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At least 91 records · Page 5

Franck-Condon factor formulae for astrophysical and other molecules

Simple closed-form, approximate, analytic expressions for Franck-Condon factors are given. They provide reliable estimates for Franck-Condon factor arrays for molecular band systems for which only vibrational-frequency, equilibrium internuclear separation and reduced mass values are known, as is often the case for astrophysically interesting molecules such as CeO, CoH, CrH, CrO, CuH, GeH, LaO, NiH, SnH, and ZnH for band systems of which Franck-Condon arrays have been calculated.

Nicholls, R. W.↗

Polysilaketals: High‐Performance Polyether‐Based Electrolytes with Tunable Disubstituted Silane Linkers

Abstract Polymer electrolytes exhibit higher energy density and improved safety in lithium‐ion batteries relative to traditionally used liquid electrolytes but are currently limited by their lower electrochemical performance. Aiming to access polymer electrolytes with competitive electrochemical properties, we developed the anionic ring‐opening polymerization (AROP) of cyclic silaketals to synthesize amorphous silicon‐containing polyether‐based electrolytes with varying substituent bulk of the general formula [OSi(R) 2 (CH 2 CH 2 O) 2 ] n (R=alkyl, phenyl). As opposed to previously reported uncontrolled polycondensation routes toward low molecular weight polysilaketals, AROP allows access to targeted molecular weights above the entanglement threshold of the polymers. The polysilaketal with the lowest steric bulk (P(OSi Me,Me ‐2EO)) exceeds the conductivity of poly(ethylene oxide) (PEO), a leading polymer electrolyte. To the best of our knowledge, this is the first solid polymer electrolyte to achieve this benchmark. Steric bulk in polysilaketals was found to impart stability and two bulkier polysilaketals, P(OSi Et,Et ‐2EO) and P(OSi Me,Ph ‐2EO), exhibited higher current fractions than PEO over a wide range of salt loadings. Moreover, the efficacy of P(OSi Et,Et ‐2EO) was competitive with that of PEO. Taken together, the tunable and competitive electrochemical properties of polysilaketals validate the systematic incorporation of silyl groups as a strategy to access high performance polymer electrolytes.

Rugh, Haley J.↗

Heat Transfer Through Turbulent Friction Layers

The "general Prandtl number" Pr(exp 1) - A(sub q)/A Pr, aside from the Reynolds number determines the ratio of turbulent to molecular heat transfer, and the temperature distribution in turbulent friction layers. A(sub q) = exchange coefficient for heat; A = exchange coefficient for momentum transfer. A formula is derived from the equation defining the general Prandtl number which describes the temperature as a function of the velocity. For fully developed thermal boundary layers all questions relating to heat transfer to and from incompressible fluids can be treated in a simple manner if the ratio of the turbulent shear stress to the total stress T(sub t)/T in the layers near the wall is known, and if the A(sub q)/A can be regarded as independent of the distance from the wall. The velocity distribution across a flat smooth channel and deep into the laminar sublayer was measured for isothermal flow to establish the shear stress ratio T(sub t)/T and to extend the universal wall friction law. The values of T(sub t)/T which resulted from these measurements can be approximately represented by a linear function of the velocity in the laminar-turbulent transition zone. The effect of the temperature relationship of the material values on the flow near the wall is briefly analyzed. It was found that the velocity at the laminar boundary (in contrast to the thickness of the laminar layer) is approximately independent of the temperature distribution. The temperature gradient at the wall and the distribution of temperature and heat flow in the turbulent friction layers were calculated on the basis of the data under two equations. The derived formulas and the figures reveal the effects of the Prandtl number, the Reynolds number, the exchange quantities and the temperature relationship of the material values.

Reichardt, H.↗

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

Kahn, L. R.↗

An investigation of the preparation of high molecular weight perfluorocarbon polyethers

High molecular weight perfluorocarbon polyether gums were obtained by photolysis of perfluorodienes and discyl fluorides containing a perfluorocarbon polyether backbond. The materials obtained are represented by chemical formulas. A method was developed whereby reactive acyl fluoride and trifluorovinyl end groups are converted into inert structures. In order to investigate the possible preparation of difunctional molecules which may be useful in polymer synthesis, the reactions of hexafluoropropene oxide (HFPO) with Grignard and organolithium reagents have been studied. Reactions of various nucleophilic reagents with HFPO were also investigated.

Watts, R. O.↗

Electron paramagnetic resonance studies of slowly tumbling vanadyl spin probes in nematic liquid crystals

The purposes of this vanadyl spin probe study are threefold: (1) to establish when the breakdown of motionally narrowed formulas occurs; (2) to analyze the experimental vanadyl EPR line shapes by the stochastic Lioville method as developed by Polnaszek et al. (1973) for slow tumbling in an anisotropic liquid; and (3) to compare the vanadyl probe study results with those of Polnaszek and Freed (1975). Spectral EPR line shapes are simulated for experimental spectra of vanadyl acetylacetonate (VOAA) in nematic liquid crystal butyl p-(p-ethoxyphenoxycarbonyl) phenyl carbonate (BEPC) and Phase V of EM laboratories. It is shown that the use of typical vanadyl complexes as spin probes for nematic liquid crystals simplifies the theoretical analysis and the subsequent interpretation. Guidelines for the breakdown of motionally narrowed formulas are established. Both the slow tumbling aspects and the effects of non-Brownian rotation should be resolved in order to extract quantitative information about molecular ordering and rotational mobility.

Bruno, G. V.↗

Water chemistry in flume channel and hyporheic zone (i.e., porewater) associated with: “Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry”

Dissolved oxygen (DO), total organic carbon (TOC), total nitrogen (TN), molecular data for organic matter, and biochemical reactions for surface water and porewater (i.e., hyporheic zone) collected from a water recirculating flume located at the University of Texas, Austin. The flume contained real river water from Lower Colorado River(Austin, TX) and clean sand. Hyporheic exchange in the flume was induced through The study aims to understand relationships between aerobic metabolism of organic matter and molecular characteristics of organic matter, such as thermodynamic signature and nitrogen content, through the extent of the hyporheic zone at 10 cm- resolution, and through time. During the experiment, organic matter (dry leaves) was added to the flume and removed after 24 hours. The water samples were collected before the addition of leaves, at the time of removal of leaves, and at hour 72. The water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and total organic carbon (TOC) and total nitrogen (TN) analysis. Dissolved oxygen content throughout the surface water and the hyporheic zone of the flume was measured with a large planar optode. This data package is associated with the publication ’ Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry’ published in Environmental Science and Technology (Turețcaia et al., 2023 https://doi.org/10.1021/acs.est.3c04765). The dataset is comprised of five folders (1) Diss_O2_pic, (2) input_files (3) output_files; (4) python_code; and (5) R_code . Diss_O2_pic contains siximages of dissolved oxygen distribution in a bedform at hours 0, 24, and 72 of the experiment conducted in a large recirculation flume. Images are in separate R and G channels (i.e., RGB). The input_files contains (1) a csv file with FTICR peaks identified within each sample, (2) a csv file with molecular information pertinent to FTICR data with Gibbs free energy calculations adjusted for environmental temperature, (3) a csv file containing concentrations of non-purgeable organic carbon measured throughout the experiment , (4) a csv file containing concentrations of total nitrogen measured throughout the experiment, (5) a csv file containing total biochemical reactions (i.e., transformations) identified in the dataset, (6) a csv containing transformation profiles, and (7) a csv file containing transformations with formulas, and (8) a jpg file with schematic representation of locations for sample collection. The output_files contains (1) and xlsx file containing percent biochemical reactions containing nitrogen identified across all 39 sample, (2) a csv file of merged FTICR data and molecular information files, (3) a csv files containing average Gibbs free energy within sampling domains and at each sampling location, (4) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 0, (5) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 24, (6) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 72, (7) a csv file with percent chemical classes identified across sampling locations at hour 0, (8) a csv file with percent chemical classes identified across sampling locations at hour 24, (9) a csv file with percent chemical classes identified across sampling locations at hour 72, and (10) a csv file containing percent nitrogen containing biochemical reactions identified across sampling locations at hours 0, 24, and 72. The python_code contains seven ipynb files which are Jupyter Notebooks used for data analysis and figures generation. The R_code contains 3 R files with R code used for data analysis and figures generation. This data package contains the processed data used in the associated manuscript. This data has not been previously published.

54 ENVIRONMENTAL SCIENCES↗

Mass fractionation during transonic escape and implications for loss of water from Mars and Venus

Hydrodynamic escape of hydrogen from a planetary atmosphere can remove heavier gases as well as hydrogen, provided that the escape rate is sufficiently large. Analytic approximations for the degree of mass fractionation of a trace species during hydrodynamic escape are compared with accurate numerical solutions for the case of transonic outflow. The analytic approximations are most accurate when the ratio of molecular weights of the heavier and lighter constituents is large so that nonlinear terms in the momentum equation for the heavy constituent become small. The simplest analytic formula is readily generalized to the case where a heavy constituent is also a major species. Application of the generalized formula to hypothetical episodes of hydrodynamic escape from Venus and Mars suggests that both hydrogen and oxygen could have escaped; thus, substantial quantities of water may have been lost without the need to oxidize large amounts of the crust.

Zahnle, Kevin J.↗

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory

The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC’s ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model’s predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport.

Biochemistry & Molecular Biology↗

Study of the 10 micron continuum of water vapor

Radiation attenuation by atmospheric water vapor is considered. A formula based on laboratory data is recommended for approximating continuous absorption in the spectra region in question. Data of full scale measurements and laboratory experiments are compared. It was concluded that only molecular absorption need be taken into account under clear atmospheric conditions during the warm part of the year, while in winter or in cloudy conditions, the effect of aerosol can be significant.

Arefyev, V. N.↗

Finite-temperature many-body perturbation theory for anharmonic vibrations: Recursions, algebraic reduction, second-quantized reduction, diagrammatic rules, linked-diagram theorem, finite-temperature self-consistent field, and general-order algorithm

A unified theory is presented for finite-temperature many-body perturbation expansions of the anharmonic vibrational contributions to thermodynamic functions, i.e., the free energy, internal energy, and entropy. The theory is diagrammatically size-consistent at any order, as ensured by the linked-diagram theorem proved in this study, and, thus, applicable to molecular gases and solids on an equal footing. It is also a basis-set-free formalism, just like its underlying Bose–Einstein theory, capable of summing anharmonic effects over an infinite number of states analytically. It is formulated by the Rayleigh–Schrödinger-style recursions, generating sum-over-states formulas for the perturbation series, which unambiguously converges at the finite-temperature vibrational full-configuration-interaction limits. Two strategies are introduced to reduce these sum-over-states formulas into compact sum-over-modes analytical formulas. One is a purely algebraic method that factorizes each many-mode thermal average into a product of one-mode thermal averages, which are then evaluated by the thermal Born–Huang rules. Canonical forms of these rules are proposed, dramatically expediting the reduction process. The other is finite-temperature normal-ordered second quantization, which is fully developed in this study, including a proof of thermal Wick’s theorem and the derivation of a normal-ordered vibrational Hamiltonian at finite temperature. The latter naturally defines a finite-temperature extension of size-extensive vibrational self-consistent field theory. These reduced formulas can be represented graphically as Feynman diagrams with resolvent lines, which include anomalous and renormalization diagrams. Two order-by-order and one general-order algorithms of computing these perturbation corrections are implemented and applied up to the eighth order. The results show no signs of Kohn–Luttinger-type nonconvergence.

74 ATOMIC AND MOLECULAR PHYSICS↗

Mass Spectrometry Adduct Calculator

We describe the Mass Spectrometry Adduct Calculator (MSAC), an automated Python tool to calculate the adduct ion masses of a parent molecule. Here, adduct refers to a version of a parent molecule [M] that is charged due to addition or loss of atoms and electrons resulting in a charged ion, e.g. [M+H] + . MSAC includes a database of 2,341 potential ions and their mass-to-charge ratios (m/z) as extracted from the NIST/EPA/NIH Mass Spectral Library (NIST17), the Global Natural Products Social Molecular Networking Public Spectral Libraries (GNPS), and MassBank of North America (MoNA). The calculator relies on user-selected subsets of the combined database to calculate expected m/z for adducts of molecules supplied as formulas This tool is intended to help researchers create identification libraries to collect evidence for the presence of molecules in mass spectrometry data. While the included adduct database focuses on adducts typically detected during liquid chromatography-mass spectrometry analyses, users may supply their own lists of adducts and charge states for calculating expected m/z. We also analyzed statistics on adducts from spectra contained in the three selected mass spectral libraries. MSAC is freely available at https://github.com/pnnl/MSAC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anisotropic angular scattering models of elastic electron-neutral collisions for Monte Carlo plasma simulations

Many laboratory and industrial plasma applications require accurate modeling techniques to understand the interplay between microscopic and macroscopic processes. A prime example of this interplay is how particle and Monte Carlo (MC) simulation codes describe angular scattering of electrons following elastic scattering events. The forward peaked nature of high energy electron elastic scattering is relatively trivial to accurately describe in plasma simulations. However, for lower energy collisions, which produce near isotropic or backward peaked differential cross sections, there is not a strong consensus among the plasma modeling community on how to best describe these angular scattering trends. Here, in this study, we propose a systematic method to approximate the aforementioned non-trivial angular scattering behavior with a formula that can be readily implemented in particle-in-cell (PIC) and/or MC plasma simulation codes. The present approach is specifically applied to fusion relevant atomic hydrogen and helium, as well as for molecular hydrogen, and results are also applicable to the atomic isotopes and homonuclear molecular isotopologues of these species. Comparisons between the present angular distribution function and benchmark scattering data were used to validate the proposed models. In addition, two-term Boltzmann calculations and PIC direct simulation MC simulations revealed that the proposed angular distribution function is accurate, agreeing very well with benchmark convergent close-coupling scattering calculations, and electron transport measurements. These studies confirmed that the present angular distribution function model can be utilized without the need of renormalization to the momentum transfer cross section (as opposed to using the elastic scattering integrated cross section), which has been suggested by several studies in order to correct for deficient angular scattering models, and to agree with transport measurements. Hence, the present anisotropic angular scattering model can be utilized to accurately model the momentum transfer as well as the electron trajectories of elastic collisions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the Rayleigh-scattering optical depth of the atmosphere

It is pointed out that revised Rayleigh-scattering optical depths published by Hoyt (1977) are not correct, because King's (1923) formula, which was used by Hoyt, requires that the rotational lines be included in the polarization measurement. To exclude them is to exclude the contribution of the Raman-shifted photons to the total molecular extinction. Hoyt's error was repeated by Froehlich and Shaw (1980), who also confused the depolarization for natural light with that for (polarized) laser light. In an effort to clarify basic concepts, attention is given to the origin of the depolarization correction, depolarization ratios, vibrational Raman effects, and extinction measurements.

Young, A. T.↗

Interstellar clouds - From a dynamical perspective on their chemistry

The possibility is examined that in the course of its dynamical evolution, a single mass of interstellar gas would exhibit properties of diffuse clouds, dense clouds and finally also of clouds perturbed by shocks or intense UV or X-ray radiation generated by a star of its own creation. This concept provides a common thread through the bewildering diversity of physical and chemical compositional properties shown by interstellar clouds. From this perspective, instead of being static objects, interstellar clouds are possibly incessantly evolving from initially diffuse to later dense state and then to star formation which ultimately restructures or disperses the remaining cloud material to begin the whole evolutionary process once again. Based on a simplified study of interstellar chemistry from a dynamical perspective, the ideas are presented as an heuristic: to encourage thought on the future direction of molecular astrophysics and the need to consider the chemical behavior of interstellar clouds in conjunction with, rather than in isolation from, their dynamical behavior. A physical basis must be sought for the semiempirical temperature formula which has been given a critical role in the collapse of diffuse clouds. Self-shielding effects in the chemistry of CO were neglected and this drawback should be removed; the ability of the model to explain the fractional abundances of more complex molecules, such as cyanopolyynes, should be examined.

Prasad, S. S.↗

Fluid Dynamics of Small, Rugged Vacuum Pumps of Viscous-Drag Type

The need to identify spikes in the concentration of hazardous gases during countdowns to space shuttle launches has led Kennedy Space Center to acquire considerable expertise in the design, construction, and operation of special-purpose gas analyzers of mass-spectrometer type. If such devices could be miniaturized so as to fit in a small airborne package or backpack them their potential applications would include integrated vehicle health monitoring in later-generation space shuttles and in hazardous material detection in airports, to name two examples. The bulkiest components of such devices are vacuum pumps, particularly those that function in the low vacuum range. Now some pumps that operate in the high vacuum range (e.g. molecular-drag and turbomolecular pumps) are already small and rugged. The present work aims to determine whether, on physical grounds, one may or may not adopt the molecular-drag principle to the low-vacuum range (in which case viscous-drag principle is the appropriate term). The deliverable of the present effort is the derivation and justification of some key formulas and calculation methods for the preliminary design of a single-spool, spiral-channel viscous-drag pump.

Russell, John M.↗

Natural organic matter composition and nanomaterial surface coating determine the nature of platinum nanomaterial-natural organic matter corona

Natural organic matter corona (NOM corona) is an interfacial area between nanomaterials (NMs) and the sur- rounding environment, which gives rise to NMs' unique surface identity. While the importance of the formation of natural organic matter (NOM) corona on engineered nanomaterials (NMs) to NM behavior, fate, and toxicity has been well-established, the understanding of how NOM molecular properties affect NOM corona composition remains elusive due to the complexity and heterogeneity of NOM. This is further complicated by the variation of NOMs from different origins. Here we use eight NOM isolates of different molecular composition and ultrahigh resolution Fourier-transform ion cyclotron resonance-mass spectrometry (ESI-FT-ICR-MS) to determine the mol- ecular composition of platinum NM-NOM corona as a function of NOM composition and NM surface coating. We observed that the composition of PtNM-NOM corona varied with the composition of the original NOM. The per- centage of NOM formulas that formed PVP-PtNM-NOM corona was higher than those formed citrate-PtNM-NOM corona, due to increased sorption of NOM formulas, in particular condensed hydrocarbons, to the PVP coating. The relative abundance of heteroatom formulas (CHON, CHOS, and CHOP) was higher in the PVP-PtNM-NOM corona than in citrate-PtNM-corona which was in turn higher than those in the original NOM isolate, indicating preferential partitioning of heteroatom-rich molecules to NM surfaces. The relative abundance of CHO, CHON, CHOS, CHOP and condensed hydrocarbons in PtNM-NOM corona increased with their increase in NOM isolates. Furthermore, PtNM-NOM corona is rich with compounds with high molecular weight. This study demonstrates that the composition and properties of PtNM-NOM corona depend on NOM molecular properties and PtNM sur- face coating. The results here provide evidence of molecular interactions between NOM and NMs, which are crit- ical to understanding NM colloidal properties (e.g., surface charge and stability), interaction forces (e.g., van der Waals and hydrphobic), environmental behaviors (e.g., aggregation, disso.

Baalousha, Mohammed↗

Mixed stochastic-deterministic density functional theoretic decomposition of Kubo–Greenwood conductivities in the projector augmented wave formalism

Pairing the accuracy of the Kohn–Sham density-functional framework with the efficiency of a stochastic algorithmic approach, mixed stochastic-deterministic density functional theory (mDFT) achieves a favorable computational scaling with system sizes and electronic temperatures. We employ the recently developed mDFT formalism to investigate the dynamic charge-transport properties of systems in the warm dense matter regime. The optical conductivity spectra are computed for single- and multi- component mixtures of carbon, hydrogen, and beryllium using two complementary approaches: Kubo–Greenwood in the mDFT picture and real-time time-dependent mDFT. We further devise a decomposition of the Onsager coefficients leading up to the Kubo–Greenwood spectra to exhibit contributions from the deterministic, stochastic, and mixed electronic state transitions at different incident photon energies.

36 MATERIALS SCIENCE↗