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At least 109 records · Page 6

Bond order predictions using deep neural networks

Machine learning is an extremely powerful tool for the modern theoretical chemist since it provides a method for bypassing costly algorithms for solving the Schrödinger equation. Already, it has proven able to infer molecular and atomic properties such as charges, enthalpies, dipoles, excited state energies, and others. Most of these machine learning algorithms proceed by inferring properties of individual atoms, even breaking down total molecular energy into individual atomic contributions. In this paper, we introduce a modified version of the Hierarchically Interacting Particle Neural Network (HIP-NN) capable of making predictions on the bonds between atoms rather than on the atoms themselves. We train the modified HIP-NN to infer bond orders for a large number of small organic molecules as computed via the Natural Bond Orbital package. We demonstrate that the trained model is extensible to molecules much larger than those in the training set by studying its performance on the COMP6 dataset. This method has applications in cheminformatics and force field parameterization and opens a promising future for machine learning models to predict other quantities that are defined between atoms such as density matrix elements, Hamiltonian parameters, and molecular reactivities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Photoabsorption in formaldehyde

Theoretical studies of the vertical electronic dipole excitation and ionization spectra in molecular formaldehyde are reported. The investigations relied on configuration-interaction calculations and moment-theory techniques. A double-zeta basis of contracted Gaussian-lobe functions supplemented with appropriate polarization and bond functions was used to construct Fock spectra in C(2 nu) symmetry for certain states near the ground state equilibrium geometry. The ionization energies, discrete vertical transition frequencies, and oscillator strengths for occupied and vertical Fock orbitals are in general accord with experimental determinations and other theoretical calculations. Stieltjes and Chebyshev vertical electronic photoionization profiles were calculated and found to be in good agreement with appropriately averaged photoionization-mass spectrometric measurements of the cross section for parent H2CO(+) ion production.

Langhoff, P. W.↗

Aeolian Sand Transport in the Planetary Context: Respective Roles of Aerodynamic and Bed-Dilatancy Thresholds

The traditional view of aeolian sand transport generally estimates flux from the perspective of aerodynamic forces creating the airborne grain population, although it has been recognized that "reptation" causes a significant part of the total airborne flux; reptation involves both ballistic injection of grains into the air stream by the impact of saltating grains as well as the "nudging" of surface grains into a creeping motion. Whilst aerodynamic forces may initiate sand motion, it is proposed here that within a fully-matured grain cloud, flux is actually governed by two thresholds: an aerodynamic threshold, and a bed-dilatancy threshold. It is the latter which controls the reptation population, and its significance increases proportionally with transport energy. Because we only have experience with terrestrial sand transport, extrapolations of aeolian theory to Mars and Venus have adjusted only the aerodynamic factor, taking gravitational forces and atmospheric density as the prime variables in the aerodynamic equations, but neglecting reptation. The basis for our perspective on the importance of reptation and bed dilatancy is a set of experiments that were designed to simulate sand transport across the surface of a martian dune. Using a modified sporting crossbow in which a sand-impelling sabot replaced the bolt-firing mechanism, individual grains of sand were fired at loose sand targets with glancing angles typical of saltation impact; grains were projected at about 80 m/s to simulate velocities commensurate with those predicted for extreme martian aeolian conditions. The sabot impelling method permitted study of individual impacts without the masking effect of bed mobilization encountered in wind-tunnel studies. At these martian impact velocities, grains produced small craters formed by the ejection of several hundred grains from the bed. Unexpectedly, the craters were not elongated, despite glancing impact; the craters were very close to circular in planform. High-speed photography showed them to grow in both diameter and depth after the impactor had ricochetted from the crater site. The delayed response of the bed was "explosive" in nature, and created a miniature ejecta curtain spreading upward and outward for many centimeters for impact of 100-300 micron-diameter grains into similar material. Elastic energy deposited in the bed by the impacting grain creates a subsurface stress regime or "quasi-Boussinesq" compression field. Elastic recovery of the bed occurs by dilatancy; shear stresses suddenly convert the grains from closed to open packing, and grains are consequently able to eject themselves forcefully from the impact site. Random jostling of the grains causes radial homogenization of stress vectors and a resulting circular crater. There is a great temptation to draw parallels with cratering produced by meteorite impacts, but a rigorous search for common modelling ground between the two phenomena has not been conducted at this time. For every impact of an aerodynamically energized grain, there are several hundred grains ejected into the wind for the high-energy transport that might occur on Mars. Many of these grains will themselves become subject to the boundary layer's aerodynamic lift forces (their motion will not immediately die and add to the creep population), and these grains will become indistinguishable from those lifted entirely by aerodynamic forces. As each grain impacts the bed, it will eject even more grains into the flow. A cascading effect will take place, but because it must be finite in its growth, damping will occur as the number of grains set in motion causes mid-air collisions that prevent much of the impact energy from reaching the surface of the bed -thus creating a dynamic equilibrium in a high-density saltation cloud. It is apparent that for a given impact energy, the stress field permits a smaller volume of grains to convert to open packing as the size of the bed grains increases, or as the energy of the "percussive" grain decreases (by decrease in velocity or mass). Thus, the mass of the "repercussive" grain population that is ejected from the impact site becomes a function of the scale of the stress field in relation to the scale of the bed material (self-similarity being applicable if both bed size and energy are simultaneously adjusted). In other words, in a very high energy aeolian system where an aerodynamically raised grain can ballistically raise many more grains, the amount of material lifted into the wind becomes largely a function of a dilatancy threshold. If this threshold is exceeded, grains are repercussively injected into the saltation cloud. The "dilatancy threshold" may be defined in terms of the saltation percussive force required to convert the bed, through elastic response, from a closed to an open packing system. If open packing cannot be created, the grains cannot escape from the impact site, even though the elastic deformation and percussive force may be able to reorganize the grains with respect to one another. As the crossbow experiments showed, for an ever-increasing bed grain size, a point is reached when no material can be moved because the energy of the percussive grain is insufficient to dilate the relatively coarse bed. Although this seems to be stating the obvious -- that too little energy will not cause the bed to splash -- the consequences of exceeding the "splash threshold" by dilatancy are not so obvious for high-energy aeolian transport. It is noted that the force required to elastically dilate the bed has to overcome Coulombic grain attractions such as dipole-dipole coupling, dielectric, monopole, contact-induced dipole attractions, van der Waals forces, molecular monolayer capillary forces, as well as the mechanical interlocking frictional resistance of the grains. On Mars, it is predicted that the dilatancy threshold may be the prime control of grain flux. Additional information is contained in the original.

Marshall, J. R.↗

Transition probabilities of the B-prime 1Sigma(u)(+) to X 1Sigma(g)(+) system of molecular hydrogen

From published potential energy curves and transition dipole moments, there are obtained by numerical integration of the equations of nuclear motion the vibrational eigenfunctions of the X 1Sigma(g)(+) and B-prime 1Sigma(u)(+) states of H2. The probabilities of radiative transitions from the discrete vibrational levels of the excited B-prime 1Sigma(u)(+) electronic state of H2 to the discrete and continuum vibrational levels of the ground X 1Sigma(g)(+) electronic state are calculated. The Franck-Condon factors are also presented.

Kwok, T. L.↗

Amphiphile Organization in Organic Solutions: An Alternative Explanation for Small-Angle X-ray Scattering Features in Malonamide/Alkane Mixtures

In this work, the role of different intermolecular interactions in the aggregation of amphiphiles in an organic solvent is studied for systems of relevance to liquid-liquid extraction (LLE), a chemical process used to selectively recover metals from complex mixtures. Of specific interest is the role, or lack thereof, of hydrogen bonding, which is often assumed to be a main driver of the organic phase structural organization that has been linked to separation efficacy. Toward that end, a series of malonamide extractants in n-dodecane have been studied in the absence of any extracted aqueous solutes, including water. The series of extractants includes N,N'-dimethyl-N,N'-dibutyltetradecylmalonamide (DMDBTDMA), two of its homologs, and N,N'-dimethyl-N,N'-dioctylhexylethoxymalonamide (DMDOHEMA). This simplified model LLE system enables systematic investigation of the role of dipole-dipole and alkyl tail steric interactions in amphiphile aggregation. Small-angle X-ray scattering (SAXS) profiles computed from molecular dynamics trajectories are in good agreement with experimental SAXS data. Molecular dynamics simulations show that malonamide aggregation results from dipole-driven self-association and lacks characteristic aggregate sizes. Mid-q correlation peaks in the SAXS profiles emerge at high concentration for each malonamide. In those densely packed solutions, the correlation peaks are observed to result from alkyl tail-induced spacing between electron-rich polar head groups, with peak positions determined by the different alkyl tail lengths present in the malonamide molecule. This explanation of the SAXS correlation peaks contrasts with the prevailing literature, which attributes mesoscale features observed in small-angle scattering to the formation of microemulsions. Instead, this work finds that these features are present in the absence of water or any reverse micellar organization of the malonamides. As such, molecular-scale malonamide self-association and packing, rather than microemulsion-based colloidal-scale descriptions, is a more appropriate framework for these LLE systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile

Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole–dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. In conclusion, this study enables the ability to predict the structure–property relations for PAN and analogues with sustainable ab initio accuracy across scales.

36 MATERIALS SCIENCE↗

Dielectric Properties of Piezoelectric Polyimides

Molecular modeling and dielectric measurements are being used to identify mechanisms governing piezoelectric behavior in polyimides such as dipole orientation during poling, as well as degree of piezoelectricity achievable. Molecular modeling on polyimides containing pendant, polar nitrile (CN) groups has been completed to determine their remanent polarization. Experimental investigation of their dielectric properties evaluated as a function of temperature and frequency has substantiated numerical predictions. With this information in hand, we are then able to suggest changes in the molecular structures, which will then improve upon the piezoelectric response.

Ounaies, Z.↗

Modeling of pressure-induced far-infrared absorption spectra Molecular hydrogen pairs

Meyer et al. (1985) have calculated the accurate induced dipole moment function of H2-H2 from first principles, using highly correlated wave functions for the first time in such work. The present paper is concerned with the collision-induced translational-rotational absorption coefficient for molecular hydrogen pairs, taking into account computations on the basis of the fundamental theory considered by Meyer et al. Data have been obtained for temperatures in the range from 40 to 300 K. Criteria are developed for choosing among various model line shapes. It is found that certain models are capable of approximating the quantum profiles closely, with rms errors of only a few percent.

Borysow, J.↗

Quantifying Species Populations in Multivalent Borohydride Electrolytes

Multivalent batteries represent an important beyond Li-ion energy storage concept. The prospect of calcium batteries, in particular, has emerged recently due to novel electrolyte demonstrations, especially that of a ground-breaking combination of the borohydride salt Ca(BH 4 ) 2 dissolved in tetrahydrofuran. Recent analysis of magnesium and calcium versions of this electrolyte led to the identification of divergent speciation pathways for Mg 2+ and Ca 2+ despite identical anions and solvents, owing to differences in cation size and attendant flexibility of coordination. To test these proposed speciation equilibria and develop a more quantitative understanding thereof, we have applied pulsed-field-gradient nuclear magnetic resonance and dielectric relaxation spectroscopy to study these electrolytes. Additionally, concentration-dependent variation in anion diffusivities and solution dipole relaxations, interpreted with the aid of molecular dynamics simulations, confirms these divergent Mg 2+ and Ca 2+ speciation pathways. These results provide a more quantitative description of the electroactive species populations. We find that these species are present in relatively small quantities, even in the highly active Ca(BH 4 ) 2 /tetrahydrofuran electrolyte. This finding helps interpret previous characterizations of metal deposition efficiency and morphology control and thus provides important fundamental insight into the dynamic properties of multivalent electrolytes for next-generation batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Angular motion of a PAH molecule in interstellar environment

Polycyclic aromatic hydrocarbon (PAH) molecules have recently been proposed as an important and hitherto undetected component of the Interstellar Medium (ISM). The theory was based on an explanation of the Unidentified IR Emission Bands by Leger et al. It has already led to a verified prediction on extended galactic and extragalactic emissions measured by IRAS, or by a recent balloon borne experiment. The physics that rules the motion of such molecules in the ISM was studied, taking into account their coupling with the ambient gas, the radiation field (absorption and emission) and the static magnetic field. This is important for many implications of the PAH theory such as the radio emission by these molecules or the expected polarization of their IR emission. A reflection nebulae is considered where the situation is rather well known. Every day life of a mean PAH molecule in such a region is as follows: every 3 hrs a UV photon is absorbed heating the molecule to a thousand degs; the temperature decay due to cooling by IR emission follows then within a few seconds. A collision with a molecule of gas occurs typically once a week, while an H atom is ejected or captured at the same rate. A typical cooling cycle after a heat impulse is given. The PAH molecules studied as representative of the family has typically 50 atoms, a radius of 4.5 A, is circular and has a molecular mass of M = 300; its permanent dipole moment is 3 Debye.

Rouan, D.↗

Range and strength of mechanical interactions of force dipoles in elastic fiber networks

Mechanical forces generated by myosin II molecular motors drive diverse cellular processes, most notably shape change, division and locomotion. These forces may be transmitted over long range through the cytoskeletal medium – a disordered, viscoelastic network of biopolymers. The resulting cell size scale force chains can in principle mediate mechanical interactions between distant actomyosin units, leading to self-organized structural order in the cell cytoskeleton. Inspired by such force transmission through elastic structures in the cytoskeleton, we consider a percolated fiber lattice network, where fibers are represented as linear elastic elements that can both bend and stretch, and the contractile activity of myosin motors is represented by force dipoles. Then, by using a variety of metrics, we show how two such contractile force dipoles interact with each other through their mutual mechanical deformations of the elastic fiber network. As a prelude to two-dipole interactions, we quantify how forces propagate through the network from a single anisotropic force dipole by analyzing clusters of nodes connected by highly strained bonds, as well as through the decay rate of strain energy with distance from a force dipole. We show that predominant fiber bending screens out force propagation, resulting in reduced and strongly network configuration-dependent dipole interactions. On the other hand, stretching-dominated networks support longer-ranged inter-dipole interactions that recapitulate the predictions of linear elasticity theory. By characterizing the differences between tensile and compressive force propagation in the fiber network, we show how inter-dipole interaction depends on the dipoles’ mutual separation and orientation. The resulting elastic interaction energy may mediate a force between multiple distant dipoles, leading to their self-organization into ordered configurations. In conclusion, this provides a potential pathway for active mechanical force-driven structural order in elastic biopolymer networks.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Molecular polarizabilities as fingerprints of perturbations to water by ions and confinement

Perturbations to water, both by ions and confining media, have been the focus of numerous experimental and theoretical studies. Yet, several open questions remain, including the extent to which such perturbations modify the structural and dielectric properties of the liquid. Here, we present a first-principles molecular dynamics study of alkali cations in water (Li + , Na + , and K + ) as well as of water and LiCl and KCl solutions under confinement within carbon nanotubes (CNTs) of small diameter (1.1-1.5 nm). Our simulations support the view that the water structure is only modified locally in the presence of cations. We found that molecular polarizabilities are fingerprints of hydrogen bonding modifications, which occur at most up to the second solvation shell for all cations in bulk water. Under confinement, we found that the overall value of the molecular polarizability of water molecules near the surface is determined by the balance of two effects, which are quantitatively different in CNTs of different radii: the presence of broken hydrogen bonds at the surface leads to a decrease in the polarizabilities of water molecules, while the interaction with the CNT enhances polarizabilities. Interestingly, the reduction in dipole moments of interfacial water molecules under confinement is instead driven only by changes in the water structure and not by interfacial interactions. As expected, confinement effects on water molecular polarizabilities and dipole moments are more pronounced in the case of the 1.1 nm CNT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectroscopy of atoms in an optical dipole trap using spectrally selective heating by a probe laser field

Spectral properties of atoms localised in an optical dipole trap are studied using the method of spectrally selective heating by a probe field. The method is based on measuring the number of atoms in a trap after they interact with a probe field. The dependence of the number of atoms on the frequency of the probe field fully characterises the shift and width of the spectral absorption line of trapped atoms. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Widespread Negative Longitudinal Piezoelectric Responses in Ferroelectric Crystals with Layered Structures

In this study, we investigate the underlying mechanisms of the universal negative piezoelectricity in low-dimensional layered materials by carrying out first-principles calculations. Two-dimensional layered ferroelectric CuInP 2 S 6 is analyzed in detail as a typical example, but the theory can be applied to any other low-dimensional layered piezoelectrics. Consistent with the theory proposed in [Phys. Rev. Lett. 119, 207601 (2017), the anomalous negative piezoelectricity in CuInP 2 S 6 also results from its negative clamped-ion term, which cannot be compensated by the positive internal-strain part. Here, we focus on a more general rule by proposing that having a negative clamped-ion term should be universal among piezoelectric materials, which is attributed to the “lag of Wannier center” effect. The internal-strain term, which is the change in polarization due to structural relaxation in response to strain, is mostly determined by the spatial structure and chemical bonding of the material. In a low-dimensional layered piezoelectric material such as CuInP 2 S 6 , the internal-strain term is approximately zero. This is because the internal structure of the molecular layers, which are bonded by the weak van der Waals interaction, responds little to the strain. As a result, the magnitude of the dipole, which depends strongly on the dimension and structure of the molecular layer, also has a small response with respect to strain. An equation bridging the internal strain responses in low-dimensional and three-dimensional piezoelectrics is also derived to analytically express this point. This work aims to deepen our understanding about this anomalous piezoelectric effect, especially in low-dimensional layered materials, and provide strategies for discovering materials with novel electromechanical properties.

2-dimensional systems↗

Capturing Ultrafast Electron Driven Chemical Reactions in Molecules

The goals of this project are to develop experimental tools to investigate the dynamics of dissociative electron attachment (DEA) reactions in real time. In a DEA reaction, the attachment of a low energy electron to a molecule results in bond breaking and the fragmentation of the molecule. A new instrument has been designed and is under construction to perform time-resolved photoelectron and photo-fragment spectroscopy following electron transfer from an iodide anion to a molecule within a mass-selected molecular dimer. Iodide binds only weakly through the dipole interaction with many polar molecules, and such molecules forming a dimer with iodide undergo only small changes from the equilibrium geometry in isolation. When the electron is transferred from the iodide, the iodine atom is no longer bound, so the electron transfer step can be considered analogous to electron attachment and brings the key advantage of ultrafast timing precision. The experiments proposed here will establish the experimental tools to interrogate the dynamics of dissociative electron attachment on the fundamental timescales of the nuclear motion, by simultaneously probing the valence electronic structure and the fragmentation pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗