X-ray and Optical Circular Dichroism as Local and Global Ultrafast Chiral Probes of [12]Helicene Racemization.

Chirality is a fundamental molecular property that plays a crucial role in biophysics and drug design. Optical circular dichroism (OCD) is a well-established chiral spectroscopic probe in the UV-visible regime. Chirality is most commonly associated with a localized chiral center. However, some compounds such as helicenes (Figure 1) are chiral due to their screwlike global structure. In these highly conjugated systems, some electric and magnetic allowed transitions are distributed across the entire molecule, and OCD thus probes the global molecular chirality. Recent advances in X-ray sources, in particular the control of their polarization and spatial profiles, have enabled X-ray circular dichroism (XCD), which, in contrast to OCD, can exploit the localized and element-specific nature of X-ray electronic transitions. XCD therefore is more sensitive to local structures, and the chirality probed with it can be referred to as local. During the racemization of helicene, between opposite helical structures, the screw handedness can flip locally, making the molecule globally achiral while retaining a local handedness. Here, we use the racemization mechanism of [12]helicene as a model to demonstrate the capabilities of OCD and XCD as time-dependent probes for global and local chiralities, respectively. Our simulations demonstrate that XCD provides an excellent spectroscopic probe for the time-dependent local chirality of molecules.

Uncovering the 3d and 4d Electronic Interactions in Solvated Ru Complexes with 2p3d Resonant Inelastic X-ray Scattering.

The electronic structure and dynamics of ruthenium complexes are widely studied given their use in catalytic and light-harvesting materials. Here we investigate three model Ru complexes, [RuIII(NH3)6]3+, [RuII(bpy)3]2+, and [RuII(CN)6]4-, with L3-edge 2p3d resonant inelastic X-ray scattering (RIXS) to probe unoccupied 4d valence orbitals and occupied 3d orbitals and to gain insight into the interactions between these levels. The 2p3d RIXS maps contain a higher level of spectral information than the L3 X-ray absorption near edge structure (XANES). This study provides a direct measure of the 3d spin-orbit splittings of 4.3, 4.0, and 4.1 eV between the 3d5/2 and 3d3/2 orbitals of the [RuIII(NH3)6]3+, [RuII(bpy)3]2+, and [RuII(CN)6]4- complexes, respectively.

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape.

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

The evolution of solvation symmetry and composition in Zn halide aqueous solutions from dilute to extreme concentrations.

The emergence of cation-anion species, or contact ion pairs, is fundamental to understanding the physical properties of aqueous solutions when moving from the ideal, low-concentration limit to the manifestly non-ideal limits of very high solute concentration or constituent ion activity. We focus here on Zn halide solutions both as a model system and also as an exemplar of the applications spanning from (i) electrical energy storage via the paradigm of water in salt electrolyte (WiSE) to (ii) the physical chemistry of brines in geochemistry to (iii) the long-standing problem of nucleation. Using a combination of experimental and theoretical approaches we quantify the halide coordination number and changing coordination geometry without embedded use of theoretical equilibrium constants. These results and the associated methods, notably including the use of valence-to-core X-ray emission spectroscopy, provide new insights into the Zn halide system and new research directions in the physical chemistry of concentrated electrolytes.

Exploring Parameter Redundancy in the Unitary Coupled-Cluster Ansätze for Hybrid Variational Quantum Computing.

One of the commonly used chemically inspired approaches in variational quantum computing is the unitary coupled-cluster (UCC) ansätze. Despite being a systematic way of approaching the exact limit, the number of parameters in the standard UCC ansätze exhibits unfavorable scaling with respect to the system size, hindering its practical use on near-term quantum devices. Efforts have been taken to propose some variants of the UCC ansätze with better scaling. In this paper, we explore the parameter redundancy in the preparation of unitary coupled-cluster singles and doubles (UCCSD) ansätze employing spin-adapted formulation, small amplitude filtration, and entropy-based orbital selection approaches. Numerical results of using our approach on some small molecules have exhibited a significant cost reduction in the number of parameters to be optimized and in the time to convergence compared with conventional UCCSD-VQE simulations. We also discuss the potential application of some machine learning techniques in further exploring the parameter redundancy, providing a possible direction for future studies.

G0W0 Ionization Potentials of First-Row Transition Metal Aqua Ions.

We report computations of the vertical ionization potentials within the GW approximation of the near-complete series of first-row transition metal (V-Cu) aqua ions in their most common oxidation states, i.e., V3+, Cr3+, Cr2+, Mn2+, Fe3+, Fe2+, Co2+, Ni2+, and Cu2+. The d-orbital occupancy of these systems spans a broad range from d2 to d9. All of the structures were first optimized at the density functional theory level using a large cluster of explicit water molecules that are embedded in a continuum solvation model. Vertical ionization potentials were computed with the one-shot G0W0 approach on a range of transition metal ion clusters (6, 18, 40, and 60 explicit water molecules), wherein the convergence with respect to the basis set size was evaluated using the systems with 40 water molecules. We assess the results using three different density functional approximations as starting points for the vertical ionization potential calculations, namely, G0W0@PBE, G0W0@PBE0, and G0W0@r2SCAN. While the predicted ground-state structures are similar to all three exchange-correlation functionals, the vertical ionization potentials were in closer agreement with experiment when using the G0W0@PBE0 and G0W0@r2SCAN approaches, with the r2SCAN-based calculations being significantly less expensive. Computed bond distances and vertical ionization potentials for all structures are in good agreement with available experimental data.

Time-Evolving Chirality Loss in Molecular Photodissociation Monitored by X-ray Circular Dichroism Spectroscopy.

The ultrafast photoinduced chirality loss of 2-iodobutane is studied theoretically by time- and frequency-resolved X-ray circular dichroism (TRXCD) spectroscopy. Following an optical excitation, the iodine atom dissociates from the chiral center, which we capture by quantum non-adiabatic molecular dynamics simulations. At variable time delays after the pump, the resonant X-ray pulse selectively probes the iodine and carbon atom involved in the chiral dissociation through a selected core-to-valence transition. The TRXCD signal at the iodine L1 edge accurately captures the timing of C-I photodissociation and thereby chirality loss, c.a 70 fs. The strong electric dipole-electric quadrupole (ED-EQ) response makes this signal particularly sensitive to vibronic coherence at the high X-ray regime. At the carbon K-edges, the signals monitor the molecular chirality of the 2-butyl radical photoproduct and the spin state of the iodine atom. The ED-EQ response is masked under the strong electric dipole-magnetic dipole response, making this signal intuitive for the electronic population. The evolution of the core electronic states and its chiral sensitivity is discussed. Overall, the element-specific TRXCD signal provides a detailed picture of molecular dynamics and offers a unique sensitive window into the time-dependent chirality of molecules.

Water Defect Stabilizes the Bi3+ Lone-Pair Electronic State Leading to an Unusual Aqueous Hydration Structure.

The aqueous hydration structure of the Bi3+ ion is probed using a combination of extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) simulations of ion-water clusters and condensed-phase solutions. Anomalous features in the EXAFS spectra are found to be associated with a highly asymmetric first-solvent water shell. The aqueous chemistry and structure of the Bi3+ ion are dramatically controlled by the water stabilization of a lone-pair electronic state involving the mixed 6s and 6p orbitals. This leads to a distinct multimodal distribution of water molecules in the first shell that are separated by about 0.2 Å. The lone-pair structure is stabilized by a collective response of multiple waters that are localized near the lone-pair anti-bonding site. The findings indicate that the lone-pair stereochemistry of aqueous Bi3+ ions plays a major role in the binding of water and ligands in aqueous solutions.

Real-Time Time-Dependent Electronic Structure Theory.

Real-time electronic structure methods provide an unprecedented view of electron dynamics and ultrafast spectroscopy on the atto- and femtosecond time scale with vast potential to yield new insights into the electronic behavior of molecules and materials. In this Review, we discuss the fundamental theory underlying various real-time electronic structure methods as well as advantages and disadvantages of each. We give an overview of the numerical techniques that are widely used for real-time propagation of the quantum electron dynamics with an emphasis on Gaussian basis set methods. We also showcase many of the chemical applications and scientific advances made by using real-time electronic structure calculations and provide an outlook of possible new directions.

Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods.

The emergence of state-of-the-art X-ray light sources has paved the way for novel spectroscopies that take advantage of their atomic specificity to shed light on fundamental physical, chemical, and biological processes both in the static and time domains. The success of these experiments hinges on the ability to interpret and predict core-level spectra, which has opened avenues for theory to play a key role. Over the last two decades, linear-response time-dependent density functional theory (LR-TDDFT), despite various theoretical challenges, has become a computationally attractive and versatile framework to study excited-state spectra including X-ray spectroscopies. In this context, we focus our discussion on LR-TDDFT approaches for the computation of X-ray Near-Edge Structure (XANES), Valence-to-Core X-ray Emission (VtC-XES), and Resonant Inelastic X-ray Scattering (RIXS) spectroscopies in molecular systems with an emphasis on Gaussian basis set implementations. We illustrate these approaches with applications and provide a brief outlook of possible new directions.

Correction: Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods.

Correction for 'Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods' by Daniel R. Nascimento et al., Phys. Chem. Chem. Phys., 2022, 24, 14680-14691, https://doi.org/10.1039/D2CP01132H.

Informed Chemical Classification of Organophosphorus Compounds via Unsupervised Machine Learning of X-ray Absorption Spectroscopy and X-ray Emission Spectroscopy.

We analyze an ensemble of organophosphorus compounds to form an unbiased characterization of the information encoded in their X-ray absorption near-edge structure (XANES) and valence-to-core X-ray emission spectra (VtC-XES). Data-driven emergence of chemical classes via unsupervised machine learning, specifically cluster analysis in the Uniform Manifold Approximation and Projection (UMAP) embedding, finds spectral sensitivity to coordination, oxidation, aromaticity, intramolecular hydrogen bonding, and ligand identity. Subsequently, we implement supervised machine learning via Gaussian process classifiers to identify confidence in predictions that match our initial qualitative assessments of clustering. The results further support the benefit of utilizing unsupervised machine learning as a precursor to supervised machine learning, which we term Unsupervised Validation of Classes (UVC), a result that goes beyond the present case of X-ray spectroscopies.

iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software.

We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time-dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0).

Unsupervised machine learning for unbiased chemical classification in X-ray absorption spectroscopy and X-ray emission spectroscopy.

We report a comprehensive computational study of unsupervised machine learning for extraction of chemically relevant information in X-ray absorption near edge structure (XANES) and in valence-to-core X-ray emission spectra (VtC-XES) for classification of a broad ensemble of sulphorganic molecules. By progressively decreasing the constraining assumptions of the unsupervised machine learning algorithm, moving from principal component analysis (PCA) to a variational autoencoder (VAE) to t-distributed stochastic neighbour embedding (t-SNE), we find improved sensitivity to steadily more refined chemical information. Surprisingly, when embedding the ensemble of spectra in merely two dimensions, t-SNE distinguishes not just oxidation state and general sulphur bonding environment but also the aromaticity of the bonding radical group with 87% accuracy as well as identifying even finer details in electronic structure within aromatic or aliphatic sub-classes. We find that the chemical information in XANES and VtC-XES is very similar in character and content, although they unexpectedly have different sensitivity within a given molecular class. We also discuss likely benefits from further effort with unsupervised machine learning and from the interplay between supervised and unsupervised machine learning for X-ray spectroscopies. Our overall results, i.e., the ability to reliably classify without user bias and to discover unexpected chemical signatures for XANES and VtC-XES, likely generalize to other systems as well as to other one-dimensional chemical spectroscopies.

Projector-Based Quantum Embedding for Molecular Systems: An Investigation of Three Partitioning Approaches.

Projector-based embedding is a relatively recent addition to the collection of methods that seek to utilize chemical locality to provide improved computational efficiency. This work considers the interactions between the different proposed procedures for this method and their effects on the accuracy of the results. The interplay between the embedded background, projector type, partitioning scheme, and level of atomic orbital (AO) truncation are investigated on a selection of reactions from the literature. The Huzinaga projection approach proves to be more reliable than the level-shift projection when paired with other procedural options. Active subsystem partitioning from the subsystem projected AO decomposition (SPADE) procedure proves slightly better than the combination of Pipek-Mezey localization and Mulliken population screening (PMM). Along with these two options, a new partitioning criteria is proposed based on subsystem von Neumann entropy and the related subsystem orbital occupancy. This new method overlaps with the previous PMM method, but the screening process is computationally simpler. Finally, AO truncation proves to be a robust option for the tested systems when paired with the Huzinaga projection, with satisfactory results being acquired at even the most severe truncation level.

Mechanistic Investigation of Dimethylmercury Formation Mediated by a Sulfide Mineral Surface.

Mercury (Hg) pollution is a global environmental problem. The abiotic formation of dimethylmercury (DMeHg) from monomethylmercury (MMeHg) may account for a large portion of DMeHg in oceans. Previous experimental work has shown that abiotic formation of DMeHg from MMeHg can be facilitated by reduced sulfur groups on sulfide mineral surfaces. In that work, a mechanism was proposed in which neighboring MMeHg moieties bound to sulfide sites on a mineral surface react through an SN2-type mechanism to form DMeHg and incorporate the remaining Hg atoms into the mineral surface. Here, we perform density functional theory calculations to explore the mechanisms of DMeHg formation on the 110 surface of a CdS(s) (hawleyite) nanoparticle. We show that coordination of MMeHg substituents to adjacent reduced sulfur groups protruding from the surface indeed facilitates DMeHg formation and that the reaction proceeds through direct transmethylation from one MMeHg substituent to another. Coordination of Hg by multiple S atoms provides a transition-state stabilization and activates a C-Hg bond for methyl transfer. In addition, solvation effects play an important role in the surface reconstruction of the nanoparticle and in decreasing the energetic barrier for DMeHg formation relative to the corresponding reaction in vacuo.

Ultrafast x-ray pump x-ray probe transient absorption spectroscopy: A computational study and proposed experiment probing core-valence electronic correlations in solvated complexes.

Femtosecond x-ray pump-x-ray probe experiments are currently possible at free electron lasers such as the linac coherent light source, which opens new opportunities for studying solvated transition metal complexes. In order to make the most effective use of these kinds of experiments, it is necessary to determine which chemical properties an x-ray probe pulse will measure. We have combined electron cascade calculations and excited-state time-dependent density functional theory calculations to predict the initial state prepared by an x-ray pump and the subsequent x-ray probe spectra at the Fe K-edge in the solvated model transition metal complex, K4FeII(CN)6. We find several key spectral features that report on the ligand-field splitting and the 3p and 3d electron interactions. We then show how these features could be measured in an experiment.

Surface Functionalization of Black Phosphorus with Nitrenes: Identification of P=N Bonds by Using Isotopic Labeling.

Surface functionalization of two-dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced herein is a mild, surface-specific protocol for the surface functionalization of few-layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational, X-ray photoelectron, solid state 31 P NMR, and UV-vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15 N-labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.

Probing Sulfur Chemical and Electronic Structure with Experimental Observation and Quantitative Theoretical Prediction of Kα and Valence-to-Core Kß X-ray Emission Spectroscopy.

An extensive experimental and theoretical study of the Kα and Kß high-resolution X-ray emission spectroscopy (XES) of sulfur-bearing systems is presented. This study encompasses a wide range of organic and inorganic compounds, including numerous experimental spectra from both prior published work and new measurements. Employing a linear-response time-dependent density functional theory (LR-TDDFT) approach, strong quantitative agreement is found in the calculation of energy shifts of the core-to-core Kα as well as the full range of spectral features in the valence-to-core Kß spectrum. The ability to accurately calculate the sulfur Kα energy shift supports the use of sulfur Kα XES as a bulk-sensitive tool for assessing sulfur speciation. The fine structure of the sulfur Kß spectrum, in conjunction with the theoretical results, is shown to be sensitive to the local electronic structure including effects of symmetry, ligand type and number, and, in the case of organosulfur compounds, to the nature of the bonded organic moiety. This agreement between theory and experiment, augmented by the potential for high-access XES measurements with the latest generation of laboratory-based spectrometers, demonstrates the possibility of broad analytical use of XES for sulfur and nearby third-row elements. The effective solution of the forward problem, i.e., successful prediction of detailed spectra from known molecular structure, also suggests future use of supervised machine learning approaches to experimental inference, as has seen recent interest for interpretation of X-ray absorption near-edge structure (XANES).

ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries.

High-throughput, comprehensive, and confident identifications of metabolites and other chemicals in biological and environmental samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent technological advances, metabolomics studies still result in the detection of a disproportionate number of features that cannot be confidently assigned to a chemical structure. This inadequacy is driven by the single most significant limitation in metabolomics, the reliance on reference libraries constructed by analysis of authentic reference materials with limited commercial availability. To this end, we have developed the in silico chemical library engine (ISiCLE), a high-performance computing-friendly cheminformatics workflow for generating libraries of chemical properties. In the instantiation described here, we predict probable three-dimensional molecular conformers (i.e., conformational isomers) using chemical identifiers as input, from which collision cross sections (CCS) are derived. The approach employs first-principles simulation, distinguished by the use of molecular dynamics, quantum chemistry, and ion mobility calculations, to generate structures and chemical property libraries, all without training data. Importantly, optimization of ISiCLE included a refactoring of the popular MOBCAL code for trajectory-based mobility calculations, improving its computational efficiency by over 2 orders of magnitude. Calculated CCS values were validated against 1983 experimentally measured CCS values and compared to previously reported CCS calculation approaches. Average calculated CCS error for the validation set is 3.2% using standard parameters, outperforming other density functional theory (DFT)-based methods and machine learning methods (e.g., MetCCS). An online database is introduced for sharing both calculated and experimental CCS values ( metabolomics.pnnl.gov ), initially including a CCS library with over 1 million entries. Finally, three successful applications of molecule characterization using calculated CCS are described, including providing evidence for the presence of an environmental degradation product, the separation of molecular isomers, and an initial characterization of complex blinded mixtures of exposure chemicals. This work represents a method to address the limitations of small molecule identification and offers an alternative to generating chemical identification libraries experimentally by analyzing authentic reference materials. All code is available at github.com/pnnl .