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At least 55 records · Page 3

Structural Phase Transitions of NbO 2 : Bulk versus Surface

The metal to insulator transition of NbO 2 has been predicted to be a result of a structural phase transition (SPT) governed by Peierls physics. However, direct observation of the SPT using experimental techniques is still restricted by the extremely high transition temperature (810 °C) and the proclivity for NbO 2 to oxidize into Nb 2 O 5 above 400 °C when exposed to air. In this work, we address these issues and employ temperature-dependent X-ray spectroscopy to describe the SPT of NbO 2 from the bulk to surface. Temperature-dependent extended X-ray absorption fine structure spectroscopy (T-EXAFS) reveals a gradual weakening of the bulk Nb dimers over a large temperature range, which is indicative of a second-order Peierls mechanism. From these measurements, we determine the critical dimer distance to be 2.77 Å. Our T-EXAFS observations are supported by density functional theory of the phonon dispersion and the electronic density of states of NbO 2 , which conclude that the dimerization is responsible for the insulating phase. The dimerization does not extend to the topmost layers, where an oxygen rich surface reconstruction is preferred irrespective of temperature even in extremely reducing environments; changes in the low-energy electron diffraction patterns are attributed to oxygen concentration and are independent of the underlying bulk phase transitions of NbO 2 .

36 MATERIALS SCIENCE↗

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique

A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Thermodynamics and Mechanism of a Photocatalyzed Stereoselective [2 + 2] Cycloaddition on a CdSe Quantum Dot

Colloidal quantum dots (QDs) have shown promise over the last few decades for a range of applications including single photon emission, in vivo imaging and photocatalysis. Recent experiments demonstrated that QDs impart stereoselectivity to triplet excited-state [2+2] cycloaddition reactions of alkenes photocatalyzed by the QD through self-assembly of the reagent molecules on the QD surface, but these experiments did not reveal the precise geometries of surface-bound molecules or their interactions with surface atoms. Here, a theoretical mechanistic approach is used to study such interactions for [2+2] cycloadditions of 4-vinylbenzoic acid derivatives on CdSe QDs. Spin-polarized periodic density functional theory (DFT) and non-periodic DFT calculations are deployed to determine the origin of the selectivity for the syn diastereomer of the resultant tetrasubstituted cyclobutane product via atomistic modelling of the CdSe surface and substrates, and determination of the thermodynamic energies of reactions for each step, the intermolecular interactions between the substrates, and the triplet state reaction paths. The calculations indicate that reaction selectivity arises from preferred binding of pairs through intermolecular interactions of substrate molecules on the QD surface in a syn-precursor structure followed by dimerization after triplet excitation. Further, these mechanisms are generalizable to other metal-enriched QD surfaces that have a similar surface structure to CdSe, such as InSe or CdTe. Design principles for anti diastereomer derivatives are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metal-organic framework supported single-site nickel catalysts for butene dimerization

Homotopic sites in a well-controlled environment are not only ideal systems for mechanistic studies, but also allow optimal control of catalytic transformations. Sites having only a single metal cation and sites consisting of metal oxo complexes with few nickel (Ni) cations supported on the nodes of UiO-66 metal-organic framework (Ni-UiO-66) are studied for 1-butene dimerization. Monomeric Ni sites, which bind to the Zr 6 node via two Zr-OH(µ3) linkages, are active and selective for the dimerization of 1-butene to linear and mono-branched C 8 isomers. Ni oxo complexes with few Ni cations show lower activity and promote the oligomerization of transiently formed C 8 isomers. In conclusion, Kohn-Sham density function theory calculations combined with spectroscopic measurements and kinetic analyses indicate that dimerization follows a Cossee-Arlman reaction mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthetic Control of Exciton Dynamics in Bioinspired Cofacial Porphyrin Dimers

Understanding how the complex interplay among excitonic interactions, vibronic couplings, and reorganization energy determines coherence-enabled transport mechanisms is a grand challenge with both foundational implications and potential payoffs for energy science. We use a combined experimental and theoretical approach to show how a modest change in structure may be used to modify the exciton delocalization, tune electronic and vibrational coherences, and alter the mechanism of exciton transfer in covalently linked cofacial Zn-porphyrin dimers (meso-beta linked AB m-β and meso-meso linked AA m-m ). While both AB m-β and AA m-m feature zinc porphyrins linked by a 1,2-phenylene bridge, differences in the interporphyrin connectivity set the lateral shift between macrocycles, reducing electronic coupling in AB m-β and resulting in a localized exciton. Pump-probe experiments show that the exciton dynamics is faster by almost an order of magnitude in the strongly coupled AA m-m dimer, and two-dimensional electronic spectroscopy (2DES) identifies a vibronic coherence that is absent in AB m-β . Theoretical studies indicate how the interchromophore interactions in these structures, and their system-bath couplings, influence excitonic delocalization and vibronic coherence-enabled rapid exciton transport dynamics. Real-time path integral calculations reproduce the exciton transfer kinetics observed experimentally and find that the linking-modulated exciton delocalization strongly enhances the contribution of vibronic coherences to the exciton transfer mechanism, and that this coherence accelerates the exciton transfer dynamics. These benchmark molecular design, 2DES, and theoretical studies provide a foundation for directed explorations of nonclassical effects on exciton dynamics in multiporphyrin assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the Origin of Negative Temperature Dependence and Activity of N-Coordinated Cobalt Sites During Ethylene Dimerization

The on-demand production of short-chain linear alpha olefins (LAOs; C4-C8) via C2H4 dimerization and oligomerization is industrially attractive, prompting extensive research on designing active, selective, and stable catalysts for industrial use. Cobalt supported on ammoniated carbon (Co(NH3)x/C) catalysts have shown remarkable activity and selectivity in this process. However, critical aspects such as the active phase, active site structure, the role of the catalyst support, cobalt loading effects, and the inverse correlation of the reaction rate with temperature remain inadequately understood. This study systematically explores these factors using a combination of steady-state differential catalytic tests, in situ molecular characterization including diffuse reflectance UV-Vis (DR-UV-Vis), Infrared, and Raman spectroscopies, and ex situ X-ray diffraction (XRD) and high annular aberration-corrected dark field transmission electron microscopy (HAADF-STEM). Various supports (SiO2, Al2O3, NH4-ZSM-5, g-C3N4, and C) and cobalt loadings (1.0-3.0 Co nm-2) were studied to determine the optimal catalyst composition and identify the active phase and sites. Carbon-supported catalysts uniquely produce C4-8 LAOs during C2H4 dimerization, with site-time-yield remaining constant (~10-3 s-1) for 1.0-4.0 Co nm-2 at prolonged reaction times (24-48?h time-on-stream). At higher loadings of 6.0 Co nm-2, the formation of crystalline CoO and Co3O4 phases reduces catalytic activity and LAO selectivity. Our findings show that active catalysts lack crystalline cobalt oxides and instead feature dispersed Co2+ sites, tetra-coordinated to a mix of N/NH3 and O/H2O ligands, which catalyze C2H4 dimerization via the Cossee-Arlman mechanism, exhibiting 1st order dependence on C2H4 concentration. The observed inverse rate-temperature correlation is attributed to compensation effects (i.e., presence of Cremer-Constable relationship) linked to changes in adsorption enthalpic and entropic factors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bond Dissociation Energy, Ionization Energy, and Electronic Structure of Thorium Dimer

Diatomic thorium, Th 2 , has been investigated using a laser ablation, supersonic expansion source to produce the molecule and resonant two-photon ionization spectroscopy to measure its bond dissociation energy (BDE) and ionization energy (IE). The molecule has a high density of states in the vicinity of its bond dissociation energy, leading to rapid predissociation as soon as this energy is exceeded. The BDE is identified from this predissociation threshold as D 0 (Th 2 ) = 2.857(7) eV, where the assigned error limit is provided in parentheses in units of the last quoted digit. Similarly, the one-photon ionization threshold has been measured, providing the ionization energy IE(Th 2 ) = 5.042(4) eV. Together with a thermochemical cycle and the atomic ionization energy, these values provide the BDE of the cation, giving D 0 (Th 2 + ) = 4.122(8) eV. Computations show that Th 2 has three nearly degenerate low-lying electronic states (1 3 Σ u + , 1 1 Σ g + , and 1 3 Δ g ) with bonding dominated by 7s and 6d orbitals, indicating predominantly transition-metal-like behavior. The 1 3 Σ u + state exhibits a triple bond, whereas the 1 1 Σ g + and 1 3 Δ g states possess quadruple-bond character and correspondingly shorter bonds. Although 1 3 Σ u + is predicted to be the lowest state without spin–orbit coupling, the large spin–orbit stabilization of the 1 3 Δ g state makes its Ω = 1 g component the ground state. Furthermore, the calculated dissociation energy (2.840 eV) and ionization energy of Th 2 (5.098 eV) are both in excellent agreement with experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling Intermolecular Interactions in Nanotubes, Fullerenes and Graphite using a New Long-Range Potential

The cohesive energy and compressibility of strands of a single-wall nanotube rope has been computed using a new long-range potential energy function derived from accurate ab initio quantum chemistry calculations of the benzene dimer and calibrated for energetic and mechanical properties of graphite (at pressures up to 12 GPa). We also use this potential to calculate a variety of properties of carbon nanotubes (both single- and multi-wall) and fullerenes. Extensive comparisons are made with previously published potentials.

Jaffe, Richard↗

Characterizing Ultrafast Intersystem Crossing Pathways in Molecular Pt Dimers Using Time-Resolved Wide-Angle X-ray Scattering

Vibronic coupling between transition metal charge transfer states is a potential mechanism for enhancing the intersystem crossing (ISC) rate. Vibronic coupling-driven ISC has been observed in Pt­(II) dimer complexes, where the trajectory across excited-state pathways is tuned by atomic displacements via Pt–Pt stretching vibrations. Time-resolved wide-angle X-ray scattering (TR-WAXS) was utilized to quantify the Pt–Pt contraction following metal–metal-to-ligand charge transfer (MMLCT) excitation in Pt dimers with different bridging ligands. Both complexes exhibit Pt–Pt bond formation with a decrease in Pt–Pt distance of ∼ 0.25 Å and coherent vibrational wavepackets (CVWPs) encoded in the Pt–Pt contraction of both dimers. However, the complexes exhibit different time-dependent evolution of their CVWPs. Analysis of interference patterns between different CVWPs is used to track the trajectory across the excited-state surfaces. Furthermore, this work demonstrates that the interference between CVWPs in ultrafast TR-WAXS encodes indirect information regarding electronic excited-states to reveal the Pt dimer bridge-dependent ISC mechanism.

Computational chemistry↗

Characterization of cured polystyrylpyridine by model compounds

The crosslinking or curing reaction of polystyrylpyridine (PSP) has been studied by means of thermal reactions of its model compounds. Compounds 2,6-distyrylpyridine, 4-stilbazole, and deuterated 4-stilbazole were pyrolyzed at 200-325 C both in air and under vacuum in a sealed tube. The major pyrolysis products were diarylethane and stilbene, and were characterized by gas chromatography-mass spectrometry. Major dimeric products were naphthalene or quinoline derivatives. Mechanisms for the pyrolysis are suggested, and a crosslinked structure for cured PSP is proposed based on the thermal reaction products of model compounds.

Hsu, M.-T. S.↗

Freestanding VO 2 membranes on epidermal nanomesh for ultra-sensitive correlated breathable sensors

The interest in highly sensitive sensors is rapidly increasing for detecting very tiny signals for Internet of Things devices. Here, we achieve ultra-sensitive correlated breathable sensors based on freestanding VO 2 membranes. We fabricate the membranes by growing VO 2 films onto sacrificial Sr 3 Al 2 O 6 layer grown on SrTiO 3 , selectively dissolving the Sr 3 Al 2 O 6 in water, and then rendering freestanding VO 2 membrane on nanomesh. The nanomeshes are extremely flexible, sweat permeable, and readily skin-adhesive. The resistance of the VO 2 membranes is reversibly tuned by human’s tiny mechanical stimuli and breath stimuli. The stimuli modulate the Peierls dimerization of one-dimensional V-V chains in the VO 2 lattice which concomitantly controls the electron correlation and hence resistivity. Since our breathable sensors operate based on quantum-mechanical correlation effects, their sensitivity is 1-2 orders of magnitude higher than conventional tactile and respiratory sensors based on other materials. Thus, the freestanding membranes of correlated oxides on epidermal nanomeshes are multifunctional platforms for developing ultra-sensitive correlated breathable sensors.

36 MATERIALS SCIENCE↗

Cleavage at the nsp5–nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form

Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP- (−6) MPro C145A(+3) -GB1-6H, 86.2 kDa) by mature WT MPro (MPro WT ) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K dimer ) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor’s nsp4–nsp5 site appears to saturate MProWT’s active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro C145A-IP ) is a homodimer with an estimated K dimer of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro C145A-IP –ensitrelvir complex is like that of the MPro WT –ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5–nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage.

60 APPLIED LIFE SCIENCES↗

Hourglass–Shaped Nanocages with Concaved Structures Based on Selective Self–Complementary Coordination Ligands and Tunable Hierarchical Self–Assembly

Three-dimensional (3D) structures constructed via coordination-driven self-assemblies have recently garnered increasing attention due to the challenges in structural design and potential applications. In particular, developing new strategy for the convenient and precise self-assemblies of 3D supramolecular structures is of utmost interest. Introducing the concept of self-coordination ligands, herein the design and synthesis of two meta-modified terpyridyl ligands with selective self-complementary coordination moiety are reported and their capability to assemble into two hourglass-shaped nanocages SA and SB is demonstrated. Within these 3D structures, the meta-modified terpyridyl unit preferably coordinates with itself to serve as concave part. By changing the arm length of the ligands, hexamer (SA) and tetramer (SB) are obtained respectively. In-depth studies on the assembly mechanism of SA and SB indicate that the dimers could be formed first via self-complementary coordination and play crucial roles in controlling the final structures. Moreover, both SA and SB can go through hierarchical self-assemblies in solution as well as on solid–liquid interface, which are characterized by transmission electron microscope (TEM) and scanning tunneling microscopy (STM). As a result, it is further demonstrated that various higher-order assembly structures can be achieved by tuning the environmental conditions.

3D metallo-supramolecules↗

Chemical ionization mass spectrometry utilizing benzene cations for measurements of volatile organic compounds and nitric oxide

We evaluate the capability of chemical ionization mass spectrometry (CIMS) using benzene cations as reagent ions (benzene CIMS) for detecting atmospheric trace gases. We characterize the ionization pathways and product ion distributions for 27 analytes spanning diverse chemical classes. To interpret the complex ion chemistry involving two reagent ions (C 6 H$^{+}_{6}$ and (C 6 H 6 )$^{+}_{2}$) and multiple ionization pathways (charge transfer, proton transfer, adduct formation, and hydride abstraction), we introduce a thermodynamics-based framework that classifies analytes into three categories based on their ionization energy (IE), relative to those of benzene monomer (9.24 eV) and dimer (8.69 eV). Each class exhibits distinct ionization mechanisms and product ions. Analytes with IE smaller than 8.69 eV (low IE) undergo charge transfer with both reagent ions; analytes with IE between 8.69 and 9.24 eV (mid IE) undergo charge transfer with C 6 H$^{+}_{6}$ and potential adduct formation with (C 6 H 6 )$^{+}_{2}$; analytes with IE larger than 9.24 eV (high IE) could undergo adduct formation, proton transfer, or hydride abstraction. Analytes within each class also show similar sensitivity, enabling sensitivity estimation for compounds lacking calibration standards. In addition to volatile organic compounds (VOCs), benzene CIMS detects nitric oxide (NO) with a detection limit of 5 pptv for 1 min integration time, exceeding the performance of most commercial NOx analyzers. Field deployments in Chicago and St. Louis demonstrate good agreement with reference NO measurements. Isoprene measurements show good agreement with a co-located gas chromatography–photoionization detector (GC-PID) in St. Louis, but exhibit substantial positive bias in Chicago, likely due to interferences from anthropogenic VOCs in the polluted urban environment. These results highlight the potential of benzene CIMS for concurrent measurements of NO, VOCs, and their oxidation products using a single instrument, while also underscoring challenges in complex atmospheric conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding

The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we describe DarR-c-di-AMP and DarR-DNA structures and complementary biochemical assays. The DarR-c-di-AMP structure reveals a unique effector binding site for a TFR, located between DarR dimer subunits. Strikingly, we show this motif also binds cAMP. The location of the adenine nucleotide binding site between subunits suggests this interaction may facilitate dimerization and hence DNA binding. Indeed, biochemical assays show cAMP enhances DarR DNA binding. Finally, DarR-DNA structures reveal a distinct TFR DNA-binding mechanism involving two interacting dimers on the DNA. Thus, the combined data unveil a newly described second messenger binding motif and DNA binding mode for this important family of regulators.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular recognition requires dimerization of a VHH antibody

Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.

60 APPLIED LIFE SCIENCES↗

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of human NADK2 reveals atypical assembly and regulation of NAD kinases from animal mitochondria

All kingdoms of life produce essential nicotinamide dinucleotide NADP(H) using NAD kinases (NADKs). A panel of published NADK structures from bacteria, eukaryotic cytosol, and yeast mitochondria revealed similar tetrameric enzymes. Here, we present the 2.8-Å structure of the human mitochondrial kinase NADK2 with a bound substrate, which is an exception to this uniformity, diverging both structurally and biochemically from NADKs. We show that NADK2 harbors a unique tetramer disruptor/dimerization element, which is conserved in mitochondrial kinases of animals (EMKA) and absent from other NADKs. EMKA stabilizes the NADK2 dimer but prevents further NADK2 oligomerization by blocking the tetramerization interface. This structural change bears functional consequences and alters the activation mechanism of the enzyme. Whereas tetrameric NADKs undergo cooperative activation via oligomerization, NADK2 is a constitutively active noncooperative dimer. Thus, our data point to a unique regulation of NADP(H) synthesis in animal mitochondria achieved via structural adaptation of the NADK2 kinase.

59 BASIC BIOLOGICAL SCIENCES↗