The Good, the Bad, and the Ugly: Pseudopotential Inconsistency Errors in Molecular Applications of Density Functional Theory.

The pseudopotential (PP) approximation is one of the most common techniques in computational chemistry. Despite its long history, the development of custom PPs has not tracked with the explosion of different density functional approximations (DFAs). As a result, the use of PPs with exchange/correlation models for which they were not developed is widespread, although this practice is known to be theoretically unsound. The extent of PP inconsistency errors (PPIEs) associated with this practice has not been systematically explored across the types of energy differences commonly evaluated in chemical applications. We evaluate PPIEs for a number of PPs and DFAs across 196 chemically relevant systems of both transition-metal and main-group elements, as represented by the W4-11, TMC34, and S22 data sets. Near the complete basis set limit, these PPs are found to cleanly approach all-electron (AE) results for noncovalent interactions but introduce root-mean-squared errors (RMSEs) upwards of 15 kcal mol-1 into predictions of covalent bond energies for a number of popular DFAs. We achieve significant improvements through the use of empirical atom- and DFA-specific PP corrections, indicating considerable systematicity of the PPIEs. The results of this work have implications for chemical modeling in both molecular contexts and for DFA design, which we discuss.

Electron-Affinity Time-Dependent Density Functional Theory: Formalism and Applications to Core-Excited States.

The lack of particle-hole attraction and orbital relaxation within time-dependent density functional theory (TDDFT) lead to extreme errors in the prediction of K-edge X-ray absorption spectra (XAS). We derive a linear-response formalism that uses optimized orbitals of the n - 1-electron system as the reference, building orbital relaxation and a proper hole into the initial density. Our approach is an exact generalization of the static-exchange approximation that ameliorates the particle-hole interaction error associated with the adiabatic approximation and reduces errors in TDDFT XAS by orders of magnitude. With a statistical performance of just 0.5 eV root-mean-square error and the same computational scaling as TDDFT under the core-valence separation approximation, we anticipate that this approach will be of great utility in XAS calculations of large systems.

Accurate core excitation and ionization energies from a state-specific coupled-cluster singles and doubles approach.

We investigate the use of orbital-optimized references in conjunction with single-reference coupled-cluster theory with single and double substitutions (CCSD) for the study of core excitations and ionizations of 18 small organic molecules, without the use of response theory or equation-of-motion (EOM) formalisms. Three schemes are employed to successfully address the convergence difficulties associated with the coupled-cluster equations, and the spin contamination resulting from the use of a spin symmetry-broken reference, in the case of excitations. In order to gauge the inherent potential of the methods studied, an effort is made to provide reasonable basis set limit estimates for the transition energies. Overall, we find that the two best-performing schemes studied here for ΔCCSD are capable of predicting excitation and ionization energies with errors comparable to experimental accuracies. The proposed ΔCCSD schemes reduces statistical errors against experimental excitation energies by more than a factor of two when compared to the frozen-core core-valence separated (FC-CVS) EOM-CCSD approach - a successful variant of EOM-CCSD tailored towards core excitations.

Relativistic Orbital-Optimized Density Functional Theory for Accurate Core-Level Spectroscopy.

Core-level spectra of 1s electrons of elements heavier than Ne show significant relativistic effects. We combine advances in orbital-optimized density functional theory (OO-DFT) with the spin-free exact two-component (X2C) model for scalar relativistic effects to study K-edge spectra of third period elements. OO-DFT/X2C is found to be quite accurate at predicting energies, yielding a ∼0.5 eV root-mean-square error versus experiment with the modern SCAN (and related) functionals. This marks a significant improvement over the >50 eV deviations that are typical for the popular time-dependent DFT (TDDFT) approach. Consequently, experimental spectra are quite well reproduced by OO-DFT/X2C, sans empirical shifts for alignment. OO-DFT/X2C combines high accuracy with ground state DFT cost and is thus a promising route for computing core-level spectra of third period elements. We also explored K and L edges of 3d transition metals to identify limitations of the OO-DFT/X2C approach in modeling the spectra of heavier atoms.

Approaching the basis set limit in Gaussian-orbital-based periodic calculations with transferability: Performance of pure density functionals for simple semiconductors.

Simulating solids with quantum chemistry methods and Gaussian-type orbitals (GTOs) has been gaining popularity. Nonetheless, there are few systematic studies that assess the basis set incompleteness error (BSIE) in these GTO-based simulations over a variety of solids. In this work, we report a GTO-based implementation for solids and apply it to address the basis set convergence issue. We employ a simple strategy to generate large uncontracted (unc) GTO basis sets that we call the unc-def2-GTH sets. These basis sets exhibit systematic improvement toward the basis set limit as well as good transferability based on application to a total of 43 simple semiconductors. Most notably, we found the BSIE of unc-def2-QZVP-GTH to be smaller than 0.7 mEh per atom in total energies and 20 meV in bandgaps for all systems considered here. Using unc-def2-QZVP-GTH, we report bandgap benchmarks of a combinatorially designed meta-generalized gradient approximation (mGGA) functional, B97M-rV, and show that B97M-rV performs similarly (a root-mean-square-deviation of 1.18 eV) to other modern mGGA functionals, M06-L (1.26 eV), MN15-L (1.29 eV), and Strongly Constrained and Appropriately Normed (SCAN) (1.20 eV). This represents a clear improvement over older pure functionals such as local density approximation (1.71 eV) and Perdew-Burke-Ernzerhof (PBE) (1.49 eV), although all these mGGAs are still far from being quantitatively accurate. We also provide several cautionary notes on the use of our uncontracted bases and on future research on GTO basis set development for solids.

Exploring spin symmetry-breaking effects for static field ionization of atoms: Is there an analog to the Coulson-Fischer point in bond dissociation?

Löwdin's symmetry dilemma is an ubiquitous issue in approximate quantum chemistry. In the context of Hartree-Fock (HF) theory, the use of Slater determinants with some imposed constraints to preserve symmetries of the exact problem may lead to physically unreasonable potential energy surfaces. On the other hand, lifting these constraints leads to the so-called broken symmetry solutions that usually provide better energetics, at the cost of losing information about good quantum numbers that describe the state of the system. This behavior has previously been extensively studied in the context of bond dissociation. This paper studies the behavior of different classes of HF spin polarized solutions (restricted, unrestricted, and generalized) in the context of ionization by strong static electric fields. We find that, for simple two electron systems, unrestricted Hartree-Fock (UHF) is able to provide a qualitatively good description of states involved during the ionization process (neutral, singly ionized, and doubly ionized states), whereas RHF fails to describe the singly ionized state. For more complex systems, even though UHF is able to capture some of the expected characteristics of the ionized states, it is constrained to a single Ms (diabatic) manifold in the energy surface as a function of field intensity. In this case, a better qualitative picture can be painted by using generalized Hartree-Fock as it is able to explore different spin manifolds and follow the lowest solution due to lack of collinearity constraints on the spin quantization axis.

Management of complex hernias with loss of domain using daily and fractioned preoperative progressive pneumoperitoneum: a retrospective single-center cohort study.

PURPOSE: The incidence of complex hernias with loss of domain (CHLD) has been increasing and the treatment of these cases may require auxiliary techniques in addition to surgery. This study aims to refine the progressive preoperative pneumoperitonium (PPP) in patients with CHLD, to achieve an increased in wall dimensions. METHODS: Patients presented with a CHLD undergoing PPP protocol were analyzed between May 2017 and May 2019. Our PPP protocol was to use two daily insufflations of 1000 ml of ambient air during a period of 14 days. We compared the abdominal cavity volume (ACV), the hernial sac volume (HSV) and the volume ratio (VR), before and after our refined PPP. RESULTS: During our evaluation period, the protocol was performed on 16 patients. The mean age was 55.73 (± 12.87), and the mean BMI was 31.35 (± 7.33). The median of HSV was 2104.53 ml; Mean ACV was 6722.36 ml, and median of VR was 29.97% (27.46-34.38 IIQ). The averages were: daily volume of gas ± 1526.66 ml, total volume ± 17,350 ml, and the PPP period of ± 10.7 days. The increase in post-PPP ACV was 52.13% (p < 0.0001), and the VR decreased to 26.9% (p < 0.609). All patients' symptoms and complications were mild (according Clavien-Dindo grades I and II), and there were no loop injuries, no catheter complications, or any surgical re-interventions. CONCLUSION: The study suggests that the use of this method results in a significant increase in ACV, and reduction of the herniated content in a safe and efficient manner, with mild complications.

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

Thermochemical and Kinetics of CH3SH + H Reactions: The Sensitivity of Coupling the Low and High-Level Methodologies.

The reaction system formed by the methanethiol molecule (CH3SH) and a hydrogen atom was studied via three elementary reactions, two hydrogen abstractions and the C-S bond cleavage (CH3SH + H → CH3S + H2 (R1); → CH2SH + H2 (R2); → CH3 + H2S (R3)). The stable structures were optimized with various methodologies of the density functional theory and the MP2 method. Two minimum energy paths for each elementary reaction were built using the BB1K and MP2 methodologies, and the electronic properties on the reactants, products, and saddle points were improved with coupled cluster theory with single, double, and connected triple excitations (CCSD(T)) calculations. The sensitivity of coupling the low and high-level methods to calculate the thermochemical and rate constants were analyzed. The thermal rate constants were obtained by means of the improved canonical variational theory (ICVT) and the tunneling corrections were included with the small curvature tunneling (SCT) approach. Our results are in agreement with the previous experimental measurements and the calculated branching ratio for R1:R2:R3 is equal to 0.96:0:0.04, with kR1 = 9.64 × 10-13 cm3 molecule-1 s-1 at 298 K.

Thermochemical and kinetics studies of the CH3SH+S (3P) hydrogen abstraction and insertion reactions.

Sulfur-containing molecules have a significant impact on atmosphere and biosphere. In this work we studied, from the point of view of electronic structure and chemical kinetics methods, the elementary reactions between a methanethiol molecule and a sulfur atom leading to hydrogen abstraction C-S bond cleavage (CH(3)SH+S; R1:→ CH(3)S+SH; R2: → CH(2)SH+SH; R3:→ CH(3)+HS(2)). The geometrical structures of the reactants, products, and saddle points for the three reaction paths were optimized using the BB1K method with the aug-cc-pV(T+d)Z basis set. The thermochemical properties were improved using single point coupled-cluster (CCSD(T)) calculations on the BB1K geometries followed by extrapolation to the complete basis set (CBS) limit. This methodology was previously applied and has given accurate values of thermochemical and kinetics properties when compared to benchmark calculations and experimental data. For each reaction, the thermal rate constants were calculated using the improved canonical variational theory (ICVT) including the zero-curvature (ICVT/ZCT) and small-curvature (ICVT/SCT) tunneling corrections. For comparison, the overall ICVT/SCT reaction rate constant at 300 K obtained with single-point CCSD(T)/CBS calculations for the CH(3)SH+S reaction is approximately 1400 times lower than the isovalent CH(3)SH+O reaction, obtained with CVT/SCT. The reaction path involving the hydrogen abstraction from the thiol group is the most important reactive path in all temperatures.

Polymorphisms of Lewis and Secretor genes are related to breast cancer and metastasis in axillary lymph nodes.

ABH and Lewis antigen expression has been associated with cancer development and prognosis, tumor differentiation, and metastasis. Considering that invasive ductal breast carcinoma (IDC) presents multiple molecular alterations, the aim of the present study was to determine whether the polymorphism of ABO, Lewis, and Secretor genes, as well as ABO phenotyping, could be associated with tumor differentiation and lymph nodes metastasis. Seventy-six women with IDC and 78 healthy female blood donors were submitted to ABO phenotyping/genotyping and Lewis and Secretor genotyping. Phenotyping was performed by hemagglutination and genotyping by the polymerase chain reaction with sequence-specific primers. ABO, Lewis, and Secretor genes were classified by individual single nucleotide polymorphism at sites 59, 1067, 202, and 314 of the Lewis gene, 428 of the Secretor gene, and 261 (O1 allele), 526 (O2 and B allele), and 703 (B allele). No association was found between breast cancer and ABO antigen expression (P = 0.9323) or genotype (P = 0.9356). Lewis-negative genotype was associated with IDC (P = 0.0126) but not with anatomoclinical parameters. Nonsecretor genotype was associated with axillary lymph node metastasis (P = 0.0149). In conclusion, Lewis and Secretor genotyping could be useful to predict respectively breast cancer susceptibility and axillary lymph nodes metastasis.