ERKALE-A flexible program package for X-ray properties of atoms and molecules

Generating interstitial water within the persisting tetrahedral H-bond network explains density increase upon compressing liquid water

Despite its ubiquitous nature, the atomic structure of water in its liquid state is still controversially debated. We use a combination of X-ray Raman scattering spectroscopy in conjunction with ab initio and path integral molecular dynamics simulations to study the local atomic and electronic structure of water under high pressure conditions. Systematically increasing fingerprints of non-hydrogen-bonded H[Formula: see text]O molecules in the first hydration shell are identified in the experimental and computational oxygen K-edge excitation spectra. This provides evidence for a compaction mechanism in terms of a continuous collapse of the second hydration shell with increasing pressure via generation of interstitial water within locally tetrahedral hydrogen-bonding environments.

Beyond Electrons: Correlation and Self-Energy in Multicomponent Density Functional Theory

Post-Kohn-Sham methods are used to evaluate the ground-state correlation energy and the orbital self-energy of systems consisting of multiple flavors of different fermions. Starting from multicomponent density functional theory, suitable ways to arrive at the corresponding multicomponent random-phase approximation and the multicomponent Green's functionG W ${GW}$ approximation, including relativistic effects, are outlined. Given the importance of both of this methods in the development of modern Kohn-Sham density functional approximations, this work will provide a foundation to design advanced multicomponent density functional approximations. Additionally, theG W ${GW}$ quasiparticle energies are needed to study light-matter interactions with the Bethe-Salpeter equation.

The tale of HORTON: Lessons learned in a decade of scientific software development

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade.

Insight on Gaussian Basis Set Truncation Errors in Weak to Intermediate Magnetic Fields with an Approximate Hamiltonian

Strong magnetic fields such as those found on white dwarfs have significant effects on the electronic structures of atoms and molecules. However, the vast majority of molecular studies in the literature in such fields are carried out with Gaussian basis sets designed for zero field, leading to large basis set truncation errors [Lehtola et al., Mol. Phys. 2020, 118, e1597989]. In this work, we aim to identify the failures of the Gaussian basis sets in atomic calculations to guide the design of new basis sets for strong magnetic fields. We achieve this by performing fully numerical electronic structure calculations at the complete basis set (CBS) limit for the ground state and low lying excited states of the atoms 1 ≤ Z ≤ 18 in weak to intermediate magnetic fields. We also carry out finite-field calculations for a variety of Gaussian basis sets, introducing a real-orbital approximation for the magnetic-field Hamiltonian. Our primary focus is on the aug-cc-pVTZ basis set, which has been used in many works in the literature. A study of the differences in total energies of the fully numerical CBS limit calculations and the approximate Gaussian basis calculations is carried out to provide insight into basis set truncation errors. Examining a variety of states over the range of magnetic field strengths from B = 0 to B = 0.6B0, we observe significant differences for the aug-cc-pVTZ basis set, while much smaller errors are afforded by the benchmark-quality AHGBSP3-9 basis set [Lehtola, J. Chem. Phys. 2020, 152, 134108]. This suggests that there is considerable room to improve Gaussian basis sets for calculations at finite magnetic fields.

A call to arms: Making the case for more reusable libraries

The traditional foundation of science lies on the cornerstones of theory and experiment. Theory is used to explain experiment, which in turn guides the development of theory. Since the advent of computers and the development of computational algorithms, computation has risen as the third cornerstone of science, joining theory and experiment on an equal footing. Computation has become an essential part of modern science, amending experiment by enabling accurate comparison of complicated theories to sophisticated experiments, as well as guiding by triage both the design and targets of experiments and the development of novel theories and computational methods. Like experiment, computation relies on continued investment in infrastructure: it requires both hardware (the physical computer on which the calculation is run) as well as software (the source code of the programs that performs the wanted simulations). In this Perspective, I discuss present-day challenges on the software side in computational chemistry, which arise from the fast-paced development of algorithms, programming models, as well as hardware. I argue that many of these challenges could be solved with reusable open source libraries, which are a public good, enhance the reproducibility of science, and accelerate the development and availability of state-of-the-art methods and improved software.

Automatic Generation of Accurate and Cost-Efficient Auxiliary Basis Sets

We have recently discussed an algorithm to automatically generate auxiliary basis sets (ABSs) of the standard form for density fitting (DF) or resolution-of-the-identity (RI) calculations in a given atomic orbital basis set (OBS) of any form, such as Gaussian-type orbitals, Slater-type orbitals, or numerical atomic orbitals [J. Chem. Theory Comput. 2021, 17, 6886]. In this work, we study two ways to reduce the cost of such automatically generated ABSs without sacrificing their accuracy. We contract the ABS with a singular value decomposition proposed by Kállay [J. Chem. Phys. 2014, 141, 244113], used here in a somewhat different setting. We also drop the high-angular momentum functions from the ABS, as they are unnecessary for global fitting methods. Studying the effect of these two types of truncations on Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) calculations on a chemically diverse set of first- and second-row molecules within the RI/DF approach, we show that accurate total and atomization energies can be achieved by a combination of the two approaches with significant reductions in the size of the ABS. While the original approach yields ABSs whose number of functions NbfABS scales with the number of functions in the OBS, NOBSbf, as NABSbf = γNOBSbf with the prefactor γ ≈ O ( 10 ) , the reduction schemes of this work afford results of essentially the same quality as the original unpruned and uncontracted ABS with γ ≈ 5-6, while an accuracy that may suffice for routine applications is achievable with a further reduced ABS with γ ≈ 3-4. The observed errors are similar at HF and MP2 levels of theory, suggesting that the generated ABSs are highly transferable and can also be applied to model challenging properties with high-level methods.

Reproducibility of density functional approximations: How new functionals should be reported

Density functional theory is the workhorse of chemistry and materials science, and novel density functional approximations are published every year. To become available in program packages, the novel density functional approximations (DFAs) need to be (re)implemented. However, according to our experience as developers of Libxc [Lehtola et al., SoftwareX 7, 1 (2018)], a constant problem in this task is verification due to the lack of reliable reference data. As we discuss in this work, this lack has led to several non-equivalent implementations of functionals such as Becke-Perdew 1986, Perdew-Wang 1991, Perdew-Burke-Ernzerhof, and Becke's three-parameter hybrid functional with Lee-Yang-Parr correlation across various program packages, yielding different total energies. Through careful verification, we have also found many issues with incorrect functional forms in recent DFAs. The goal of this work is to ensure the reproducibility of DFAs. DFAs must be verifiable in order to prevent the reappearance of the above-mentioned errors and incompatibilities. A common framework for verification and testing is, therefore, needed. We suggest several ways in which reference energies can be produced with free and open source software, either with non-self-consistent calculations with tabulated atomic densities or via self-consistent calculations with various program packages. The employed numerical parameters-especially the quadrature grid-need to be converged to guarantee a ≲0.1 μEh precision in the total energy, which is nowadays routinely achievable in fully numerical calculations. Moreover, as such sub-μEh level agreement can only be achieved when fully equivalent implementations of the DFA are used, the source code of the reference implementation should also be made available in any publication describing a new DFA.

Meta-GGA Density Functional Calculations on Atoms with Spherically Symmetric Densities in the Finite Element Formalism

Density functional calculations on atoms are often used for determining accurate initial guesses as well as generating various types of pseudopotential approximations and efficient atomic-orbital basis sets for polyatomic calculations. To reach the best accuracy for these purposes, the atomic calculations should employ the same density functional as the polyatomic calculation. Atomic density functional calculations are typically carried out employing spherically symmetric densities, corresponding to the use of fractional orbital occupations. We have described their implementation for density functional approximations (DFAs) belonging to the local density approximation (LDA) and generalized gradient approximation (GGA) levels of theory as well as Hartree-Fock (HF) and range-separated exact exchange [Lehtola, S. Phys. Rev. A 2020, 101, 012516]. In this work, we describe the extension to meta-GGA functionals using the generalized Kohn-Sham scheme, in which the energy is minimized with respect to the orbitals, which in turn are expanded in the finite element formalism with high-order numerical basis functions. Furnished with the new implementation, we continue our recent work on the numerical well-behavedness of recent meta-GGA functionals [Lehtola, S.; Marques, M. A. L. J. Chem. Phys. 2022, 157, 174114]. We pursue complete basis set (CBS) limit energies for recent density functionals and find many to be ill-behaved for the Li and Na atoms. We report basis set truncation errors (BSTEs) of some commonly used Gaussian basis sets for these density functionals and find the BSTEs to be strongly functional dependent. We also discuss the importance of density thresholding in DFAs and find that all of the functionals studied in this work yield total energies converged to 0.1 μEh when densities smaller than 10-11a0-3 are screened out.

Thermochemical evaluation of adaptive and fixed density functional theory quadrature schemes

A systematic study is made of the accuracy and efficiency of a number of existing quadrature schemes for molecular Kohn-Sham Density-Functional Theory (DFT) using 408 molecules and 254 chemical reactions. Included are the fixed SG-x (x = 0-3) grids of Gill et al., Dasgupta, and Herbert, the 3-zone grids of Treutler and Ahlrichs, a fixed five-zone grid implemented in Molpro, and a new adaptive grid scheme. While all methods provide a systematic reduction of errors upon extension of the grid sizes, significant differences are observed in the accuracies for similar grid sizes with various approaches. For the tests in this work, the SG-x fixed grids are less suitable to achieve high accuracies in the DFT integration, while our new adaptive grid performed best among the schemes studied in this work. The extra computational time to generate the adaptive grid scales linearly with molecular size and is negligible compared with the time needed for the self-consistent field iterations for large molecules. A comparison of the grid accuracies using various density functionals shows that meta-GGA functionals need larger integration grids than GGA functionals to reach the same degree of accuracy, confirming previous investigations of the numerical stability of meta-GGA functionals. On the other hand, the grid integration errors are almost independent of the basis set, and the basis set errors are mostly much larger than the errors caused by the numerical integrations, even when using the smallest grids tested in this work.

Extracting Inelastic Scattering Cross Sections for Finite and Aperiodic Materials from Electronic Dynamics Simulations

Explicit time-dependent electronic structure theory methods are increasingly prevalent in the areas of condensed matter physics and quantum chemistry, with the broad-band optical absorptivity of molecular and small condensed-phase systems nowadays routinely studied with such approaches. In this paper, it is demonstrated that electronic dynamics simulations can similarly be employed to study cross sections for the scattering-induced electronic excitations probed in nonresonant inelastic X-ray scattering and momentum-resolved electron energy loss spectroscopies. A method is put forth for evaluating the electronic dynamic structure factor, which involves the application of a momentum boost-type perturbation and transformation of the resulting reciprocal space density fluctuations into the frequency domain. Good agreement is first demonstrated between the dynamic structure factor extracted from these electronic dynamics simulations and the corresponding transition matrix elements from linear response theory. The method is then applied to some extended (quasi)one-dimensional systems, for which the wave vector becomes a good quantum number in the thermodynamic limit. Finally, the dispersion of many-body excitations in a series of hydrogen-terminated graphene flakes (and twisted bilayers thereof) is investigated to highlight the utility of the presented approach for capturing morphology-dependent effects in the inelastic scattering cross sections of nanostructured and/or noncrystalline materials.

X-ray Raman Scattering: A Hard X-ray Probe of Complex Organic Systems

This paper provides a review of the characterization of organic systems via X-ray Raman scattering (XRS) and a step-by-step guidance for its application. We present the fundamentals of XRS required to use the technique and discuss the main parameters of the experimental set-ups to optimize spectral and spatial resolution while maximizing signal-to-background ratio. We review applications that target the analysis of mixtures of organic compounds, the identification of minor spectral features, and the spatial discrimination in heterogeneous systems. We discuss the recent development of the direct tomography technique, which utilizes the XRS process as a contrast mechanism for assessing the three-dimensional spatially resolved carbon chemistry of complex organic materials. We conclude by exposing the current limitations and provide an outlook on how to overcome some of the existing challenges and advance future developments and applications of this powerful technique for complex organic systems.

Chemical bonding theories as guides for self-interaction corrected solutions: Multiple local minima and symmetry breaking

Fermi-Löwdin orbitals (FLOs) are a special set of localized orbitals, which have become commonly used in combination with the Perdew-Zunger self-interaction correction (SIC) in the FLO-SIC method. The FLOs are obtained for a set of occupied orbitals by specifying a classical position for each electron. These positions are known as Fermi-orbital descriptors (FODs), and they have a clear relation to chemical bonding. In this study, we show how FLOs and FODs can be used to initialize, interpret, and justify SIC solutions in a common chemical picture, both within FLO-SIC and in traditional variational SIC, and to locate distinct local minima in either of these approaches. We demonstrate that FLOs based on Lewis theory lead to symmetry breaking for benzene-the electron density is found to break symmetry already at the symmetric molecular structure-while ones from Linnett's double-quartet theory reproduce symmetric electron densities and molecular geometries. Introducing a benchmark set of 16 planar cyclic molecules, we show that using Lewis theory as the starting point can lead to artifactual dipole moments of up to 1 D, while Linnett SIC dipole moments are in better agreement with experimental values. We suggest using the dipole moment as a diagnostic of symmetry breaking in SIC and monitoring it in all SIC calculations. We show that Linnett structures can often be seen as superpositions of Lewis structures and propose Linnett structures as a simple way to describe aromatic systems in SIC with reduced symmetry breaking. The role of hovering FODs is also briefly discussed.

Straightforward and Accurate Automatic Auxiliary Basis Set Generation for Molecular Calculations with Atomic Orbital Basis Sets

Density fitting (DF), also known as the resolution of the identity (RI), is a widely used technique in quantum chemical calculations with various types of atomic basis sets─Gaussian-type orbitals, Slater-type orbitals, as well as numerical atomic orbitals─to speed up density functional, Hartree-Fock (HF), and post-HF calculations. Traditionally, custom auxiliary basis sets are hand-optimized for each orbital basis set; however, some automatic schemes have also been suggested. In this work, we propose a simple yet numerically stable automated scheme for forming auxiliary basis sets with the help of a pivoted Cholesky decomposition, which is applicable to any type of atomic basis function. We exemplify the scheme with proof-of-concept calculations with Gaussian basis sets and show that the proposed approach leads to negligible DF/RI errors in HF and second-order Møller-Plesset (MP2) total energies of the non-multireference part of the W4-17 test set when used with orbital basis sets of at least polarized triple-ζ quality. The results are promising for future applications employing Slater-type orbitals or numerical atomic orbitals, as well as schemes based on the use of local fitting approaches. Global fitting approaches can also be used, in which case the high-angular-momentum functions produced by the present scheme can be truncated to minimize the computational cost.

Ion association in hydrothermal aqueous NaCl solutions: implications for the microscopic structure of supercritical water

Knowledge of the microscopic structure of fluids and changes thereof with pressure and temperature is important for the understanding of chemistry and geochemical processes. In this work we investigate the influence of sodium chloride on the hydrogen-bond network in aqueous solution up to supercritical conditions. A combination of in situ X-ray Raman scattering and ab initio molecular dynamics simulations is used to probe the oxygen K-edge of the alkali halide aqueous solution in order to obtain unique information about the oxygen's local coordination around the ions, e.g. solvation-shell structure and the influence of ion pairing. The measured spectra exhibit systematic temperature dependent changes, which are entirely reproduced by calculations on the basis of structural snapshots obtained via ab initio molecular dynamics simulations. Analysis of the simulated trajectories allowed us to extract detailed structural information. This combined analysis reveals a net destabilizing effect of the dissolved ions which is reduced with rising temperature. The observed increased formation of contact ion pairs and occurrence of larger polyatomic clusters at higher temperatures can be identified as a driving force behind the increasing structural similarity between the salt solution and pure water at elevated temperatures and pressures with drawback on the role of hydrogen bonding in the hot fluid. We discuss our findings in view of recent results on hot NaOH and HCl aqueous fluids and emphasize the importance of ion pairing in the interpretation of the microscopic structure of water.

Sulfur Molecules in Space by X-rays: A Computational Study

X-ray astronomy lacks high resolution spectra of interstellar dust analogues and molecules, severely hampering interstellar medium studies based on upcoming X-ray missions. Various theoretical approaches may be used to address this problem, but they must first be shown to reproduce reliable spectra compared to the experiment. In this work, we calculate the sulfur K edge X-ray absorption spectra of H₂S, SO₂, and OCS, whose spectra are already known from X-ray experiments and predict the X-ray spectrum of CS, which as far as we are aware has not been measured, thereby hampering its detection by X-ray telescopes. We chose these four molecules as the astrochemistry of sulfur is an unsolved problem and as the four molecules are already known to exist in space. We consider three types of methods for modeling the X-ray spectra: more accurate calculations with the algebraic-diagrammatic construction (ADC) and the CC2, CCSD, and CC3 coupled cluster (CC) approaches as well as more affordable ones with transition potential density functional theory (TP-DFT). A comparison of our computational results to previously reported experimental spectra shows that the core-valence separation (CVS) approaches CVS-ADC(2)-x and CVS-CC3 generally yield a good qualitative level of agreement with the experiment, suggesting that they can be used for interpreting measured spectra, while the TP-DFT method is not reliable for these molecules. However, quantitative agreement with the experiment is still outside the reach of the computational methods studied in this work.

X-ray Raman scattering for bulk chemical and structural insight into green carbon

X-ray Raman scattering (XRS) spectroscopy is an emerging inelastic scattering technique which uses hard X-rays to study the X-ray absorption edges of low-Z elements (e.g. C, N, O) in bulk. This study applies XRS spectroscopy to pyrolysis and hydrothermal carbons. These materials are thermochemically-produced carbon from renewable resources and represent a route for the sustainable production of carbon materials for many applications. Results confirm local structural differences between biomass-derived (Oak, Quercus Ilex) pyrolysis and hydrothermal carbon. In comparison with NEXAFS, XRS spectroscopy has been shown to be more resilient to experimental artefacts such as self-absorption. Density functional theory XRS calculations of potential structural sub-units confirm that hydrothermal carbon is a highly disordered carbon material formed principally of furan units linked by the α carbon atoms. Comparison of two pyrolysis temperatures (450 °C and 650 °C) shows the development of an increasingly condensed carbon structure. Based on our results, we have proposed a semi-quantitative route to pyrolysis condensation.

PSIXAS: A Psi4 plugin for efficient simulations of X-ray absorption spectra based on the transition-potential and Δ-Kohn-Sham method

Near edge X-ray absorption fine structure (NEXAFS) spectra and their pump-probe extension (PP-NEXAFS) offer insights into valence- and core-excited states. We present PSIXAS, a recent implementation for simulating NEXAFS and PP-NEXAFS spectra by means of the transition-potential and the Δ-Kohn-Sham method. The approach is implemented in form of a software plugin for the Psi4 code, which provides access to a wide selection of basis sets as well as density functionals. We briefly outline the theoretical foundation and the key aspects of the plugin. Then, we use the plugin to simulate PP-NEXAFS spectra of thymine, a system already investigated by others and us. It is found that larger, extended basis sets are needed to obtain more accurate absolute resonance positions. We further demonstrate that, in contrast to ordinary NEXAFS simulations, where the choice of the density functional plays a minor role for the shape of the spectrum, for PP-NEXAFS simulations the choice of the density functional is important. Especially hybrid functionals (which could not be used straightforwardly before to simulate PP-NEXAFS spectra) and their amount of "Hartree-Fock like" exact exchange affects relative resonance positions in the spectrum.

Curing basis set overcompleteness with pivoted Cholesky decompositions

The description of weakly bound electronic states is especially difficult with atomic orbital basis sets. The diffuse atomic basis functions that are necessary to describe the extended electronic state generate significant linear dependencies in the molecular basis set, which may make the electronic structure calculations ill-convergent. We propose a method where the overcomplete molecular basis set is pruned by a pivoted Cholesky decomposition of the overlap matrix, yielding an optimal low-rank approximation that is numerically stable, the pivot indices determining a reduced basis set that is complete enough to describe all the basis functions in the original overcomplete basis. The method can be implemented either by a simple modification to the usual canonical orthogonalization procedure, which hides the excess functions and yields fewer efficiency benefits, or by generating custom basis sets for all the atoms in the system, yielding significant cost reductions in electronic structure calculations. The pruned basis sets from the latter choice allow accurate calculations to be performed at a lower cost even at the self-consistent field level, as illustrated on a solvated (H₂O)₂₄ ^- anion. Our results indicate that the Cholesky procedure allows one to perform calculations with accuracies close to standard augmented basis sets with cost savings which increase with the size of the basis set, ranging from 9% fewer functions in single-ζ basis sets to 28% fewer functions in triple-ζ basis sets.

Stretched or noded orbital densities and self-interaction correction in density functional theory

Semilocal approximations to the density functional for the exchange-correlation energy of a many-electron system necessarily fail for lobed one-electron densities, including not only the familiar stretched densities but also the less familiar but closely related noded ones. The Perdew-Zunger (PZ) self-interaction correction (SIC) to a semilocal approximation makes that approximation exact for all one-electron ground- or excited-state densities and accurate for stretched bonds. When the minimization of the PZ total energy is made over real localized orbitals, the orbital densities can be noded, leading to energy errors in many-electron systems. Minimization over complex localized orbitals yields nodeless orbital densities, which reduce but typically do not eliminate the SIC errors of atomization energies. Other errors of PZ SIC remain, attributable to the loss of the exact constraints and appropriate norms that the semilocal approximations satisfy, suggesting the need for a generalized SIC. These conclusions are supported by calculations for one-electron densities and for many-electron molecules. While PZ SIC raises and improves the energy barriers of standard generalized gradient approximations (GGAs) and meta-GGAs, it reduces and often worsens the atomization energies of molecules. Thus, PZ SIC raises the energy more as the nodality of the valence localized orbitals increases from atoms to molecules to transition states. PZ SIC is applied here, in particular, to the strongly constrained and appropriately normed (SCAN) meta-GGA, for which the correlation part is already self-interaction-free. This property makes SCAN a natural first candidate for a generalized SIC.

Assessment of Initial Guesses for Self-Consistent Field Calculations. Superposition of Atomic Potentials: Simple yet Efficient

Electronic structure calculations, such as in the Hartree-Fock or Kohn-Sham density functional approach, require an initial guess for the molecular orbitals. The quality of the initial guess has a significant impact on the speed of convergence of the self-consistent field (SCF) procedure. Popular choices for the initial guess include the one-electron guess from the core Hamiltonian, the extended Hückel method, and the superposition of atomic densities (SAD). Here, we discuss alternative guesses obtained from the superposition of atomic potentials (SAP), which is easily implementable even in real-space calculations. We also discuss a variant of SAD which produces guess orbitals by purification of the density matrix that could also be used in real-space calculations, as well as a parameter-free variant of the extended Hückel method, which resembles the SAP method and is easy to implement on top of existing SAD infrastructure. The performance of the core Hamiltonian, the SAD, and the SAP guesses as well as the extended Hückel variant is assessed in nonrelativistic calculations on a data set of 259 molecules ranging from the first to the fourth periods by projecting the guess orbitals onto precomputed, converged SCF solutions in single- to triple-ζ basis sets. It is shown that the proposed SAP guess is the best guess on average. The extended Hückel guess offers a good alternative, with less scatter in accuracy.

A Trip to the Density Functional Theory Zoo: Warnings and Recommendations for the User

This account is written for general users of density functional theory (DFT) methods as well as experimental researchers who are new to the field and would like to conduct such calculations. Its main emphasis lies on how to find a way through the confusing ‘zoo’ of DFT by addressing common misconceptions and highlighting those modern methods that should ideally be used in calculations of energetic properties and geometries. A particular focus is on highly popular methods and the important fact that popularity does not imply accuracy. In this context, we present a new analysis of the openly available data published in Swart and co-workers’ famous annual ‘DFT poll’ (http://www.marcelswart.eu/dft-poll/) to demonstrate the existing communication gap between the DFT user and developer communities. We show that despite considerable methodological advances in the field, the perception of some parts of the user community regarding their favourite approaches has changed little. It is hoped that this account makes a contribution towards changing this status and that users are inspired to adjust their current computational protocols to accommodate strategies that are based on proven robustness, accuracy, and efficiency rather than popularity.

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals

The VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicate that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, ωB97X-V and ωB97M-V, and a value of b = 6.2 is recommended for both ωB97X-rV and ωB97M-rV.

Open source molecular modeling

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.

Complex Orbitals, Multiple Local Minima, and Symmetry Breaking in Perdew-Zunger Self-Interaction Corrected Density Functional Theory Calculations

Implentation of seminumerical stability analysis for calculations using the Perdew-Zunger self-interaction correction is described. It is shown that real-valued solutions of the Perdew-Zunger equations for gas phase atoms are unstable with respect to imaginary orbital rotations, confirming that a proper implementation of the correction requires complex-valued orbitals. The orbital density dependence of the self-interaction corrected functional is found to lead to multiple local minima in the case of the acrylic acid, H6, and benzene molecules. In the case of benzene, symmetry breaking that results in incorrect ground state geometry is found to occur, erroneously leading to alternating bond lengths in the molecule.

Sulphur Kβ emission spectra reveal protonation states of aqueous sulfuric acid

In this paper we report an X-ray emission study of bulk aqueous sulfuric acid. Throughout the range of molarities from 1 M to 18 M the sulfur Kβ emission spectra from H2SO4 (aq) depend on the molar fractions and related deprotonation of H2SO4. We compare the experimental results with results from emission spectrum calculations based on atomic structures of single molecules and structures from ab initio molecular dynamics simulations. We show that the S Kβ emission spectrum is a sensitive probe of the protonation state of the acid molecules. Using non-negative matrix factorization we are able to extract the fractions of different protonation states in the spectra, and the results are in good agreement with the simulation for the higher part of the concentration range.

Planning, performing and analyzing X-ray Raman scattering experiments

A compilation of procedures for planning and performing X-ray Raman scattering (XRS) experiments and analyzing data obtained from them is presented. In particular, it is demonstrated how to predict the overall shape of the spectra, estimate detection limits for dilute samples, and how to normalize the recorded spectra to absolute units. In addition, methods for processing data from multiple-crystal XRS spectrometers with imaging capability are presented, including a super-resolution method that can be used for direct tomography using XRS spectra as the contrast. An open-source software package with these procedures implemented is also made available.

Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride

We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting future experiments.