Lancifodilactone G : insights about an unusually stable enol

From quantum mechanics calculations we confirm that the naturally occurring enol lancifodilactone G is stable over the keto form (by 2.6 kcal/mol in water), the only known stable aliphatic enol (devoid of conjugated or bulky aromatics and lacking a 1,3-diketone structural motif known to stabilize enols). We determine architectural elements responsible for the enol stabilization and find a mechanism for keto-enol conversion in solution. In addition, we correct previously reported computational results that were performed on the misinterpreted structure demonstrating that the enol form of this natural product is more stable than previously thought

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor−liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations

Mechanisms of Auger-induced chemistry derived from wave packet dynamics

To understand how core ionization and subsequent Auger decay lead to bond breaking in large systems, we simulate the wave packet dynamics of electrons in the hydrogenated diamond nanoparticle C_(197)H_(112). We find that surface core ionizations cause emission of carbon fragments and protons through a direct Auger mechanism, whereas deeper core ionizations cause hydrides to be emitted from the surface via remote heating, consistent with results from photon-stimulated desorption experiments [Hoffman A, Laikhtman A, (2006) J Phys Condens Mater 18:S1517–S1546]. This demonstrates that it is feasible to study the chemistry of highly excited large-scale systems using simulation and analysis tools comparable in simplicity to those used for classical molecular dynamics

Electromagnetic field application to underground power cable detection

Before commencing excavation or other work where power or other cables may be buried, it is important to determine the location of cables to ensure that they are not damaged. This paper describes a method of power-cable detection and location that uses measurements of the magnetic field produced by the currents in the cable, and presents the results of tests performed to evaluate the method. The cable detection and location program works by comparing the measured magnetic field signal with values predicted using a simple numerical model of the cable. Search coils are used as magnetic field sensors, and a measurement system is setup to measure the magnetic field of an underground power cable at a number of points above the ground so that it can detect the presence of an underground power cable and estimate its position. Experimental investigations were carried out using a model and under real site test conditions. The results show that the measurement system and cable location method give a reasonable prediction for the position of the target cable

Detection and Location of Underground Power Cable using Magnetic Field Technologies

The location of buried underground electricity cables is becoming a major engineering and social issue worldwide. Records of utility locations are relatively scant, and even when records are available, they almost always refer to positions relative to ground-level physical features that may no longer exist or that may have been moved or altered. The lack of accurate positioning records of existing services can cause engineering and construction delays and safety hazards when new construction, repairs, or upgrades are necessary. Hitting unknown underground obstructions has the potential to cause property damage, injuries and, even deaths. Thus, before commencing excavation or other work where power or other cables may be buried, it is important to determine the location of the cables to ensure that they are not damaged during the work. This paper describes the use of an array of passive magnetic sensors (induction coils) together with signal processing techniques to detect and locate underground power cables. The array consists of seven identical coils mounted on a support frame; one of these coils was previously tested under laboratory conditions, and relevant results have been published in [1]. A measurement system was constructed that uses a battery powered data acquisition system with two NI 9239 modules connected to the coil array, and controlled by a laptop. The system is designed to measure the magnetic field of an underground power cable at a number of points above the ground. A 3 by 3 m test area was chosen in one of our campus car parks. This area was chosen because the university’s utility map shows an isolated power cable there. Measurements were taken with the array in 16 different test positions, and compared with the values predicted for a long straight horizontal cable at various positions. Finally, error maps were plotted for different Z-coordinate values, showing the minimum fitting error for each position in this plane. One such map is shown in Figure 1; the low error values of 4-5% give a high degree of confidence that most of the measured signal is due to a cable near to these positions. This view is supported by the fact that the university’s utility map shows the cable at X = 1.4 m, and by amplitude measurements taken with a hand-held magnetic field meter

Structure of polyamidoamide dendrimers up to limiting generations : a mesoscale description

The polyamidoamide (PAMAM) class of dendrimers was one of the first dendrimers synthesized by Tomalia and co-workers at Dow. Since its discovery the PAMAMs have stimulated many discussions on the structure and dynamics of such hyperbranched polymers. Many questions remain open because the huge conformation disorder combined with very similar local symmetries have made it difficult to characterize experimentally at the atomistic level the structure and dynamics of PAMAM dendrimers. The higher generation dendrimers have also been difficult to characterize computationally because of the large size (294852 atoms for generation 11) and the huge number of conformations. To help provide a practical means of atomistic computational studies, we have developed an atomistically informed coarse-grained description for the PAMAM dendrimer. We find that a two-bead per monomer representation retains the accuracy of atomistic simulations for predicting size and conformational complexity, while reducing the degrees of freedom by tenfold. This mesoscale description has allowed us to study the structural properties of PAMAM dendrimer up to generation 11 for time scale of up to several nanoseconds. The gross properties such as the radius of gyration compare very well with those from full atomistic simulation and with available small angle x-ray experiment and small angle neutron scattering data. The radial monomer density shows very similar behavior with those obtained from the fully atomistic simulation. Our approach to deriving the coarse-grain model is general and straightforward to apply to other classes of dendrimers

Effects of Surface Roughness on the Electrochemical Reduction of CO2 over Cu

We have investigated the role of surface roughening on the CO2 reduction reaction (CO2RR) over Cu. The activity and product selectivity of Cu surfaces roughened by plasma pretreatment in Ar, O2, or N2 were compared with that of electrochemically polished Cu samples. Differences in total and product current densities, the ratio of current densities for HER (the hydrogen evolution reaction) to CO2RR, and the ratio of current densities for C2+ to C1 products depend on the electrochemically active surface and are nearly independent of plasma composition. Theoretical analysis of an electropolished and roughened Cu surface reveals a higher fraction of undercoordinated Cu sites on the roughened surface, sites that bind CO preferentially. Roughened surfaces also contain square sites similar to those on a Cu(100) surface but with neighboring step sites, which adsorb OC-COH, a precursor to C2+ products. These findings explain the increases in the formation of oxygenates and hydrocarbons relative to CO and the ratio of oxygenates to hydrocarbons observed with increasing surface roughness

Understanding DNA based Nanostructures

We use molecular dynamics (MD) simulations to understand the structure, and stability of various Paranemic crossover (PX) DNA molecules and their topoisomer JX molecules, synthesized recently by Seeman and coworkers at New York University (NYU). Our studies include all atoms (4432 to 6215) of the PX structures with an explicit description of solvent and ions (for a total of up to 42,000 atoms) with periodic boundary conditions. We report the effect of divalent counterions Mg(+2) on the structural and thermodynamic properties of these molecules and compare them to our previously reported results in presence of monovalent Na+ ions. The dynamic structures averaged over the 3-nanosecond simulations preserves the Watson-Crick hydrogen bonding as well as the helical structure. We find that PX65 is the most stable structure both in Na+ and Mg(+2) in accordance with the experimental results. PX65 has helical twist and other helical structural parameters close to the values for normal B-DNA of similar length and sequence. Our strain energy calculations demonstrate that stability of the crossover structure increases with the increase in crossover points

The role of preview validity in predictability and frequency effects on eye movements in reading

Epub 2018 Apr 12A word’s predictability, as measured by its cloze probability, has a robust influence on the time a reader’s eyes spend on the word, with more predictable words receiving shorter fixations. However, several previous studies using the boundary paradigm have found no apparent effect of predictability on early reading time measures when the reader does not have valid parafoveal preview of the target word. The present study directly assesses this pattern in two experiments, demonstrating evidence for a null effect of predictability on first fixation and gaze duration with invalid preview, supported by Bayes factor analyses. While the effect of context independent word frequency is shown to survive with invalid preview, consistent with previous studies, the effect of predictability is eliminated with both unrelated word previews and random letter string previews. These results suggest that a word’s predictability influences early stages of orthographic processing, and does so only when perceptual evidence is equivocal, as is the case when the word is initially viewed in parafoveal vision. Word frequency may influence not only early orthographic processing, but also later processing stages. (PsycINFO Database Record (c) 2018 APA, all rights reserved)This work was supported by a grant from the National Science Foundation (BCS 1732008) to the Adrian Stau