Mid-Scale Instrumentation: Regional Facilities to Address Grand Challenges in Chemistry

A regional workshop sponsored by the National Science Foundation, Arlington, Virginia, September 29-30, 2016. To determine what needs and opportunities might exist for mid-scale instrumentation (MSI), two workshops were held in fall of 2016 to explore opportunities within the discipline that could be provided by such investment. One workshop was convened to explore the need for co-localization of existing instrumentation at a regional or cyber-enabled facilities (addressed in this report, “Mid-Scale Instrumentation: Regional Facilities to Address Grand Challenges in Chemistry”). In this report, we identify different areas where investment in such MSI facilities would be highly beneficial. These appear as six “grand challenges” that can be summarized here as follows: 1. Structure and dynamics at interfaces 2. Highly parallel chemical synthesis and characterization 3. Transient intermediates 4. New science arising from the characterization of heterogeneous mixtures 5. Multi-scale dynamics of complex systems: integrating transport with reaction 6. Structure-function relationship in disordered and/or heterogeneous system

Multiplex ligation dependent probe amplification (MLPA) for rapid distinction between unique sequence positive and negative marker chromosomes in prenatal diagnosis

Background: Small supernumerary marker chromosomes (sSMC) are extra structurally abnormal chromosomes that cannot be unambiguously identified with conventional chromosome banding techniques. These marker chromosomes may cause an abnormal phenotype or be harmless depending on different factors such as genetic content, chromosomal origin and level of mosaicism. When a sSMC is found during prenatal diagnosis, the main question is whether the sSMC contains euchromatin since in most cases this will lead to phenotypic abnormalities. We present the use of Multiplex Ligation Dependent probe Amplification (MLPA) for rapid distinction between non-euchromatic and euchromatic sSMC. Results: 29 well-defined sSMC found during prenatal diagnosis were retrospectively investigated with MLPA with the SALSA MLPA centromere kits P181 and P182 as well as with the SALSA MLPA telomere kits P036B and P070 (MRC Holland BV, Amsterdam, The Netherlands). All unique-sequence positive sSMC were correctly identified with MLPA, whereas the unique-sequence negative sSMC had normal MLPA results. Conclusions: Although different techniques exist for identification of sSMC, we show that MLPA is a valuable adjunctive tool for rapidly distinguishing between unique-sequence positive and negative sSMC. In case of positive MLPA results, genetic microarray analysis or, if not available, targeted FISH can be applied for further identification and determination of the exact breakpoints, which is important for prediction of the fetal phenotype. In case of a negative MLPA result, which means that the sSMC most probably does not contain genes, the parents can already be reassured and parental karyotyping can be initiated to assess the heritability. In the mean time, FISH techniques are needed for determination of the chromosomal origin

Influence of the Spatial Distribution of Cationic Functional Groups at Nanoparticle Surfaces on Bacterial Viability and Membrane Interactions

While positively charged nanomaterials induce cytotoxicity in many organisms, much less is known about how the spatial distribution and presentation of molecular surface charge impact nanoparticle–biological interactions. We systematically functionalized diamond nanoparticle surfaces with five different cationic surface molecules having different molecular structures and conformations, including four small ligands and one polymer, and we then probed the molecular-level interaction between these nanoparticles and bacterial cells. Shewanella oneidensis MR-1 was used as a model bacterial cell system to investigate how the molecular length and conformation of cationic surface charges influence their interactions with the Gram-negative bacterial membranes. Nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) demonstrate the covalent modification of the nanoparticle surface with the desired cationic organic monolayers. Surprisingly, bacterial growth-based viability (GBV) and membrane damage assays both show only minimal biological impact by the NPs functionalized with short cationic ligands within the concentration range tested, yet NPs covalently linked to a cationic polymer induce strong cytotoxicity, including reduced cellular viability and significant membrane damage at the same concentration of cationic groups. Transmission electron microscopy (TEM) images of these NP-exposed bacterial cells show that NPs functionalized with cationic polymers induce significant membrane distortion and the production of outer membrane vesicle-like features, while NPs bearing short cationic ligands only exhibit weak membrane association. Our results demonstrate that the spatial distribution of molecular charge plays a key role in controlling the interaction of cationic nanoparticles with bacterial cell membranes and the subsequent biological impact. Nanoparticles functionalized with ligands having different lengths and conformations can have large differences in interactions even while having nearly identical zeta potentials. While the zeta potential is a convenient and commonly used measure of nanoparticle charge, it does not capture essential differences in molecular-level nanoparticle properties that control their biological impact

Electronic structure of Fe- vs. Ru-based dye molecules

In order to explore whether Ru can be replaced by inexpensive Fe in dye molecules for solar cells, the differences in the electronic structure of Fe- and Ru-based dyes are investigated by X-ray absorption spectroscopy and first-principles calculations. Molecules with the metal in a sixfold, octahedral N cage, such as tris(bipyridines) and tris(phenanthrolines), exhibit a systematic downward shift of the N 1s-to-π* transition when Ru is replaced by Fe. This shift is explained by an extra transfer of negative charge from the metal to the N ligands in the case of Fe, which reduces the binding energy of the N 1s core level. The C 1s-to-π* transitions show the opposite trend, with an increase in the transition energy when replacing Ru by Fe. Molecules with the metal in a fourfold, planar N cage (porphyrins) exhibit a more complex behavior due to a subtle competition between the crystal field, axial ligands, and the 2+ vs. 3+ oxidation states.This work was supported by the National Science Foundation (NSF) under Award Nos. CHE-1026245, DMR-1121288 (MRSEC), DMR-0537588 (SRC), and by the (U.S.) Department of Energy (DOE) under Contract Nos. DE-FG02-01ER45917 (end station) and DE-AC02-05CH11231 (ALS). P. L. Cook acknowledges support from the University of Wisconsin System 2012-2013 Applied Research Grant. J. M. García-Lastra and A. Rubio acknowledge financial support from the European Research Council (ERC-2010-AdG-Proposal No. 267374), Spanish Grants (FIS2011-65702-C02-01 and PIB2010US-00652), Grupos Consolidados (IT-319-07), and European Commission project CRONOS (280879-2).Peer Reviewe

Covalently bonded adducts of deoxyribonucleic acid (DNA) oligonucleotides with single-wall carbon nanotubes: synthesis and hydridization

ABSTRACT We have developed a multistep route to the formation of covalently linked adducts of single-wall carbon nanotubes (SWNT) and deoxyribonucleic acid (DNA) oligonucleotides. X-ray photoelectron spectroscopy was used to characterize the initial chemical modification to form amineterminated SWNTs, which were then covalently linked to DNA. The resulting DNA−SWNT adducts hybridize selectively with complementary sequences, with only minimal interaction with noncomplementary sequences

High Temperature Treatment of Diamond Particles Toward Enhancement of Their Quantum Properties

Fluorescence of the negatively charged nitrogen-vacancy (NV-) center of diamond is sensitive to external electromagnetic fields, lattice strain, and temperature due to the unique triplet configuration of its spin states. Their use in particulate diamond allows for the possibility of localized sensing and magnetic-contrast-based differential imaging in complex environments with high fluorescent background. However, current methods of NV(-)production in diamond particles are accompanied by the formation of a large number of parasitic defects and lattice distortions resulting in deterioration of the NV(-)performance. Therefore, there are significant efforts to improve the quantum properties of diamond particles to advance the field. Recently it was shown that rapid thermal annealing (RTA) at temperatures much exceeding the standard temperatures used for NV(-)production can efficiently eliminate parasitic paramagnetic impurities and, as a result, by an order of magnitude improve the degree of hyperpolarization of(13)C via polarization transfer from optically polarized NV(-)centers in micron-sized particles. Here, we demonstrate that RTA also improves the maximum achievable magnetic modulation of NV(-)fluorescence in micron-sized diamond by about 4x over conventionally produced diamond particles endowed with NV-. This advancement can continue to bridge the pathway toward developing nano-sized diamond with improved qualities for quantum sensing and imaging

Interpretasi Lingkungan Pengendapan Formasi Talang Akar Berdasarkan Data Cutting dan Wireline Log pada Lapangan X Cekungan Sumatera Selatan

A sedimentary environment is a part of earth\u27s surface which is physically, chemically and biologically distinct from adjacent terrains (Selley, 1988). The study of the depositional environment is one goal of many studiesconducted for academic purpose and economically purpose in oil and gas exploration. The study of the depositionalenvironment requires a fairly comprehensive analysis as to sequencestratigraphy facies analysis to obtain detailedinterpretations or conclusions. The purpose of this study is to analyze cutting and wireline logs to determinelithology, facies and sedimentation history of theTalang Akar formation field X in South Sumatra basin. The method used to analyze the formation of depositional environment of Talang Akar field X in SouthSumatra basin is the cutting description in order to know the composition of the constituent formations. While theanalysis conducted is cutting analysis to get lithofacies interpretation, second is well log analysis method to getsubsurface data such as physical rock properties then electrofacies analysis based on gamma ray log pattern andthird is stratigraphy sequence analysis method so sea level changed can be known. Stratigraphy sequenceinterpretation did base on facies and gamma ray log pattern changed. Pratama-1 well lithology consists of shale, siltstone, very fine sandstone until medium sandstone andlimestones. While the well lithology Pratama-2 is composed of shale, very fine until medium sandstone and siltstone.Facies found in wells Pratama-1 consists of distributary channel fill, prodelta, distal bar, distributary mouth bar,and marsh. Facies in wells Pratama-2 is a mud flat and mixed flat. In Pratama-1 wells are 2 sets sequence that bounded by 2 sequence boundary, with a stratigraphic unit LST, TST and HST with progradation andretrogradation stacking patterns. While the Pratama-2 wells contained one stratigraphic unit sequence that is onlyTST in progradation and agradation stacking patterns. Based on this analysis the Talang Akar formation field X inSouth Sumatra basin has a transitional depositional environment

Nanoscale battery cathode materials induce DNA damage in bacteria

The increasing use of nanoscale lithium nickel manganese cobalt oxide (LixNiyMnzCo1−y−zO2, NMC) as a cathode material in lithium-ion batteries poses risk to the environment. Learning toxicity mechanisms on molecular levels is critical to promote proactive risk assessment of these complex nanomaterials and inform their sustainable development. We focused on DNA damage as a toxicity mechanism and profiled in depth chemical and biological changes linked to DNA damage in two environmentally relevant bacteria upon nano-NMC exposure. DNA damage occurred in both bacteria, characterized by double-strand breakage and increased levels of many putative chemical modifications on bacterial DNA bases related to direct oxidative stress and lipid peroxidation, measured by cutting-edge DNA adductomic techniques. Chemical probes indicated elevated intracellular reactive oxygen species and transition metal ions, in agreement with DNA adductomics and gene expression analysis. By integrating multi-dimensional datasets from chemical and biological measurements, we present rich mechanistic insights on nano-NMC-induced DNA damage in bacteria, providing targets for biomarkers in the risk assessment of reactive materials that may be extrapolated to other nano–bio interactions