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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller–Plesset perturbation method

Here, using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller–Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ~0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2000

Laboratory Astrophysics: The Universe in the Palm of Your Hand

Polycyclic aromatic compounds (PACs), a class of organic molecules whose structures are characterized by the presence of two or more fused aromatic rings, have been the subject of astrophysical interest for nearly two decades. Large by interstellar standards (from as few as 20 to perhaps as many as several hundred atoms), it has been suggested that these species are among the most abundant interstellar molecules impacting a wide range of astrophysical phenomena including: (1) the ubiquitous family of infrared emission bands observed in an ever-increasing assortment of astronomical objects; (2) the subtle but rich array of discrete visible/near-infrared interstellar molecular absorption features known as the diffuse interstellar bands (DIBs); (3) the broad near-infrared quasi-continuum observed in a number of nebulae known as excess red emission (ERE); (4) the interstellar ultraviolet extinction curve and broad '2200 Angstrom bump'; and (5) the heating/cooling mechanisms of interstellar clouds. Nevertheless, until recently a lack of good-quality laboratory spectroscopic data on PACs under astrophysically relevant conditions (i.e. isolated, ionized molecules, ionized molecular clusters, etc.) has hindered critical evaluation and extension of this model. Fortunately, the last decade has seen an explosion of experimental and theoretical techniques aimed specifically at addressing these issues. Indeed, many of these techniques will be explored in the series of talks which constitute this forum. This talk will provide an overview of the studies of the spectroscopic properties of isolated, neutral, and ionized PACs that have been conducted in the Astrochemistry Laboratory at NASA Ames, together with a consideration of their implications for astrophysics. Particular attention will be paid to models of the interstellar infrared emission spectra generated using the available database of laboratory PAC infrared spectra and the natural ability of this database to accommodate the variations observed in the astronomical spectra. Such models provide insight into the structure, abundance, and ionization state of the interstellar PAC population and, in turn, provide direct insight into the processes of carbon nucleation, growth and evolution as matter is processed through the interstellar medium. These models will be followed by a more in depth look at some specific aspects of the interstellar infrared emission spectrum, considering both what we can learn about them and what we can learn from them. Finally, some of the limitations of the current model and the available spectroscopic dataset will be 'dered along with future experimental directions designed to address these shortcomings. Further information about this and the related areas of research currently ongoing in the Astrochemistry Laboratory can be found at our world wide web site. http://www-space.arc.nasa.gov/(tilda)astrochem

Hudgins, Douglas M.↗
NASA NTRS2001

NATO Advanced Study Institute on Spectroscopy

This booklet presents an account of the course 'Spectroscopy of Systems with Spatially Confined Structures' held in Erice-Sicily, Italy, from June 15 to June 30, 2001. This meeting was organized by the International School of Atomic and Molecular Spectroscopy of the 'Ettore Majorana' Centre for Scientific Culture. The purpose of this course was to present and discuss nanometer-scale physics, a rapidly progressing field. The top-down approach of semiconductor technology will soon meet the scales of the bottom-up approaches of supramolecular chemistry and of spatially localized excitations in ionic crystals. This course dealt with the fabrication, measurement and understanding of the relevant structures and brought together the scientific communities responsible for these development. The advances in this area of physics have already let to applications in optoelectronics and will likely lead to many more. The subjects of the course included spatially resolved structures such as quantum wells, quantum wires and quantum dots, single atoms and molecules, clusters, fractal systems, and the development of related techniques like near-field spectroscopy and confocal microscopy to study such systems.

DiBartolo, Baldassare↗
DOE OSTI2022

A combined theoretical and experimental study of small anthracene–water clusters

Water-cluster interactions with polycyclic aromatic hydrocarbons (PAHs) are of paramount interest in many chemical and biological processes. Here we report a study of anthracene monomers and dimers with water (up to four)-cluster systems utilizing molecular beam vacuum-UV photoionization mass spectrometry and density functional calculations. Structural loss in photoionization efficiency curves when adding water indicates that various isomers are generated, while theory indicates only a slight shift in energy in photoionization states of different isomers. Calculations reveal that the energetic tendency of water is to remain clustered and not to disperse around the PAH. Theoretically, we observe water confinement exclusively in the case of four water clusters and only when the anthracenes are in a cross configuration due to optimal OH∙∙∙π interactions, indicating dependence on the size and structure of the PAH. Furthermore theory sheds light on the structural changes that occur in water upon ionization of anthracene, due to the optimal interactions of the resulting hole and water hydrogen atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Theoretical research program to study chemical reactions in AOTV bow shock tubes

The main focus was the development, implementation, and calibration of methods for performing molecular electronic structure calculations to high accuracy. These various methods were then applied to a number of chemical reactions and species of interest to NASA, notably in the area of combustion chemistry. Among the development work undertaken was a collaborative effort to develop a program to efficiently predict molecular structures and vibrational frequencies using energy derivatives. Another major development effort involved the design of new atomic basis sets for use in chemical studies: these sets were considerably more accurate than those previously in use. Much effort was also devoted to calibrating methods for computing accurate molecular wave functions, including the first reliable calibrations for realistic molecules using full CI results. A wide variety of application calculations were undertaken. One area of interest was the spectroscopy and thermochemistry of small molecules, including establishing small molecule binding energies to an accuracy rivaling, or even on occasion surpassing, the experiment. Such binding energies are essential input to modeling chemical reaction processes, such as combustion. Studies of large molecules and processes important in both hydrogen and hydrocarbon combustion chemistry were also carried out. Finally, some effort was devoted to the structure and spectroscopy of small metal clusters, with applications to materials science problems.

Taylor, Peter R.↗
DOE OSTI2026

Redox Potentials for Hydrogen Species in Acetonitrile and Tetrahydrofuran

The properties of the fundamental hydrogen species, proton (H+), hydrogen atom (H•), and hydride anion (H-) are critical to a vast range of chemical processes, yet their thermodynamic properties in nonaqueous solvents are not well established. A hybrid supermolecule-continuum approach is used to predict the Gibbs free energies of solvation (?G°solv) and standard redox potentials (E°) for the 2H+/H2 and H•/H- couples in acetonitrile (MeCN) and tetrahydrofuran (THF) following the approach previously used for water. Gas phase geometry optimizations were done using density functional theory (DFT) with the ?B97XD functional, Møller-Plesset second-order perturbation theory (MP2) with augmented correlation-consistent basis sets and composite-correlated molecular orbital theory (G3MP2 and G3MP2B3). Additional single point calculations in gas phase were performed for H- affinity for MeCN and THF at the coupled cluster CCSD(T) level using MP2 geometries. Solvation was included using the self-consistent reaction field SMD model. For H+, the ?G°solv values are predicted to be -252.2 kcal/mol in MeCN and -261.0 kcal/mol in THF. The redox potentials for the 2H+/H2 couple are +0.49 V in MeCN and +0.11 V in THF relative to the aqueous SHE, consistent with the available experimental data. The ?G°solv for H- is predicted to be -80 kcal/mol in MeCN and -68 in THF, and for H•, ?G°solv is predicted to be -1.3 kcal/mol in THF and -2.0 kcal/mol in MeCN. These solvation energies yield respective calculated redox potentials for the H•/H- couple of -0.14 V in MeCN and -0.68 V in THF relative to the aqueous SHE. H2 solvation is slightly exergonic in MeCN (-3.3 kcal/mol) and near thermoneutral in THF (+1.3 kcal/mol). The pKa(H2) is predicted to be 45.4 in MeCN and 47.8 in THF. The proton-coupled electron transfer (PCET) accounting term CG was evaluated giving values on the ferrocene scale within approximately 2 kcal/mol of literature in both solvents. These results provide benchmarks for hydrogen redox chemistry in MeCN and THF and improve consistency across E°, ?G°solv, pKa, and CG. These results provide benchmarks for hydrogen redox chemistry in nonaqueous media challenging previous estimates based on indirect extrapolations and assumptions.

Duda, Damian P.↗
NASA NTRS1995

A Coupled-Cluster Study of the Molecular Structure, Vibrational Spectrum, and Heats of Formation of XONO2 (X=H, F, Cl)

The equilibrium structures, harmonic vibrational frequencies, dipole moments, and IR intensities of nitric acid, fluorine nitrate, and chlorine nitrate have been investigated by using the singles and doubles coupled cluster method that also includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). A standard triple-zeta double-polarized basis set was utilized. The equilibrium geometries and vibrational spectra of HONO2 and ClONO2 are shown to be in excellent agreement with the available experimental data. The ab initio vibrational spectrum of FONO2 is also shown to be in excellent agreement with experiment. Unlike the FOOF and FON molecules, but similar to the cis- and trans-FONO molecules, FONO2 is shown to possess normal bond distances. The bonding in FONO2 is shown to be more similar to that in ClONO2 than that in HONO2, although there are still significant differences, especially in the partial atomic charges as deduced from Mulliken populations. This causes FONO2 to possess almost no dipole moment, which is very different to both HONO2 and ClONO2. By using large atomic natural orbital basis sets, CCSD(T) energies are computed for four isodesmic reactions in order to determine an accurate heat of formation for FONO2. Our best estimate for DELTA H(raised circle) (sub f,298) is 3.1 plus or minus 2.0 kcal/mol, indicating that the F-ONO2 bond energy is 31.3 kcal/mol.

Lee, Timothy J.↗
DOE OSTI2020

Structural Rearrangements of Subnanometer Cu Oxide Clusters Govern Catalytic Oxidation

Sub-nanometer metal oxide clusters are very important materials that are widely used, for example, in catalysis or electronic devices such as sensors. Hence, it is critical to understand the atomic structures and properties of sub-nanometer metal oxide clusters under a reactive gas environment, such as O 2 . We consider here experimentally accessible precise-size Cu clusters (Cu 4 ) supported on partially hydroxylated amorphous alumina and show that such clusters can access, in catalytic conditions at high temperature under a pressure of O 2 , a large ensemble of oxidized structures, representing a large variety of oxygen content, of geometries in link with the support, and of catalytic activities for oxidation reactions, as seen from their reducibilities. A grand canonical basin hopping method based on first-principles energy reveals an ensemble of 24 configurations for the Cu 4 O x cluster of low free energy, less than 0.8 eV above the global minimum. The low free energy ensemble consists of clusters of different stoichiometries, which are mainly Cu 4 O 3 and Cu 4 O 4 in the temperature range of 200–400 °C and under a pressure of 0.5 bar of O 2 . The presence of several competitive isomers at each composition implies that cluster fluxionality impacts the phase diagram, which should be ensemble-averaged. In terms of catalytic oxidation activity, Cu 4 O 3 isomers present highly variable O abstraction energy: the most stable isomers are inactive for alkane oxidative dehydrogenation, but isomerization to metastable isomers, that proceed with low barrier, enable to create active configurations with low O abstraction energy. O atoms with the lowest anionic character, and thus of more electrophilic nature, present the best oxidation capability. In contrast, all Cu 4 O 4 isomers show a low O abstraction energy and a high potential catalytic activity. Here, this manuscript demonstrates the unique structural and electronic properties of sub-nano Cu oxide clusters and illustrates the critical roles of configuration ensembles and rearrangement to highly reactive metastable cluster isomers in nanocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Robust Tensor Hypercontraction of the Particle–Particle Ladder Term in Equation-of-Motion Coupled Cluster Theory

One method of representing a high-rank tensor as a (hyper-)product of lower-rank tensors is the tensor hypercontraction (THC) method of Hohenstein et al. This strategy has been found to be useful for reducing the polynomial scaling of coupled-cluster methods by representation of a four-dimensional tensor of electron-repulsion integrals in terms of five two-dimensional matrices. Pierce et al. have already shown that the application of a robust form of THC to the particle–particle ladder (PPL) term reduces the cost of this term in couple-cluster singles and doubles (CCSD) from O(N 6 ) to O(N 5 ) with negligible errors in energy with respect to the density-fitted variant. In this work, we have implemented the least-squares variant of THC (LS-THC) which does not require a nonlinear tensor factorization, including the robust form (R-LS-THC), for the calculation of the excitation and electron attachment energies using equation-of-motion coupled cluster methods EOMEE-CCSD and EOMEA-CCSD, respectively. We have benchmarked the effect of the R-LS-THC-PPL approximation on excitation energies using the comprehensive QUEST database and the accuracy of electron attachment energies using the NAB22 database. Here, we find that errors on the order of 1 meV are achievable with a reduction in total calculation time of approximately 5x.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Incorporating Electronic Information into Machine Learning Potential Energy Surfaces via Approaching the Ground-State Electronic Energy as a Function of Atom-Based Electronic Populations

Machine learning (ML) approximations to density functional theory (DFT) potential energy surfaces (PESs) are showing great promise for reducing the computational cost of accurate molecular simulations, but at present, they are not applicable to varying electronic states, and in particular, they are not well suited for molecular systems in which the local electronic structure is sensitive to the medium to long-range electronic environment. With this issue as the focal point, we present a new machine learning approach called "BpopNN" for obtaining efficient approximations to DFT PESs. Conceptually, the methodology is based on approaching the true DFT energy as a function of electron populations on atoms; in practice, this is realized with available density functionals and constrained DFT (CDFT). Additionally, the new approach creates approximations to this function with neural networks. These approximations thereby incorporate electronic information naturally into a ML approach, and optimizing the model energy with respect to populations allows the electronic terms to self-consistently adapt to the environment, as in DFT. We confirm the effectiveness of this approach with a variety of calculations on LinHn clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A molecular ground electronic state with an occupied 5g spinor—The superheavy (E125)F molecule

Fully relativistic calculations, primarily at the 4-component coupled-cluster singles and doubles with perturbative triples [CCSD(T)] level of theory with the Dirac–Coulomb (DC) Hamiltonian, have been carried out for the superheavy (E125)F molecule using large Gaussian basis sets. The electronic ground state is determined to have an [Og]8s 2 5g 1 6f 3 configuration on E125 with an Ω = 6 ground state and an 8p electron largely donated to F. A Mulliken population analysis indicates that the ground state is mainly ionic with a partial charge of +0.79 on E125 and a single sigma bond involving the F 2p and E125 8p spinors. The occupied g spinor is not involved in the bonding. With the largest basis set used in this work, the (0 K) dissociation energy was calculated at the DC-CCSD(T) level of theory to be 7.02 eV. Analogous calculations were also carried out for the E125 atom, both the neutral and its cation. The lowest energy electron configuration of E125 + , [Og]$8s$$^{2}_{1/2}$$5g$$^{1}_{7/2}$$6f$$^{3}_{5/2}$ with a J = 6 ground state, was found to be similar to that in (E125)F, while the neutral E125 atom has an [Og]$8s$$^{2}_{1/2}$$5g$$^{1}_{7/2}$$6f$$^{2}_{5/2}$$7d$$^{1}_{3/2}$$8p$$^{1}_{1/2}$ ground state electron configuration with a J = 17/2 ground state. The ionization energy (IE) of E125 is reported for the first time and is calculated to be 4.70 eV at the DC-CCSD(T) level of theory. Non-relativistic calculations were also carried out on the E125 atom and the (E125)F molecule. Here, the non-relativistic ground state of the E125 atom was calculated to have a 5g 5 ground state with an IE of just 3.4 eV. The net effect of relativity on (E125)F is to stabilize its bonding.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2025

Multiscale Physics of Atomic Nuclei from First Principles

Atomic nuclei exhibit multiple energy scales ranging from hundreds of MeV in binding energies to fractions of an MeV for low-lying collective excitations. As the limits of nuclear binding are approached near the neutron and proton drip lines, traditional shell structure starts to melt with an onset of deformation and an emergence of coexisting shapes. It is a long-standing challenge to describe this multiscale physics starting from nuclear forces with roots in quantum chromodynamics. Here, we achieve this within a unified and nonperturbative quantum many-body framework that captures both short- and long-range correlations starting from modern nucleon-nucleon and three-nucleon forces from chiral effective field theory. The short-range (dynamic) correlations which account for the bulk of the binding energy are included within a symmetry-breaking framework, while long-range (static) correlations (and fine details about the collective structure) are included by employing symmetry projection techniques. Our calculations accurately reproduce—within theoretical error bars—available experimental data for low-lying collective states and the electromagnetic quadrupole transitions in 20−30 Ne. In addition, we reveal coexisting spherical and deformed shapes in 30 Ne, which indicates the breakdown of the magic neutron number 𝑁 = 20 as the key nucleus 28 O is approached, and we predict that the drip line nuclei 32,34 Ne are strongly deformed and collective. By developing reduced-order models for symmetry-projected states, we perform a global sensitivity analysis and find that the subleading singlet 𝑆-wave contact and a pion-nucleon coupling strongly impact nuclear deformation in chiral effective field theory. The techniques developed in this work clarify how microscopic nuclear forces generate the multiscale physics of nuclei spanning collective phenomena as well as short-range correlations and allow one to capture emergent and dynamical phenomena in finite fermion systems such as atom clusters, molecules, and atomic nuclei.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

How good are polarizable and flexible models for water: Insights from a many-body perspective

We present a systematic analysis of state-of-the-art polarizable and flexible water models from a many-body perspective, with a specific focus on their ability to represent the Born–Oppenheimer potential energy surface of water from the gas to the liquid phase. Using coupled cluster data in the completed basis set limit as a reference, we examine the accuracy of the polarizable models in reproducing individual many-body contributions to interaction energies and harmonic frequencies of water clusters and compare their performance with that of MB-pol, an explicit many-body model that has been shown to correctly predict the properties of water across the entire phase diagram. Based on these comparisons, we use MB-pol as a reference to analyze the ability of the polarizable models to reproduce the energy landscape of liquid water under ambient conditions. We find that, while correctly reproducing the energetics of minimum-energy structures, the polarizable models examined in this study suffer from inadequate representations of many-body effects for distorted configurations. To investigate the role played by geometry-dependent representations of 1-body charge distributions in reproducing coupled cluster data for both interaction and many-body energies, we introduce a simplified version of MB-pol that adopts fixed atomic charges and demonstrate that the new model retains the same accuracy as the original MB-pol model. Based on the analyses presented in this study, we believe that future developments of both polarizable and explicit many-body models should continue in parallel and would benefit from synergistic efforts aimed at integrating the best aspects of the two theoretical/computational frameworks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The Rise of Neural Networks for Materials and Chemical Dynamics

Machine learning (ML) is quickly becoming a premier tool for modeling chemical processes and materials. ML-based force fields, trained on large data sets of high-quality electron structure calculations, are particularly attractive due their unique combination of computational efficiency and physical accuracy. This Perspective summarizes some recent advances in the development of neural network-based interatomic potentials. Designing high-quality training data sets is crucial to overall model accuracy. One strategy is active learning, in which new data are automatically collected for atomic configurations that produce large ML uncertainties. Another strategy is to use the highest levels of quantum theory possible. Transfer learning allows training to a data set of mixed fidelity. A model initially trained to a large data set of density functional theory calculations can be significantly improved by retraining to a relatively small data set of expensive coupled cluster theory calculations. These advances are exemplified by applications to molecules and materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Determining the three-dimensional atomic structure of an amorphous solid

Amorphous solids such as glass, plastics and amorphous thin films are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells 1-4 . However, owing to the lack of long-range order, the three-dimensional (3D) atomic structure of amorphous solids has so far eluded direct experimental determination 5-15 . Here we develop an atomic electron tomography reconstruction method to experimentally determine the 3D atomic positions of an amorphous solid. Using a multi-component glass-forming alloy as proof of principle, we quantitatively characterize the short- and medium-range order of the 3D atomic arrangement. We observe that, although the 3D atomic packing of the short-range order is geometrically disordered, some short-range-order structures connect with each other to form crystal-like superclusters and give rise to medium-range order. We identify four types of crystal-like medium-range order-face-centred cubic, hexagonal close-packed, body-centred cubic and simple cubic-coexisting in the amorphous sample, showing translational but not orientational order. These observations provide direct experimental evidence to support the general framework of the efficient cluster packing model for metallic glasses 10,12-14,16 . Finally, we expect that this work will pave the way for the determination of the 3D structure of a wide range of amorphous solids, which could transform our fundamental understanding of non-crystalline materials and related phenomena.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Exploring the Role of Inorganic and Organic Interfaces on CO 2 and CH 4 Partitioning: Case Study of Silica, Illite, Calcite, and Kerogen Nanopores on Gas Adsorption and Nanoscale Transport Behaviors

The adsorption, partitioning, and diffusion of CO 2 and CH 4 in organic–inorganic pores composed of kerogen with silica, illite, or calcite are studied using density functional theory and classical molecular dynamics simulations. The adsorption and partitioning behavior of CO 2 and CH 4 molecules is found to be a function of chemistry of the solid interface, pore size, and surface area. CO 2 molecules are preferentially adsorbed compared to CH 4 molecules on silica, illite, calcite, and kerogen surfaces due to significant contributions of electrostatic interactions with the atoms of the associated surfaces. CO 2 and CH 4 molecules display higher adsorption energy on calcite and silica compared to those on illite and kerogen because of enhanced interactions with the positively charged calcium ions on the calcite surface and the hydroxyl group (-OH) on the silica surface. Enhanced internal nanopores and the availability of adsorption active sites in illite and kerogen matrices aid in higher partitioning of the gas molecules into these pores. CO 2 has a significant influence on the clustering and swelling of kerogen fragments compared to CH 4 . Higher CO 2 adsorption on inorganic and kerogen surfaces results in lower overall self-diffusivities compared to CH 4 . This study illustrates surface and pore size controls on the adsorption, partitioning, and self-diffusivities of CO 2 and CH 4 at conditions relevant for subsurface energy applications. The chemistry of the surfaces along with the availability of internal pores and active adsorption sites influences the adsorption behavior of gases. Our results suggest that CO 2 stored in depleted gas reservoirs may preferentially inhabit nanoconfined pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗
DOE OSTI2022

Reticular chemistry for the rational design of mechanically robust mesoporous merged-net metal-organic frameworks

Access to metal-organic frameworks (MOFs) with enhanced mechanical stability is key to their successful deployment in practical applications. However, the high porosity of the material often affects mechanical stability. In this article, to achieve highly porous MOFs with enhanced mechanical stability, we explored the merged-net approach where two relatively fragile frameworks were merged into a robust MOF structure. We demonstrate the effectiveness of this approach by computationally evaluating mechanical properties of sph-MOFs with varying lengths of linkers. Prominently, we pinpoint the significance of triangular rigidity on the robustness of large-pore MOFs and, subsequently, designed and synthesized a rare earth (RE)-based RE-sph-MOF-5 by the reticulation of hexanuclear RE clusters, tritopic linkers, and unprecedentedly large planar hexatopic linkers containing 19 phenyl rings. The mechanical properties of sph-MOFs were characterized and quantified using amplitude-frequency modulation (AM-FM) bimodal atomic force microscopy (AFM) analyses. Markedly, the mesoporous RE-sph-MOF-5 expresses high mechanical stability despite its large mesoporous cavities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗