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At least 91 records · Page 5

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First-principles modeling of chemistry in mixed solvents: Where to go from here?

Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solar nebula chemistry - Implications for volatiles in the solar system

Current theoretical models of solar nebula chemistry which take into account the interplay between chemistry and dynamics are presented for the abundant reactive volatile elements including hydrogen, carbon, nitrogen, oxygen, and sulfur. Results of these models indicate that, in the solar nebula, the dominant carbon and nitrogen gases were CO and NO, whereas, in giant planet subnebulae, the dominant carbon and nitrogen gases were CH4 and NH3; in the solar nebula, the Fe metal grains catalyzed the formation of organic compounds from CO and H2 via the Fischer-Tropsch-type reaction. It was also found that, in solar nebula, bulk FeS formation was kinetically favorable, while FeO incorporation into silicates and bulk Fe3O4 formation were kinetically inhibited. Furthermore, clathrate formation was kinetically inhibited in the solar nebula, while it was kinetically favorable in giant planet subnebulae.

Fegley, Bruce, Jr.↗

Theoretical insights into the surface physics and chemistry of redox-active oxides

Redox active oxides are ubiquitous in materials applications, including catalysis, photovoltaics, self-cleaning glasses, chemical sensors, and electronic components. Their utility derives from their unique ability to access multiple metal charge states within a finite energy window. However, this property also confounds our ability to study reducible oxides, because it leads to structural, compositional, and electronic complexities that elude simplistic models of materials structure and function. Oxygen vacancies play a critical role in shaping the functional properties of such oxides; most notably, they lead to mobile charge imbalances that impact surface processes at significant distances from the originating defect. Atomistic simulations are inherently equipped to illuminate these phenomena at a fundamental level; however, reducible oxides pose great challenges due to the high level of electron correlation needed to correctly describe them. Knowing how defects form, couple, propagate, agglomerate, or repel each other and influence the surface properties of reducible oxides is only now coming into the grasp of modern theory and simulation capabilities. This knowledge is also key to discovering and controlling emergent materials processes at nanometer scale and beyond. The manuscript was written with support of all three authors from U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Work by RR and VG was performed at Pacific Northwest National Laboratory (PNNL), which is a multi-program laboratory operated by Battelle for DOE under Contract DE AC05 76RL01830. AS was supported under Award DE-SC0007347.

Rousseau, Roger J.↗

The physics and chemistry of dusty plasmas: A laboratory and theoretical investigation

Theoretical work on dusty plasmas was conducted in three areas: collective effects in a dusty plasma, the role of dusty plasmas in cometary atmospheres, and the role of dusty plasmas in planetary atmospheres (particularly in the ring systems of the giant planets). Laboratory investigations consisted of studies of dust/plasma interactions and stimulated molecular excitation and infrared emission by charged dust grains. Also included is a list of current publications.

Whipple, E. C.↗

Chemistry of chlorine in dense interstellar clouds

Laboratory experiments and theoretical modeling show that the chemistry of chlorine is fairly simple in dense interstellar clouds, with Cl and HCl as the only species whose fractional abundances are significant. The estimated fraction of gas-phase chlorine present as HCl lies between 25-65 percent, in good agreement with the recent observations of the ground state HCl transition by Blake, Keene, and Philips (1985). These results, combined with the observational limits on HCl, indicate that chlorine is not severely depleted in dense interstellar clouds.

Blake, G. A.↗

MXene-Derived Potassium-Preintercalated Bilayered Vanadium Oxide Nanostructures for Cathodes in Nonaqueous K-Ion Batteries

Bilayered vanadium oxides (BVOs) are promising cathode materials for beyond-Li-ion batteries due to their tunable chemistries and high theoretical capacities. However, the large size of beyond-Li + ions limits electrochemical cycling and rate capability of BVO electrodes. Recent reports of MXene-derived BVOs with nanoscale flower-like morphology have shown improved electrochemical stability at high rates up to 5C in nonaqueous lithium-ion batteries. Here, we report how morphological stabilization can lead to improved rate capability in potassium-ion batteries (PIBs) through the synthesis and electrochemical characterization of MXene-derived K-preintercalated BVOs (MD-KVOs), which were derived from two V 2 CT x precursor materials prepared using two different etching protocols. We show that the etching conditions affect the surface chemistry of the MXene, which plays a role in the MXene-to-oxide transformation process. MXene derived from a milder etchant transformed into a nanoflower MD-KVO with two-dimensional (2D) nanosheet petals (KVO-DMAE) while a more aggressive etchant produced a MXene that transformed into a MD-KVO with one-dimensional (1D) nanorod morphology (KVO-CMAE). Electrochemical cycling of the produced MD-KVOs after drying at 200 °C under vacuum (KVO-DMAE-200 and KVO-CMAE-200) in PIBs showed that electrochemical stability of MD-KVO at high rates improved through the morphological stabilization of 2D particles combined with the control of interlayer water and K + ion content. Structure refinement of KVO-DMAE-200 further corroborates the behavior observed during K + ion cycling, connecting structural and compositional characteristics to the improved rate capability. This work demonstrates how proper synthetic methodology can cause downstream effects in the control of structure, chemical composition, and morphology of nanostructured layered oxide materials, which is necessary for development of future materials for beyond-Li-ion battery technologies.

25 ENERGY STORAGE↗

Understanding flavin electronic structure and spectra

Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

59 BASIC BIOLOGICAL SCIENCES↗

Diffusion Monte Carlo approaches for studying nuclear quantum effects in fluxional molecules

Abstract Diffusion quantum Monte Carlo (DMC) provides a powerful approach for obtaining the ground state energy and wave function of molecules, ions, and molecular clusters. The approach is uniquely well suited for studies of fluxional molecules, which undergo large amplitude vibrational motions even in their ground state. In contrast to the electronic structure problem, where the wave function must be antisymmetric with respect to exchange of any pair of electrons, the wave function for the ground vibrational state is nodeless. This greatly simplifies the application of DMC for vibrational problems. Because there is not a single potential function that can be used to describe the intramolecular and intermolecular interactions in all molecular systems, most methods that are used to describe nuclear quantum effects rely on a carefully chosen zero‐order description of the molecular vibrations. In contrast, DMC calculations can be performed in Cartesian coordinates, making the DMC algorithm easily transferable between different chemical systems. In this contribution, the theory that underlies DMC will be discussed along with important considerations for performing DMC calculations. Extensions for evaluating vibrationally excited states and molecular properties are also discussed. Insights that can be obtained from DMC calculations are illustrated in the context of the protonated water clusters. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Theoretical and Physical Chemistry > Spectroscopy

Chemistry↗

Interstellar sulfur chemistry

The results of a chemical model of SO, CS, and OCS chemistry in dense clouds are summarized. The results are obtained from a theoretical study of sulfur chemistry in dense interstellar clouds using a large-scale time-dependent model of gas-phase chemistry. Among the results are the following: (1) owing to activation energy, the reaction of CS with O atoms is efficient as a loss mechanism of CS during the early phases of cloud evolution or in hot and oxygen-rich sources such as the KL nebula; (2) if sulfur is not abnormally depleted in dense clouds, then the observed abundances of SO, SO2, H2S, CS, OCS, H2CS, and SiS indicate that sulfur is mostly atomic in dense clouds; and (3) OCS is stable against reactions with neutral atoms and radicals in dense clouds.

Prasad, S. S.↗

Experimental basis for a Titan probe organic analysis

The recent Voyager flyby of Titan produced evidence for at least nine organic compounds in that atmosphere that are heavier than methane. Several models of Titan's atmosphere, as well as laboratory simulations, suggest the presence of organics considerably more complex that those observed. To ensure that the in situ measurements are definitive with respect to Titan's atmosphere, experiment concepts, and the related instrumentation, must be carefully developed specifically for such a mission. To this end, the possible composition of the environment to be analyzed must be bracketed and model samples must be provided for instrumentation development studies. Laboratory studies to define the optimum flight experiment and sampling strategy for a Titan entry probe are currently being conducted. Titan mixtures are being subjected to a variety of energy sources including high voltage electron from a DC discharge, high current electric shock, and laser detonation. Gaseous and solid products are produced which are then analyzed. Samples from these experiements are also provided to candidate flight experiments as models for instrument development studies. Preliminary results show that existing theoretical models for chemistry in Titan's atmosphere cannot adequetely explain the presence and abundance of all trace gases observed in these experiments.

Mckay, C. P.↗

The Schwinger Variational Method

Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. The application of the Schwinger variational (SV) method to e-molecule collisions and molecular photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions. Since this is not a review of cross section data, cross sections are presented only to server as illustrative examples. In the SV method, the correct boundary condition is automatically incorporated through the use of Green's function. Thus SV calculations can employ basis functions with arbitrary boundary conditions. The iterative Schwinger method has been used extensively to study molecular photoionization. For e-molecule collisions, it is used at the static exchange level to study elastic scattering and coupled with the distorted wave approximation to study electronically inelastic scattering.

Huo, Winifred M.↗

The Schwinger Variational Method

Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. For collisional problems they can be grouped into two types: those based on the Schroedinger equation and those based on the Lippmann-Schwinger equation. The application of the Schwinger variational (SV) method to e-molecule collisions and photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions.

Huo, Winifred M.↗

Organic Chemistry in Space

Astronomical observations, theoretical modeling, laboratory simulation and analysis of extraterrestrial material have enhanced our knowledge of the inventory of organic matter in the interstellar medium (ISM) and on small bodies such as comets and asteroids (Ehrenfreund & Charnley 2000). Comets, asteroids and their fragments, meteorites and interplanetary dust particles (IDPs), contributed significant amounts of extraterrestrial organic matter to the young Earth. This material degraded and reacted in a terrestrial prebiotic chemistry to form organic structures that may have served as building blocks for life on the early Earth. In this talk I will summarize our current understanding of the organic composition and chemistry of interstellar clouds. Molecules of astrobiological relevance include the building blocks of our genetic material: nucleic acids, composed of subunits such as N-heterocycles (purines and pyrimidines), sugars and amino acids. Signatures indicative of inheritance of pristine and modified interstellar material in comets and meteorites will also be discussed.

Charnley, Steven↗

Physics, chemistry and pulmonary sequelae of thermodegradation events in long-mission space flight

An event in which electronic insulation consisting of polytetrafluoroethylene undergoes thermodegradation on the Space Station Freedom is considered experimentally and theoretically from the initial chemistry and convective transport through pulmonary deposition in humans. The low-gravity enviroment impacts various stages of event simulation. Vapor-phase and particulate thermodegradation products were considered as potential spacecraft contaminants. A potential pathway for the production of ultrafine particles was identified. Different approaches to the simulation and prediction of contaminant transport were studied and used to predict the distribution of generic vapor-phase products in a Space Station model. A lung transport model was used to assess the pulmonary distribution of inhaled particles, and, finally, the impact of adaptation to low gravity on the human response to this inhalation risk was explored on the basis of known physiological modifications of the immune, endocrine, musculoskeletal and pulmonary systems that accompany space flight.

Todd, Paul↗

Multiscale Ecosystem for solving Maxwell-Schrodinger equations of open quantum systems (OpenMS)

Light-matter interactions play an important role in many branches of physics, chemistry, energy, and materials science. In the strong coupling regime, light-matter interactions are able to tune the materials properties via the formation of new quasiparticles, such as plasmons and polaritons. However, theoretical and numerical modeling of the light-matter interaction-mediated processes remain a big challenge because light-matter interactions are fundamentally multiscale and multiphysics problems involving multiple interactions between electrons, nuclei, and photons at different time/length scales. In the current community, light-matter interactions were treated at different levels of theoretical complexity in quantum chemistry and quantum optics. In quantum optics or quantum photonics, the matter is usually simplified as a few-level system, and the light is treated quantum-mechanically. On the other hand, quantum chemistry explores first-principles methods, including both single-particle and many-body-based techniques, to describe the electronic properties of matter in detail. However, light is usually prescribed as a classical electromagnetic field, and the light-matter interaction is taken into account as an external potential via classical approximations. This software is designed to fill current modeling shortcomings by delivering a first-ever scalable multiscale platform for simulating light-matter interactions in realistic electromagnetic environments. The software solves Maxwell and Schrodinger equations self-consistent on the heterogeneous platforms. It implements HF/DFT, TDDFT, and coupled-cluster counterparts for light-matter interactions and adopts modular programming to offload massively parallel algorithms on a large number of CPU/GPUs.

Zhang, Yu↗

Teaching Nonradiative Transitions with MATLAB and Python

Nonradiative transitions are changes in energy states of atoms, ions, or molecules that do not involve the emission or absorption of photons. Despite their importance in understanding luminescent properties and photochemical reaction mechanisms, nonradiative transitions are rarely given more than a qualitative overview in undergraduate and even graduate physical chemistry curricula. To supplement the coverage of nonradiative transition topics, we provide here a set of active learning exercises to help students develop an intuitive understanding of the factors that determine the rate of nonradiative transitions. Here, we start by outlining the theoretical background through the formulations of the Franck–Condon factor and its relation to the rate of nonradiative transition. We then introduce three teaching modules, with associated MATLAB and Python codes, to explore how (1) the excited state nuclear displacement, (2) the electronic energy gap between excited and ground state and (3) the excited/ground state vibrational mode frequencies affect the magnitude of the Franck–Condon factor and thereby the rate of nonradiative transitions. The wave function overlap plots that accompany all teaching modules provide direct visualization of the effect of input parameters on the magnitude of Franck–Condon overlap integral.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗