arXiv subjects

Heather J. Kulik

Publications and source records attributed to Heather J. Kulik.

At least 37 records · Page 2Linked to original sources

arXiv2022

Ligand additivity relationships enable efficient exploration of transition metal chemical space

To accelerate exploration of chemical space, it is necessary to identify the compounds that will provide the most additional information or value. A large-scale analysis of mononuclear octahedral transition metal complexes deposited in an experimental database confirms an under-representation of lower-symmetry complexes. From a set of around 1000 previously studied Fe(II) complexes, we show that the theoretical space of synthetically accessible complexes formed from the relatively small number of unique ligands is significantly (ca. 816k) larger. For the properties of these complexes, we validate the concept of ligand additivity by inferring heteroleptic properties from a stoichiometric combination of homoleptic complexes. An improved interpolation scheme that incorporates information about cis and trans isomer effects predicts the adiabatic spin-splitting energy to around 2 kcal/mol and the HOMO level to less than 0.2 eV. We demonstrate a multi-stage strategy to discover leads from the 816k Fe(II) complexes within a targeted property region. We carry out a coarse interpolation from homoleptic complexes that we refine over a subspace of ligands based on the likelihood of generating complexes with targeted properties. We validate our approach on 9 new binary and ternary complexes predicted to be in a targeted zone of discovery, suggesting opportunities for efficient transition metal complex discovery.

physics.chem-ph↗

arXiv2022

A Transferable Recommender Approach for Selecting the Best Density Functional Approximations in Chemical Discovery

Approximate density functional theory (DFT) has become indispensable owing to its cost-accuracy trade-off in comparison to more computationally demanding but accurate correlated wavefunction theory. To date, however, no single density functional approximation (DFA) with universal accuracy has been identified, leading to uncertainty in the quality of data generated from DFT. With electron density fitting and transfer learning, we build a DFA recommender that selects the DFA with the lowest expected error with respect to gold standard but cost-prohibitive coupled cluster theory in a system-specific manner. We demonstrate this recommender approach on vertical spin-splitting energy evaluation for challenging transition metal complexes. Our recommender predicts top-performing DFAs and yields excellent accuracy (ca. 2 kcal/mol) for chemical discovery, outperforming both individual transfer learning models and the single best functional in a set of 48 DFAs. We demonstrate the transferability of the DFA recommender to experimentally synthesized compounds with distinct chemistry.

physics.chem-ph↗

arXiv2022

Putting Density Functional Theory to the Test in Machine-Learning-Accelerated Materials Discovery

Accelerated discovery with machine learning (ML) has begun to provide the advances in efficiency needed to overcome the combinatorial challenge of computational materials design. Nevertheless, ML-accelerated discovery both inherits the biases of training data derived from density functional theory (DFT) and leads to many attempted calculations that are doomed to fail. Many compelling functional materials and catalytic processes involve strained chemical bonds, open-shell radicals and diradicals, or metal-organic bonds to open-shell transition-metal centers. Although promising targets, these materials present unique challenges for electronic structure methods and combinatorial challenges for their discovery. In this Perspective, we describe the advances needed in accuracy, efficiency, and approach beyond what is typical in conventional DFT-based ML workflows. These challenges have begun to be addressed through ML models trained to predict the results of multiple methods or the differences between them, enabling quantitative sensitivity analysis. For DFT to be trusted for a given data point in a high-throughput screen, it must pass a series of tests. ML models that predict the likelihood of calculation success and detect the presence of strong correlation will enable rapid diagnoses and adaptation strategies. These "decision engines" represent the first steps toward autonomous workflows that avoid the need for expert determination of the robustness of DFT-based materials discoveries.

cond-mat.mtrl-sci↗

arXiv2022

Exploiting Ligand Additivity for Transferable Machine Learning of Multireference Character Across Known Transition Metal Complex Ligands

Accurate virtual high-throughput screening (VHTS) of transition metal complexes (TMCs) remains challenging due to the possibility of high multi-reference (MR) character that complicates property evaluation. We compute MR diagnostics for over 5,000 ligands present in previously synthesized transition metal complexes in the Cambridge Structural Database (CSD). To accomplish this task, we introduce an iterative approach for consistent ligand charge assignment for ligands in the CSD. Across this set, we observe that MR character correlates linearly with the inverse value of the averaged bond order over all bonds in the molecule. We then demonstrate that ligand additivity of MR character holds in TMCs, which suggests that the TMC MR character can be inferred from the sum of the MR character of the ligands. Encouraged by this observation, we leverage ligand additivity and develop a ligand-derived machine learning representation to train neural networks to predict the MR character of TMCs from properties of the constituent ligands. This approach yields models with excellent performance and superior transferability to unseen ligand chemistry and compositions.

cond-mat.mtrl-sci↗

arXiv2022

Ligand Additivity and Divergent Trends in Two Types of Delocalization Errors from Approximate Density Functional Theory

Despite its widespread use, the predictive accuracy of density functional theory (DFT) is hampered by delocalization errors, especially for correlated systems such as transition-metal complexes. Two complementary tuning strategies have been developed to reduce delocalization error: eliminating the global curvature with respect to charge addition or removal, and computing a linear response Hubbard U as a measure of local curvature at the metal center at fixed charge and applying it to the transition-metal complex in a DFT+U framework. We investigate the relationship between the two measures of delocalization error as we manipulate the ligand field strength by varying the number of strong-field ligands in a series of heteroleptic complexes or by geometrically constraining the metal-ligand bond length in homoleptic octahedral complexes. We show that across these sets of complexes with varying ligand fields, an inverse relationship generally exists between global and local curvatures. We find that effects of ligand substitution on both measures of delocalization are typically additive, but the two quantities seldom coincide. The observation of ligand additivity suggests opportunities for evaluating errors on homoleptic complexes to infer corrections for lower-symmetry complexes.

cond-mat.mtrl-sci↗

arXiv2022

Machine learning models predict calculation outcomes with the transferability necessary for computational catalysis

Virtual high throughput screening (VHTS) and machine learning (ML) have greatly accelerated the design of single-site transition-metal catalysts. VHTS of catalysts, however, is often accompanied with high calculation failure rate and wasted computational resources due to the difficulty of simultaneously converging all mechanistically relevant reactive intermediates to expected geometries and electronic states. We demonstrate a dynamic classifier approach, i.e., a convolutional neural network that monitors geometry optimization on the fly, and exploit its good performance and transferability for catalyst design. We show that the dynamic classifier performs well on all reactive intermediates in the representative catalytic cycle of the radical rebound mechanism for methane-to-methanol despite being trained on only one reactive intermediate. The dynamic classifier also generalizes to chemically distinct intermediates and metal centers absent from the training data without loss of accuracy or model confidence. We rationalize this superior model transferability to the use of on-the-fly electronic structure and geometric information generated from density functional theory calculations and the convolutional layer in the dynamic classifier. Combined with model uncertainty quantification, the dynamic classifier saves more than half of the computational resources that would have been wasted on unsuccessful calculations for all reactive intermediates being considered.

physics.chem-ph↗

arXiv2022

Two Wrongs Can Make a Right: A Transfer Learning Approach for Chemical Discovery with Chemical Accuracy

Appropriately identifying and treating molecules and materials with significant multi-reference (MR) character is crucial for achieving high data fidelity in virtual high throughput screening (VHTS). Nevertheless, most VHTS is carried out with approximate density functional theory (DFT) using a single functional. Despite development of numerous MR diagnostics, the extent to which a single value of such a diagnostic indicates MR effect on chemical property prediction is not well established. We evaluate MR diagnostics of over 10,000 transition metal complexes (TMCs) and compare to those in organic molecules. We reveal that only some MR diagnostics are transferable across these materials spaces. By studying the influence of MR character on chemical properties (i.e., MR effect) that involves multiple potential energy surfaces (i.e., adiabatic spin splitting, $ΔE_\mathrm{H-L}$, and ionization potential, IP), we observe that cancellation in MR effect outweighs accumulation. Differences in MR character are more important than the total degree of MR character in predicting MR effect in property prediction. Motivated by this observation, we build transfer learning models to directly predict CCSD(T)-level adiabatic $ΔE_\mathrm{H-L}$ and IP from lower levels of theory. By combining these models with uncertainty quantification and multi-level modeling, we introduce a multi-pronged strategy that accelerates data acquisition by at least a factor of three while achieving chemical accuracy (i.e., 1 kcal/mol) for robust VHTS.

physics.chem-ph↗

arXiv2021

Molecular orbital projectors in non-empirical jmDFT recover exact conditions in transition metal chemistry

Low-cost, non-empirical corrections to semi-local density functional theory are essential for accurately modeling transition metal chemistry. Here, we demonstrate the judiciously-modified density functional theory (jmDFT) approach with non-empirical U and J parameters obtained directly from frontier orbital energetics on a series of transition metal complexes. We curate a set of nine representative Ti(III) and V(IV) $d^1$ transition metal complexes and evaluate their flat plane errors along the fractional spin and charge lines. We demonstrate that while jmDFT improves upon both DFT+U and semi-local DFT with the standard atomic orbital projectors (AOPs), it does so inefficiently. We rationalize these inefficiencies by quantifying hybridization in the relevant frontier orbitals for both the case of fractional spins and fractional charges. To overcome these limitations, we introduce a procedure for computing a molecular orbital projector (MOP) basis for use with jmDFT. We demonstrate this single set of $d^1$ MOPs to be suitable for nearly eliminating all energetic delocalization error and static correlation error. In all cases, the MOP jmDFT outperforms AOP jmDFT, and it eliminates most flat plane errors at non-empirical values. Unlike widely employed DFT+U or hybrid functionals, jmDFT nearly eliminates energetic delocalization error and static correlation error within a non-empirical framework.

cond-mat.mtrl-sci↗

arXiv2021

Eliminating Delocalization Error to Improve Heterogeneous Catalysis Predictions with Molecular DFT+U

Approximate semi-local density functional theory (DFT) is known to underestimate surface formation energies yet paradoxically overbind adsorbates on catalytic transition-metal oxide surfaces due to delocalization error. The low-cost DFT+U approach only improves surface formation energies for early transition-metal oxides or adsorption energies for late transition-metal oxides. In this work, we demonstrate that this inefficacy arises due to the conventional usage of metal-centered atomic orbitals as projectors within DFT+U. We analyze electron density rearrangement during surface formation and O atom adsorption on rutile transition-metal oxides to highlight that a standard DFT+U correction fails to tune properties when the corresponding density rearrangement is highly delocalized across both metal and oxygen sites. To improve both surface properties simultaneously while retaining the simplicity of a single-site DFT+U correction, we systematically construct multi-atom-centered molecular-orbital-like projectors for DFT+U. We demonstrate this molecular DFT+U approach for tuning adsorption energies and surface formation energies of minimal two-dimensional models of representative early (i.e., TiO2) and late (i.e., PtO2) transition-metal oxides. Molecular DFT+U simultaneously corrects adsorption energies and surface formation energies of multi-layer models of rutile TiO2(110) and PtO2(110) to resolve the paradoxical description of surface stability and surface reactivity of semi-local DFT.

cond-mat.mtrl-sci↗

arXiv2021

Audacity of huge: overcoming challenges of data scarcity and data quality for machine learning in computational materials discovery

Machine learning (ML)-accelerated discovery requires large amounts of high-fidelity data to reveal predictive structure-property relationships. For many properties of interest in materials discovery, the challenging nature and high cost of data generation has resulted in a data landscape that is both scarcely populated and of dubious quality. Data-driven techniques starting to overcome these limitations include the use of consensus across functionals in density functional theory, the development of new functionals or accelerated electronic structure theories, and the detection of where computationally demanding methods are most necessary. When properties cannot be reliably simulated, large experimental data sets can be used to train ML models. In the absence of manual curation, increasingly sophisticated natural language processing and automated image analysis are making it possible to learn structure-property relationships from the literature. Models trained on these data sets will improve as they incorporate community feedback.

physics.chem-ph↗

arXiv2021

Deciphering Cryptic Behavior in Bimetallic Transition Metal Complexes with Machine Learning

The rational tailoring of transition metal complexes is necessary to address outstanding challenges in energy utilization and storage. Heterobimetallic transition metal complexes that exhibit metal-metal bonding in stacked "double decker" ligand structures are an emerging, attractive platform for catalysis, but their properties are challenging to predict prior to laborious synthetic efforts. We demonstrate an alternative, data-driven approach to uncovering structure-property relationships for rational bimetallic complex design. We tailor graph-based representations of the metal-local environment for these heterobimetallic complexes for use in training of multiple linear regression and kernel ridge regression (KRR) models. Focusing on oxidation potentials, we obtain a set of 28 experimentally characterized complexes to develop a multiple linear regression model. On this training set, we achieve good accuracy (mean absolute error, MAE, of 0.25 V) and preserve transferability to unseen experimental data with a new ligand structure. We trained a KRR model on a subset of 330 structurally characterized heterobimetallics to predict the degree of metal-metal bonding. This KRR model predicts relative metal-metal bond lengths in the test set to within 5%, and analysis of key features reveals the fundamental atomic contributions (e.g., the valence electron configuration) that most strongly influence the behavior of complexes. Our work provides guidance for rational bimetallic design, suggesting that properties including the formal shortness ratio should be transferable from one period to another.

cond-mat.mtrl-sci↗

arXiv2021

Mapping the Electronic Structure Origins of Surface- and Chemistry-Dependent Doping Trends in III-V Quantum Dots

Modifying the optoelectronic properties of nanostructured materials through introduction of dopant atoms has attracted intense interest. Nevertheless, the approaches employed are often trial and error, preventing rational design. We demonstrate the power of large-scale electronic structure calculations with density functional theory (DFT) to build an atlas of preferential dopant sites for a range of M(II) and M(III) dopants in the representative III-V InP magic sized cluster (MSC). We quantify the thermodynamic favorability of dopants, which we identify to be both specific to the sites within the MSC (i.e., interior vs surface) and to the nature of the dopant atom (i.e., smaller Ga(III) vs larger Y(III) or Sc(III)). These observations motivate development of maps of the most and least favorable doping sites, which are consistent with some known experimental expectations but also yield unexpected observations. For isovalent doping (i.e., Y(III)/Sc(III) or Ga(III), we observed stronger sensitivity of the predicted energetics to the type of ligand orientation on the surface than to the dopant type, but divergent behavior is observed for whether interior doping is favorable. For charge balancing with M(II) (i.e., Zn or Cd) dopants, we show that the type of ligand removed during the doping reaction is critical. We show that limited cooperativity with dopants up to moderate concentrations occurs, indicating rapid single-dopant estimations of favorability from DFT can efficiently guide rational design. Our work emphasizes the strong importance of ligand chemistry and surface heterogeneity in determining paths to favorable doping in quantum dots, an observation that will be general to other III-V and II-VI quantum dot systems generally synthesized with carboxylate ligands.

cond-mat.mtrl-sci↗

arXiv2021

Machine learning to tame divergent density functional approximations: a new path to consensus materials design principles

Computational virtual high-throughput screening (VHTS) with density functional theory (DFT) and machine-learning (ML)-acceleration is essential in rapid materials discovery. By necessity, efficient DFT-based workflows are carried out with a single density functional approximation (DFA). Nevertheless, properties evaluated with different DFAs can be expected to disagree for the cases with challenging electronic structure (e.g., open shell transition metal complexes, TMCs) for which rapid screening is most needed and accurate benchmarks are often unavailable. To quantify the effect of DFA bias, we introduce an approach to rapidly obtain property predictions from 23 representative DFAs spanning multiple families and "rungs" (e.g., semi-local to double hybrid) and basis sets on over 2,000 TMCs. Although computed properties (e.g., spin-state ordering and frontier orbital gap) naturally differ by DFA, high linear correlations persist across all DFAs. We train independent ML models for each DFA and observe convergent trends in feature importance; these features thus provide DFA-invariant, universal design rules. We devise a strategy to train ML models informed by all 23 DFAs and use them to predict properties (e.g., spin-splitting energy) of over 182k TMCs. By requiring consensus of the ANN-predicted DFA properties, we improve correspondence of these computational lead compounds with literature-mined, experimental compounds over the single-DFA approach typically employed. Both feature analysis and consensus-based ML provide efficient, alternative paths to overcome accuracy limitations of practical DFT.

cond-mat.mtrl-sci↗

arXiv2021

Using Machine Learning and Data Mining to Leverage Community Knowledge for the Engineering of Stable Metal-Organic Frameworks

Although the tailored metal active sites and porous architectures of MOFs hold great promise for engineering challenges ranging from gas separations to catalysis, a lack of understanding of how to improve their stability limits their use in practice. To overcome this limitation, we extract thousands of published reports of the key aspects of MOF stability necessary for their practical application: the ability to withstand high temperatures without degrading and the capacity to be activated by removal of solvent molecules. From nearly 4,000 manuscripts, we use natural language processing and automated image analysis to obtain over 2,000 solvent-removal stability measures and 3,000 thermal degradation temperatures. We analyze the relationships between stability properties and the chemical and geometric structures in this set to identify limits of prior heuristics derived from smaller sets of MOFs. By training predictive machine learning (ML, i.e., Gaussian process and artificial neural network) models to encode the structure-property relationships with graph- and pore-structure-based representations, we are able to make predictions of stability orders of magnitude faster than conventional physics-based modeling or experiment. Interpretation of important features in ML models provides insights that we use to identify strategies to engineer increased stability into typically unstable 3d-containing MOFs that are frequently targeted for catalytic applications. We expect our approach to accelerate the time to discovery of stable, practical MOF materials for a wide range of applications.

cond-mat.mtrl-sci↗

arXiv2021

Representations and Strategies for Transferable Machine Learning Models in Chemical Discovery

Strategies for machine-learning(ML)-accelerated discovery that are general across materials composition spaces are essential, but demonstrations of ML have been primarily limited to narrow composition variations. By addressing the scarcity of data in promising regions of chemical space for challenging targets like open-shell transition-metal complexes, general representations and transferable ML models that leverage known relationships in existing data will accelerate discovery. Over a large set (ca. 1000) of isovalent transition-metal complexes, we quantify evident relationships for different properties (i.e., spin-splitting and ligand dissociation) between rows of the periodic table (i.e., 3d/4d metals and 2p/3p ligands). We demonstrate an extension to graph-based revised autocorrelation (RAC) representation (i.e., eRAC) that incorporates the effective nuclear charge alongside the nuclear charge heuristic that otherwise overestimates dissimilarity of isovalent complexes. To address the common challenge of discovery in a new space where data is limited, we introduce a transfer learning approach in which we seed models trained on a large amount of data from one row of the periodic table with a small number of data points from the additional row. We demonstrate the synergistic value of the eRACs alongside this transfer learning strategy to consistently improve model performance. Analysis of these models highlights how the approach succeeds by reordering the distances between complexes to be more consistent with the periodic table, a property we expect to be broadly useful for other materials domains.

physics.chem-ph↗

arXiv2021

Harder, better, faster, stronger: large-scale QM and QM/MM for predictive modeling in enzymes and proteins

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Trade-offs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multi-scale QM/MM or iterative approach. Limitations to both conventional density functional theory (DFT) and classical MM force fields remain for describing non-covalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e., electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.

physics.chem-ph↗

arXiv2021

An Irreversible Synthetic Route to an Ultra-Strong Two-Dimensional Polymer

Polymers that extend covalently in two dimensions have attracted recent attention as a means of combining the mechanical strength and in-plane energy conduction of conventional two-dimensional (2D) materials with the low densities, synthetic processability, and organic composition of their one-dimensional counterparts. Efforts to date have proven successful in forms that do not allow full realization of these properties, such as polymerization at flat interfaces or fixation of monomers in immobilized lattices. A frequently employed synthetic approach is to introduce microscopic reversibility, at the cost of bond stability, to achieve 2D crystals after extensive error correction. Herein we demonstrate a synthetic route to 2D irreversible polycondensation directly in the solution phase, resulting in covalently bonded 2D polymer platelets that are chemically stable and highly processable. Further fabrication offers highly oriented, free-standing films which exhibit exceptional 2D elastic modulus and yield strength at 50.9 +- 15.0 GPa and 0.976 +- 0.113 GPa, respectively. Platelet alignment is evidenced by polarized photoluminescence centered at 580 and 680 nm from different dipole transitions. This new synthetic route provides opportunities for 2D polymers in applications ranging from composite structures to molecular sieving membranes.

cond-mat.soft↗

arXiv2021

Molecular DFT+U: A Transferable, Low-Cost Approach to Eliminate Delocalization Error

While density functional theory (DFT) is widely applied for its combination of cost and accuracy, corrections (e.g., DFT+U) that improve it are often needed to tackle correlated transition-metal chemistry. In principle, the functional form of DFT+U, consisting of a set of localized atomic orbitals (AO) and a quadratic energy penalty for deviation from integer occupations of those AOs, enables the recovery of the exact conditions of piecewise linearity and the derivative discontinuity. Nevertheless, for practical transition-metal complexes, where both atomic states and ligand orbitals participate in bonding, standard DFT+U can fail to eliminate delocalization error (DE). Here, we show that by introducing an alternative valence-state (i.e., molecular orbital or MO) basis to the DFT+U approach, we recover exact conditions in cases where standard DFT+U corrections have no error-reducing effect. This MO-based DFT+U also eliminates DE where standard AO-based DFT+U is already successful. We demonstrate the transferability of our approach on a range of ligand field strengths (i.e., from H_2O to CO), electron configurations (i.e., from Sc to Fe to Zn), and spin states (i.e., low-spin and high-spin) in representative transition-metal complexes.

physics.chem-ph↗