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Results for “molecular functionalization”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Enzymatic Nitrogen Insertion into Unactivated C–H Bonds

Selective functionalization of aliphatic C–H bonds, ubiquitous in molecular structures, could allow ready access to diverse chemical products. While enzymatic oxygenation of C–H bonds is well established, the analogous enzymatic nitrogen functionalization is still unknown; nature is reliant on pre-oxidized compounds for nitrogen incorporation. Likewise, synthetic methods for selective nitrogen derivatization of unbiased C–H bonds remain elusive. In this work, new-to-nature heme-containing nitrene transferases were used as starting points for the directed evolution of enzymes to selectively aminate and amidate unactivated C(sp3)–H sites. The desymmetrization of methyl- and ethylcyclohexane with divergent site selectivity is offered as demonstration. The evolved enzymes in these lineages are highly promiscuous and show activity towards a wide array of substrates, providing a foundation for further evolution of nitrene transferase function. Computational studies and kinetic isotope effects (KIEs) are consistent with a stepwise radical pathway involving an irreversible, enantiodetermining hydrogen atom transfer (HAT), followed by a lower-barrier diastereoselectivity determining radical rebound step. In-enzyme molecular dynamics (MD) simulations reveal a predominantly hydrophobic pocket with favorable dispersion interactions with the substrate. Here, by offering a direct path from saturated precursors, these enzymes present a new biochemical logic for accessing nitrogen-containing compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Controlling reversible phase transitions in rare-earth nickelates for novel memory devices

Resistive switching in correlated complex oxides is lucrative for emerging applications in neuromorphic computing, and densely scaled non-volatile memory. Electrical conductance of such complex oxides can be controllable switched across multiple orders of magnitude by either (a) electroforming a conduction channel (e.g., in tungsten oxide), or (b) inducing Mott-Hubbard transition (e.g., in rare-earth nickelates)– both via controlled migration of defects (such as oxygen vacancies) under applied bias. Nevertheless, the promise of such defect-driven electronic transitions are far from realized due to a lack of fundamental understanding of the atomic-scale processes that underlie migration and spatiotemporal evolution of oxygen vacancies over nano-to-mesoscopic length/timescales under applied electric field. In this project, we employ a synergistic integration of density functional theory (DFT) calculations, ab initio/classical molecular dynamics (AIMD/CMD) simulations, machine learning (ML), precision synthesis, and multi-modal X-ray imaging experiments to address this knowledge gap. Such an integrated approach offers to elucidate the correlations between subtle structural distortion and oxidation states; treat localized charge carriers; describe defect/ion transport in the presence of electric field; and, in turn, greatly advance the current understanding of microstructural evolution in complex oxides under applied bias. The fundamental knowledge gained from this work will enable precise control over hierarchical defect structures and unravel new routes to manipulate resistance states in complex oxides. This, in turn, will accelerate design of novel devices with desired set of neural functionalities, and high-speed densely-scaled resistive random access memory technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Pd-Ru pair on Pt surface for promoting hydrogen oxidation and evolution in alkaline media

Hydrogen oxidation reaction in alkaline media is critical for alkaline fuel cells and electrochemical ammonia compressors. The slow hydrogen oxidation reaction in alkaline electrolytes requires large amounts of scarce and expensive platinum catalysts. While transition metal decoration can enhance Pt catalysts’ activity, it often reduces the electrochemical active surface area, limiting the improvement in Pt mass activity. Here, we enhance Pt catalysts’ activity without losing surface-active sites by using a Pd-Ru pair. Utilizing a mildly catalytic thermal pyrolysis approach, Pd-Ru pairs are decorated on Pt, confirmed by extended X-ray absorption fine structure and high-angle annular dark-field scanning transmission electron microscopy. Density functional theory and ab-initio molecular dynamics simulations indicate preferred Pd and Ru dopant adsorption. The Pd-Ru decorated Pt catalyst exhibits a mass-based exchange current density of 1557 ± 85 A g –1 metal for hydrogen oxidation reaction, demonstrating superior performance in an ammonia compressor.

25 ENERGY STORAGE↗
DOE OSTI2023

Why Dissolving Salt in Water Decreases Its Dielectric Permittivity

The dielectric permittivity of salt water decreases on dissolving more salt. For nearly a century, this phenomenon has been explained by invoking saturation in the dielectric response of the solvent water molecules. Herein, we employ an advanced deep neural network (DNN), built using data from density functional theory, to study the dielectric permittivity of sodium chloride solutions. Notably, the decrease in the dielectric permittivity as a function of concentration, computed using the DNN approach, agrees well with experiments. Detailed analysis of the computations reveals that the dominant effect, caused by the intrusion of ionic hydration shells into the solvent hydrogen-bond network, is the disruption of dipolar correlations among water molecules. Accordingly, the observed decrease in the dielectric permittivity is mostly due to increasing suppression of the collective response of solvent waters.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Hunt for Starspots in HARPS Spectra of G and K Stars

We present a method for detecting starspots on cool stars using the cross-correlation function (CCF) of high-resolution molecular spectral templates applied to archival high-resolution spectra of G and K stars observed with the High Accuracy Radial Velocity Planet Searcher (HARPS)/HARPS-N. We report nondetections of starspots on the Sun even when the Sun was spotted, the solar twin 18 Scorpii, and the very spotted Sun-like star HAT-P-11, suggesting that Sun-like starspot distributions will be invisible to the CCF technique, and should not produce molecular absorption signals that might be confused for signatures of exoplanet atmospheres. We detect strong TiO absorption in the T Tauri K-dwarfs LkCa 4 and AA Tau, consistent with significant coverage by cool regions. We show that despite the nondetections, the technique is sensitive to relatively small spot coverages on M dwarfs and large starspot areas on Sun-like stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Molecular Tuning of Ether Cosolvent Chemistry for High-Voltage Sodium-Ion Batteries

Ethers as electrolyte cosolvents in sodium-ion batteries (SIBs) provide favorable Na + solvation and interfacial properties, but their low oxidative stability limits their use in high-voltage SIBs. Herein, we address this limitation via molecular tuning of ether cosolvents for high-voltage (4.2 V) hard carbon || NaNi 0.33 Fe 0.33 Mn 0.33 O 2 full cells. Tetrahydropyran (THP) is functionalized with a nitrile group to form tetrahydropyran-4-carbonitrile (THPCN). To delineate the effect of nitrile functionalization and benchmark ether against a conventional carbonate, THP, THPCN, and diethyl carbonate (DEC) are evaluated as cosolvents with ethylene carbonate. Nitrile functionalization lowers the HOMO energy of the ether, extends the electrolyte stability window, and alters Na⁺ solvation. Spectroscopic techniques and molecular dynamics simulations reveal that THPCN exhibits predominantly aggregate-dominated solvation (95.1 %) with weakened Na + -solvent interactions, producing the most anion-rich environment relative to DEC and THP cosolvents. THPCN-modified solvation promotes the formation of highly conductive, fluorine-enriched interphases that suppress parasitic reactions. Pouch full cells with THPCN sustained ~ 600 cycles at 4.2 V, outperforming THP and DEC. Operando gas analysis reveals that THPCN reduces CO 2 generation by 45% and H 2 generation by 30% relative to THP. Furthermore, the findings demonstrate nitrile functionalization as a molecular design strategy to stabilize ethers and enable high-voltage SIBs.

25 ENERGY STORAGE↗
DOE OSTI2022

Workhorse minimally empirical dispersion-corrected density functional with tests for weakly bound systems: r 2 SCAN + rVV 10

SCAN+rVV10 has been demonstrated to be a versatile van der Waals (vdW) density functional that delivers good predictions of both energetic and structural properties for many types of bonding. Recently, the r 2 SCAN functional was devised as a revised form of SCAN with improved numerical stability. In this work, we refit the rVV10 functional to optimize the r 2 SCAN+rVV10 vdW density functional and test its performance for molecular interactions and layered materials. Our molecular tests demonstrate that r 2 SCAN+rVV10 outperforms its predecessor SCAN+rVV10 in both efficiency (numerical stability) and accuracy. This good performance is also found in lattice-constant predictions. In comparison with benchmark results from higher-level theories or experiments, r 2 SCAN+rVV10 yields excellent interlayer binding energies and phonon dispersions for layered materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Feasibility of a Novel Density Functional Method Outside the Kohn-Sham Framework for Modeling Global Potential Energy Surfaces of Molecular Chemical Reactions (Final Technical Report)

The project aimed towards the construction of computational methods capable of modeling the global potential energy surface (PES) of small molecules, molecular ions, and radicals — including the parts of the PES which correspond to chemical reactions, and the reaction paths connecting reactants, intermediates, and reaction products. This goal may seem humble at first glance, but for chemical systems with more than about six atoms in total, at the time the project was proposed, there were no established theoretical methods capable of simulating such systems reliably, not even for small molecules in the gas phase which are electronically benign. This restriction severely hampers our ability to model and control chemical processes under harsh conditions. With the goal of constructing a method capable of modeling such chemical systems, we proposed to pursue a novel approach towards a Multi-Configuration (MC) DFT outside the traditional frameworks of Kohn-Sham theory and other methods of coupling wave function theory with DFT. Rather than being a complete active space (CAS) method, the proposed DOCI-DFT would employ a special restricted form of the active space wave function, called Doubly-Occupied CI (DOCI)—this wave function form is sufficient to describe not only heterolytic, but also homolytic bond dissociation processes at the zeroth order (i.e., as active space wave function). There are no other standard mean field methods which can do so. In the original proposal, we also outlined strong formal and practical arguments speaking for this method. The project proposal was accepted by the Department of Energy and provided two years of seed funding for one graduate student, as well as two years of two weeks PI summer-salary for the PI. However, ultimately the project could not be effectively pursued due to severe interferences outside the context scientific problems and was cancelled. Apart from two weeks of PI salary (and associated fringe & overhead costs issues by the performing institution), no costs were charged against the award, with the entire rest of funding returned to the Department of Energy. This report reiterates the primary background information regarding the project, its original goals, and outlines the preliminary work performed during the two weeks of DOE funding charged.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Charge Transport in Zirconium-Based Metal–Organic Frameworks

Metal–organic frameworks (MOFs) are a class of crystalline porous materials characterized by inorganic nodes and multitopic organic linkers. Because of their molecular-scale porosity and periodic intraframework chemical functionality, MOFs are attractive scaffolds for supporting and/or organizing catalysts, photocatalysts, chemical-sensing elements, small enzymes, and numerous other functional-property-imparting, nanometer-scale objects. Notably, these objects can be installed after the synthesis of the MOF, eliminating the need for chemical and thermal compatibility of the objects with the synthesis milieu. Thus, postsynthetically functionalized MOFs can present three-dimensional arrays of high-density, yet well-separated, active sites. Depending on the application and corresponding morphological requirements, MOF materials can be prepared in thin-film form, pelletized form, isolated single-crystal form, polycrystalline powder form, mixed-matrix membrane form, or other forms. For certain applications, most obviously catalytic hydrolysis and electro- or photocatalytic water splitting, but also many others, an additional requirement is water stability. MOFs featuring hexa-zirconium(IV)-oxy nodes satisfy this requirement. For applications involving electrocatalysis, charge storage, photoelectrochemical energy conversion, and chemiresistive sensing, a further requirement is electrical conductivity, as embodied in electron or hole transport. As most MOFs, under most conditions, are electrically insulating, imparting controllable charge-transport behavior is both a chemically intriguing and chemically compelling challenge. Herein, we describe three strategies to render zirconium-based metal–organic frameworks (MOFs) tunably electrically conductive and, therefore, capable of transporting charge on the few nanometers (i.e., several molecular units) to few micrometers (i.e., typical dimensions for MOF microcrystallites) scale. The first strategy centers on redox-hopping between periodically arranged, chemically equivalent sites, essentially repetitive electron (or hole) self-exchange. Zirconium nodes are electrically insulating, but they can function as grafting sites for (a) redox-active inorganic clusters or (b) molecular redox couples. Alternatively, charge hopping based on linker redox properties can be exploited. Marcus’s theory of electron transfer has proven useful for understanding/predicting trends in redox-hopping based conductivity, most notably, in accounting for variations as great as 3000-fold depending on the direction of charge propagation through structurally anisotropic MOFs. In MOF environments, propagation of electronic charge via redox hopping is necessarily accompanied by movement of charge-compensating ions. Consequently, rates of redox hopping can depend on both the identity and concentration of ions permeating the MOF. In the context of electrocatalysis, an important goal is to transport electronic charge fast enough to match or exceed the inherent activity of MOF-based or MOF-immobilized catalysts. Bandlike electronic conductivity is the focus of an alternative strategy: one based on the introduction of molecular guests capable of forming donor–acceptor charge transfer complexes with the host framework. Theory again can be applied predictively to alter conductivity. A third strategy similarly emphasizes electronic conductivity, but it makes use of added bridges in the form of molecular oligomers or inorganic clusters that can then be linked to span the length of a MOF crystallite. For all strategies, retention of molecular-scale porosity is emphasized, as this property is key to many applications. Lastly, while our focus is on Zr-MOFs, the described approaches clearly are extendable to other MOF compositions, as has already been demonstrated, in part, in studies by others.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Redox and Thiols in Archaea

Low molecular weight (LMW) thiols have many functions in bacteria and eukarya, ranging from redox homeostasis to acting as cofactors in numerous reactions, including detoxification of xenobiotic compounds. The LMW thiol, glutathione (GSH), is found in eukaryotes and many species of bacteria. Analogues of GSH include the structurally different LMW thiols: bacillithiol, mycothiol, ergothioneine, and coenzyme A. Many advances have been made in understanding the diverse and multiple functions of GSH and GSH analogues in bacteria but much less is known about distribution and functions of GSH and its analogues in archaea, which constitute the third domain of life, occupying many niches, including those in extreme environments. Archaea are able to use many energy sources and have many unique metabolic reactions and as a result are major contributors to geochemical cycles. As LMW thiols are major players in cells, this review explores the distribution of thiols and their biochemistry in archaea.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Impact of functional groups on the electrocatalytic hydrogenation of aromatic carbonyls to alcohols

We report that electrocatalytic hydrogenation (ECH) of biomass-derived feedstocks has a critical dependence on the molecular structure of the organic and its adsorption on the electrode surface. In this study, we investigated the role of functional groups in the adsorption of the organic molecule on the charged Pd (111) surface and its subsequent effect on organic reduction in electrochemical hydrogenation of organic molecules. With three aromatic carbonyls of benzaldehyde (BZD), acetophenone (ACE), and vanillin (VAN), we rationalize molecular-scale adsorption and interfacial charge transfer processes by employing density-functional-theory based ab initio molecular dynamics simulations. We observe that the functional group and electrode charge strongly affect the proximity of organic molecule to the Pd (111) surface, where distances of aromatic ring and carbonyl group of the organic on the electrode change distinctively with functional groups and charge state of electrode, which strongly impact reduction of organics on the surface. Calculations of differential electron density show the strongest reduction with benzaldehyde via interfacial electron transfer from the charged Pd surface. We also observe that the interaction between the functional groups and solvent (VAN > BZD > ACE) significantly influence the organic interaction with the charged electrode (BZD > VAN > ACE), resulting in the net interaction energy between the organic and the electrode in the order of BZD > ACE > VAN. Experimental measurement of ECH rate also show the same trend of the net interaction energy. These results demonstrate the significance of solvent effect on the reducibility of organic molecules on electrodes.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Combined density functional theory/kinetic Monte Carlo investigation of surface morphology during cycling of Li-Cu electrodes

In this work, we employed a combined density functional theory and kinetic Monte Carlo approach in order to investigate the nanoscale behavior of lithium stripping and plating on lithium-copper nanoalloys. Density functional theory calculations were used to develop an atom-by-atom understanding of the nucleation behavior of lithium on copper surfaces with different surface morphologies. We found that nanometric pits resulted in significantly more favorable lithium deposition when compared to pristine or lightly-defective Cu surfaces, which is in agreement with previous experimental studies. We then used density functional theory and constrained ab initio molecular dynamics to develop interaction and reaction parameters for a larger-scale kinetic Monte Carlo model in order to provide insight into the stripping and plating behavior of nanostructured Li-Cu nanoalloy anodes. Substantial losses in capacity and strong indications of morphological change were observed for a wide range of Cu:Li ratios over 100 cycles. We observed a complex relationship between the nanoparticle composition and the properties of the formed solid-electrolyte interphase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Tunable noninteracting free-energy density functionals for high-energy-density physics applications

In this work, we introduce the concept of a tunable noninteracting free-energy density functional and present two examples realized: (i) via a simple one-parameter convex combination of two existing functionals and (ii) via the construction of a generalized gradient approximation (GGA) enhancement factor that contains one free parameter and is designed to satisfy a set of incorporated constraints. Functional (i), constructed as a combination of the local Thomas–Fermi and a pseudopotential-adapted GGA for the noninteracting free-energy, has already demonstrated its practical usability for establishing the high temperature end of the equation of state of deuterium [Phys. Rev. B 104, 144104 (2021)] and CHON resin [Phys. Rev. E 106, 045207 (2022)] for inertial confinement fusion applications. Hugoniot calculations for liquid deuterium are given as another example of how the application of computationally efficient orbital-free density functional theory (OF-DFT) can be utilized with the employment of the developed functionals. Once the functionals have been tuned such that the OF-DFT Hugoniot calculation matches the Kohn–Sham solution at some low-temperature point, agreement with the reference Kohn–Sham results for the rest of the high temperature Hugoniot path is very good with relative errors for compression and pressure on the order of 2% or less.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Molecular-Level Insights into the Influence of Ionic Liquids on the Structure and Dynamics of Neutral and Charged Polyimides

We use all-atom molecular dynamics simulations to investigate how increasing ionic functionalization influences polyimide (PI) behavior in ionic liquid (IL) solvation environments. Here, we examine three polymer systems with varying charge densities: a neutral polyimide [N−PI] containing imidazole rings and progressively introduce charge through quaternization to create singly [C−PI] + and doubly charged [C−2PI] 2+ variants across a wide range of IL concentration (0−90 wt %). Through comprehensive structural, mechanical, and electrostatic analyses, we reveal that polymer charge density plays a central role in shaping IL organization and interaction with the polymer matrix. At low IL content, charged systems exhibit strong electrostatic complexation, leading to chain compaction, localized ESP environments, and elevated dielectric constants. As IL concentration increases, the effect of the different polymer charge states becomes less significant. Notably, an intermediate composition regime at approximately 50 wt % IL is associated with changes in IL-rich domain connectivity and overall system behavior across all three PI systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Assessing density functionals for describing methane dissociative chemisorption on Pt(110)-(2×1) surface

In this work, we explore the suitability of several density functionals with the generalized gradient approximation (GGA) and beyond for describing the dissociative chemisorption of methane on the reconstructed Pt(110)-(2×1) surface. The bulk and surface structures of the metal, methane adsorption energy, and dissociation barrier are used to assess the functionals. A van der Waals corrected GGA functional (optPBE-vdW) and a metaGGA functional with van der Waals correction (MS PBEl-rVV10) are selected for ab initio molecular dynamics calculations of the sticking probability. Our results suggest that the use of these two functionals may lead to a better agreement with existing experimental results, thus serving as a good starting point for future development of reliable machine-learned potential energy surfaces for the dissociation of methane on the Pt(110)-(2×1) surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗