Vacuum-ultraviolet photochemistry. V - Molecular elimination of nitrogen in the photolysis of hydrazine.
Molecular elimination of nitrogen from hydrazine from single molecule and not radical-radical combination
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SEARCH · Engineering Papers
Results for “single molecule”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Virial expansion of the second layer in physical adsorption - An ab initio calculation for helium on argon crystal
A model of helium adsorption on an argon crystal is built up from the premise that local adsorption predominates in the first layer and nonlocal adsorption in the second. Application of the virial expansion theorem to the second layer gives a series in which the first term represents the motion of a single molecule in the external potential field and the second a two-body interaction under this field. The thermodynamic functions of the adsorbed phase are calculated ab initio, the gas-solid interaction potential being derived from lattice summation and the partition function from an appropriate choice of a site-spacing polynomial to describe the periodic potential. The mutual interaction of adsorbed molecules is calculated with a two-dimensional Lennard-Jones potential. The second virial coefficient is calculated and its dependence on temperature and choice of potential is studied. It is found that the second virial coefficient is very well approximated by a two-dimensional gas in free space. The adsorption isotherm, isosteric heat, and specific heat are obtained and compared with the results of Ross and Steele, giving excellent agreement.
Oh, B. K.↗
Gene-Based Detection of Microorganisms in Environmental Samples Using PCR
Contaminating microorganisms pose a serious potential risk to the crew's well being and water system integrity aboard the International Space Station (ISS). We are developing a gene-based microbial monitor that functions by replicating specific segments of DNA as much as 10(exp 12) x. Thus a single molecule of DNA can be replicated to detectable levels, and the kinetics of that molecule's accumulation can be used to determine the original concentration of specific microorganisms in a sample. Referred to as the polymerase chain reaction (PCR), this enzymatic amplification of specific segments of the DNA or RNA from contaminating microbes offers the promise of rapid, sensitive, quantitative detection and identification of bacteria, fungi, viruses, and parasites. We envision a small instrument capable of assaying an ISS water sample for 48 different microbes in a 24 hour period. We will report on both the developments in the chemistry necessary for the PCR assays to detect microbial contaminants in ISS water, and on progress towards the miniaturization and automation of the instrumentation.
Glass, John I.↗
Biosensors for DNA sequence detection
DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.
Review↗
Fabrication of Buried Nanochannels From Nanowire Patterns
A method of fabricating channels having widths of tens of nanometers in silicon substrates and burying the channels under overlying layers of dielectric materials has been demonstrated. With further refinement, the method might be useful for fabricating nanochannels for manipulation and analysis of large biomolecules at single-molecule resolution. Unlike in prior methods, burying the channels does not involve bonding of flat wafers to the silicon substrates to cover exposed channels in the substrates. Instead, the formation and burying of the channels are accomplished in a more sophisticated process that is less vulnerable to defects in the substrates and less likely to result in clogging of, or leakage from, the channels. In this method, the first step is to establish the channel pattern by forming an array of sacrificial metal nanowires on an SiO2-on-Si substrate. In particular, the wire pattern is made by use of focused-ion-beam (FIB) lithography and a subsequent metallization/lift-off process. The pattern of metal nanowires is then transferred onto the SiO2 layer by reactive-ion etching, which yields sacrificial SiO2 nanowires covered by metal. After removal of the metal covering the SiO2 nanowires, what remains are SiO2 nanowires on an Si substrate. Plasma-enhanced chemical vapor deposition (PECVD) is used to form a layer of a dielectric material over the Si substrate and over the SiO2 wires on the surface of the substrate. FIB milling is then performed to form trenches at both ends of each SiO2 wire. The trenches serve as openings for the entry of chemicals that etch SiO2 much faster than they etch Si. Provided that the nanowires are not so long that the diffusion of the etching chemicals is blocked, the sacrificial SiO2 nanowires become etched out from between the dielectric material and the Si substrate, leaving buried channels. At the time of reporting the information for this article, channels 3 m long, 20 nm deep, and 80 nm wide (see figure) had been fabricated by this method.
Choi, Daniel↗
Rapid Polymer Sequencer
Solid-state nanopore-based analysis of nucleic acid polymers is revolutionary. No other technique can determine information content in single molecules of genetic material at the speed of 1 subunit per microsecond. Because individual molecules are counted, the output is intrinsically quantitative. The nanopore approach is more generalized than any other method and in principle may be used to analyze any polymer molecule, including proteins. The approach to the development of a solid-state nanopore device is novel in the use of nanofabrication, nanoelectronic components, and high-speed signal acquisition. A novel geometry of the solid-state nanopore (less than 5 nm in length and 5 nm in diameter) will enable 1 to 5 nucleotide resolution measurements. This means that maximum resolution will be improved at least 100-fold compared to biological ion-channel measurements. The solid-state nanopore sensor will be made to enable sequencing DNA at a much faster rate than presently possible without the need for extensive sample preparation procedures, such as enzymatic amplification and labeling reactions. It will analyze electronic properties of individual subunits of DNA or RNA, to obtain linear composition of each genetic polymer molecule.
technology opportunity↗
Counting mRNA copies in intact bacterial cells by fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH)
A method for measuring mRNA copies in intact bacterial cells by fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) is presented. Unlike conventional single molecule FISH, where the presence of a transcript is determined by fluorescence intensity, fliFISH relies on On-Off duty cycles of photo-switching dyes to set a predetermined threshold for distinguishing true signals from background noise. The method provides a quantitative approach for detecting and counting true mRNA copies and rejecting false signals with high accuracy.
Hu, Dehong↗
Viscous flow properties and hydrodynamic diameter of phenothiazine-based redox-active molecules in different supporting salt environments
We report viscous flow properties of a redox-active organic molecule, N-(2-(2-methoxyethoxy)ethyl)phenothiazine (MEEPT), a candidate for non-aqueous redox flow batteries, and two of its radical cation salts. A microfluidic viscometer enabled the use of small sample volumes in determining viscosity as a function of shear rate and concentration in the non-aqueous solvent, acetonitrile, both with and without supporting salts. All solutions tested show Newtonian behavior over shear rates of up to 30 000 s−1, which was rationalized by scaling arguments for the diffusion-based relaxation time of a single MEEPT molecule without aggregation. Neat MEEPT is flowable but with a large viscosity (412 mPa⋅s at room temperature), which is ∼1000 times larger than that of acetonitrile. MEEPT solutions in acetonitrile have low viscosities; at concentrations up to 0.5 M, the viscosity increases by less than a factor of two. From concentration-dependent viscosity measurements, molecular information was inferred from intrinsic viscosity (hydrodynamic diameter) and the Huggins coefficient (interactions). Model fit credibility was assessed using the Bayesian Information Criterion. It is found that the MEEPT and its charged cations are “flowable” and do not flocculate at concentrations up to 0.5 M. MEEPT has a hydrodynamic diameter of around 8.5 Å, which is almost insensitive to supporting salt and state of charge. This size is comparable to molecular dimensions of single molecules obtained from optimized structures using density functional theory calculations. The results suggest that MEEPT is a promising candidate for redox flow batteries in terms of its viscous flow properties.
Wang, Yilin (ORCID:0000000316102995)↗
Effect of Confinement on the Density and Diffusivity of Organic Molecules in Single-Digit Nanopores Relative to Bulk Fluid Behavior
Prediction of fluid properties in microporous and mesoporous confinement is non-trivial due to distinct influences from pore surface functionality and shape and fluid molecular characteristics. The vast majority of literature focuses nearly exclusively on a small number of components that are generally low molecular weight gases and vapors. Missing are studies that utilize a relatively large number of compounds that are liquid at ambient conditions to probe the impact of molecular shape and size on confined fluid properties. Such materials are of great interest in the extraction of oil and gas from shale reservoirs or for the design of selective adsorbents for chemical separation. In this work, we reveal non-intuitive relationships that emerge when comparing bulk fluid properties to those when confined in amorphous silica single-digit nanopores (approx. 5 nm SBA-15), specifically the confined density and self-diffusivity. A counterintuitive result was obtained where larger molecules had relatively faster self-diffusivities; however, this behavior was revealed to be caused by these larger compounds exhibiting a relatively low density when confined. As the prediction of confined fluid properties impacts a diversity of disciplines, the results highlight the need for additional investigations where consistent and large-scale experimental procedures are employed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multifunctional nanopore electrode array method for characterizing and manipulating single entities in attoliter-volume enclosures
Structurally regular nanopore arrays fabricated to contain independently controllable annular electrodes represent a new kind of architecture capable of electrochemically addressing small collections of matter—down to the single entity (molecule, particle, and biological cell) level. Furthermore, these nanopore electrode arrays (NEAs) can also be interrogated optically to achieve single entity spectroelectrochemistry. Larger entities such as nanoparticles and single bacterial cells are investigated by dark-field scattering and potential-controlled single-cell luminescence experiments, respectively, while NEA-confined molecules are probed by single molecule luminescence. By carrying out these experiments in arrays of identically constructed nanopores, massively parallel collections of single entities can be investigated simultaneously. The multilayer metal–insulator design of the NEAs enables highly efficient redox cycling experiments with large increases in analytical sensitivity for chemical sensing applications. NEAs may also be augmented with an additional orthogonally designed nanopore layer, such as a structured block copolymer, to achieve hierarchically organized multilayer structures with multiple stimulus-responsive transport control mechanisms. Finally, NEAs constructed with a transparent bottom layer permit optical access to the interior of the nanopore, which can result in the cutoff of far-field mode propagation, effectively trapping radiation in an ultrasmall volume inside the nanopore. Furthermore, the bottom metal layer may be used as both a working electrode and an optical cladding layer, thus, producing bifunctional electrochemical zero-mode waveguide architectures capable of carrying out spectroelectrochemical investigations down to the single molecule level.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography
Abstract The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.
59 BASIC BIOLOGICAL SCIENCES↗
Mechanistic studies of small molecule ligands selective to RNA single G bulges
Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.
Biochemistry & Molecular Biology↗
Traction-separation response of bilayer graphene interfaces: The role of an intercalated single atomic layer of water molecules and hydroxyl groups
Molecular dynamics simulations of the normal and shear traction-separation response of dry and wet bilayer graphene interfaces were performed. The influence of a single, atomic layer of water molecules sandwiched between graphene layers and hydroxyl functionalization on one or both layers were investigated. Hydroxyl groups provided a shielding effect during normal separation while favoring stick-slip friction under sliding conditions. The single, atomic layer of water molecules confined between hydrophilic and asymmetric hydrophobic/hydrophilic surfaces was found to ease sliding friction. The mechanisms arose from the balance between the attractive and repulsive graphene/water interactions through bridges of single water molecules between the two surfaces and the structure of the water monolayer under confinement for which an out-of-plane water/water hydrogen bond network could not be developed. The single, atomic layer of water molecules reduced the sliding friction the most when both surfaces were hydrophilic and lowered the sliding friction of the asymmetric hydrophobic/hydrophilic interfaces to that when both surfaces were hydrophobic. An optimal hydroxyl surface coverage of less than 10% may exist for efficient water lubrication, with diminishing effect with increasing number of hydroxyl groups. Finally, the findings offer a design strategy for assembling bilayer graphene interfaces with tailored friction and sliding contact properties.
36 MATERIALS SCIENCE↗
Novel Materials Containing Single-Wall Carbon Nanotubes Wrapped in Polymer Molecules
In this design, single-wall carbon nanotubes (SWNTs) have been coated in polymer molecules to create a new type of material that has low electrical conductivity, but still contains individual nanotubes, and small ropes of individual nanotubes, which are themselves good electrical conductors and serve as small conducting rods immersed in an electrically insulating matrix. The polymer is attached through weak chemical forces that are primarily non-covalent in nature, caused primarily through polarization rather than the sharing of valence electrons. Therefore, the electronic structure of the SWNT involved is substantially the same as that of free, individual (and small ropes of) SWNT. Their high conductivity makes the individual nanotubes extremely electrically polarizable, and materials containing these individual, highly polarizable molecules exhibit novel electrical properties including a high dielectric constant.
Smalley, Richard E.↗
Reply to: Insufficient evidence for ageing in protein dynamics
Reference 1 states that we claimed that internal motions in single protein molecules exhibit ageing over 13 decades of time. In contrast, our primary conclusion, as expressed in the title, was that over these timescales the dynamics of single protein molecules is non-equilibrium and self-similar. Notwithstanding, we demonstrate in this reply that protein dynamics does indeed exhibit ageing according to the criteria of ref. 1.
59 BASIC BIOLOGICAL SCIENCES↗
Space-Time Quantum Information from the Entangled States of Magnetic Molecule (STI Product)
This collaborative project combines synthesis, measurement, and theory by three faculty members at the Eddleman Quantum Institute of UC Irvine to effectively investigate the quantum properties of molecules in the space, time, and frequency domains. Through synthetic chemistry, molecules are tailored for their magnetic and coherent properties. By combining femtosecond (fs) terahertz (THz) light and a continuous wave (cw) THz laser with a low temperature scanning tunneling microscope (STM), quantum phenomena are probed with simultaneous femtosecond temporal and atomic-scale spatial resolution. In particular, the invention of the quantum superposition microscope (QSM) advances quantum sensing for enhanced spectroscopy and imaging capabilities. Coupling theory to the experimental efforts offers a deeper understanding and predictive power for the molecular systems. The phenomena of superposition, entanglement, and coherence is central to quantum information science and can be realized in qubit states. Many systems can be modeled by a double-well potential in which two levels are formed in the two lowest energy states interacting with the environment and external radiation. In focusing on molecules as two-level systems, the underlying expectation is that their tunable composition and structure allows an effective parameter space to optimize their use as qubits for quantum sensing and computing. The THz radiation induces the superposition between the two states, appearing as temporal oscillations that damp in amplitude. Enhanced spectroscopy and imaging in the time and frequency domains is achieved through the extreme sensitivity of the frequency and damping of coherence of two-level systems to its environment. A single hydrogen molecule trapped in the STM tunneling gap experiences a double-well potential and absorption of THz femtosecond pulses of light creates the superposition of its two levels, appearing as damped oscillations in the light induced direct current (DC). The oscillation frequency depends sensitively on the electric field distribution of the copper nitride (Cu 2 N) surface, through the Stark effect, and associated with the different charge distributions at the copper and nitrogen sites and in between. This QSM can resolve variation in the surface electric field with 0.02 nanometer resolution. In addition, the single hydrogen molecule entaes with nearby hydrogen molecules as seen in the avoided level crossings of energy (oscillation frequency) versus the voltage across the tunneling gap. Thus, the first application of the QSM senses and images the surface electric field at the atomic scale. Results from this project advance fundamental understanding of quantum phenomena, develop novel synthesis, measurement, and theory, provide the knowledge foundation for molecule-based qubits and sensing that enable the development of the QSM and emergent technologies. This project trained researchers in quantum information science, extended knowledge in classrooms, and outreached to the community.
47 OTHER INSTRUMENTATION↗
Structure of Gas Phase Monohydrated Nicotine: Implications for Nicotine’s Native Structure in the Acetylcholine Binding Protein
In this work, we report a joint experimental–theoretical study of the never reported before structure and infrared spectra of gas phase monohydrated nicotine (NIC) and nornicotine (NOR) and use them to assign their protonation sites. NIC’s biological activity is strongly affected by its protonation site, namely, the pyrrolidine (Pyrro-NICH + , anticipated active form) and pyridine (Pyri-NICH + ) forms; however, these have yet to be directly experimentally determined in either the nicotinic acetylcholine receptor (nAChR, no water present) or the acetylcholine-binding protein (AChBP, a single water molecule is present) but can only be inferred to be Pyrro-NICH + from the intermolecular distance to the neighboring residues (i.e., tryptophan). Our temperature-controlled double ion trap infrared spectroscopic experiments assisted by the collisional stripping method and high-level theoretical calculations yield the protonation ratio of Pyri:Pyrro = 8:2 at 240 K for the gas phase NICH + ···(H 2 O) complex, which resembles the molecular cluster present in the AChBP. Therefore, a single water molecule in the gas phase enhances this ratio in NICH + relative to the 3:2 for the nonhydrated gas phase NICH + in a trend that contrasts with the almost exclusive presence of Pyrro-NICH + in aqueous solution. In contrast, the Pyri-NORH + protomer is exclusively observed, a fact that may correlate with its weaker biological activity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Numerical single-center self-consistent-field function for the hydrogen molecule.
Hartree-Fock single determinant wavefunction calculated numerically for normal state of hydrogen molecule
Taylor, H. S.↗