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Yang, Weitao

Publications and source records attributed to Yang, Weitao.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales

Enterobacterales, a large order of Gram-negative bacteria, including Escherichia coli and Klebsiella pneumoniae, are major causes of urinary tract and gastrointestinal infections, pneumonia, and other diseases in healthcare settings and communities. ESBL-producing Enterobacterales and carbapenem-resistant Enterobacterales can break down commonly used antibiotics, with some strains being resistant to all available antibiotics. This public health threat necessitates the development of novel antibiotics, ideally targeting new pathways in these bacteria. Gram-negative bacteria possess an outer membrane enriched with lipid A, a saccharolipid that serves as the membrane anchor of lipopolysaccharides and the active component of the bacterial endotoxin, causing septic shock. The biosynthesis of lipid A is crucial for the viability of Gram-negative bacteria, and as an essential enzyme in this process, LpxH has emerged as a promising target for developing novel antibiotics against multidrugresistant Gram-negative pathogens. Here, we report the development of pyridinyl sulfonyl piperazine LpxH inhibitors. Among them, ortho-substituted pyridinyl compounds significantly boost LpxH inhibition and antibiotic activity over the original phenyl series. Structural and QM/MM analyses reveal that these improved activities are primarily due to the enhanced interaction between F141 of the LpxH insertion lid and the pyridinyl group. Incorporation of the N-methyl-N-phenyl-methanesulfonamide moiety into the pyridinyl sulfonyl piperazine backbone results in JHLPH- 106 and JH-LPH-107, both of which exhibit potent antibiotic activity against wild-type Enterobacterales such as K. pneumoniae and E. coli. JH-LPH-107 exhibits a low rate of spontaneous resistance and a high safety window in vitro, rendering it an excellent lead for further clinical development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Energy Frontier Research Centers: Center for the Computational Design of Functional Layered Materials (CCDM) August 1, 2014 - July 31, 2018; Center for Complex Materials from First Principles (CCM) August 1, 2018 - July 31, 2021 (Final Report)

The mission of the DOE Energy Frontier Research Centers CCDM (2014-2018) and CCM (2018-2021) was to theoretically develop, computationally apply, and experimentally validate electronic structure methods for all materials, with a focus on the complex materials, especially layered and two-dimensional materials, strongly-correlated materials, and liquid water. This was achieved by over 200 published journal articles authored by about 17 senior investigators from physics and chemistry and from theory, computation, and experiment, plus their collaborators. In particular, the Centers confirmed the predictive power of the SCAN (strongly constrained and appropriately normed) density functional, which was constructed to satisfy 17 known exact constraints and several appropriate norms. Without being fitted to real bonded systems, and at a modest computational cost, SCAN correctly predicted covalent, ionic, metallic, hydrogen, and van der Waals bonds in many challenging materials. SCAN gave an improved description of defects in semiconductors, surface properties of metals, seven phases of ice, liquid water, liquid and supercooled silicon, subtle structural distortions in ferroelectrics, formation energies and structural predictions for solids, and critical pressures for structural phase transitions. Perhaps most remarkably, SCAN correctly described some strongly-correlated materials that were previously believed to be beyond the reach of density-functional approximations. SCAN is the only density functional that correctly predicts the band gap closing under chemical doping of the cuprate high-temperature superconducting materials. SCAN also predicts a landscape of competing stripe and magnetic phases in the cuprates. For some materials with some codes, SCAN has convergence problems that are greatly reduced by the CCM-developed r 2 SCAN, without loss of accuracy or rigor. SCAN and r 2 SCAN still make some self-interaction error, which is greatly reduced by the CCDM/ CCM-developed local orbital scaling correction (LOSC). These Centers further proved that the fundamental energy gaps of a solid from an orbital energy difference and from total energy differences are the same for a large class of generalized Kohn-Sham (GKS) functionals, including SCAN and standard hybrid functionals, and that symmetry breaking arises when a dynamic density fluctuation drops to zero frequency. The Centers identified new mechanisms for catalysis in layered materials with ions intercalated between the layers, investigated charge density waves both in model systems and in real layered materials, studied changes of band gap with the number of layers, and explored topological ultrathin films, bent nanoribbons, and defects.

08 HYDROGEN↗
DOE OSTI2020

Arene Substitution Design for Controlled Conformational Changes of Dibenzocycloocta-1,5-dienes

We report that the agile eight-mernbered cycloalkane can be stabilized by fusing two rigid benzene rings, substituted with proper functional groups. The conformational change of dibenzocycloocta-1,S-diene (DBCOD), a rigid-flexible-rigidorganic moiety, from Boat to Chair conformation requires an activation energy of 42 kJ/mol that is substantially lower than that of existing submolecular shape-changing unit. Experimental data corroborated by theory calculations demonstrate that intramolecular hydrogen bonding can stabilize Boat whereas electron repulsive interaction from opposing ester substituents favors Chair. Intramolecular hydrogen bonding, formed by 1,10-diamide substitution stabilizes Boat, spiking the temperature at which Boat and Chair can readily interchange from -60 °C to 60 °C. Concomitantly this intramolecular attraction raises the energy barrier from 42 kJ/mol of unsubstituted DBCOD to 68 kJ/mol of diamide-substituted DBCOD. Remarkably, this value falls within the range of the activation energy of highly efficient enzyme catalyzed biological reactions. With shape changes once considered only possible with high-energy, our work reveals a potential pathway exemplified by a specific submolecular structure to achieve low-energy driven shape changes for the first time. Together with intrinsic cycle stability and high energy output systems that would have incurred damage under high-energy stimuli, could particularly benefit from this new kind of low-energy driven shape-changing mechanism. This work has laid the basis to construct systems for low-energy driven stimuli-responsive applications, hitherto a challenge to overcome.

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

Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections

The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier’s wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine–cytosine (GC) base pairs and among 3 adenine–thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π–π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.

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

Preserving Symmetry and Degeneracy in the Localized Orbital Scaling Correction Approach

Symmetry is a fundamental concept that plays a critical role in many chemical and physical phenomena and processes, which highlights the importance of theoretical methods to correctly handle symmetry. The recently developed localized orbital scaling correction (LOSC1) shows great improvement on the description of band gaps, photoemission spectra, and dissociation limits of cationic species. However, issues remain with LOSC1 in dealing with the symmetry and degeneracy of electronic states, which are also relevant to other methods using localization. In this work, we utilize a new method that deals with the physical-space and the energy-space localization on an equal footing. The resulting localized orbitals, i.e., orbitalets, are able to maintain more symmetry and the desired state degeneracy, which is important in calculating the electronic structure of both molecules and periodic bulk systems. Furthermore, the curvature matrix is redefined to improve potential energy curves for systems with stretched bonds, while retaining the correct dissociation limits. This new approach, termed LOSC2, includes only two fitting parameters. It maintains accuracy similar to that of LOSC1 over many properties, while overcoming LOSC1’s deficiencies in symmetry and degeneracy. Our tests have shown that LOSC2 orbitalets possess the full- or subgroup of molecular symmetry if allowed, which preserves the state degeneracy. Tests on differently sized planar annulenes, odd-numbered allenes, and triphenylene again verify that LOSC2 is able to maintain the state degeneracy, while LOSC1 cannot. Finally, all the tests demonstrate the advantage of LOSC2 in the calculation of molecular systems and its potential for application to periodic bulk systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Charge transfer excitation energies from ground state density functional theory calculations

Calculating charge transfer (CT) excitation energies with high accuracy and low computational cost is a challenging task. Kohn-Sham density functional theory (KS-DFT), due to its efficiency and accuracy, has achieved great success in describing ground state problems. To extend to excited state problems, our group recently demonstrated an approach with good numerical results to calculate low-lying and Rydberg excitation energies of an N-electron system from a ground state KS or generalized KS calculations of an (N-1)-electron system via its orbital energies. In the present work, we explore further the same methodology to describe CT excitations. Numerical results from this work show that performance of conventional density functional approximations (DFAs) is not as good for CT excitations as for other excitations due to the delocalization error. Applying localized orbital scaling correction (LOSC) to conventional DFAs, a recently developed method in our group to effectively reduce the delocalization error, can improve the results. Overall, the performance of this methodology is better than time dependent DFT (TDDFT) with conventional DFAs. In addition, it shows that results from LOSC-DFAs in this method reach similar accuracy to other methods, such as ΔSCF, G 0 W 0 with Bethe-Salpeter equations, particle-particle random phase approximation, and even high-level wavefunction methods like CC2. Our analysis shows that the correct 1/R trend for CT excitation can be captured from LOSC-DFA calculations, stressing that the application of DFAs with the minimal delocalization error is essential within this methodology. This work provides an efficient way to calculate CT excitation energies from ground state DFT.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Excitation Energies from the Single-Particle Green’s Function with the GW Approximation

Quasi-particle energies are vital to predicting molecular ionization energies and bulk band structures. The state-of-the-art method for quasi-particle energy calculations, particularly for bulk systems, is the GW approximation. For excited state calculations, one needs to go beyond the GW approximation. The Bethe–Salpeter equation (BSE) is the commonly used approach for bulk-system excited state calculations beyond the GW approximation, which is accurate but computationally cumbersome. In this Article, we create a new method to extract excitation energies directly from the quasi-particle energies based on the GW approximation. Starting from the (N – 1)-electron system, we are able to calculate molecular excitation energies with orbital energies at the GW level for HOMO excitations. Our calculations demonstrate that this method can accurately capture low-lying local excitations as well as charge transfer excitations in many molecular systems. This approach is shown to outperform the time-dependent density functional theory (TDDFT) and are comparable with higher level excited state calculations, including the equation-of-motion couple cluster (EOM-CC) theory and the BSE, but with less computational effort. This new approach provides an efficient alternative to the BSE method for accurate excited state calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Renormalized Singles Green’s Function for Quasi-Particle Calculations beyond the G 0 W 0 Approximation

Quasi-particle energies and band gaps in particular are critical for investigating novel materials. Commonly used density functional approximations (DFAs) systematically underestimate band gaps, and GW approximation is the established method of choice for good accuracy and reliability. However, G 0 W 0 has some undesired dependence on the DFA, while self-consistent GW (scGW) is expensive and not consistent in accuracy improvement. Here a simple and efficient G RS W 0 approach has been developed: a subspace diagonalization of the Hartree-Fock (HF) Hamiltonian with the DFA density matrix provides the new reference Green's function GRS that incorporates the effect of all single excitation contributions to the self-energy, thereby essentially eliminating the starting-point dependence. Calculations for molecules and large band gap solids demonstrate the significant improvement over G 0 W 0 and greatly reduced dependence on the initial DFA. GRS W0 approach also improve results for other bulks over G 0 W 0 but to a lesser extent, which could be due to the limitations in current implementation for bulks. The results demonstrate that to achieve good accuracy, it is not necessary to use hybrid DFA, which is expensive for bulks. Lastly, this work should be greatly significant in making GW a more robust approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Approximating Quasiparticle and Excitation Energies from Ground State Generalized Kohn–Sham Calculations

Quasiparticle energies and fundamental band gaps specifically are critical properties of molecules and materials. It was rigorously established that the generalized Kohn–Sham HOMO and LUMO orbital energies are the chemical potentials of electron removal and addition and thus good approximations to band edges and fundamental gaps from a density functional approximation (DFA) with minimal delocalization error. For other quasiparticle energies, their connection to the generalized Kohn–Sham orbital energies has not been established but remains highly interesting. We provide the comparison of experimental quasiparticle energies for many finite systems with calculations from the GW Green function and localized orbitals scaling correction (LOSC), a recently developed correction to semilocal DFAs, which has minimal delocalization error. Extensive results with over 40 systems clearly show that LOSC orbital energies achieve slightly better accuracy than the GW calculations with little dependence on the semilocal DFA, supporting the use of LOSC DFA orbital energies to predict quasiparticle energies. This also leads to the calculations of excitation energies of the N-electron systems from the ground state DFA calculations of the (N – 1)-electron systems. Findings show good performance with accuracy similar to TDDFT and the delta SCF approach for valence excitations with commonly used DFAs with or without LOSC. For Rydberg states, good accuracy was obtained only with the use of LOSC DFA. Our report highlights the pathway to quasiparticle and excitation energies from ground density functional calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Describing strong correlation with fractional-spin correction in density functional theory

Significance The static correlation error inherent in commonly used density functional approximations (DFAs) has seriously hindered the application of density functional theory (DFT) to strongly correlated systems. Here, an effective fractional-spin correction against the important issue of static/strong correlation in DFT is developed. With this, the flat-plane behavior of various DFAs is largely restored, and the potential energy curves of dissociation of ionic species, single bonds, and multiple bonds are properly described, which demonstrates great improvement in the treatment of strong correlation. This work should have a significant impact on the development and application of DFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Activating MoS 2 for pH-Universal Hydrogen Evolution Catalysis

MoS 2 presents a promising catalyst for the hydrogen evolution reaction (HER) in water splitting, but its worse catalytic performance in neutral and alkaline media than in acidic environment may be problematic for practical application. This is because the other half reaction of water splitting, i.e., oxygen evolution reaction, often needs to be implemented in alkaline environment. Here we demonstrate a universal strategy that may be used to significantly improve the HER catalysis of MoS 2 in all kinds of environments from acidic to alkaline, proton intercalation. Protons may be enabled to intercalate between monolayer MoS 2 and underlying substrates or in the interlayer space of thicker MoS 2 by two processes: electrochemically polarizing MoS 2 at negative potentials (vs RHE) in acidic media or immersing MoS2 into certain acid solutions like TFSI. The improvement in catalytic performance is due to the activity enhancement of the active sites in MoS 2 by the intercalated protons, which might be related with the effect of the intercalated protons on electrical conductance and the adsorption energy of hydrogen atoms. The enhancement in catalytic activity by the intercalated proton is very stable even in neutral and alkaline electrolytes.

, mechanical behavior↗
DOE OSTI2017

pH-Dependent Assembly of Porphyrin–Silica Nanocomposites and Their Application in Targeted Photodynamic Therapy

Structurally controlled nanoparticles, such as core–shell nanocomposite particles by combining two or more compositions, possess enhanced or new functionalities that benefited from the synergistic coupling of the two components. In this paper, we report new nanocomposite particles with self-assembled porphyrin arrays as the core surrounded by amorphous silica as the shell. The synthesis of such nanocomposite nanoparticles was conducted through a combined surfactant micelle confined self-assembly and silicate sol–gel process using optically active porphyrin as a functional building block. Depending on kinetic conditions, these particles exhibit structure and function at multiple length scales and locations. At the molecular scale, the porphyrins as the building blocks provide well-defined macromolecular structures for noncovalent self-assembly and unique chemistry for high-yield generation of singlet oxygen for photodynamic therapy (PDT). On the nanoscale, controlled noncovalent interactions of the porphyrin building block result in an extensive self-assembled porphyrin network that enables efficient energy transfer and impressive fluorescence for cell labeling, evidenced by absorption and photoluminescence spectra. The thin silicate shell on the nanoparticle surface allows easy functionalization, and the resultant targeting porphyrin-silica nanocomposites can selectively destroy tumor cells upon receiving light irradiation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials

The optimized effective potential (OEP) that gives accurate Kohn-Sham (KS) orbitals and orbital energies can be obtained from a given reference electron density. These OEP-KS orbitals and orbital energies are used here for calculating electronic excited states with the particle-particle random phase approximation (pp-RPA). Our calculations allow the examination of pp-RPA excitation energies with the exact KS density functional theory (DFT). Various input densities are investigated. Specifically, the excitation energies using the OEP with the electron densities from the coupled-cluster singles and doubles method display the lowest mean absolute error from the reference data for the low-lying excited states. This study probes into the theoretical limit of the pp-RPA excitation energies with the exact KS-DFT orbitals and orbital energies. We believe that higher-order correlation contributions beyond the pp-RPA bare Coulomb kernel are needed in order to achieve even higher accuracy in excitation energy calculations.

74 ATOMIC AND MOLECULAR PHYSICS↗