arXiv subjects

Frederick R. Manby

Publications and source records attributed to Frederick R. Manby.

15 recordsLinked to original sources

arXiv2024

NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models

Structure determination is essential to a mechanistic understanding of diseases and the development of novel therapeutics. Machine-learning-based structure prediction methods have made significant advancements by computationally predicting protein and bioassembly structures from sequences and molecular topology alone. Despite substantial progress in the field, challenges remain to deliver structure prediction models to real-world drug discovery. Here, we present NeuralPLexer3 -- a physics-inspired flow-based generative model that achieves state-of-the-art prediction accuracy on key biomolecular interaction types and improves training and sampling efficiency compared to its predecessors and alternative methodologies. Examined through newly developed benchmarking strategies, NeuralPLexer3 excels in vital areas that are crucial to structure-based drug design, such as physical validity and ligand-induced conformational changes.

cs.LG↗

arXiv2022

Informing Geometric Deep Learning with Electronic Interactions to Accelerate Quantum Chemistry

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. By developing a physics-inspired equivariant neural network, we introduce a method to learn molecular representations based on the electronic interactions among atomic orbitals. Our method, OrbNet-Equi, leverages efficient tight-binding simulations and learned mappings to recover high fidelity quantum chemical properties. OrbNet-Equi models a wide spectrum of target properties with an accuracy consistently better than standard machine learning methods and a speed orders of magnitude greater than density functional theory. Despite only using training samples collected from readily available small-molecule libraries, OrbNet-Equi outperforms traditional methods on comprehensive downstream benchmarks that encompass diverse main-group chemical processes. Our method also describes interactions in challenging charge-transfer complexes and open-shell systems. We anticipate that the strategy presented here will help to expand opportunities for studies in chemistry and materials science, where the acquisition of experimental or reference training data is costly.

cs.LG↗

arXiv2022

OrbNet: Deep Learning for Quantum Chemistry Using Symmetry-Adapted Atomic-Orbital Features

We introduce a machine learning method in which energy solutions from the Schrodinger equation are predicted using symmetry adapted atomic orbitals features and a graph neural-network architecture. \textsc{OrbNet} is shown to outperform existing methods in terms of learning efficiency and transferability for the prediction of density functional theory results while employing low-cost features that are obtained from semi-empirical electronic structure calculations. For applications to datasets of drug-like molecules, including QM7b-T, QM9, GDB-13-T, DrugBank, and the conformer benchmark dataset of Folmsbee and Hutchison, \textsc{OrbNet} predicts energies within chemical accuracy of DFT at a computational cost that is thousand-fold or more reduced.

physics.chem-ph↗

arXiv2021

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 million DFT calculations on molecules and geometries. This dataset covers the most common elements in bio- and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) as well as charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformers benchmark set, OrbNet Denali has a median correlation coefficient of R^2=0.90 compared to the reference DLPNO-CCSD(T) calculation, and R^2=0.97 compared to the method used to generate the training data (wB97X-D3/def2-TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for non-covalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of wB97X-D3/def2-TZVP with an average MAE of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

physics.chem-ph↗

arXiv2020

Reliable transition properties from excited-state mean-field calculations

Delta-self-consistent field theory (delta-SCF) is a conceptually simple and computationally inexpensive method for finding excited states. Using the maximum overlap method to guide optimization of the excited state, delta-SCF has been shown to predict excitation energies with a level of accuracy that is competitive with, and sometimes better than, that of TDDFT. Here we benchmark delta-SCF on a larger set of molecules than has previously been considered, and, in particular, we examine the performance of delta-SCF in predicting transition dipole moments, the essential quantity for spectral intensities. A potential downfall for delta-SCF transition dipoles is origin dependence induced by the nonorthogonality of delta-SCF ground and excited states. We propose and test the simplest correction for this problem, based on symmetric orthogonalization of the states, and demonstrate its use on bacteriochlorophyll structures sampled from the photosynthetic antenna in purple bacteria.

physics.chem-ph↗

arXiv2020

Multi-task learning for electronic structure to predict and explore molecular potential energy surfaces

We refine the OrbNet model to accurately predict energy, forces, and other response properties for molecules using a graph neural-network architecture based on features from low-cost approximated quantum operators in the symmetry-adapted atomic orbital basis. The model is end-to-end differentiable due to the derivation of analytic gradients for all electronic structure terms, and is shown to be transferable across chemical space due to the use of domain-specific features. The learning efficiency is improved by incorporating physically motivated constraints on the electronic structure through multi-task learning. The model outperforms existing methods on energy prediction tasks for the QM9 dataset and for molecular geometry optimizations on conformer datasets, at a computational cost that is thousand-fold or more reduced compared to conventional quantum-chemistry calculations (such as density functional theory) that offer similar accuracy.

physics.chem-ph↗

arXiv2020

Coupling electrons and vibrations in molecular quantum chemistry

We derive an electron-vibration model Hamiltonian in a quantum chemical framework, and explore the extent to which such a Hamiltonian can capture key effects of nonadiabatic dynamics. The model Hamiltonian is a simple two-body operator, and we make preliminary steps at applying standard quantum chemical methods to evaluating its properties, including mean-field theory, linear response, and a primitive correlated model. The Hamiltonian can be compared to standard vibronic Hamiltonians, but is constructed without reference to potential energy surfaces, through direct differentiation of the one- and two-electron integrals at a single reference geometry. The nature of the model Hamiltonian in the harmonic and linear-coupling regime is investigated for pyrazine, where a simple time-dependent calculation including electron-vibration correlation is demonstrated to exhibit the well-studied population transfer between the S$_2$ and S$_1$ excited states.

physics.chem-ph↗

arXiv2019

Polaritonic Coupled-Cluster Theory

We develop coupled-cluster theory for systems of electrons strongly coupled to photons, providing a promising theoretical tool in polaritonic chemistry with a perspective of application to all types of fermion-boson coupled systems. We show benchmark results for model molecular Hamiltonians coupled to cavity photons. By comparing to full configuration interaction results for various ground-state properties and optical spectra, we demonstrate that our method captures all key features present in the exact reference, including Rabi splittings and multi-photon processes. Further, a path on how to incorporate our bosonic extension of coupled-cluster theory into existing quantum chemistry programs is given.

physics.chem-ph↗

arXiv2019

Analytical Gradients for Projection-Based Wavefunction-in-DFT Embedding

Projection-based embedding provides a simple, robust, and accurate approach for describing a small part of a chemical system at the level of a correlated wavefunction method while the remainder of the system is described at the level of density functional theory. Here, we present the derivation, implementation, and numerical demonstration of analytical nuclear gradients for projection-based wavefunction-in-density functional theory (WF-in-DFT) embedding. The gradients are formulated in the Lagrangian framework to enforce orthogonality, localization, and Brillouin constraints on the molecular orbitals. An important aspect of the gradient theory is that WF contributions to the total WF-in-DFT gradient can be simply evaluated using existing WF gradient implementations without modification. Another simplifying aspect is that Kohn-Sham (KS) DFT contributions to the projection-based embedding gradient do not require knowledge of the WF calculation beyond the relaxed WF density. Projection-based WF-in-DFT embedding gradients are thus easily generalized to any combination of WF and KS-DFT methods. We provide numerical demonstration of the method for several applications, including calculation of a minimum energy pathway for a hydride transfer in a cobalt-based molecular catalyst using the nudged-elastic-band method at the CCSD-in-DFT level of theory, which reveals large differences from the transition state geometry predicted using DFT.

physics.chem-ph↗

arXiv2019

Structure and efficiency in bacterial photosynthetic light-harvesting

Photosynthetic organisms use networks of chromophores to absorb sunlight and deliver the energy to reaction centres, where charge separation triggers a cascade of chemical steps to store the energy. We present a detailed model of the light-harvesting complexes in purple bacteria, including explicit interaction with sunlight; energy loss through radiative and non-radiative processes; and dephasing and thermalizing effects of coupling to a vibrational bath. An important feature of the model is that we capture the effect of slow vibrational modes by introducing time-dependent disorder. Our model describes the experimentally observed high efficiency of light harvesting, despite the absence of long-range quantum coherence. The one-exciton part of the quantum state fluctuates due to slow vibrational changes, but remains highly mixed at all times. This lack of long-range coherence suggests a relatively minor role for structure in determining the efficiency of bacterial light harvesting. To investigate this we built hypothetical models with randomly arranged chromophores, but still observed high efficiency when typical nearest-neighbour distances are comparable with those found in nature. This helps to explain the efficiency of energy transport in organisms whose chromophore networks differ widely in structure, while also suggesting new design criteria for efficient artificial light-harvesting devices.

physics.bio-ph↗

arXiv2018

Even-handed subsystem selection in projection-based embedding

Projection-based embedding offers a simple framework for embedding correlated wavefunction methods in density functional theory. Partitioning between the correlated wavefunction and density functional subsystems is performed in the space of localized molecular orbitals. However, during a large geometry change--such as a chemical reaction--the nature of these localized molecular orbitals, as well as their partitioning into the two subsystems, can change dramatically. This can lead to unphysical cusps and even discontinuities in the potential energy surface. In this work, we present an even-handed framework for localized orbital partitioning that ensures consistent subsystems across a set of molecular geometries. We illustrate this problem and the even-handed solution with a simple example of an SN2 reaction. Applications to a nitrogen umbrella flip in a cobalt-based CO2 reduction catalyst and to the binding of CO to Cu clusters are presented. In both cases, we find that even-handed partitioning enables chemically accurate embedding with modestly-sized embedded regions for systems in which previous partitioning strategies are problematic.

physics.chem-ph↗

arXiv2013

The distinguishable cluster approximation

A new method that accurately describes strongly correlated states and captures dynamical correlation is presented. It is derived as a modification of coupled-cluster theory with single and double excitations (CCSD) through consideration of particle distinguishability between dissociated fragments, whilst retaining the key desirable properties of particle-hole symmetry, size extensivity, invariance to rotations within the occupied and virtual spaces, and exactness for two-electron subsystems. The resulting method called the distinguishable cluster approximation, smoothly dissociates difficult cases such as the nitrogen molecule, with the modest N^6 computational cost of CCSD. Even for molecules near their equilibrium geometries, the new model outperforms CCSD. It also accurately describes the massively correlated states encountered when dissociating hydrogen lattices, a proxy for the metal-insulator transition, and the fully dissociated system is treated exactly.

physics.chem-ph↗

arXiv2013

Machine learning for predictive condensed-phase simulation

We show how machine learning techniques based on Bayesian inference can be used to reach new levels of realism in the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density-functional theory (DFT) give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable corrections to DFT. The resulting corrected DFT scheme gives remarkably accurate predictions for the relative energies of small water clusters and of different ice structures, and greatly improves the description of the structure and dynamics of liquid water.

cond-mat.mtrl-sci↗

arXiv2012

Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes

Density functional theory (DFT) embedding provides a formally exact framework for interfacing correlated wave-function theory (WFT) methods with lower-level descriptions of electronic structure. Here, we report techniques to improve the accuracy and stability of WFT-in-DFT embedding calculations. In particular, we develop spin-dependent embedding potentials in both restricted and unrestricted orbital formulations to enable WFT-in-DFT embedding for open-shell systems, and we develop an orbital-occupation-freezing technique to improve the convergence of optimized effective potential (OEP) calculations that arise in the evaluation of the embedding potential. The new techniques are demonstrated in applications to the van-der-Waals-bound ethylene-propylene dimer and to the hexaaquairon(II) transition-metal cation. Calculation of the dissociation curve for the ethylene-propylene dimer reveals that WFT-in-DFT embedding reproduces full CCSD(T) energies to within 0.1 kcal/mol at all distances, eliminating errors in the dispersion interactions due to conventional exchange-correlation (XC) functionals while simultaneously avoiding errors due to subsystem partitioning across covalent bonds. Application of WFT-in-DFT embedding to the calculation of the low-spin/high-spin splitting energy in the hexaaquairon(II) cation reveals that the majority of the dependence on the DFT XC functional can be eliminated by treating only the single transition-metal atom at the WFT level; furthermore, these calculations demonstrate the substantial effects of open-shell contributions to the embedding potential, and they suggest that restricted open-shell WFT-in-DFT embedding provides better accuracy than unrestricted open-shell WFT-in-DFT embedding due to the removal of spin contamination.

physics.chem-ph↗

arXiv2010

Tensor factorizations of local second-order Møller Plesset theory

Efficient electronic structure methods can be built around efficient tensor representations of the wavefunction. Here we describe a general view of tensor factorization for the compact representation of electronic wavefunctions. We use these ideas to construct low-complexity representations of the doubles amplitudes in local second order Møller-Plesset perturbation theory. We introduce two approximations - the direct orbital specific virtual approximation and the full orbital specific virtual approximation. In these approximations, each occupied orbital is associated with a small set of correlating virtual orbitals. Conceptually, the representation lies between the projected atomic orbital representation in Pulay-Saebø local correlation theories and pair natural orbital correlation theories. We have tested the orbital specific virtual approximations on a variety of systems and properties including total energies, reaction energies, and potential energy curves. Compared to the Pulay-Saebø ansatz, we find that these approximations exhibit favourable accuracy and computational times, while yielding smooth potential energy curves.

physics.comp-ph↗