgaDNA pairs were available for concordance analysis. Mean kappa for gDNA-wgaDNA pairs was 0.99. Concordance between gDNA-wgaDNA pairs was higher than amongst wgaDNA pairs (mean kappa for the 29 independently amplified pairs of wgaDNA was 0.95; interquartile range: 0.93-1.00). A statistical analysis of those SNPs which failed to genotype from amplified DNA only revealed that those loci were more likely to be closer to the telomeres and in locally GC-rich sequences. In summary, the MDA method produces wgaDNA samples that can be genotyped using high-throughput technology with a very high reproducibility to the original DNA but with slightly lower call rates. DNA amplification methodologies provide a useful solution for current and future large-scale genetic analyses especially with limited quantities of samples and DNA.     

State of the art in the delivery of photosensitizers for photodynamic therapy

In photodynamic therapy, one of the problems limiting the use of many photosensitizers (PS) is the difficulty in preparing pharmaceutical formulations that enable their parenteral administration. Due to their low water solubility, the hydrophobic PS cannot be simply injected intravenously. Different strategies, including polymer-PS conjugation or encapsulation of the drug in colloidal carriers such as oil-dispersions, liposomes and polymeric particles, have been investigated. Although these colloidal carriers tend to accumulate selectively in tumour tissues, they are rapidly taken up by the mononuclear phagocytic system. In order to reduce this undesirable uptake by phagocytic cells, long-circulating carriers that consist of surface modified carriers have been developed. Moreover, considerable effort has been directed towards using other types of carriers to improve tumour targeting and to minimize the side effects. One of the approaches is to entrap PS into the lipophilic core of low-density lipoproteins (LDL) without altering their biological properties. The LDL receptor pathway is an important factor in the selective accumulation of PS in tumour tissue owing to the increased number of LDL receptors on the proliferating cell surface. Specific targeting can also be achieved by binding of monoclonal antibodies or specific tumour-seeking molecules to PS or by the coating of PS loaded carriers.