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DOE OSTI2020

Third-Order Møller–Plesset Theory Made More Useful? The Role of Density Functional Theory Orbitals

The practical utility of Møller–Plesset (MP) perturbation theory is severely constrained by the use of Hartree–Fock (HF) orbitals. It has recently been shown that the use of regularized orbital-optimized MP2 orbitals and scaling of MP3 energy could lead to a significant reduction in MP3 error. In this work, we examine whether density functional theory (DFT)-optimized orbitals can be similarly employed to improve the performance of MP theory at both the MP2 and MP3 levels. We find that the use of DFT orbitals leads to significantly improved performance for prediction of thermochemistry, barrier heights, noncovalent interactions, and dipole moments relative to the standard HF-based MP theory. Indeed, MP3 (with or without scaling) with DFT orbitals is found to surpass the accuracy of coupled-cluster singles and doubles (CCSD) for several data sets. We also found that the results are not particularly functional sensitive in most cases (although range-separated hybrid functionals with low delocalization error perform the best). As such, MP3 based on DFT orbitals thus appears to be an efficient, noniterative O(N 6 ) scaling wave-function approach for single-reference electronic structure computations. Scaled MP2 with DFT orbitals is also found to be quite accurate in many cases, although modern double hybrid functionals are likely to be considerably more accurate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Push it to the limit: comparing periodic and local approaches to density functional theory for intermolecular interactions

With the aim of systematically comparing two popular approaches to density functional theory–all-electron calculations with local basis sets, and periodic calculations employing plane wave basis sets and norm-conserving pseudopotentials–we have computed complete-basis binding energies across the S22 set of intermolecular interactions, a dataset consisting of noncovalent interactions of small- and medium-sized molecules containing first- and second-row atoms, using the Troullier-Martins norm-conserving pseudopotentials with SPW92, a local spin-density approximation; and PBE, a generalised gradient approximation. Here, we have found that it is challenging to reach the basis set limit with these periodic calculations; for the methods and systems examined, a minimum vacuum distance of 30 Å between a system and its nearest images is necessary–unless some form of dipole correction is employed–as is a kinetic energy cutoff of at least 80 Ry. The trends in convergence with respect to vacuum size and kinetic energy cutoff are largely independent of the level of density functional approximation employed. A sense of the impact of each hyperparameter on basis set error provides a foundation for ensuring quality calculations in future studies and allows us to quantify the basis set errors incurred in existing studies on similar systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Giant Dipole Moments: Remarkable Effects Mono‐, Di‐, and Tri‐ Hydrated 5,6‐Diaminobenzene‐1,2,3,4‐Tetracarbonnitrile

The molecule 5,6-diaminobenzene-1,2,3,4-tetracarbonnitrile (MOI) was first synthesized by Müllen and coworkers in 2016 and boasts an ultrastrong dipole moment of $14.1\pm 0.7$ Debye in THF. Gas phase DFT computations do not fully reflect this ultrastrong dipole moment, demonstrating the role of solvent in increasing this dipole moment. Here, we investigate the effect of solvent molecule position on the dipole moment of this species, computationally examining systems with giant dipole moments. These systems are optimized in the gas phase with the B3LYP functional, employing the aug-cc-pVTZ and def2-TZVP basis sets, as well as the B3LYP-D3BJ/aug-cc-pVTZ functional in Orca. Single point DLPNO-CCSD/aug-cc-pVDZ results were obtained from Orca and Psi4, as well as DLPNO-CCSD(T)/CBS information from Psi4. Additionally, these are compared to the dipole moments of di- and tri-hydrated systems, and the SMD models for THF and water at the B3LYP/aug-cc-pVTZ level of theory. The dissociation energies, HOMO-LUMO energy gaps, and dipole moments are presented. These metrics show the nh1nh1′ THF system boasts the largest dissociation energy and dipole moment of the singly solvated systems, due to its strong hydrogen bonding. The importance of solvent placement is highlighted and may guide the synthesis of macromolecules or organic frameworks incorporating the MOI or MOI-like subunits. Remarkably, a single solvent molecule provides a good model for the difference between the gas phase and solvated species. The predicted gas phase dipole moments computed with B3LYP/aug-cc-pVTZ for the MOI, its monohydrated complex, dihydrated complex, and its trihydrated complex are 9.6, 14.2, 16.0, and 16.8 Debye, respectively.

dipole↗

NASA NTRS2010

GOATS - Orbitology Component

The GOATS Orbitology Component software was developed to specifically address the concerns presented by orbit analysis tools that are often written as stand-alone applications. These applications do not easily interface with standard JPL first-principles analysis tools, and have a steep learning curve due to their complicated nature. This toolset is written as a series of MATLAB functions, allowing seamless integration into existing JPL optical systems engineering modeling and analysis modules. The functions are completely open, and allow for advanced users to delve into and modify the underlying physics being modeled. Additionally, this software module fills an analysis gap, allowing for quick, high-level mission analysis trades without the need for detailed and complicated orbit analysis using commercial stand-alone tools. This software consists of a series of MATLAB functions to provide for geometric orbit-related analysis. This includes propagation of orbits to varying levels of generalization. In the simplest case, geosynchronous orbits can be modeled by specifying a subset of three orbit elements. The next case is a circular orbit, which can be specified by a subset of four orbit elements. The most general case is an arbitrary elliptical orbit specified by all six orbit elements. These orbits are all solved geometrically, under the basic problem of an object in circular (or elliptical) orbit around a rotating spheroid. The orbit functions output time series ground tracks, which serve as the basis for more detailed orbit analysis. This software module also includes functions to track the positions of the Sun, Moon, and arbitrary celestial bodies specified by right ascension and declination. Also included are functions to calculate line-of-sight geometries to ground-based targets, angular rotations and decompositions, and other line-of-site calculations. The toolset allows for the rapid execution of orbit trade studies at the level of detail required for the early stage of mission concept development.

Haber, Benjamin M.↗

NASA NTRS1979

Astrophysical gamma-ray production by inverse Compton interactions of relativistic electrons

The inverse Compton scattering of background photon gases by relativistic electrons is a good candidate for the production of high-energy gamma rays in the diffuse interstellar medium as well as in discrete sources. By discussing the special case of the scattering of the diffuse starlight in the interstellar medium by cosmic ray electrons, we demonstrate that previous derivations of the gamma ray source function for this process on the basis of the Thomson limit of the Klein-Nishina cross section lead to incorrect values for gamma-ray energies above 100 MeV. It is shown that the Thomson limit is not applicable for the calculation of gamma-ray source functions in astrophysical circumstances in which target photons with energies greater than 1 eV are scattered by relativistic electrons.

Schlickeiser, R.↗

DOE OSTI2016

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Structure of human dual-specificity phosphatase 27 at 2.38 Å resolution

There are over 100 genes in the human genome that encode protein tyrosine phosphatases (PTPs) and approximately 60 of these are classified as dual-specificity phosphatases (DUSPs). Although many dual-specificity phosphatases are still not well characterized, novel functions have been discovered for some of them that have led to new insights into a variety of biological processes and the molecular basis for certain diseases. Indeed, as the functions of DUSPs continue to be elucidated, a growing number of them are emerging as potential therapeutic targets for diseases such as cancer, diabetes and inflammatory disorders. Here, the overexpression, purification and structure determination of DUSP27 at 2.38 {angstrom} resolution are presented.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

3-[4-Bromo-α(R)-methoxybenzyl]-6-chloro-3(S),4(S*)-dihydroxychroman: X-ray and DFT Studies

Sodium borohydride reduction of E-3-benzylidenechromanone epoxides in dry methanol has afforded 3(S*), 4(S*)-dihydroxy-3-[α(R*)-methoxybenzyl]chromans as an interesting class of products, the structures of which have been assigned mainly from spectral data and consideration of the mechanistic aspects. X-ray diffraction study of one of them, 3-[4-bromo-α(R*)-methoxybenzyl]-6-chloro-3(S*),4(S*)- dihydroxychroman, is performed. The title compound crystallizes in the monoclinic sp. gr. P2{sub 1}/n, with a = 13.336(6) Å, b = 10.866(5) Å, c = 27.166(11) Å, β = 95.193(6)°, V = 3920(3) Å{sup 3}, and Z = 8. Supramolecular construction of the compound involves O–H···O intermolecular hydrogen bonds as well as three other types of non-covalent interactions which are responsible for crystal packing. Density functional theory was applied for geometry optimization, molecular orbital calculations, and prediction of UV spectral features. The geometric parameters (bond lengths, bond angles, and dihedral angles) for the representative compound obtained from density functional theory with B3LY6-31G basis set were in good agreement with experimental values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Non-additive non-interacting kinetic energy of rare gas dimers

We show approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE. We use numerically accurate inversions to study the exact NAKE of several rare-gas dimers within partition density functional theory, a method that provides the uniqueness for the exact NAKE. We find that the NAKE decreases nearly exponentially with atomic separation for the rare-gas dimers. We compute the logarithmic derivative of the NAKE with respect to the bond length for our numerically accurate inversions as well as for several approximate NAKE functionals. We show that standard approximate NAKE functionals do not reproduce the correct behavior for this logarithmic derivative and propose two new NAKE functionals that do. The first of these is based on a re-parametrization of a conjoint Perdew-Burke-Ernzerhof (PBE) functional. The second is a simple, physically motivated non-decomposable NAKE functional that matches the asymptotic decay constant without fitting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2005

Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

Lee, Timothy J.↗

DOE OSTI2022

Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost

Hybrid or “extended” symmetry-adapted perturbation theory (XSAPT) replaces traditional SAPT’s treatment of dispersion with better performing alternatives while at the same time extending two-body (dimer) SAPT to a many-body treatment of polarization using a self-consistent charge embedding procedure. The present work presents a systematic study of how XSAPT interaction energies and energy components converge with respect to the choice of Gaussian basis set. Errors can be reduced in a systematic way using correlation-consistent basis sets, with aug-cc-pVTZ results converged within <0.1 kcal/mol. Similar (if slightly less systematic) behavior is obtained using Karlsruhe basis sets at much lower cost, and we introduce new versions with limited augmentation that are even more efficient. Pople-style basis sets, which are more efficient still, often afford good results if a large number of polarization functions are included. The dispersion models used in XSAPT afford much faster basis-set convergence as compared to the perturbative description of dispersion in conventional SAPT, meaning that “compromise” basis sets (such as jun-cc-pVDZ) are no longer required and benchmark-quality results can be obtained using triple-ζ basis sets. The use of diffuse functions proves to be essential, especially for the description of hydrogen bonds. As a result, the “δ(Hartree–Fock)” correction for high-order induction can be performed in double-ζ basis sets without significant loss of accuracy, leading to a mixed-basis approach that offers 4× speedup over the existing (cubic scaling) XSAPT approach.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2018

Compressive Deformation Behavior of Open-Cell Cu-Zn-Al Alloy Foam Made Through P/M Route Using Mechanically Alloyed Powder

Cu-Zn-Al foams of varying porosity fractions using mechanical alloyed powder have been made through powder metallurgy route. Here, NH{sub 4} (HCO{sub 3}) was used as a space holder. Mechanically alloyed Cu-Zn-Al is made using a planetary ball mill taking the ratio of Cu/Zn/Al = 70:25:5 (by weight ratio). The ball/powder ratios were varied in the four ranges 10:1, 15:1, 20:1, and 25:1. Green compacts of milled powder and space holder samples were sintered at three stages at three different temperatures 350, 550, and 850 °C for 1 h at each stage. The crystalline size and particle size as a function of ball/powder ratios were examined. The compressive deformation responses of foams are varied with relative density and the ball/powder ratio. The plateau stress and energy absorption of these foams increase with an increase in relative density but decreases with increase in ball/powder ratio, even though crystalline size decreases. This has further been explained on the basis of particle morphology as a function of ball/powder ratio.

36 MATERIALS SCIENCE↗

NASA NTRS1987

A method of calculating the total flow from a given sea surface topography

Using a simple dynamical model of a wind-driven ocean circulation of the Stommel type, and an analytical basis developed to objectively analyze the sea surface height residuals from an altimeter and, in the process, to determine the total flow instead of just the near surface geostrophic component associated with the given sea surface topography. The method is based on first deriving the solution to the forced problem for a given wind stress required to develop a hypothetical true or perfect data field and to establishing the basis for the objective analysis. The stream function and the surface height field for the forced problem are developed in terms of certain characteristic functions with the same expansion coefficients for both fields. These characteristic functions are simply the solutions for a homogeneous elliptic equation for the stream function and the solutions of an inhomogeneous balance equation for the height field. For the objective analysis, using a sample of randomly selected height values from the true data field, the height field characteristic functions are used to fit the given topography in a least squares sense. The resulting expansion coefficients then permit the synthesis of the total flow field via the stream function characteristic modes and the solution is perfectly well behaved even along the equator. The method of solution is easily adaptable to realistic ocean basis by straight forward numerical methods. The analytical basis of the theory and the results for an ideal rectangular basin on a beta plane are described.

Rao, Desiraju B.↗

DOE OSTI2017

On extending Kohn-Sham density functionals to systems with fractional number of electrons

Here, we analyze four ways of formulating the Kohn-Sham (KS) density functionals with a fractional number of electrons, through extending the constrained search space from the Kohn-Sham and the generalized Kohn-Sham (GKS) non-interacting $\mathcal{v}$-representable density domain for integer systems to four different sets of densities for fractional systems. In particular, these density sets are (I) ensemble interacting N -representable densities, (II) ensemble non-interacting N -representable densities, (III) non-interacting densities by the Janak construction, and (IV) non-interacting densities whose composing orbitals satisfy the Aufbau occupation principle. By proving the equivalence of the underlying first order reduced density matrices associated with these densities, we show that sets (I), (II), and (III) are equivalent, and all reduce to the Janak construction. Moreover, for functionals with the ensemble v-representable assumption at the minimizer, (III) reduces to (IV) and thus justifies the previous use of the Aufbau protocol within the (G)KS framework in the study of the ground state of fractional electron systems, as defined in the grand canonical ensemble at zero temperature. By further analyzing the Aufbau solution for different density functional approximations (DFAs) in the (G)KS scheme, we rigorously prove that there can be one and only one fractional occupation for the Hartree Fock functional, while there can be multiple fractional occupations for general DFAs in the presence of degeneracy. This has been confirmed by numerical calculations using the local density approximation as a representative of general DFAs. This work thus clarifies important issues on density functional theory calculations for fractional electron systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Robust, Accurate, and Efficient: Quantum Embedding Using the Huzinaga Level-Shift Projection Operator for Complex Systems

Using wave function (WF) in density functional theory (DFT) embedding methods provides a framework for performing localized, high-accuracy WF calculations on a system, while not incurring the full computational cost of the WF calculation on the full system. To effectively partition a system into localized WF and DFT subsystems, we utilize the Huzinaga level-shift projection operator within an absolutely localized basis. In this work, we study the ability of the absolutely localized Huzinaga level-shift projection operator method to study complex WF and DFT partitions, including partitions between multiple covalent bonds, a double bond, and transition-metal–ligand bonds. We find that our methodology can accurately describe all of these complex partitions. Additionally, we study the robustness of this method with respect to the WF method, specifically where the embedded systems were described using a multiconfigurational WF method. We found that the method is systematically improvable with respect to both the number of atoms in the WF region and the size of the basis set used, with energy errors less than 1 kcal/mol. Additionally, we calculated the adsorption energy of H2 to a model of an iron metal–organic framework (Fe-MOF-74) to within 1 kcal/mol compared to CASPT2 calculations performed on the full model while incurring only a small fraction of the full computational cost. In conclusion, this work demonstrates that the absolutely localized Huzinaga level-shift projection operator method is applicable to very complex systems with difficult electronic structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

We present that the fast-growing Gram-negative bacterium Vibrio natriegens is an attractive microbial system for molecular biology and biotechnology due to its remarkably short generation time and metabolic prowess. However, efforts to uncover and utilize the mechanisms underlying its rapid growth are hampered by the scarcity of functional genomic data. Here, we develop a pooled genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) screen to identify a minimal set of genes required for rapid wild-type growth. Targeting 4,565 (99.7%) of predicted protein-coding genes, our screen uncovered core genes comprising putative essential and growth-supporting genes that are enriched for respiratory pathways. We found that 96% of core genes were located on the larger chromosome 1, with growth-neutral duplicates of core genes located primarily on chromosome 2. Lastly, our screen also refines metabolic pathway annotations by distinguishing functional biosynthetic enzymes from those predicted on the basis of comparative genomics. Taken together, this work provides a broadly applicable platform for high-throughput functional genomics to accelerate biological studies and engineering of V. natriegens.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1990

On the dissociation energy of Mg2

The bonding in the X 1Sigma(+)g state of Mg2 is investigated using near-complete valence one-particle Slater and Gaussian basis sets containing up to h functions. It is shown that the four-electron complete CI limit can be approached using a sequence of either second-order CI (SOCI) or interacting correlated fragment (ICF) calculations. At the valence level, the best estimate of the dissociation energy D(e) was 464/cm. This is a lower limit and is probably within 5/cm of the complete basis value.

Partridge, Harry↗

NASA NTRS1990

Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets

Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.

Dyall, Kenneth G.↗