Engineering topics

Ji, Zhe

Publications and source records attributed to Ji, Zhe.

4 records

DOE OSTI2023

Enhanced active-site electric field accelerates enzyme catalysis

In this study, the design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme’s activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn 2+ with Co 2+ . Based on the electric field enhancement, we make a quantitative prediction of rate acceleration—50-fold faster than the wild-type enzyme—which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity—electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Protein Electric Fields Enable Faster and Longer-Lasting Covalent Inhibition of β-Lactamases

The widespread design of covalent drugs has focused on crafting reactive groups of proper electrophilicity and positioning towards targeted amino-acid nucleophiles. In this work, we found that environmental electric fields projected onto a reactive chemical bond, an overlooked design element, play essential roles in the covalent inhibition of TEM-1 beta-lactamase by avibactam. Using the vibrational Stark effect, the magnitudes of the electric fields that are exerted by TEM active sites onto avibactam’s reactive C=O were measured and demonstrate an electrostatic gating effect that promotes bond formation yet relatively suppresses the reverse dissociation. These results suggest new principles of covalent drug design and off-target site prediction. Unlike shape and electrostatic complementary which address binding constants, electrostatic catalysis drives reaction rates, essential for covalent inhibition, and deepens our understanding of chemical reactivity, selectivity, and stability in complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site

We report the catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C–D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that, despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active-site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, which provides direct evidence for the fundamental difference between the electrostatic environment of solvents and that of a preorganized enzyme active site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Ester-Linked Crystalline Covalent Organic Frameworks

Ester-linked, crystalline, porous covalent organic frameworks (COFs) have been synthesized and structurally characterized. Transesterification reactions between ditopic 2-pyridinyl aromatic carboxylates and tri- or tetratopic phenols gave the corresponding ester-linked COFs. They crystallize as 2D structures in kgm (COF-119) and hcb (COF-120, 121, 122) topologies with surface areas of up to 2092 m 2 /g. Notably, crystalline COF-122 comprises edges spanning over 10 phenylene units, an aspect that had only been achieved in metal-organic frameworks. Finally, this work expands the scope of reticular chemistry to include, for the first time, crystalline ester-linked COFs related to common polyesters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗