Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in ...materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY 1. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.
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•Virtual reality and materials.•Interactive molecular dynamics.•Fast ion conduction.•Zeolite catalysis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Background ApoAI (apolipoproteins AI) and apoAII (apolipoprotein AII) are structural and functional proteins of high-density lipoproteins (HDL) which undergo post-translational modifications at ...specific residues, creating distinct proteoforms. While specific post-translational modifications have been reported to alter apolipoprotein function, the full spectrum of apoAI and apoAII proteoforms and their associations with cardiometabolic phenotype remains unknown. Herein, we comprehensively characterize apoAI and apoAII proteoforms detectable in serum and their post-translational modifications and quantify their associations with cardiometabolic health indices. Methods and Results Using top-down proteomics (mass-spectrometric analysis of intact proteins), we analyzed paired serum samples from 150 CARDIA (Coronary Artery Risk Development in Young Adults) study participants from year 20 and 25 exams. Measuring 15 apoAI and 9 apoAII proteoforms, 6 of which carried novel post-translational modifications, we quantified associations between percent proteoform abundance and key cardiometabolic indices. Canonical (unmodified) apoAI had inverse associations with HDL cholesterol and HDL-cholesterol efflux, and positive associations with obesity indices (body mass index, waist circumference), and triglycerides, whereas glycated apoAI showed positive associations with serum glucose and diabetes mellitus. Fatty-acid‒modified ApoAI proteoforms had positive associations with HDL cholesterol and efflux, and inverse associations with obesity indices and triglycerides. Truncated and dimerized proteoforms of apoAII were associated with HDL cholesterol (positively) and obesity indices (inversely). Several proteoforms had no significant associations with phenotype. Conclusions Associations between apoAI and AII and cardiometabolic indices are proteoform-specific. These results provide "proof-of-concept" that precise chemical characterization of human apolipoproteins will yield improved insights into the complex pathways through which proteins signify and mediate health and disease.
Neutral and especially dianionic 6- and 12-vertex closo ortho-carboranes (o-carboranes) 1,2-R2-1,2-C2B n H n (R = H, CH3, NH2, OH, F, SiH3, PH2, SH, Cl, as well as e -, CH2 -, NH-, O-, SiH2 -, PH-, ...and S-) exhibit extremely large variations (over 1 Å!) of the cage CC distances, from 1.626 to 2.638 Å, at the B3LYP/6-31G*//B3LYP/6-31G* DFT level. These CC “bond lengths,” among the longest ever reported, generally are greater in the icosahedral than those in the corresponding octahedral systems and depend strongly on the substituents. While 1,2-(NH2)2-1,2-C2B10H10 has the longest Cc···Cc separation in neutral species (1.860 Å), Cc···Cc distances can be much larger in the corresponding dianions. These range from 1.823 Å (R- = e - ) to 2.638 Å (R- = CH2 -) for 1,2-(R-)2-1,2-C2B10H10 and from 1.626 Å (R- = SiH2 -) to 3.099 Å (R- = NH-) for 1,2-(R-)2-1,2-C2B4H4. Remarkably, there is no abrupt discontinuity over the entire range of CC lengths. Consequently, the relationship between the gradual changes in the distances and the nature of the bonding was analyzed by means of the form of the Kohn−Sham orbitals, the Wiberg Cc···Cc bond indices, and Bader AIM method. Cluster carboranes, and possibly other heteroboranes, thus appear to offer unique opportunities for modulating Cc···Cc distances.
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IJS, KILJ, NUK, PNG, UL, UM
Top-down proteomics (TDP) allows precise determination/characterization of the different proteoforms derived from the expression of a single gene. In this study, we targeted apolipoprotein A-I ...(ApoA-I), a mediator of high-density-lipoprotein cholesterol efflux (HDL-E), which is inversely associated with coronary heart disease risk. Absolute ApoA-I concentration and allelic variation only partially explain interindividual HDL-E variation. Therefore, we hypothesize that differences in HDL-E are associated with the abundances of different ApoA-I proteoforms. Here, we present a targeted TDP methodology to characterize ApoA-I proteoforms in serum samples and compare their abundances between individuals. We characterized 18 ApoA-I proteoforms using selected-ion monitoring coupled to electron-transfer dissociation mass spectrometry. We then compared the abundances of these proteoforms between two groups of four participants, representing the individuals with highest and lowest HDL-E values within the Chicago Healthy Aging Study (n = 420). Six proteoforms showed significantly (p < 0.0005) higher intensity in high HDL-E individuals: canonical ApoA-I fold difference (fd) = 1.17, carboxymethylated ApoA-I (fd = 1.24) and, with highest difference, four fatty acylated forms: palmitoylated (fd = 2.16), oleoylated (fd = 2.08), arachidonoylated (fd = 2.31) and one bearing two modifications: palmitoylation and truncation (fd = 2.13). These results demonstrate translational potential for targeted TDP in revealing, with high sensitivity, associations between interindividual proteoform variation and physiological differences underlying disease risk.
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In the field of solar water splitting, searching for and modifying bulk compositions have been the conventional approaches to enhancing visible-light activity. In this work, manipulation of ...heterointerfaces in ZnS–GaP multilayer films is demonstrated as a successful alternative approach to achieving visible-light-active photoelectrodes. The photocurrent measured under visible light increases with the increasing number of interfaces for ZnS–GaP multilayer films with the same total thickness, indicating it to be a predominantly interface-driven effect. The activity extends to long wavelengths (650 nm), much longer than those expected for pure ZnS and also longer than those previously reported for GaP. Density functional theory calculations of ZnS–GaP multilayers predict the presence of electronic states associated with atoms at the interfaces between ZnS and GaP that are different from those found within the layers away from the interfaces; these states, formed due to unique bonding environments found at the interfaces, lead to a lowering of the band gap and hence the observed visible-light activity. The presence of these electronic states attributed to the interfaces is confirmed by depth-resolved X-ray photoelectron spectroscopy. Thus, we show that interface engineering is a promising route for overcoming common deficiencies of individual bulk materials caused by both wide band gaps and indirect band gaps and hence enhancing visible-light absorption and photoelectrochemical performance.
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Spreading of sessile water droplets on a solid graphite surface has been studied using atomistic molecular dynamics techniques. The system is in the partial wetting regime and a straightforward ...scheme is applied to extract the contact angle from the atomistic simulations. Even for droplets containing a thousand molecules, the calculated contact angle for water is 83°, which is close to the experimental macroscopic value. On addition of ethanol, the contact angle decreases to 30° and we approach complete wetting. Time-averaged structural analyses show that the ethanol molecules form a monolayer on top of the solid surface. A few Å above the solid surface, the ethanol molecules are preferentially located at the liquid/vapor interface rather than in the bulk of the droplet.
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Recent periodic density functional calculations have predicted the existence of ultra-flexible low-energy forms of boron oxides in which rigid boron-oxygen heterocycles are linked by flexible B-O-B ...bridges. The minima in the energy landscapes of these frameworks are remarkably broad, with widths in excess of those of many hybrid metal-organic frameworks. Enormous changes in cell volume, which can exceed a factor of two, are accompanied by negligible changes in energy. Here we explore the underlying reasons for this behaviour using molecular electronic-structure calculations, periodic density functional theory and template-based geometric simulations. The angular flexibility of the B-O-B bridge depends only upon the geometry of the local B
2
O
5
unit, independent of the configuration of neighbouring bridges. Unique cooperativity between the bending and twisting motions of the bridges leads to considerable anisotropy in framework flexibility. Exceptional flexibility is conferred not only by the intrinsic bending flexibility of the bridges but by topological factors, crucially the relaxation of torsional constraints when B
3
O
3
rings are present. We test these conclusions by showing how the flexibility of the frameworks can be tuned by decoration with isoelectronic rings. The new nanoporous boron oxides presented in this work are predicted to be potential novel guest-host materials because of their flat energy landscapes. Furthermore, such structures can be generated systematically from silicates by the substitution of B
2
O
5
4−
for SiO
4
4−
. A borate analogue of β-cristobalite is shown to be isoenergetic with the known B
2
O
3
-I polymorph. We raise the possibility of new families of frameworks and zeolite analogues.
We predict a wide range of ultra-flexible low-energy forms of boron oxides in which rigid B-O-B bridges link boron-oxygen heterocycles.
The energy landscapes of ultra-thin nanofilms of ZnO and ZnS are examined in detail using periodic hybrid density functional calculations. We predict new staggered graphitic forms, which are stable ...only for the thinnest films and are of particular interest as the electronic structure shows a spontaneous symmetry breaking across the film and consequently a marked decrease in band gap with thickness. The relative energies of the various forms, their structural and electronic properties and their variation with film thickness are discussed. Possible kinetic pathways for transitions from the graphitic forms are examined by explicit evaluation of transition state energies. For polar surfaces, such as (0001) würtzite and (111) zinc blende, many different mechanisms operate to remove or reduce the surface dipole depending on the number of layers in the nanofilm. The polar ZnS nanofilms, but not the polar ZnO analogues or any non-polar film, are predicted to spontaneously become non-stoichiometric by loss of zinc atoms from the surface. The behaviour of adsorbed water on the ultra-thin films is also examined. There is no dissociation on any ZnS film. For ZnO, dissociation into OH
−
and H
+
takes place not only on (101&cmb.macr;0) würtzite, but also on (110) zinc blende. This result that does not appear to have been reported previously and deserves future experimental study. While we concentrate on ZnO and ZnS, similar energy landscapes are expected for any oxide or sulphide which adopts the würtzite or zinc blende structure in the bulk.
Ab initio
energy landscapes of thin ZnO and ZnS films reveal new structures, non-stoichiometry and different behaviour of adsorbed water.
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•Domain decomposition Monte Carlo.•Million atom simulation cells.•Solid state structure.
We propose a method for the simulation of large ionic systems with long-range forces using the ...Monte Carlo method. This method employs a domain decomposition strategy for subdividing the simulation cell and parallelisation of these subdomains using a thread based strategy. This is thus ideally suited to modern day multi-core architectures.
Evaluation of the long range interactions that is incompatible with a domain decomposition strategy has been replaced by the direct calculation of the Coulomb sum (Fennell and Gezelter, 2006). We compare this approach with that of “standard” Monte Carlo simulations that employ the Ewald technique. A relatively large two-body cutoff is required to reproduce the Ewald results accurately. Finally, as a pilot application, we demonstrate that our novel approach can be applied to very large simulation cells (>1 million atoms); results for enthalpies, are presented for a typical non-ideal oxide solid solution (MnO–MgO) as a function of composition and highlight the formation of nano-sized domains in the very large simulation cells. Well defined structures such as exsolution lamellae are not observed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The existence of ultra‐flexible low‐energy forms of boron oxides (B2O3 and BO) is demonstrated, in particular structures in which B3O3 or B4O2 six‐membered rings are linked by single B‐O‐B bridges. ...The minima in the energy landscapes are remarkably broad; the variation in the internal energies is very small over a very large range of volumes. Such volume changes may even exceed 200%. This remarkable behavior is attributed predominantly to the pronounced angular flexibility of the B‐O‐B bridges linking the rings, which is unusual for a covalent bond. At larger volumes, the structures are nanoporous; the pores collapse upon compression with negligible change in energy, making these suitable as guest‐host materials. In marked contrast, in other materials where low density frameworks have been reported or predicted, such low‐density phases are considerably higher in energy. The flexibility of the structures also offers a resolution of the long‐standing controversy reconciling the structure and density of vitreous B2O3.
Low‐energy 3D networks of boron oxide based on six‐membered rings connected by B‐O‐B bridges are reported. The B‐O‐B connections are extremely flexible, enabling volume changes exceeding 200% with very little internal energy change (<10 kJ mol−1). At larger volumes these materials exhibit a nanoporous microstructure, which collapses to a closed form with negligible energy change.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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