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At least 109 records · Page 6

Enhancing the formation of ionic defects to study the ice Ih/XI transition with molecular dynamics simulations

Ice Ih, the common form of ice in the biosphere, contains proton disorder. Its proton-ordered counterpart, ice XI, is thermodynamically stable below 72 K. However, the formation of ice XI is kinetically hindered, and experimentally it is obtained by doping with KOH. Doping creates ionic defects that promote the migration of protons and the associated change in proton configuration. In this article, we mimic the effect of doping with a bias potential that enhances the formation of ionic defects in molecular dynamics simulations. The recombination of the ions thus formed proceeds through fast migration of the hydroxide along hydrogen bond loops, providing a physical and expedite way to change the proton configuration. Here, a key ingredient of this approach is a machine learning potential trained with density functional theory data and capable of modelling molecular dissociation. We exemplify the usefulness of this idea by studying the order-disorder transition using an appropriate order parameter that distinguishes the proton environments in ice Ih and XI. We calculate the changes in free energy, enthalpy, and entropy associated with the transition. Our estimated entropy agrees with experiment within the error bars of the calculation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Predicting the Dissolution Rate of Borosilicate Glasses using QSPR analysis based on molecular dynamics simulations

Quantitative Structure Property Relationship (QSPR) analysis based on molecular dynamics (MD) simulations is a promising approach for establishing the composition-property relationships of glass and other materials with complex structures. A series of 20 borosilicate and boroaluminosilicate glasses have been modeled by using MD simulations with recently developed effective potentials. Short- and medium-range structures of these glasses were analyzed and, based on these structural information, QSPR analysis of the initial dissolution rate (r0) was made and compared with measured r0 at 90°C and pH 9 using various structural descriptors such as percentage of bridging oxygen species, network connectivity and average ring size. The structural descriptors, Fnet, containing energetic information such as single bond strength and other structural information were also used. It was found that overall network connectivity, average ring size and Fnet give reasonable predictions of the r0 of studied glasses, given the conditions that the glasses are homogeneous and dissolve congruently. Modifying glass compositions to account preferential release of modifiers gives a better prediction for incongruently dissolving glasses. The results were compared with our recent work of predicting glass dissolution behavior from compositions using the topological-constraints-based models.

Du, Jincheng↗

Combining scaling relationships overcomes rate vs. overpotential tradeoffs in O2 molecular electrocatalysis

The development of advanced chemical-to-electrical energy conversions requires fast and efficient electrocatalysis of multi-electron/multi-proton reactions, such as the oxygen reduction reaction 10 (ORR). Using molecular catalysts, correlations between the reaction rate and energy efficiency have recently been identified. Improved catalysis requires circumventing the rate vs. overpotential tradeoffs implied by such ‘scaling relationships.’ Described here is an ORR system—using a soluble iron-porphyrin and weak acids—with the best reported combination of rate and efficiency for a soluble ORR catalyst. This advance is achieved not by “breaking” scaling relationships but 15 rather by combining two of them. Key to this behavior is a polycationic ligand, which enhances anionic ligand binding and changes the catalyst E1/2. These results show how combining scaling relationships is powerful way towards improved electrocatalysis.

Martin, Daniel J.↗

Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation

While drug resistance mutations can often be attributed to the loss of direct or solvent-mediated protein−ligand interactions in the drug-mutant complex, in this study we show that a resistance mutation for the picomolar HIV-1 capsid (CA)-targeting antiviral (GS-6207) is mainly due to the free energy cost of the drug-induced protein side chain reorganization in the mutant protein. Among several mutations, M66I causes the most suppression of the GS-6207 antiviral activity (up to ~84,000-fold), and only 83- and 68-fold reductions for PF74 and ZW-1261, respectively. To understand the molecular basis of this drug resistance, we conducted molecular dynamics free energy simulations to study the structures, energetics, and conformational free energy landscapes involved in the inhibitors binding at the interface of two CA monomers. To minimize the protein−ligand steric clash, the I66 side chain in the M66I−GS-6207 complex switches to a higher free energy conformation from the one adopted in the apo M66I. In contrast, the binding of GS-6207 to the wild-type CA does not lead to any significant M66 conformational change. Based on an analysis that decomposes the absolute binding free energy into contributions from two receptor conformational states, it appears that it is the free energy cost of side chain reorganization rather than the reduced protein−ligand interaction that is largely responsible for the drug resistance against GS-6207.

Sun, Qinfang (ORCID:0000000173621543)↗

Molecular relaxations, molecular orientation, and the friction characteristics of polyimide films

The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were interpreted in terms of molecular orientation and thermomechanical data obtained by torsional braid analysis (TBA). A large friction transition was found to occur at 40 + or - 10 C in a dry argon atmosphere (10 ppm H2O). It was postulated that the mechanical stresses of sliding transform or reorder the molecules on the surface into a configuration conducive to easy shear, such as an extended chain. The molecular relaxation which occurs in this temperature region appears to give the molecules the necessary freedom for this reordering process to occur. The effects of velocity, reversibility, and thermal prehistory on the friction properties of polyimide were also studied.

Fusaro, R. L.↗

Molecular relaxations, molecular orientation and the friction characteristics of polyimide films

The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were interpreted in terms of molecular orientation and thermomechanical data obtained by torsional braid analysis (TBA). A large friction transition was found to occur at 40 plus or minus 10 C in a dry argon atmosphere (10 ppm H2O). It was postulated that the mechanical stresses of sliding transform or reorder the molecules on the surface into a configuration conducive to easy shear, such as an extended chain. The molecular relaxation which occurs in this temperature region appears to give the molecules the necessary freedom for this reordering process to occur. The effects of velocity, reversibility, and thermal prehistory on the friction properties of polyimide were also studied.

Fusaro, R. L.↗

Computer programs for the interpretation of low resolution mass spectra: Program for calculation of molecular isotopic distribution and program for assignment of molecular formulas

Two FORTRAN computer programs for the interpretation of low resolution mass spectra were prepared and tested. One is for the calculation of the molecular isotopic distribution of any species from stored elemental distributions. The program requires only the input of the molecular formula and was designed for compatability with any computer system. The other program is for the determination of all possible combinations of atoms (and radicals) which may form an ion having a particular integer mass. It also uses a simplified input scheme and was designed for compatability with any system.

Miller, R. A.↗

Detection of the 12.28 micron rotational line of molecular hydrogen in the Orion molecular cloud

The pure rotational S(2) transition of molecular hydrogen at 12.28 microns has been detected in emission from the region of vibrational-rotational line emission in Orion. The line was resolved both spectrally and spatially, and the line shapes, widths, and velocities are consistent with those observed in the upsilon = 1-0 transitions. The results put new constraints on the structure, temperature, and dynamics of the region of molecular hydrogen emission.

Beck, S. C.↗

The energetics of molecular clouds. V - The S37 molecular cloud

The molecular clouds of S37, which coincides with a region of visual obscuration, is observed at several molecular transition frequencies and at IR wavelengths in the 2-125 micron range. It is found that the temperature and the column density peak near the reflection nebulae vdB 118 and 119, with line splitting and possible self-absorption being observed near the latter. Although many 2-micron sources are observed in the direction of the cloud, no bright, 10-micron sources are seen, and far-IR emission is found over an extensive region in the cloud. An energetics analysis leads to the prediction of a dust cooling rate consistent with the far-IR observations, which indicate not less than 15,000-35,000 solar luminosities, and more detailed energetics examinations show that the conditions necessary for collision heating of the gas by warm dust exist.

Evans, N. J., II↗

Molecular orbital predictions of the vibrational frequencies of some molecular ions

The initial detections of IR vibration-rotation bands in polyatomic molecular ions by recent spectroscopic advances were guided by ab initio prediction of vibrational frequencies. The present calculations predict the vibrational frequencies of additional ions which are candidates for laboratory analysis. Neutral molecule vibrational frequencies were computed at three levels of theory and then compared with experimental data; the effect of scaling was also investigated, in order to determine how accurately vibrational frequencies could be predicted. For 92 percent of the frequencies examined, the relatively simple HF/6-31G theory's vibrational frequencies were within 100/cm of experimental values, with a mean absolute error of 49/cm. On this basis, the frequencies of 30 molecular ions (many possessing astrophysical significance) were computed.

Defrees, D. J.↗

Thermal instabilities in diffuse molecular clouds - Formation of molecular cloud cores

The stability of diffuse clouds to thermal instabilities is examined using the semiempirical cooling function derived by Tarafdar et al. (1985) for these clouds. It is found that diffuse clouds which obey such a cooling function are susceptible to thermal instability at densities n of less than about 70-80/cu cm. The growth rate for instability is large and the mass contained in unstable regions ranges from about 0.001 to 1 solar mass. It is suggested that such instabilities may trigger formation of molecular cloud cores of the type found in low-mass molecular clouds (e.g., TMC-2). Criteria for thermal instability in self-gravitating systems are also derived.

Graziani, Frank R.↗

Molecular outflows in the Monoceros OB1 molecular cloud

Observations of J = 1-0 emission from CO in nine suspected molecular outflows in the Monoceros OB1 molecular cloud are presented. It is found that, if the five sources which are confirmed to be outflows conserve momentum as they evolve, they will sweep up at least 0.6 percent of the mass of the entire cloud before coming into pressure equilibrium with the ambient gas. This number indicates that it should take at most 160 episodes of similar outflow activity in order to sweep up the bulk of the Mon OB1 cloud to highly supersonic speeds.

Margulis, Michael↗

Information storage at the molecular level - The design of a molecular shift register memory

The control of electron transfer rates is discussed and a molecular shift register memory at the molecular level is described. The memory elements are made up of molecules which can exist in either an oxidized or reduced state and the bits can be shifted between the cells with photoinduced electron transfer reactions. The device integrates designed molecules onto a VLSI substrate. A control structure to modify the flow of information along a shift register is indicated schematically.

Beratan, David N.↗

Molecular abundances in the Sagittarius A molecular cloud

We have obtained column densities for HCO(+), HCO, HCS(+), C3H2, HC5N, SiO, OCS, HCOOH, CH3CH2OH, and CH3CCH toward Sgr A. The fractional abundance of SiO relative to molecular hydrogen in Sgr A is comparable to that for the Orion plateau, about 10 exp-7 to 10 exp -8, which may be a typical value for hot clouds. The abundances of HCO, CH3CH2OH, and CH3CCH all appear to be enhanced relative to other molecular clouds such as Sgr B2.

Minh, Y. C.↗

Considerations on the Design of a Molecular Frequency Standard Based on the Molecular Beam Electric Resonance Method

The use of a rotational state transition as observed by the molecular beam electric resonance method is discussed as a possible frequency standard particularly in the millimeter wavelength range. As a promising example the 100 kMc transition between the J = 0 and J = 1 rotational states of Li 6F19 is considered. The relative insensitivity of the transition frequency to external electric and magnetic fields and the low microwave power requirements appear favorable; the small fraction of the molecular beam that is in a single rotational state is a limiting factor.

Hughes, Vernon W.↗

Autonomous Molecular Structure Imaging with High-Resolution Atomic Force Microscopy for Molecular Mixture Discovery

Due to its single-molecule sensitivity, high-resolution atomic force microscopy (HR-AFM) has proved to be a valuable and uniquely advantageous tool to study complex molecular mixtures, which hold promise for developing clean energy and achieving environmental sustainability. However, significant challenges remain to achieve the full potential of the sophisticated and time-consuming experiments. Automation combined with machine learning (ML) and artificial intelligence (AI) is key to overcoming these challenges. Here we present Auto-HR-AFM, an AI tool to automatically collect HR-AFM images of petroleum-based mixtures. In this study, we trained an instance segmentation model to teach Auto-HR-AFM how to recognize features in HR-AFM images. Auto-HR-AFM then uses that information to optimize the imaging by adjusting the probe-molecule distance for each molecule in the run. Auto-HR-AFM is the initial tool that will lead to fully automated scanning probe microscopy (SPM) experiments, from start to finish. This automation will allow SPM to become a mainstream characterization technique for complex mixtures, an otherwise unattainable target.

36 MATERIALS SCIENCE↗

Room Temperature to 150 °C Lithium Metal Batteries Enabled by a Rigid Molecular Ionic Composite Electrolyte

Molecular ionic composites (MICs), made from ionic liquids and a rigid-rod polymer poly(2,2'-disulfonyl-4,4'-benzidine terephthalamide) (PBDT), are a new type of rigid gel electrolyte that combine fast ion transport with high thermal stability and mechanical strength. In this work, a MIC electrolyte membrane is prepared that is composed of PBDT, lithium bis(trifluoromethylsulfonyl)imide (LiTFSI), and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (Pyr 14 TFSI) in a mass ratio of 10:10:80. The ionic conductivity at 25 °C is 0.56 mS cm –1 with no added flammable/volatile components. Although the polymer content is only 10 wt%, this MIC membrane is rigid with a tensile modulus of 410 MPa at room temperature. The MIC membrane remains stable and rigid at 200 °C with the shear storage modulus (G') only slightly decreasing by 35%. Li/MIC/LiFePO 4 cells demonstrate stable cycling performance over a wide temperature range from 23 to 150 °C. The specific discharge capacity at 100 and 150 °C at 1 C rate exceeds 160 mAh g –1 . The discharge capacity retention is 99% after 50 cycles at 150 °C. Furthermore, this stable battery performance shows that this low polymer content MIC membrane qualifies for use as a solid electrolyte in lithium metal batteries operating over a wide temperature range.

25 ENERGY STORAGE↗