The myosin II coiled-coil domain atomic structure in its native environment
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Rahmani, Hamidreza↗
SEARCH · Engineering Papers
Results for “atomic and molecular clusters”
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From Electronic Structure to Ion Transport: Photoelectron Spectroscopy and Molecular Dynamics Simulations Reveal the Role of Anions in Lithium Battery Electrolytes
Electrolyte anions are pivotal for lithium battery performance, yet their fundamental electronic structural properties are not well understood. In this work, we employ a combination of negative-ion photoelectron spectroscopy (NIPES), ab initio calculations, and molecular dynamics (MD) simulations to investigate the electronic structures of three representative electrolyte anions. This multiscale approach enables us to elucidate how their intrinsic electronic properties govern anion–solvent interactions in gas-phase clusters, as well as lithium-ion (Li + ) solvation structures and ion transport behavior in the condensed phase. NIPES reveals that difluoro(oxalato)borate (DFOB – ), bis(fluorosulfonyl)imide (FSI – ), and bis(oxalato)borate (BOB – ) all exhibit high electron binding energies, with vertical/adiabatic detachment energies increasing from DFOB – (6.09/5.70 eV) to FSI – (6.80/6.10 eV) to BOB – (6.82/6.40 eV), correlating with enhanced oxidation stability. Ab initio calculations reveal that DFOB – /FSI – –solvent complexes bind Li + ∼ 10 kcal/mol stronger than BOB – series, aligning with the strength of a Li + –anion model. DFOB – exhibits pronounced charge localization on both oxygen and fluorine atoms, enabling their involvement in Li + coordination. In contrast, fluorine atoms in FSI – are largely electron-depleted and remain excluded from direct Li + binding. MD simulations further demonstrate that LiDFOB and LiFSI systems exhibit Li + diffusion coefficients three and five times higher than those of LiBOB across four common solvents. Notably, LiFSI salt in acetonitrile (AN) exhibits the fastest Li + diffusion among 12 electrolyte systems, highlighting the synergistic effect of FSI – and AN in promoting ion mobility. In conclusion, these findings provide a molecular-level understanding of the critical roles of anion and its microsolvation in optimizing Li + diffusion dynamics, once again emphasizing the positioning of FSI – and DFOB – as prime candidates for next-generation electrolytes.
25 ENERGY STORAGE↗
Supercooling of Alaskan Beetle Larvae as a Winter Survival Strategy
Insects are able to survive subfreezing temperatures by either limiting ice crystal formation in their bodies or through freeze avoidance. Beetle larvae are able to avoid freezing in winter by dehydrating in the fall months and replacing their body water content with high concentrations of glycerol. This enables the body fluid of the insect to supercool, and even vitrify, recovering unharmed when the temperature warms in the spring. Using nondestructive, high‐energy X‐ray synchrotron diffraction experiments, direct insight into how cryopreservation occurs at the atomic level within the beetle larvae has been obtained. The results shed light on the molecular‐level interactions associated with the mechanism responsible for surviving freezing temperatures. The molecular models of severely dehydrated Alaskan beetle larvae, based on glycerol‐water mixtures, yield a total of 4.2 ± 1.2 intermolecular hydrogen bonds per glycerol molecule at 275 K, in good agreement with existing molecular dynamics simulations. Most importantly, they show that if just over half the body fluid content is water, the water clusters are too small to form ice crystals that cause cellular damage.
Benmore, Chris J. [X‐Ray Science Division Advanced↗
Excited-State Dynamics during Primary C–I Homolysis in Acetyl Iodide Revealed by Ultrafast Core-Level Spectroscopy
In typical carbonyl-containing molecules, bond dissociation events follow initial excitation to $nπ_{C=O}$$^*$ states. However, in acetyl iodide, the iodine atom gives rise to electronic states with mixed $nπ_{C=O}$$^*$ and $nπ_{C–I}$$^*$ character, leading to complex excited-state dynamics, ultimately resulting in dissociation. Using ultrafast extreme ultraviolet (XUV) transient absorption spectroscopy and quantum chemical calculations, we present an investigation of the primary photodissociation dynamics of acetyl iodide via time-resolved spectroscopy of core-to-valence transitions of the I atom after 266 nm excitation. The probed I 4d-to-valence transitions show features that evolve on sub-100-fs time scales, reporting on excited-state wavepacket evolution during dissociation. These features subsequently evolve to yield spectral signatures corresponding to free iodine atoms in their spin–orbit ground and excited states with a branching ratio of 1.1:1 following dissociation of the C–I bond. Calculations of the valence excitation spectrum via equation-of-motion coupled cluster with single and double substitutions (EOM-CCSD) show that initial excited states are of spin-mixed character. From the initially pumped spin-mixed state, we use a combination of time-dependent density functional theory (TDDFT)-driven nonadiabatic ab initio molecular dynamics and EOM-CCSD calculations of the N$_{4,5}$ edge to reveal a sharp inflection point in the transient XUV signal that corresponds to rapid C–I homolysis. Here, by examining the molecular orbitals involved in the core-level excitations at and around this inflection point, we are able to piece together a detailed picture of C–I bond photolysis in which d → σ* transitions give way to d → p excitations as the bond dissociates. We also report theoretical predictions of short-lived, weak 4d → 5d transitions in acetyl iodide, validated by weak bleaching in the experimental transient XUV spectra. This joint experimental–theoretical effort has thus unraveled the detailed electronic structure and dynamics of a strongly spin–orbit coupled system.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Theoretical study of the structures and electron affinities of the dimers and trimers of the group IB metals (Cu, Ag, and Au)
The molecular structure of both the neutral and negatively charged diatomic and triatomic systems containing the Cu, Ag, and Au metals are determined from ab initio calculations. For the neutral triatomic systems, the lowest energy structure is found to be triangular. The relative stability of the 2A1 and 2B2 structures can be predicted simply by knowing the constituent diatomic bond distances and atomic electron affinities (EAs). The lowest energy structure is linear for all of the negative ions. For anionic clusters containing Au, the Au atom(s) preferentially occupy the terminal position(s). The EAs of the heteronuclear systems can be predicted relatively accurately from a weighted average of the corresponding homonuclear systems. Although the theoretical EAs are systematically too small, accurate predictions for the EAs of the triatomics are obtained by uniformly scaling the ab initio results using the accurate experimental EA values available for the atoms and homonuclear diatomics.
Bauschlicher, Charles W., Jr.↗
Multifunctional Catalysts for the Tandem Reactions of Oxygenates
Industrially-relevant catalytic reactions rarely consist of a simple sequence of elementary steps. Moreover, kinetic coupling of multiple reactions on a catalyst surface is highly desired for process intensification and improved energy efficiency for large scale chemical transformations. The shifting landscape of hydrocarbon chemical feedstocks in the US also motivates research on the selective conversion of more complex molecules. One desirable type of catalytic reaction is the reduction of carboxylic acids that are produced from biomass feedstocks to their corresponding alcohols. The proposed research explores the fundamental importance of hydrogen spillover on a multifunctional catalyst for carboxylic acid reduction with H 2 composed of metal particles coupled to metal oxide particles. Recent work has demonstrated the excellent performance of supported tungsten oxide clusters for carboxylic acid reduction, but only after they are promoted with a late transition metal such as palladium. Elucidating the active state of the catalyst and the associated reaction mechanism for acid reduction on that active state are the overall goals of the proposed project and successful completion will enable future design of efficient multifunctional catalysts. The critically important role of the metal promoter is hypothesized to be its ability to dissociate H2 and spillover atomic H to the support. Although hydrogen spillover is a well-recognized phenomenon in catalysis, its role in both catalyst activation and catalytic turnover are still unresolved. The study combined materials synthesis, characterization, reactivity testing, and molecular simulations, to explore the effect of hydrogen chemical potential on the formation of the active catalytic sites and on the steady state catalytic reduction of carboxylic acid. Varying the hydrogen chemical potential through modification of the gas conditions, support composition, and metal loading to modulated the structure and catalytic performance of the reducible metal oxide. Dual function catalysts containing supported Pd and WO x species co-located on a non-reducible carrier (silica) and a reducible carrier (titania) were synthesized and characterized by electron microscopy, temperature-programmed reduction, and chemisorption. Spectroscopic methods such as X-ray absorption and UV-vis were also used to evaluate the catalysts, which were used in the reduction of propionic acid to aldehyde and alcohol. Quantum chemical calculations, including ab initio phase diagrams provided molecular insights into the H spillover phenomenon.
09 BIOMASS FUELS↗
DFTpy : An efficient and object-oriented platform for orbital-free DFT simulations
Not provided.
Chemistry↗
Molecular cluster theory of CO chemisorption on a nickel /100/ surface
Self-consistent Hartree-Fock-Slater molecular cluster models for the chemisorption of carbon monoxide on a (100) transition metal surface are presented. Energy levels and charge distribution for the CO:Ni5 cluster in C sub 4v symmetry are obtained, and the variation of binding energies with height of the CO molecule above the surface of nickel is studied in detail. Comparison is made with experimental binding energy spectra and with the multiple-scattering results of Batra and Bagus. The redistribution in energy of free-atom valence levels is studied by means of local-densities-of-states diagrams.
Ellis, D. E.↗
Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules
Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ferroelectric phase transition in group-IV monochalcogenides from an equivariant machine learned force field
Group-IV monochalcogenides are a class of layered ferroelectric semiconductors that have demonstrated spontaneous intrinsic polarization above room temperature. Here, in this study, we use the multi-atomic cluster expansion (MACE) machine learning architecture to train and test a force field capable of modeling the structural properties and second-order ferroelectric-to-paraelectric phase transition in a Group-IV monochalcogenide, GeSe. The model captures the double-well potential energy surface associated with the onset of macroscopic polarization in bulk GeSe within 12.5 meV/atom, as well as near-equilibrium properties like the phonon dispersion. The development of this quantitatively accurate force field enables long-time molecular dynamics simulations, which predict the critical temperature of the ferroelectric-to-paraelectric phase transition in bulk GeSe to be T c = 600 K. This study demonstrates the capabilities of equivariant force-fields to accurately describe phenomena associated with structural symmetry breaking.
ferroelectricity↗
Co-Design of Charge Transport Superhighways to Connect Catalytic Sites in Soft Photoelectrochemical Systems
Efficient photon-to-electron-to-molecule conversion requires multi-length scale control over charge transport pathways, where electronic charges are delivered to catalytic sites under high mass transport flux. A fundamental question is how can we co-design charge transport pathways to promote efficient charge transfer to/from catalytic sites in complex three-dimensional architectures? Soft conducting polymer systems offer exceptional promise to provide three-dimensional charge transport networks, where electrolyte (ion and solvent) can interdiffuse to promote long-lived charge carriers and the molecular nature allows for strategic synthetic design of catalytic sites. Herein we combine theoretical and experimental approaches to investigate the earliest stages of photoelectrochemical deposition of near-surface catalytic sites (Pt) on soft bulk heterojunction polymeric semiconductors composed of a prototype donor (PTB7-Th) and a prototype acceptor (N2200) as a model system towards better understanding molecular catalyst-polymer site interactions. We focus initially on photoelectrochemical deposition of low Pt loadings, nanoparticle sizes (formed by progressive nucleation) below 20 nm, for both density functional theory (DFT) modeling studies and for spectroscopic characterization using surface-sensitive X-ray and UV-photoemission (XPS/UPS). DFT modeling of “n-type” N2200 slabs reveal for the first time that sulfur atoms in the thiophene units serve as the lowest-energy adsorption sites for single Pt atoms, while larger Pt clusters engage more complexly with both thiophene and naphthalene diimide (NDI) core sites. Changes in chemical composition observed by X-ray photoelectron spectroscopy (XPS) support the DFT predictions, and the angle-resolved measurements reveal that Pt nucleation initiates at subsurface sites which appear to be localized active domains that promote charge transport/transfer and enable vertical growth toward the surface. These results suggest that light-activated Pt nanoparticle deposition decorates energetically distinct sites, where photoactivity is dictated by the local energetics of those sites, and the fact that they represent the termini of charge transport “super-highways” – a small percentage of the total volume of the donor/acceptor polymeric active layer which carries most of the photocurrent generated during both Pt deposition and photoelectrochemical HER. We posit that these initial studies provide a foundational strategy for design of catalytic sites in the near surface regions of complex polymeric materials and advancing soft semiconductor-based photoelectrochemical systems. Achieving a nanometer-scale understanding of catalyst deposition and the impact of local composition and energetics on that placement, should ultimately provide the design guidelines (co-design) for a broad array of catalysts at sites that optimize that efficiency and maximize platform durability.
14 SOLAR ENERGY↗
The Effect of Bonding on the Fragmentation of Small Systems
Recent dissociative recombination (DR) experiments have reported that the observed reaction products depend on the structure, bonding, and charge centre of the molecular ion. For examples, the dominant product channel observed in the DR of D5(+)(2), N2O2(+)(1), and D5O2(+)(3) suggests that the former two ions have the form D3(+) D2, and NO(+) NO(1), respectively, whilst the latter is known to have the form D2O D(+) D2O (3). Here we compare and contrast these observations by investigating the DR of one of the simplest such systems, Li(+) H2. This system, a weakly bound cluster with the charge centre located on the lithium atom, will provide us with an excellent opportunity for investigating the role played by the type of bonds and charge centre in the DR process.
Thomas, R. D.↗
Anion photoelectron spectroscopy and chemical bonding of ThS 2 – and ThSO –
Anion photoelectron spectra of ThSO – and ThS 2 – were recorded using the third (355 nm) harmonic of an Nd-YAG laser; these provided the measured vertical detachment energies of each anion. The experiments are supported by extensive coupled cluster calculations on ThSO, ThSO – , ThS 2 , and ThS 2 – , as well as the oxygen congeners ThO 2 and ThO 2 – . The ab initio calculations, which included complete basis set extrapolations, spin–orbit effects using four-component coupled cluster, and higher-order correlation contributions through CCSDT(Q), yielded an adiabatic electron affinity for ThO 2 – that was within 0.02 eV of the previously determined experimental value. The singly occupied molecular orbital (SOMO) in all three anions corresponds primarily to the 7s orbital on Th. Successive substitution of S for each O in ThO 2 leads to larger electron affinities and smaller bond angles in the neutral molecules, but larger angles in the anions. As demonstrated by Franck–Condon simulations of the spectra using the CCSD(T) spectroscopic constants, substitution of O by S significantly complicates the resulting detachment spectra due to the lower vibrational frequencies in the sulfur species. Altogether the calculated vertical detachment energies are in very good agreement with the experiment. In addition to the adiabatic electron affinities of each species, atomization energies and heats of formation have also been determined via the FPD approach with expected uncertainties of 1–2 kcal/mol.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Solution and Interface Structure and Dynamics in Geochemistry: Gateway to Link Elementary Processes to Mineral Nucleation and Growth
Our understanding of the process of mineral nucleation is starting to evolve from the solely thermodynamical aspects in classical nucleation theory toward a mechanistic study of reactions influenced by solvation structures of ions and their dynamics. A knowledge of how these atomic and molecular interactions respond to changing solution composition and/or the nature of an interface will form a fundamental foundation to understand rate-limiting reactions and processes for nucleation and growth. Here, we review recent advances from multidisciplinary experimental and computational approaches of the structure and dynamics of aqueous solutions and mineral–liquid interfaces that will influence rates of nucleation (and growth behavior) both homogeneously in aqueous solutions and heterogeneously at mineral–liquid interfaces. Furthermore, these processes include structure (and extent) of solute clustering, solvent degrees of freedom, and the presence of noninnocent charge-balancing ions, all of which can drive the selectivity and exert control over nucleation mechanisms. Similar controlling reactions can also occur at interfaces with the added complexities of how solute ions interact with and assemble on surface sites and use different mechanisms from bulk solutes, such as lateral solvent exchanges between distinct surface sites. To gain a predictive understanding of nucleation chemistry, we emphasize several key knowledge gaps that will need to be addressed in this field and highlight the importance of combining computations and experiments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms
The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.
Lee, Timothy J.↗
Performance of an atomic mean-field spin–orbit approach within exact two-component theory for perturbative treatment of spin–orbit coupling
The paper reports development of an atomic mean-field (AMF) spin–orbit approach within the spin-free exact two-component theory in its one-electron variant (SFX2C-1e), a new relativistic quantum-chemical method for treating spin-orbit coupling in molecules. The effective one-electron spin–orbit integral matrix in the four-component representation is assembled as a direct sum of one-centre spin–orbit integral matrices with the mean-field two-electron contributions evaluated using atomic SFX2C-1e Hartree–Fock density matrices. It is then transformed into two-component representation using analytic SFX2C-1e energy derivative formulation. The resulting two-component spin–orbit integral matrix is by design suitable for use in perturbative calculations of spin–orbit coupling, treating SFX2C-1e wavefunctions as unperturbed states. The accuracy of the present AMF approach has been demonstrated using benchmark calculations of spin–orbit splittings for representative diatomic radicals at the equation-of-motion coupled-cluster singles and doubles level. In conclusion, to demonstrate the applicability and accuracy of the present perturbative spin–orbit scheme in calculations of challenging heavy-element containing systems, a thorough computational investigation of six low-lying electronic states of ThO+ is reported.
74 ATOMIC AND MOLECULAR PHYSICS↗
Cost-effective carbon fiber precursor selections of polyacrylonitrile-derived blend polymers: carbonization chemistry and structural characterizations
Blending polyacrylonitrile (PAN) with plastic wastes and bio-based polymers provides a convenient and inexpensive method to realize cost-effective carbon fiber (CF) precursors. In this work, PAN-based blend precursors are investigated using ReaxFF reactive molecular dynamics simulations with respect to the formation of all-carbon rings, the evolutions of oxygen-containing and nitrogen-containing species, and the migration of carbon atoms to form turbostratic graphene. From these simulations, we identify that PAN/cellulose (CL) blend manifests the highest carbon yield and the most substantial all-carbon ring formation. This ReaxFF-based finding is confirmed by Raman and TEM experiments indicating high crystallinity for PAN/CL-derived blend CFs. We trace the pathway of gasification and carbonization of PAN/CL to elaborate the mechanism of the formation of all-carbon ring networks. We discover that the acetals of CL can catalyze the cyclization of the blend precursor, allowing for the search for CL derivatives or the other kinds of bio-based polymers with similar functionalities as alternative blends. In addition, we examine the structural characteristics using the carbon–carbon (C–C) radial distribution functions, C–C bond length distributions, and sp2 C atom ratios for the four representative precursors, i.e., PAN, oxidized PAN, PAN/nylon 6,6, and PAN/CL. Our simulation results show the most extensive all-carbon ring cluster and graphitic structure growths for PAN/CL. Here, we propose PAN/CL as a cost-effective alternative CF precursor, since (a) CL is naturally abundant and eco-friendly for production, (b) the blend precursor PAN/CL does not require oxidation treatment, (c) PAN/CL has a high carbon yield with substantial all-carbon ring formation, and (d) PAN/CL based CFs potentially provide a mechanical property enhancement.
36 MATERIALS SCIENCE↗
TaTi_BCC_SolidSolution_128atoms_VASP6
We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys tantalum-titanium (Ta-Ti). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Hf and Nb. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on Air Force HPC11 cluster using the VASP 6.5.1. Additional methodology and file structure information is available in the dataset README.txt file.
36 MATERIALS SCIENCE↗