A great need exists for computationally efficient quantum simulation approaches that can achieve an accuracy similar to high-level theories at a fraction of the computational cost. In this regard, we have leveraged a machine-learned interaction potential based on Chebyshev polynomials to improve density functional tight binding (DFTB) models for organic materials. The benefit of our approach is two-fold: (1) many-body interactions can be corrected for in a systematic and rapidly tunable process, and (2) high-level quantum accuracy for a broad range of compounds can be achieved with ∼0.3% of data required for one advanced deep learning potential. Our model exhibits both transferability and extensibility through comparison to quantum chemical results for organic clusters, solid carbon phases, and molecular crystal phase stability rankings. Our efforts thus allow for high-throughput physical and chemical predictions with up to coupled-cluster accuracy for systems that are computationally intractable with standard approaches.
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http://dx.doi.org/10.1021/acs.jpclett.2c00453 | DOI Listing |
J Chem Theory Comput
January 2025
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physical principles into these models, or utilizing them in a Δ-ML scheme, significantly enhances their robustness and transferability. This paper introduces PM6-ML, a Δ-ML method that synergizes the semiempirical quantum-mechanical (SQM) method PM6 with a state-of-the-art ML potential applied as a universal correction.
View Article and Find Full Text PDFMethods Mol Biol
October 2024
Research Department, New England Biolabs, Ipswich, MA, USA.
Golden Gate Assembly depends on the accurate ligation of overhangs at fragment fusion sites to generate full-length products with all parts in the desired order. Traditionally, fusion-site sequences are selected by using validated sets of overhang sequences or by applying a handful of semi-empirical rules to guide overhang choice. While these approaches allow dependable assembly of 6-8 fragments in one pot, recent work has demonstrated that comprehensive measurement of ligase fidelity allows prediction of high-fidelity junction sets that enable much more complex assemblies of 12, 24, or even 36+ fragments in a single reaction that will join with high accuracy and efficiency.
View Article and Find Full Text PDFJ Chem Inf Model
April 2024
Nobias Therapeutics, Inc., 144 S Whisman Rd, Suite C, Mountain View, California 94041, United States.
We present a diffusion-based generative model for conformer generation. Our model is focused on the reproduction of the bonded structure and is constructed from the associated terms traditionally found in classical force fields to ensure a physically relevant representation. Techniques in deep learning are used to infer atom typing and geometric parameters from a training set.
View Article and Find Full Text PDFJ Nat Prod
April 2024
Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China.
Nuclear magnetic resonance (NMR) chemical shift calculations are powerful tools for structure elucidation and have been extensively employed in both natural product and synthetic chemistry. However, density functional theory (DFT) NMR chemical shift calculations are usually time-consuming, while fast data-driven methods often lack reliability, making it challenging to apply them to computationally intensive tasks with a high requirement on quality. Herein, we have constructed a 54-layer-deep graph convolutional network for C NMR chemical shift calculations, which achieved high accuracy with low time-cost and performed competitively with DFT NMR chemical shift calculations on structure assignment benchmarks.
View Article and Find Full Text PDFPhys Rev Lett
November 2023
1Department of Chemistry, Columbia University, New York, New York 10027, USA.
Coupled-cluster theory with single, double, and perturbative triple excitations (CCSD(T))-often considered the "gold standard" of main-group quantum chemistry-is inapplicable to three-dimensional metals due to an infrared divergence, preventing its application to many important problems in materials science. We study the full, nonperturbative inclusion of triple excitations (CCSDT) and propose a new, iterative method, which we call ring-CCSDT, that resums the essential triple excitations with the same N^{7} run-time scaling as CCSD(T). CCSDT and ring-CCSDT are used to calculate the correlation energy of the uniform electron gas at metallic densities and the structural properties of solid lithium.
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