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At least 235 records · Page 13

General Protocol for the Accurate Prediction of Molecular 13 C/ 1 H NMR Chemical Shifts via Machine Learning Augmented DFT

An accurate prediction of NMR chemical shifts at affordable computational cost is very important for different types of structural assignments in experimental studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) are two of the most popular computational methods for NMR calculation, yet they often fail to resolve ambiguities in structural assignments. In this work, we present a new method that uses machine learning (ML) techniques (DFT + ML) that significantly increases the accuracy of 13 C/ 1 H NMR chemical shift prediction for a variety of organic molecules. The input of the generalizable DFT + ML model contains two critical parts: one is a vector providing insights into chemical environments, which can be evaluated without knowing the exact geometry of the molecule; the other one is the DFT-calculated isotropic shielding constant. The DFT + ML model was trained with a data set containing 476 13 C and 270 1 H experimental chemical shifts. For the DFT methods used here, the root mean square deviations (RMSDs) for the errors between predicted and experimental 13 C/ 1 H chemical shifts can be as small as 2.10/0.18 ppm, which is much lower than those from simple DFT (5.54/0.25 ppm), or DFT + linear regression (LR) (4.77/0.23 ppm) approaches. It also has a smaller maximum absolute error than two previously proposed NMR-predicting ML models. The robustness of the DFT + ML model is tested on two classes of organic molecules (TIC10 and hyacinthacines), where the correct isomers were unambiguously assigned to the experimental ones. Overall, the DFT + ML model shows promise for structural assignments in a variety of systems, including stereoisomers, that are often challenging to determine experimentally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free energy methods that furnish an estimation of relative binding free energies (RBFE) of similar molecules. Recent advances in these methods have increased their speed, accuracy, and precision. This is evident from the increasing number of retrospective as well as prospective studies employing them. However, such methods still have limited applicability in real-world scenarios due to a number of important yet unresolved issues. Here, we report the findings from a large data set comprising over 500 ligand transformations spanning over 300 ligands binding to a diverse set of 14 different protein targets which furnish statistically robust results on the accuracy, precision, and reproducibility of RBFE calculations. We use ensemble-based methods which are the only way to provide reliable uncertainty quantification given that the underlying molecular dynamics is chaotic. These are implemented using TIES (Thermodynamic Integration with Enhanced Sampling). Results achieve chemical accuracy in all cases. Ensemble simulations also furnish information on the statistical distributions of the free energy calculations which exhibit non-normal behavior. We find that the “enhanced sampling” method known as replica exchange with solute tempering degrades RBFE predictions. We also report definitively on numerous associated alchemical factors including the choice of ligand charge method, flexibility in ligand structure, and the size of the alchemical region including the number of atoms involved in transforming one ligand into another. Our findings provide a key set of recommendations that should be adopted for the reliable application of RBFE methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Fragment-based quantum chemistry methods offer a way to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Materials for the biorefinery: high bio-content, shape memory Kraft lignin-derived non-isocyanate polyurethane foams using a non-toxic protocol

Polyurethanes are among the top six polymers produced in the world and are widely used in the automotive, furniture, construction and appliance industry for their light weight, impact resistance, and insulating properties. However, the use of hazardous diisocyanates used in polyurethane formulations has led many to search for more sustainable alternatives. The lignin component of biomass has been targeted to replace the often toxic and petroleum-derived precursors to polymer synthesis in support of the biorefinery concept where natural materials are used as the feedstock for commodity plastics. The use of lignin is often hampered due to its low reactivity, heterogeneity and the necessity of employing extensive purification and/or functionalization measures to ensure materials are of comparable quality. In this report, a unique method is presented for the synthesis and processing of a non-toxic, non-isocyanate polyurethane foam utilizing unmodified Kraft lignin and a biobased curing agent. Here, raw Kraft lignin is functionalized with green organic carbonates and a non-toxic approach is taken to solubilize the precursors with a curing agent from renewable fatty acids enabling rapid gel-times. For the first time, a NIPU foam from lignin is synthesized while the structure–property relationship of different reaction mixtures is studied demonstrating shape memory capacity and 100% biobased carbon content.

36 MATERIALS SCIENCE↗

Evaluation protocol for revealing magnonic contrast in TR-STXM measurements

We present a statistically motivated method to extract magnonic contrast from time-resolved scanning transmission x-ray microscopy (TR-STXM) measurements. TR-STXM is an element-specific method for resolving spin-dynamics in space and time. It offers nanometer spatial resolution and picosecond temporal resolution. The presented method makes it possible to obtain phase and amplitude profiles of spin-waves from STXM measurements. Furthermore, it allows for a rigorous transformation to reciprocal magnon k⃗-space, revealing k⃗-dependent magnon properties such as the magnon dispersion in three dimensions and for all directions of the magnetic anisotropy. We demonstrate our method using X-band ferromagnetic resonance on a micrometer-sized permalloy assembly.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Optimizing immunization protocols to elicit broadly neutralizing antibodies

Significance The global health burden could be substantially alleviated by the creation of universal vaccines against highly mutable pathogens like HIV and influenza. Broadly neutralizing antibodies (bnAbs) are encouraging targets for such vaccines, because they can bind to diverse strains of these pathogens. BnAbs typically develop only after the immune system has been exposed to many mutated versions of a pathogen, and then too in few people and low numbers. Thus, sequentially administering multiple different pathogen-like proteins is a promising strategy to elicit bnAbs through vaccination. However, it remains unclear how best to design/administer these proteins. We explore this using physics-based simulations and provide mechanistic insights into antibody evolution that could guide creation of universal vaccines against highly mutable pathogens.

Sprenger, Kayla G.↗

Learning to learn by using nonequilibrium training protocols for adaptable materials

Evolution in time-varying environments naturally leads to adaptable biological systems that can easily switch functionalities. Advances in the synthesis of environmentally responsive materials therefore open up the possibility of creating a wide range of synthetic materials which can also be trained for adaptability. We consider high-dimensional inverse problems for materials where any particular functionality can be realized by numerous equivalent choices of design parameters. By periodically switching targets in a given design algorithm, we can teach a material to perform incompatible functionalities with minimal changes in design parameters. We exhibit this learning strategy for adaptability in two simulated settings: elastic networks that are designed to switch deformation modes with minimal bond changes and heteropolymers whose folding pathway selections are controlled by a minimal set of monomer affinities. The resulting designs can reveal physical principles, such as nucleation-controlled folding, that enable such adaptability.

Science & Technology - Other Topics↗

Protocols for x-ray transient grating pump/optical probe experiments at x-ray free electron lasers

Abstract Transient grating spectroscopy is a specialized application of the four-wave-mixing methodology and constitutes a versatile technique for investigating the dynamics of vibrational, magnetic and electronic degrees of freedom of matter in a background-free fashion. Recent developments in free-electron laser sources have enabled the extension of this technique into the extreme ultraviolet range. Ongoing efforts to expand transient grating spectroscopy into the x-ray regime promise numerous advantages: (1) substantial penetration depths that allow for probing bulk material properties, (2) element specificity via specific core-excited states, and (3) short wavelengths that allow for excitation gratings with higher momentum transfer and improved spatial resolution. In this study, we comprehensively outline the procedures for conducting x-ray transient grating pump/optical probe experiment. The process encompasses the design and alignment of the experimental setup, as well as the subsequent steps involved in data acquisition and analysis. This paper is intended as a comprehensive guide for researchers interested in implementing x-ray transient grating spectroscopy, providing valuable insights into the intricacies of the experimental workflow required for this novel technique. Furthermore, we discuss the potential for extending this methodology to an x-ray pump/x-ray probe scheme, envisioning a future direction that holds promise for enhancing the capabilities and scope of x-ray transient grating spectroscopy, opening new opportunities for studying ultrafast processes with unprecedented temporal and spatial resolutions.

Optics↗

Quantum error mitigation by hidden inverses protocol in superconducting quantum devices

We present a method to improve the convergence of variational algorithms based on hidden inverses (HIs) to mitigate coherent errors. In the context of error mitigation, this means replacing the hardware implementation of certain Hermitian gates with their inverses. Doing so results in noise cancellation and a more resilient quantum circuit. This approach improves performance in a variety of two-qubit error models where the noise operator also inverts with the gate inversion. We apply the mitigation scheme on superconducting quantum processors running the variational quantum eigensolver (VQE) algorithm to find the H 2 ground-state energy. When implemented on superconducting hardware we find that the mitigation scheme effectively reduces the energy fluctuations in the parameter learning path in VQE, reducing the number of iterations for a converged value. We also provide a detailed numerical simulation of VQE performance under different noise models and explore how HIs and randomized compiling affect the underlying loss landscape of the learning problem. These simulations help explain our experimental hardware outcomes, helping to connect lower-level gate performance to application-specific behavior in contrast to metrics like fidelity which often do not provide an intuitive insight into observed high level performance.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗