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1. Enhancing exciton diffusion in porphyrin thin films using peripheral carboalkoxy groups to influence molecular assembly

Author

Angy L. Ortiz, Gaurav Singh, Taesoo Lee, Nikolas Hall, Michael G. Walter, Meesha Kaushal, and Jennifer A. Kassel

Subjects
chemistry.chemical_classification, Quenching (fluorescence), Photoluminescence, Materials science, biology, Diffusion, Exciton, 02 engineering and technology, General Chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, biology.organism_classification, Photochemistry, 01 natural sciences, Porphyrin, 0104 chemical sciences, chemistry.chemical_compound, chemistry, Materials Chemistry, Tetra, Physical chemistry, Singlet state, 0210 nano-technology, Alkyl
Abstract

The effects of molecular arrangement on the singlet exciton diffusion properties of free-base carboalkoxyphenylporphyrins containing a variety of alkyl substituents were investigated in solution-cast thin films. Exciton diffusivity was calculated using relative quenching efficiencies (Q) obtained by measuring the singlet photoluminescent decay lifetime PL(t) of pristine porphyrin films and films doped with 0.06–0.2% volume fraction of [6,6]-phenyl-C61-butryic acid methyl ester (PCBM). The quenching efficiency and PL lifetime decay data was used in a 3D exciton diffusion Monte Carlo simulation model to extract the exciton diffusion coefficient (D) and diffusion length (LD). Five carboalkoxyphenyl porphyrins (TCAPPs) were synthesized and analyzed in solution-cast thin films, tetra(4-carbomethoxyphenyl)porphyrin (TCM4PP), tetra(4-carbobutoxyphenyl) porphyrin (TCB4PP), tetra(4-carbohexoxyphenyl)porphyrin (TCH4PP), tetra(4-carbo-2-ethylhexoxyphenyl) porphyrin (TCEH4PP), and tetra(4-carbooctoxyphenyl)porphyrin (TCO4PP). Longer alkyl chain derivatives yielded increased PL decay lifetimes and extended the exciton diffusion lengths (LD) for octyl (TCO4PP) and hexyl (TCH4PP) porphyrin derivatives. We observed an increase in the LD from 15 nm for TCM4PP to 25 nm for TCH4PP, while a branched alkyl chain derivative (TCEH4PP) showed the lowest LD of 14 nm. UV-Vis and XRD data indicate that molecular organization is strongly dependent upon the peripheral carboalkoxy chain, and that nematic molecular organization resulted in an increase in the exciton diffusion length. Our findings are an important step toward a deeper understanding of the exciton diffusivity and molecular packing relationship of simple free-base porphyrins.

Published
2016
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2. Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions

Author

Nikolas Hallberg Thuesen, Michael Schantz Klausen, Shyam Gopalakrishnan, Thomas Trolle, and Gabriel Renaud

Subjects
human leukycote antigen, next-generation sequencing (NGS), whole exome sequencing, depth of coverage, algorithm, benchmark, Immunologic diseases. Allergy, RC581-607
Abstract

Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype’s typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools’ robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA’s typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype’s typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.

Published
2022
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