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Xantheas, Sotiris S.

Publications and source records attributed to Xantheas, Sotiris S..

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Importance of Electron Correlation on the Geometry and Electronic Structure of [2Fe–2S] Systems: A Benchmark Study of the [Fe 2 S 2 (SCH 3 ) 4 ] 2–,3–,4– , [Fe 2 S 2 (SCys) 4 ] 2– , [Fe 2 S 2 (S- p -tol) 4 ] 2– , and [Fe 2 S 2 (S- o -xyl) 4 ] 2– Complexes

Iron–sulfur clusters are crucial for biological electron transport and catalysis. Obtaining accurate geometries, energetics, manifolds of their excited electronic states, and reduction energies is important to understand their role in these processes. Here, using a [2Fe–2S] model complex with Fe II and Fe III oxidation states, which leads to different charges, i.e., [Fe 2 S 2 (SMe) 4 ] 2–,3–,4– , we benchmarked a variety of computational methodologies ranging from density functional theory (DFT) to post-Hartree–Fock methods, including complete active space self-consistent field (CASSCF), multireference configuration interaction, the second-order N-electron valence state perturbation theory (NEVPT2), and the linearized integrand approximation of adiabatic connection (AC0) approaches. Additionally, we studied three experimentally well-characterized complexes, [Fe 2 S 2 (SCys) 4 ] 2– , [Fe 2 S 2 (S-o-tol) 4 ] 2– , and [Fe 2 S 2 (S-o-xyl) 4 ] 2– , via DFT methods. We conclude that the dynamic electron correlation is important for accurately predicting the geometry of these complexes. Broken symmetry (BS) DFT correctly predicts experimental geometries of low-spin multiplicity, while CASSCF does not. However, BS-DFT significantly overestimates the difference between the low- and high-spin electronic states for a given oxidation state. At the same time, CASSCF underestimates it but provides relative energies closer to the reference NEVPT2 results. Finally, AC0 provides energetics of NEVPT2 quality with the additional advantage of being able to use large CASSCF sizes. NEVPT2 gives the best estimates of the Fe III /Fe III → Fe II /Fe III (4.27 eV) and Fe II /F III → Fe II /F II (7.72 eV) reduction energies. The results provide insight into the electronic structure of these complexes and assist in the understanding of their physical properties.

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

Electronic structure simulations in the cloud computing environment

The transformative impact of modern computational paradigms and technologies, such as high-performance computing, quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on the performance of various quantum chemical formulations, ranging from low-order methods to high-accuracy approaches, implemented in different computational chemistry packages, such as NWChem, NWChemEx, SPEC, ExaChem, and FLOSIC codes on the Azure Quantum Element (AQE) Microsoft cloud services. We pay particular attention to the intricate workflows for performing composite chemistry simulations, associated data curation, and mechanisms for accuracy assessment, as defined by the enabling cloud Computational Chemistry as a Service (CCaaS). Our focus also extends to Arrows' automated workflow for high throughput simulations. Finally, we provide a perspective on the role of cloud computing in supporting the mission of leadership computational facilities (LCFs).

computational chemistry, electronic structure, Clo↗
DOE OSTI2024

The Gas Phase Protonation Sites of Six Naturally Occurring Nicotinoids

We have determined the gas phase protonation sites of six naturally occurring nicotinoids, namely nicotine (NIC), nornicotine (NOR), anabasine (ANB), anatabine (ANT), cotinine (COT) and myosmine (MYO) from experimental cryogenic ion trap infrared spectroscopy and first principles electronic structure calculations. The structural motif of these compounds consists of a common Pyridine and a differing non-Pyridine rings. The protonation site on either of these two rings correlates with the nicotinoid’s biological activity (addiction). At room temperature NIC is a mixture of Pyridine and Pyrrolidine (non-Pyridene) protomers, NOR, ANB, ANT and COT are pure Pyridine protomers and finally MYO is mostly a Pyroline (non-Pyridine) protomer. Their biological activity (addiction) correlates with the protonation preference in the nonPyridine protomer, with the exception of MYO, which, although is protonated in the Pyroline (non-Pyridine) protomer, it is not addictive because of a conjugated p system that induces a flat structure that is not optimally interacting with the environment in the in the binding pocket of the human brain.

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

Affinity of Nicotinoids to a Model Nicotinic Acetylcholine Receptor (nAChR) Binding Pocket in the Human Brain

The binding affinity of nicotinoids to the binding residues of the a4ß2 variant of the nicotinic acetylcholine receptor (nAChR) was identified as a strong predictor of the nicotinoid’s addictive character. Using ab-iniito calculations for model binding pockets of increasing size comprising of 3, 6, and 14 amino acids (3AA, 6AA, and 14AA) that are derived from the crystal structure, the differences in binding affinity of 6 nicotinoids, namely nicotine (NIC), nornicotine (NOR), anabasine (ANB), anatabine (ANT), myosmine (MYO), and cotinine (COT) were correlated to their previously reported doses required for increases in intracranial self-stimulation (ICSS) thresholds, a metric for their addictive function. By employing the many body decomposition, the differences in the binding affinities of the various nicotinoids could be attributed mainly to the proton exchange energy between the Pyridine and non-Pyridine rings of the nicotinoids and the interactions between them and a handful of proximal amino acids, namely Trp156, Trpß57, Tyr100, and Tyr204. Interactions between the guest nicotinoid and the amino acids of the binding pocket were found to be mainly classical in nature, except for those between the nicotinoid and Trp156. The larger pockets were found to model binding structures more accurately and predicted the addictive character of all nicotinoids while smaller models, which are more computationally feasible, would only predict the addictive character of nicotinoids that are similar to nicotine. Here, the present study identifies the binding affinity of the guest nicotinoid to the host binding pocket as a strong descriptor of the nicotinoid’s addiction potential and as such it can be employed as a fast screening technique for the potential addiction of nicotine analogs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units

Atomic structure prediction and associated property calculations are the bedrock of chemical physics. Since high-fidelity ab initio modeling techniques for computing the structure and properties can be prohibitively expensive, this motivates the development of machine-learning (ML) models that make these predictions more efficiently. Training graph neural networks over large atomistic databases introduces unique computational challenges such as the need to process millions of small graphs with variable size and support communication patterns that are distinct from learning over large graphs such as social networks. We demonstrate a novel hardware-software co-design approach to scale up the training of atomistic graph neural networks (GNN) for structure and property prediction. First, to eliminate redundant computation and memory associated with alternative padding techniques and to improve throughput via minimizing communication, we formulate the effective coalescing of the batches of variable-size atomistic graphs as the bin packing problem and introduce a hardware-agnostic algorithm to pack these batches. In addition, we propose hardware-specific optimizations including a planner and vectorization for the gather-scatter operations targeted for Graphcore’s Intelligence Processing Unit (IPU), as well as model-specific optimizations such as merged communication collectives and optimized softplus. Putting these all together, we demonstrate the effectiveness of the proposed co-design approach by providing an implementation of a well-established atomistic GNN on the Graphcore IPUs. We evaluate the training performance on multiple atomistic graph databases with varying degrees of graph counts, sizes and sparsity. Here, we demonstrate that such a co-design approach can reduce the training time of atomistic GNNs and can improve the performance by up to 1.5× compared to the baseline implementation of the model on the IPUs. Additionally, we compare our IPU implementation with a Nvidia GPU-based implementation and show that our atomistic GNN implementation on the IPUs can run 1.8× faster on average compared to the execution time on the GPUs.

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

Descriptors of water aggregation

For this work, we rely on a total of 23 (cluster size, 8 structural, and 14 connectivity) descriptors to investigate structural patterns and connectivity motifs associated with water cluster aggregation. In addition to the cluster size n (number of molecules), the 8 structural descriptors can be further categorized into (i) one-body (intramolecular): covalent OH bond length (r OH ) and HOH bond angle (θ HOH ), (ii) two-body: OO distance (r OO ), OHO angle (θ OHO ), and HOOX dihedral angle ($\phi$ HOOX ), where X lies on the bisector of the HOH angle, (iii) three-body: OOO angle (θ OOO ), and (iv) many-body: modified tetrahedral order parameter (q) to account for two-, three-, four-, five-coordinated molecules (q m , m = 2, 3, 4, 5) and radius of gyration (R g ). The 14 connectivity descriptors are all many-body in nature and consist of the AD, AAD, ADD, AADD, AAAD, AAADD adjacencies [number of hydrogen bonds accepted (A) and donated (D) by each water molecule], Wiener index, Average Shortest Path Length, hydrogen bond saturation (% HB), and number of non-short-circuited three-membered cycles, four-membered cycles, five-membered cycles, six-membered cycles, and seven-membered cycles. We mined a previously reported database of 4 948 959 water cluster minima for (H 2 O) n , n = 3–25 to analyze the evolution and correlation of these descriptors for the clusters within 5 kcal/mol of the putative minima. It was found that r OH and % HB correlated strongly with cluster size n, which was identified as the strongest predictor of energetic stability. Marked changes in the adjacencies and cycle count were observed, lending insight into changes in the hydrogen bond network upon aggregation. A Principal Component Analysis (PCA) was employed to identify descriptor dependencies and group clusters into specific structural patterns across different cluster sizes. The results of this study inform our understanding of how water clusters evolve in size and what appropriate descriptors of their structural and connectivity patterns are with respect to system size, stability, and similarity. The approach described in this study is general and can be easily extended to other hydrogen-bonded systems.

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

Erratum: “Breaking covalent bonds in the context of the many-body expansion (MBE). I. The purported ‘first row anomaly’ in XH n (X = C, Si, Ge, Sn; n = 1–4)” [J. Chem. Phys. 156, 244303 (2022)]

We have noted typographical errors in TABLE V of J. Chem. Phys. 156, 244303 (2022). Specifically, the values of the angles φ HχH for the XH 2 species in both the ( 3 B 1 ) and ( 1 A 1 ) states were incorrectly reported as half of the correct values. Additionally, the values of the same angles for the XH 3 and XH 4 species were reported correctly.

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

Switching of Protonation Sites in Hydrated Nicotine via a Grotthuss Mechanism

The switching of the protonation sites in hydrated nicotine, probed by experimental infrared (IR) spectroscopy and theoretical ab initio calculations, is facilitated via a Grotthuss instead of a bimolecular proton transfer (vehicle) mechanism at the experimental temperature (T = 130 K) as unambiguously confirmed by experiments with deuterated water. In contrast, the bimolecular vehicle mechanism is preferred at higher temperatures (T = 300 K) as determined by theory. Further, the Grotthuss mechanism for the concerted proton transfer results in the production of nicotine’s bioactive and addictive pyrrolidine-protonated (Pyrro-H + ) protomer with just 5 water molecules. Theoretical analysis suggests that the concerted proton transfer occurs via hydrogen-bonded bridges consisting of a 3 water molecule “core” that connects the pyridine protonated (Pyri-H + ) with the pyrrolidine-protonated (Pyrro-H + ) protomers. Additional water molecules attached as acceptors to the hydrogen-bonded “core” bridge result in lowering the reaction barrier of the concerted proton transfer down to less than 6 kcal/mol, which is consistent with the experimental observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Accurate calculation of many-body energies in water clusters using a classical geometry-dependent induction model

We incorporate geometry-dependent distributed multipole and polarizability surfaces into an induction model that is used to describe the 3- and 4-body terms of the interaction between water molecules. The expansion is carried out up to hexadecapole with the multipoles distributed on the atom sites. Dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole distributed polarizabilities are used to represent the response of the multipoles to an electric field. We compare the model against two large databases consisting of 43,844 3-body terms and 3,603 4-body terms obtained from high level ab initio calculations previously used to fit the MB-pol and q-AQUA interaction potentials. The classical induction model with no adjustable parameters reproduces the ab-initio 3- and 4-body terms contained in these teo Databases with a Root-Mean-Square-Error (RMSE) of 0.104/0.058 and a Mean-Absolute-Error (MAE) of 0.054/0.026 kcal/mol, respectively, results that are on a par with those obtained 1 by fitting the same data using tens of thousands of Permutationally Invariant Polynomials (PIPs). This demonstrates the accuracy of this physically motivated model in describing the 3- and 4-body terms in the interactions between water molecules with no adjustable parameters. The triple-dipole-dispersion energy was included in the 3-body energy and was found to be small but not quite negligible. The model represents a practical, efficient and transferable approach for obtaining accurate non-additive interactions for multi-component systems without the need of performing tens of thousands of high level electronic structure calculations and fitting them with tens of thousands of PIPs.

molecular analysis water, aqueous↗
DOE OSTI2023

A Perspective on Sustainable Computational Chemistry Software Development and Integration

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Back Door to the Surface Hydrated Electron

We use a Mg + metal to extend the size regime of water clusters to extrapolate to the bulk limit of the Vertical Detachment Energy (VDE) of the solvated electron to >3,200, a value between one to over two orders of magnitude for clusters previously measured experimentally or computed theoretically. We relate the VDE to the energy difference between the Mg + (H 2 O) $n$ and Mg 2+ (H 2 O) $n$ systems and the metal’s second ionization potential. The extrapolated bulk VDEs of the localized surface electron, which moves away from the metal as n increases, are 1.89 ± 0.01 eV for semiempirical ($n$ ~ 3,200; PM6-D 3 H 4 ) and 1.73 ± 0.03 eV ($n$ ~ 150; HF), 1.83 ± 0.02 eV ($n$ ~ 150; MP2) for ab-initio, in excellent agreement with the 1.6 – 1.8 eV range of experimental results. In conclusion, the VDEs converge from above (larger values) to the bulk limit, in a manner qualitatively different than previous studies and experiments, a fact justifying the “back door” approach to the solvated electron.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Isotope Effects in the Zundel–Eigen Isomerization of H + (H 2 O) 6

The isomerization pathway between the energetically low-lying Zundel and Eigen isomers of the protonated water hexamer was investigated using high-level ab initio calculations including a treatment of zero-point corrections. On the basis of these calculations, the Zundel–Eigen isomerization was found to proceed through a stable intermediate isomer, which consists of a four-membered ring with two single acceptor water molecules. Further, the inclusion of vibrational zero-point energy is shown to be important for accurately establishing the relative energies of the three relevant isomers involved in the Zundel–Eigen isomerization. Diffusion Monte Carlo calculations including anharmonic vibrational effects show that all three isomers of H + (H 2 O) 6 and D + (D 2 O) 6 have well-defined structures. The energetic ordering of the three isomers changes upon deuteration. The implications of these results for the vibrational spectra of H + (H 2 O) 6 and D + (D 2 O) 6 are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development

Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born–Oppenheimer potential energy surface. In particular, we focus on ab initio–based force fields that aim to explicitly reproduce many-body terms and are fitted to high-level electronic structure results. These force fields generally incorporate many-body effects through ( a) parameterization of distributed multipoles, ( b) explicit fitting of the MBE, ( c) inclusion of many-atom features in a neural network, and ( d) coarse-graining of many-body terms into an effective two-body term. We also discuss the emerging use of the MBE to improve the accuracy and speed of ab initio molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Many-body expansion for light nuclear systems

Here we extend the many-body expansion (MBE), previously applied to hydrogen bonded and molecular systems, to the light nuclear systems 3 H and 3 He by considering the nucleonic degrees of freedom as fundamental in the expansion. The analysis is based on the Pauli nucleonic dynamics (PND) model, a simple antisymmetrized dynamical code, inspired by the sophisticated constrained molecular dynamics (CoMD) model. The total energy of the 2 H nucleus is calculated with this model at -2.312 MeV, which is within 4% of the experimental value of -2.225 MeV. The application of the MBE yields results for the three-body term in the 3 H nucleus that is comparable with previous estimates, while it is reported for the first time for the nucleus of 3 He . The energies of 3 H and 3 He that include the sum of the one- and two-body terms with the model are - 6.97 ± 0.21 MeV and - 6.19 ± 0.21 MeV and the three-body terms, estimated from the difference of the sum of the one- and two-body terms from the experimentally measured energies, are -1.51 ± 0.21 MeV and -1.53 ± 0.21 MeV, respectively. The MBE for the 3 H and 3 He nuclei is qualitatively similar to the one previously reported for the water trimer: the two- and three-body terms are negative with the latter amounting to ~3% of the former. Additionally, the three-body terms correspond to about 16–23% of the total energy of the bound systems, a percentage that is also comparable to the one in the water trimer (17%). In this manner, the MBE analysis can be applied to light nuclear systems following the same protocol as the one that has been previously extensively used for hydrogen bonded molecular systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Helical Organic and Inorganic Polymers

Despite being a staple of synthetic plastics and biomolecules, helical polymers are scarcely studied with Gaussian-basis-set ab initio electron-correlated methods on an equal footing with molecules. This article introduces an ab initio second-order many-body Green’s-function [MBGF(2)] method with nondiagonal, frequency-dependent Dyson self-energy for infinite helical polymers using screw-axis-symmetry-adapted Gaussian-spherical-harmonics basis functions. Together with the Gaussian-basis-set density-functional theory for energies, analytical atomic forces, translational-period force, and helical-angle force, it can compute correlated energy, quasiparticle energy bands, structures, and vibrational frequencies of an infinite helical polymer, which smoothly converge at the corresponding oligomer results. These methods can handle incommensurable structures, which have an infinite translational period and are hard to characterize by any other method, just as efficiently as commensurable structures. We apply them to polyethylene (2/1 helix), polyacetylene (Peierls’ system), and polytetrafluoroethylene (13/6 helix) to establish the quantitative accuracy of MBGF(2)/cc-pVDZ in simulating their (angle-resolved) ultraviolet photoelectron spectra, and of B3LYP/cc-pVDZ or 6-31G** in reproducing their structures, infrared and Raman band positions, phonon dispersions, and (coherent and incoherent) inelastic neutron scattering spectra. We then predict the same properties for infinitely catenated chains of nitrogen or oxygen and discuss their possible metastable existence under ambient conditions. They include planar zigzag polyazene (N2)x (Peierls’ system), 11/3-helical isotactic polyazane (NH)x, 9/4-helical isotactic polyfluoroazane (NF)x, and 7/2-helical polyoxane (O)x as potential high-energy-density materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The nature of the chemical bond

The nature of the chemical bond has long been a topic of much interest, beginning with the speculations of Isaac Newton about the “forces” that hold atoms together to the famous book by Linus Pauling with this title. For chemists, the existence of bonds between the atoms in a molecule is without question, but what are they, how can they be categorized, and what accounts for their existence? Furthermore, early theories focused on the attraction of electrical charges of opposite sign, which could account for the binding in many inorganic molecules. But what would account for the binding in electrically neutral organic molecules? Slightly more than a century ago, G. N. Lewis noted that the chemical bond appeared to be associated with electron pairs. Shortly after the discovery of the wave equation by Irwin Schrödinger in 1925-6, Heitler and London showed that quantum mechanics, in the form of what would eventually be called valence bond (VB) theory, accounted for the binding in that most improbable of molecules, the simple H 2 molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The primary gas phase hydration shell of hydroxide

The number of water molecules in hydroxide’s primary hydration shell has been long debated to be three from the interpretation of experimental data and four from theoretical studies. Here, we provide direct evidence for the presence of a fourth water molecule in hydroxide’s primary hydration shell from a combined study based on high-resolution cryogenic experimental photoelectron spectroscopy and high-level quantum chemical computations. Well-defined spectra of OH - (H 2 O) n clusters (n = 2 to 5) yield accurate electron binding energies, which are, in turn, used as key signatures of the underlying molecular conformations. Although the smaller OH - (H 2 O) 3 and OH - (H 2 O) 4 clusters adopt close-lying conformations with similar electron binding energies that are hard to distinguish, the OH - (H 2 O) 5 cluster clearly has a predominant conformation with a four-coordinated hydroxide binding motif, a finding that unambiguously determines the gas phase coordination number of hydroxide to be four.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗