Basis Set Dependence Research Articles

Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals.

Metalloproteins widely exist in biology, playing pivotal roles in diverse life processes. Meanwhile, molecular dynamics (MD) simulations based on classical force fields has emerged as an important tool in scientific research. Partial charges are critical parameters within classical force fields and usually derived from quantum mechanical (QM) calculations. However, QM calculations are often time-consuming and prone to basis set dependence. Alternatively, fluctuating charge (FQ) models offer another avenue for partial charge derivation, which has significant speed advantages and can be used for large-scale screening. Building upon our previous work, which introduced an FQ model for zinc-containing complexes, herein we extend this model to include additional 3d transition metals which are important to the life sciences, namely chromium, manganese, iron, cobalt, and nickel. Employing CM5 charges as target for parametrization, our FQ model accurately reproduces partial charges for 3d metal complexes featuring biologically relevant ligands. Furthermore, by using atomic charges derived by our FQ model, MD simulations have been performed. These charges showed excellent performance in simulating proteomic metal sites housing multiple metal ions, specifically, a metalloprotein containing an iron-sulfur cluster and another containing a dimanganese metal site, showcasing comparable performance to those of RESP charges. We anticipate that our study can accelerate the parametrization of atomic charges for metalloproteins featuring 3d transition metals, thereby facilitating simulations of relevant systems.

Adaptive-Partitioning Multilayer Dynamics Simulations: 2. Implementations of the Permuted and Interpolated Adaptive-Partitioning Gradients.

Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1 and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the molecular-mechanical force fields. Such a multilayer model resembles the ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) model by Morokuma and co-workers, but it is distinguished by on-the-fly reclassifying atoms to be Q1, Q2, or MM in dynamics simulations. To smoothly blend the levels of descriptions of the atoms, buffer zones are introduced between adjacent layers, and the energy is smoothly interpolated. In particular, the Q1/Q2 interaction energy was expressed in two different formalisms: permuted and interpolated adaptive-partitioning (PAP and IAP), respectively. While the PAP energy is based on a weighted many-body expansion, the IAP energy is derived via alchemical quantum calculations with interpolated Fock and overlap matrices. In this article, we examine in-depth the irregularities in the IAP energy near the boundary between the buffer and Q2 zones, which were found prominent in some calculations. These irregularities are due to basis-set linear dependencies, which can be effectively suppressed using a cutoff for the weighted atomic orbital coefficients. Furthermore, we derived and implemented the gradients for both PAP and IAP. Test calculations on a series of water cluster models show perfectly smooth gradients in PAP, while a minor discontinuity occurs in IAP gradients at the buffer/Q2 boundary. The energy and gradient discontinuities in IAP become smaller when moving the buffer/Q2 boundary further away from the Q1 center and when increasing the size of the basis sets used. Overall, those discontinuities are controllable, and possible ways to further diminish them are discussed.

Decoding Chemical Bonds: Assessment of the Basis Set Effect on Overlap Electron Density Descriptors and Topological Properties in Comparison to QTAIM.

Quantum chemical bonding descriptors based on the total and overlap density can provide valuable information about chemical interactions in different systems. However, these descriptors can be sensitive to the basis set used. To address this, different numerical treatments of electron density have been proposed to reduce the basis set dependency. In this work, we introduce overlap properties (OPs) obtained through numerical treatment of the electron density and present the topology of overlap density (TOP) for the first time. We compare the basis set dependency of numerical OP and TOP descriptors with their quantum theory of atoms in molecules (QTAIM) counterparts, considering the total electron density. Three single (C-C, C-O, and C-F) bonds in ethane, methanol, and fluoromethane and two double (C═C and C═O) bonds in ethene and formaldehyde were analyzed. Diatomic molecules Li-X with X = F, Cl, and Br were also analyzed. Eight parameters, including QTAIM descriptors and OP/TOP descriptors, are used to assess the basis dependency at the ωB97X-D level of theory using 28 basis sets from three classes: Pople, Ahlrichs, and Dunning. The study revealed that the topological overlap electron density properties exhibit comparatively lesser dependence on the basis set compared to their total electron density counterparts. Remarkably, these properties retain their chemical significance even with reduced basis set dependency. Similarly, numerical OP descriptors show less basis set dependency than their QTAIM counterparts. The excess of polarization functions increases charge concentration in the interatomic region and influences both QTAIM and OP descriptors. The basis sets Def2TZVP, 6-31++G(d,p), 6-311++G(d,p), cc-pVDZ, cc-pVTZ, and cc-pVQZ demonstrate reduced variability for the tested bond classes in this study, with particular emphasis on the triple-ζ quality Ahlrichs' basis set. We recommend against using basis sets with numerous polarization functions, such as augmented Dunning's and Ahlrichs' quadruple-ζ.

Accurate Calculation of Isomerization and Conformational Energies of Larger Molecules Using Explicitly Correlated Local Coupled Cluster Methods in Molpro and ORCA.

An overview of the approximations in the explicitly correlated local coupled cluster methods PNO-LCCSD(T)-F12 in Molpro and DLPNO-CCSD(T)F12 in ORCA is given. Options to select the domains of projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and triples natural orbitals (TNOs) in both programs are described and compared in detail. The two programs are applied to compute isomerization and conformational energies of the ISOL24 and ACONFL test sets, where the former is part of the GMTKN55 benchmark suite. Thorough studies of basis set effects are presented for selected systems. These revealed large intramolecular basis set superposition effects that make it practically impossible to reliably determine the complete basis set (CBS) limits without including explicitly correlated terms. The latter strongly reduce the basis set dependence and at the same time also errors caused by the local domain approximations. On the basis of these studies, the PNO-LCCSD(T)-F12 method is applied to determine new reference energies for the above-mentioned benchmark sets. We are confident that our results should agree within a few tenths of a kcal mol-1 with the (unknown) CCSD(T)/CBS values, which therefore allowed us to define computational settings for accurate explicitly correlated local coupled cluster methods with moderate computational effort. With these protocols, especially PNO-LCCSD(T)-F12b/AVTZ', reliable reference values for comprehensive benchmark sets can be generated efficiently. This can significantly advance the development and evaluation of the performance of approximate electronic structure methods, especially improved density functional approximations or machine learning approaches.

Semi-experimental equilibrium (re SE) and theoretical structures of hydrazoic acid (HN3).

Hydrazoic acid (HN3) is used as a case study for investigating the accuracy and precision by which a molecular structure-specifically, a semi-experimental equilibrium structure (re SE)-may be determined using current state-of-the-art methodology. The influence of the theoretical corrections for effects of vibration-rotation coupling and electron-mass distribution that are employed in the analysis is explored in detail. The small size of HN3 allowed us to deploy considerable computational resources to probe the basis-set dependence of these corrections using a series of coupled-cluster single, double, perturbative triple [CCSD(T)] calculations with cc-pCVXZ (X = D, T, Q, 5) basis sets. We extrapolated the resulting corrections to the complete basis set (CBS) limit to obtain CCSD(T)/CBS corrections, which were used in a subsequent re SE structure determination. The re SE parameters obtained using the CCSD(T)/cc-pCV5Z corrections are nearly identical to those obtained using the CCSD(T)/CBS corrections, with uncertainties in the bond distances and angles of less than 0.0006 Å and 0.08°, respectively. The previously obtained re SE structure using CCSD(T)/ANO2 agrees with that using CCSD(T)/cc-pCV5Z to within 0.000 08 Å and 0.016° for bond distances and angles, respectively, and with only 25% larger uncertainties, validating the idea that re SE structure determinations can be carried out with significantly smaller basis sets than those needed for similarly accurate, strictly ab initio determinations. Although the purely computational re structural parameters [CCSD(T)/cc-pCV6Z] fall outside of the statistical uncertainties (2σ) of the corresponding re SE structural parameters, the discrepancy is rectified by applying corrections to address the theoretical limitations of the CCSD(T)/cc-pCV6Z geometry with respect to basis set, electron correlation, relativity, and the Born-Oppenheimer approximation, thereby supporting the contention that the semi-experimental approach is both an accurate and vastly more efficient method for structure determinations than is brute-force computation.

Benchmarking of the Fock-space coupled-cluster method and uncertainty estimation: Magnetic hyperfine interaction in the excited state of BaF

We present an investigation of the performance of the relativistic multi-reference Fock-space coupled cluster (FSCC) method for predicting molecular hyperfine structure (HFS) constants, including a thorough computational study to estimate the associated uncertainties. In particular, we considered the $^{19}$F HFS constant in the ground and excited states of BaF. Due to a larger basis set dependence, the uncertainties on the excited state results (16-85%) were found to be significantly larger than those on the ground state constants ($\sim$2%). The ab initio values were compared to the recent experimental results, and good overall agreement within the theoretical uncertainties was found. This work demonstrates the predictive power of the FSCC method and the reliability of the established uncertainty estimates, which can be crucial in cases where the calculated property cannot be directly compared to experiment.

Basis Set Dependence of Optical Rotation Calculations with Different Choices of Gauge.

In this work, the basis set dependence of optical rotation (OR) calculations is examined for various choices of gauge/level of theory. The OR is calculated for a set of 50 molecules using B3LYP and CAM-B3LYP and 17 molecules using coupled cluster with single and double excitations (CCSD). The calculations employ the correlation-consistent basis sets, aug-cc-pVζZ with ζ = D, T, Q. An inverse-power extrapolation formula is then utilized to obtain OR values at the complete basis set (CBS) limit. We investigate the basis set convergence for these methods and three choices of gauge: length gauge (with gauge-including atomic orbitals, LG(GIAOs), for DFT), the origin-invariant length gauge [LG(OI)], and the modified velocity gauge (MVG). The results show that all methods converge smoothly to the CBS limit and that the LG(OI) approach has a slightly faster convergence rate than the other choices of gauge. While the DFT methods reach gauge invariance at the CBS limit, CCSD does not. The significant difference between the MVG and LG(OI) results at the CBS limit, 26%, indicates that CCSD is not quite at convergence in the description of electron correlation for this property. On the other hand, gauge invariance at the CBS limit for DFT does not lead to the same OR values for the two density functionals, which is also due to electron correlation incompleteness. A limited comparison to gas-phase experimental OR values for the DFT methods shows that CAM-B3LYP seems more accurate than B3LYP. Overall, this study shows that the LG(OI) approach with the aug-cc-pVTZ basis set for DFT, and with the CBS(DT) extrapolation for CCSD, provides a good cost/accuracy balance.

All-Electron BSE@GW Method for K-Edge Core Electron Excitation Energies.

We present an accurate computational approach to calculate absolute K-edge core electron excitation energies as measured by X-ray absorption spectroscopy. Our approach employs an all-electron Bethe-Salpeter equation (BSE) formalism based on GW quasiparticle energies (BSE@GW) using numeric atom-centered orbitals (NAOs). The BSE@GW method has become an increasingly popular method for the computation of neutral valence excitation energies of molecules. However, it was so far not applied to molecular K-edge excitation energies. We discuss the influence of different numerical approximations on the BSE@GW calculation and employ in our final setup (i) exact numeric algorithms for the frequency integration of the GW self-energy, (ii) G0W0 and BSE starting points with ∼50% of exact exchange, (iii) the Tamm-Dancoff approximation and (iv) relativistic corrections. We study the basis set dependence and convergence with common Gaussian-type orbital and NAO basis sets. We identify the importance of additional spatially confined basis functions as well as of diffuse augmenting basis functions. The accuracy of our BSE@GW method is assessed for a benchmark set of small organic molecules, previously used for benchmarking the equation-of-motion coupled cluster method [Peng et al., J. Chem. Theory Comput., 2015, 11, 4146], as well as the medium-sized dibenzothiophene (DBT) molecule. Our BSE@GW results for absolute excitation energies are in excellent agreement with the experiment, with a mean average error of only 0.63 eV for the benchmark set and with errors <1 eV for the DBT molecule.

Basis sets dependency in constructing spectroscopy-accuracy Ab Initio global electric dipole moment functions

Recently, more attention have been paid on the construction of dipole moment functions (DMF) using theoretical methods. However, the computational methods to construct DMFs are not validated as much as those for potential energy surfaces do. In this letter, using Ar ⋯ He as an example, we tested how spectroscopy-accuracy DMFs can be constructed using ab initio methods. We especially focused on the basis set dependency in this scenario, i.e., the convergence of DMF with the sizes of basis sets, basis set superposition error, and mid-bond functions. We also tested the explicitly correlated method, which converges with smaller basis sets than the conventional methods do. This work can serve as a pictorial sample of all these computational technologies behaving in the context of constructing DMFs.

Calculation of vertical and adiabatic ionization potentials for some benzaldehydes using hybrid DFT, multilevel G3B3 and MP2 methods

The adiabatic ionization potential (AIP) and vertical ionization potential (VIP) for eight benzaldehydes were calculated using DFT (B3LYP, CAM-B3LYP and ωB97XD), MP2, G3B3 and CBS-QB3 methods. Basis set dependence was checked using four different basis sets 6-311G(d,p), 6-31+G(d,p), 6-311++G(2df,2p) and cc-pVTZ. Computed results were compared with the experimental data. Error metrics and statistical tools were used to validate the methods tested. Results showed an excellent agreement between the computed results and the experimental ones. Nature of the substituted groups and solvent effect on AIP values were investigated. Changes in the geometrical structures of cationic species were compared with neutral ones.

Recent Progress in the Simulation of Chiral Systems with Real Time Propagation Methods

AbstractIn this brief review, an overview about recent efforts to simulate the spectroscopic signatures of chiral molecules is given with focus on real time propagation approaches to solve the time‐dependentSchrödingerequation. In particular the simulation of electric circular dichroism spectra and vibrationalRamanoptical activity is discussed. In comparison to linear absorption spectra, where only the response of the electric dipole moment is necessary, the response of the magnetic dipole moment and electric quadrupole moment is more intricate. Issues such as gauge origin dependence, basis set dependence, non‐local potentials and the dipole approximation are addressed.

The curious case of DMSO: A CCSD(T)/CBS(aQ56+d) benchmark and DFT study.

This work addresses the pathological behavior of the energetics of dimethyl sulfoxide and related sulfur-containing compounds by providing the computational benchmark energetics of R2E2 species, where R = H/CH3 and E = O/S, with bent and pyramidal geometries using state-of-the-art methodologies. These 22 geometries were fully characterized with coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)], second-order Møller-Plesset perturbation theory (MP2), and 22 density functional theory (DFT) methods with 8, 12, and 12, respectively, correlation consistent basis sets of double-, triple-, or quadruple-ζ quality. The relative energetics were determined at the MP2 and CCSD(T) complete basis set (CBS) limits using 17 basis sets up to sextuple-ζ and include augmented, tight-d, and core-valence correlation consistent basis sets. The relative energies of oxygen-/sulfur-containing compounds exhibit exceptionally slow convergence to the CBS limit with canonical methods as well as significant basis set dependence. CCSD(T) with quadruple-ζ basis sets can give qualitatively incorrect relative energies. Explicitly correlated MP2-F12 and CCSD(T)-F12 methods dramatically accelerate the convergence of the relative energies to the CBS limit for these problematic compounds. The F12 methods with a triple-ζ quality basis set give relative energies that deviate no more than 0.41kcal mol-1 from the benchmark CBS limit. The correlation consistent Composite Approach (ccCA), ccCA-TM (TM for transition metals), and G3B3 deviated by no more than 2kcal mol-1 from the benchmark CBS limits. Relative energies for oxygen-/sulfur-containing systems fully characterized with DFT are quite unreliable even with triple-ζ quality basis sets, and 13 out of 45 combinations fortuitously give a relative energy that is within 1kcal mol-1 on average from the benchmark CCSD(T) CBS limit for these systems.

Efficient Four-Component Dirac-Coulomb-Gaunt Hartree-Fock in the Pauli Spinor Representation.

Four-component Dirac-Hartree-Fock is an accurate mean-field method for treating molecular systems where relativistic effects are important. However, the computational cost and complexity of the two-electron interaction make this method less common, even though we can consider the Dirac-Hartree-Fock Hamiltonian the "ground truth" of the electronic structure, barring explicit quantum electrodynamical effects. Being able to calculate these effects is then vital to the design of lower scaling methods for accurate predictions in computational spectroscopy and properties of heavy element complexes that must include relativistic effects for even qualitative accuracy. In this work, we present a Pauli quaternion formalism of maximal component and spin separation for computing the Dirac-Coulomb-Gaunt Hartree-Fock ground state, with a minimal floating point operation count algorithm. This approach also allows one to explicitly separate different spin physics from the two-body interactions, such as spin-free, spin-orbit, and spin-spin contributions. Additionally, we use this formalism to examine relativistic trends in the periodic table and analyze the basis set dependence of atomic gold and gold dimer systems.

A critical analysis of least-squares tensor hypercontraction applied to MP3.

The least-squares tensor hypercontraction (LS-THC) approach is a promising method of reducing the high polynomial scaling of wavefunction methods, for example, those based on many-body perturbation theory or coupled cluster. Here, we focus on LS-THC-MP3 and identify four variants with differing errors and efficiency characteristics. The performance of LS-THC-MP3 is analyzed for regular test systems with up to 40 first-row atoms. We also analyze the size-extensivity/size-consistency and grid- and basis set dependence of LS-THC-MP3. Overall, the errors observed are favorably small in comparison with standard density fitting, and a more streamlined method of generating grids via pruning is suggested. A practical crossover (the point at which LS-THC-MP3 is cheaper than the canonical method) is achieved around 240 correlated electrons. Despite several drawbacks of LS-THC that have been identified: an initial non-linearity of error when increasing system size, poor description of angular correlation, and a potentially large increase in error with the basis set size, the results show that LS-THC has significant potential for practical application to MP3 and other wavefunction methods.

Optimized Atomic Partial Charges and Radii Defined by Radical Voronoi Tessellation of Bulk Phase Simulations.

We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Voronoi integration. The approach is particularly well suited for the calculation of partial charges in periodic bulk phase systems. We apply the method to five exemplary liquid phase simulations and show how the optimized charges can help to understand the interactions in the systems. Well-known effects such as reduced ion charges below unity in ionic liquid systems are correctly predicted without any tuning, empiricism, or rescaling. We show that the basis set dependence of our method is very small. Only the total electron density is evaluated, and thus, the approach can be combined with any electronic structure method that provides volumetric total electron densities—it is not limited to Hartree–Fock or density functional theory (DFT). We have implemented the method into our open-source software tool TRAVIS.

A Simple Range-Separated Double-Hybrid Density Functional Theory for Excited States.

A simple and robust range-separated (RS) double-hybrid (DH) time-dependent density functional approach is presented for the accurate calculation of excitation energies of molecules within the Tamm–Dancoff approximation. The scheme can be considered as an excited-state extension of the ansatz proposed by Toulouse and co-workers [J. Chem. Phys. 2018, 148, 164105], which is based on the two-parameter decomposition of the Coulomb potential, for which both the exchange and correlation contributions are range-separated. A flexible and efficient implementation of the new scheme is also presented, which facilitates its extension to any combination of exchange and correlation functionals. The performance of the new approximation is tested for singlet excitations on several benchmark compilations and thoroughly compared to that of representative DH, RS hybrid, and RS DH functionals. The one-electron basis set dependence and computation times are also assessed. Our results show that the new approach improves on standard DHs in most cases, and it can provide a more robust and accurate alternative. In addition, on average, it noticeably surpasses the existing RS hybrid and RS DH functionals.

Systematic comparison and cross-validation of fixed-node diffusion Monte Carlo and phaseless auxiliary-field quantum Monte Carlo in solids

Quantum Monte Carlo (QMC) methods are some of the most accurate methods for simulating correlated electronic systems. We investigate the compatibility, strengths and weaknesses of two such methods, namely, diffusion Monte Carlo (DMC) and auxiliary-field quantum Monte Carlo (AFQMC). The multi-determinant trial wave functions employed in both approaches are generated using the configuration interaction using a perturbative selection made iteratively (CIPSI) technique. Complete basis set full configuration interaction (CBS-FCI) energies estimated with CIPSI are used as a reference in this comparative study between DMC and AFQMC. By focusing on a set of canonical finite size solid state systems, we show that both QMC methods can be made to systematically converge towards the same energy once basis set effects and systematic biases have been removed. AFQMC shows a much smaller dependence on the trial wavefunction than DMC while simultaneously exhibiting a much larger basis set dependence. We outline some of the remaining challenges and opportunities for improving these approaches.

A theoretical study for the role of complex in hydrogen abstraction of OH

A theoretical study was presented to discuss complex formation on hydrogen abstraction of OH radicals based on detailed potential energy surface at different levels. Three different triple-ζ basis sets and the corresponding augmented sets were compared to discuss the basis set dependence for weak atomic and molecular interactions. The generalized internal coordinates of the geometric centres were scanned to describe monomer collision. Hydrogen bond interactions and steric effects were visualized by wave function analyses. Rate constant calculation results compared well with experiments and highly accurate potential energy surface in terms of state-to-state accuracy especially in low temperature range.

DFT benchmark study of the O–O bond dissociation energy in peroxides validated with high-level ab initio calculations

Peroxides play a central role in many chemical and biological processes such as the Fenton reaction. The relevance of these compounds lies in the low stability of the O–O bond which upon dissociation results in radical species able to initiate various chemical or biological processes. In this work, a set of 64 DFT functional-basis set combinations has been validated in terms of their capability to describe bond dissociation energies (BDE) for the O–O bond in a database of 14 ROOH peroxides for which experimental values of BDE are available. Moreover, the electronic contributions to the BDE were obtained for four of the peroxides and the anion $$\hbox {H}_2\hbox {O}_2^-$$ at the CBS limit at CCSD(T) level with Dunning’s basis sets up to triple- $$\zeta$$ quality providing a reference value for the hydrogen peroxide anion as a model. Almost all the functionals considered here yielded mean absolute deviations around $$5.0\hbox { kcal mol}^{-1}$$ . The smallest values were observed for the $$\omega$$ B97 family and the Minnesota M11 functional with a marked basis set dependence. Despite the mean deviation, order relations among BDE experimental values of peroxides were also considered. The $$\omega$$ B97 family was able to reproduce the relations correctly whereas other functionals presented a marked dependence on the chemical nature of the R group. Interestingly, M11 functional did not show a very good agreement with the established order despite its good performance in the mean error. The obtained results support the use of similar validation strategies for proper prediction of BDE or other molecular properties by DFT methods in subsequent related studies.

Spin-Orbit Matrix Elements for a Combined Spin-Flip and IP/EA approach.

We present a practical approach for computing the Breit-Pauli spin-orbit matrix elements of multiconfigurational systems with both spin and spatial degeneracies based on our recently developed RAS-nSF-IP/EA method (Houck, S. E.; et al. J. Chem. Theory Comput. 2019, 15, 2278). The spin-orbit matrix elements over all the multiplet components are computed using a single one-particle reduced density matrix as a result of the Wigner-Eckart theorem. A mean field spin-orbit approximation was used to account for the two-electron contributions. Basis set dependence as well as the effect of including additional excitations is presented. The effect of correlating the core and semicore orbitals is also examined. Surprisingly accurate results are obtained for spin-orbit coupling constants, despite the fact that the efficient wave function approximations we explore neglect the bulk of dynamical correlation.