Interoperable workflows by exchanging grid-based data between quantum-chemical program packages.

Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.

Comparison of Different Types of Palatal Expanders: Scoping Review.

Maxillary bone contraction is caused by genetics or ambiental factors and is often accompanied by dental crowding, with the possibility of canine inclusion, crossbite, class II and III malocclusion, temporomandibular joint disorder, and obstructive sleep apnea (OSAS). Transverse maxillary deficits, in which the maxillary growth is unusually modest, are frequently treated with maxillary expansion. The purpose of this study is to compare the dental and skeletal effects of different types of expanders, particularly the Leaf Expander, rapid and slow dental-anchored or skeletal-anchored maxillary expanders. METHODS: We chose studies that compared effects determined by palatal expansion using a rapid palatal expander, expander on palatal screws, and leaf expander. RESULTS: Reports assessed for eligibility are 26 and the reports excluded were 11. A final number of 15 studies were included in the review for qualitative analysis. CONCLUSIONS: Clinically and radiographically, the outcomes are similar to those obtained with RME and SME appliances; Therefore, it might be a useful treatment choice as an alternative to RME/SME equipment in cases of poor patient compliance or specific situations. Finally, all of the devices studied produce meaningful skeletal growth of the palate. The use of skeletally anchored devices does, without a doubt, promote larger and more successful growth in adolescent patients.

Conservative Treatment of Dental Non-Carious Cervical Lesions: A Scoping Review.

This scoping review aims to evaluate methods of conservative reconstruction of dental enamel lesions resulting from abrasions and evaluate the effect of diode laser in reducing the symptoms of tooth sensitivity. The cementoenamel junction is more prone to substance loss because the enamel thickness is substantially decreased, resulting in a much weaker enamel-dentin bond. METHODS: Dental abrasion was examined in the mechanical cause alone. Pubmed, Scopus, and Web of Science were used to discover publications that matched our topic from 1 January 2018 to 20 March 2023. A comparison of various non-carious cervical lesion (NCCL) restoration treatments was generated mostly by mechanical considerations. RESULTS: A final number of 11 clinical trials and randomized controlled trials were included in the review for qualitative analysis. Composite resins performed well in clinical trials for the restoration of NCCLs. CONCLUSIONS: Composite, in its different forms of filling and consistency, preceded by the use of adhesives, is an efficient and effective material for the treatment of NCCLs. Diode laser use prior to NCCL restoration of teeth does not diminish restoration retention rate, may lessen hypersensitivity, and may affect restoration success.

Analysis of Dental Enamel Remineralization: A Systematic Review of Technique Comparisons.

The demineralization process conditions the structure of the enamel and begins with a superficial decalcification procedure that makes the enamel surface porous and gives it a chalky appearance. White spot lesions (WSLs) are the first clinical sign that can be appreciated before caries evolves into cavitated lesions. The years of research have led to the testing of several remineralization techniques. This study's objective is to investigate and assess the various methods for remineralizing enamel. The dental enamel remineralization techniques have been evaluated. A literature search on PubMed, Scopus, and Web of Science was performed. After screening, identification, and eligibility processes 17 papers were selected for the qualitative analysis. This systematic review identified several materials that, whether used singly or in combination, can be effective in the process of remineralizing enamel. All methods have a potential for remineralization when they come into contact with tooth enamel surfaces that have early-stage caries (white spot lesions). From the studies conducted in the test, all of the substances used to which fluoride has been added contribute to remineralization. It is believed that by developing and researching new remineralization techniques, this process might develop even more successfully.

New geochemical data for defining origin and distribution of mercury in groundwater of a coastal area in southern Tuscany (Italy).

A geochemical study was conducted in a coastal plain in the Orbetello Lagoon area in southern Tuscany (Italy), acquiring new data on groundwater, lagoon water, and stream sediment for insights into the origin, distribution, and behaviour of mercury in a Hg-enriched carbonate aquifer. The main hydrochemical features of the groundwater are ruled by the mixing of Ca-SO4 and Ca-Cl continental fresh waters of the carbonate aquifer and Na-Cl saline waters of the Tyrrhenian Sea and Lagoon of Orbetello. Groundwater had highly variable Hg concentrations (< 0.1-11 µg/L) that were not correlated with the percentage of saline water, depth in the aquifer, or distance from the lagoon. This excluded the possibility that saline water could be the direct source of Hg in groundwater and responsible for release of the element through interaction with the carbonate lithologies of the aquifer. The origin of Hg in groundwater could be ascribed to the Quaternary continental sediments overlying the carbonate aquifer because i) high Hg concentrations were found in the continental sediments of the coastal plain and in the contiguous lagoon sediments; ii) waters from the upper part of aquifer had the highest Hg concentrations; iii) Hg levels in groundwater increased with increasing thickness of the continental deposits. The high Hg content in the continental and lagoon sediments is geogenic due to regional and local Hg anomalies and to sedimentary and pedogenetic processes. It can be assumed that i) water circulating in these sediments dissolves the solid Hg-bearing constituents and mobilises this element mainly as chloride complexes; ii) Hg-enriched water moves from the upper part of the carbonate aquifer due to the cone of depression generated by intense pumping of groundwater by fish farms in the study area.

Frozen-Density Embedding for Including Environmental Effects in the Dirac-Kohn-Sham Theory: An Implementation Based on Density Fitting and Prototyping Techniques.

Frozen density embedding (FDE) represents an embedding scheme in which environmental effects are included from first-principles calculations by considering the surrounding system explicitly by means of its electron density. In the present paper, we extend the full four-component relativistic Dirac-Kohn-Sham (DKS) method, as implemented in the BERTHA code, to include environmental and confinement effects with the FDE scheme (DKS-in-DFT FDE). The implementation, based on the auxiliary density fitting techniques, has been enormously facilitated by BERTHA's python API (PyBERTHA), which facilitates the interoperability with other FDE implementations available through the PyADF framework. The accuracy and numerical stability of this new implementation, also using different auxiliary fitting basis sets, has been demonstrated on the simple NH3-H2O system, in comparison with a reference nonrelativistic implementation. The computational performance has been evaluated on a series of gold clusters (Aun, with n = 2, 4, 8) embedded into an increasing number of water molecules (5, 10, 20, 40, and 80 water molecules). We found that the procedure scales approximately linearly both with the size of the frozen surrounding environment (consistent with the underpinnings of the FDE approach) and with the size of the active system (in line with the use of density fitting). Finally, we applied the code to a series of heavy (Rn) and super-heavy elements (Cn, Fl, Og) embedded in a C60 cage to explore the confinement effect induced by C60 on their electronic structure. We compare the results from our simulations, with respect to more-approximate models employed in the atomic physics literature. Our results indicate that the specific interactions described by FDE are able to improve upon the cruder approximations currently employed, and, thus, they provide a basis from which to generate more-realistic radial potentials for confined atoms.

Environment Effects on X-Ray Absorption Spectra With Quantum Embedded Real-Time Time-Dependent Density Functional Theory Approaches.

In this work we implement the real-time time-dependent block-orthogonalized Manby-Miller embedding (rt-BOMME) approach alongside our previously developed real-time frozen density embedding time-dependent density functional theory (rt-TDDFT-in-DFT FDE) code, and investigate these methods' performance in reproducing X-ray absorption spectra (XAS) obtained with standard rt-TDDFT simulations, for model systems comprised of solvated fluoride and chloride ions ([X@ ( H 2 O ) 8 - , X = F, Cl). We observe that for ground-state quantities such as core orbital energies, the BOMME approach shows significantly better agreement with supermolecular results than FDE for the strongly interacting fluoride system, while for chloride the two embedding approaches show more similar results. For the excited states, we see that while FDE (constrained not to have the environment densities relaxed in the ground state) is in good agreement with the reference calculations for the region around the K and L1 edges, and is capable of reproducing the splitting of the 1s1 (n + 1)p1 final states (n + 1 being the lowest virtual p orbital of the halides), it by and large fails to properly reproduce the 1s1 (n + 2)p1 states and misses the electronic states arising from excitation to orbitals with important contributions from the solvent. The BOMME results, on the other hand, provide a faithful qualitative representation of the spectra in all energy regions considered, though its intrinsic approximation of employing a lower-accuracy exchange-correlation functional for the environment induces non-negligible shifts in peak positions for the excitations from the halide to the environment. Our results thus confirm that QM/QM embedding approaches are viable alternatives to standard real-time simulations of X-ray absorption spectra of species in complex or confined environments.

Spectroscopic/Bond Property Relationship in Group 11 Dihydrides via Relativistic Four-Component Methods.

Group 11 dihydrides MH2- (M = Cu, Ag, Au, Rg) have been much less studied than the corresponding MH compounds, despite having potentially several interesting applications in chemical research. In this work, their main spectroscopic constants (bond lengths, dissociation energies, and force constants) have been evaluated by means of highly accurate relativistic four-component coupled cluster (4c-CCSD(T)) calculations in combination with large basis sets. Periodic trends have been quantitatively explained by the charge-displacement/natural orbitals for chemical valence (CD-NOCV) analysis based on the four-component relativistic Dirac-Kohn-Sham method, which allows a consistent picture of the nature of the M-H bond to be obtained on going down the periodic table in terms of Dewar-Chatt-Duncanson bonding components. A strong ligand-to-metal donation drives the M-H bond and it is responsible for the heterolytic (HM···H-) dissociation energies to increase monotonically from Cu to Rg, with RgH2- showing the strongest and most covalent M-H bond. The "V"-shaped trend observed for the bond lengths, dissociation energies, and stretching frequencies can be explained in terms of relativistic effects and, in particular, of the relativistically enhanced sd hybridization occurring at the metal, which affects the metal-ligand distances in heavy transition-metal complexes. The sd hybridization is very small for Cu and Ag, whereas it becomes increasingly important for Au and Rg, being responsible for the increasing covalent character of the bond, the sizable contraction of the Au-H and Rg-H bonds, and the observed trend. This work rationalizes the spectroscopic/bond property relationship in group 11 dihydrides within highly accurate relativistic quantum chemistry methods, paving the way for their applications in chemical bond investigations involving heavy and superheavy elements.

Environmental Effects with Frozen-Density Embedding in Real-Time Time-Dependent Density Functional Theory Using Localized Basis Functions.

Frozen-density embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane waves and periodic boundary conditions [Pavanello, M.; J. Chem. Phys. 2015, 142, 154116]. In the current paper, we extend our recent formulation of the real-time time-dependent Kohn-Sham method based on localized basis set functions and developed within the Psi4NumPy framework to the FDE scheme. The latter has been implemented in its "uncoupled" flavor (in which the time evolution is only carried out for the active subsystem, while the environment subsystems remain at their ground state), using and adapting the FDE implementation already available in the PyEmbed module of the scripting framework PyADF. The implementation was facilitated by the fact that both Psi4NumPy and PyADF, being native Python API, provided an ideal framework of development using the Python advantages in terms of code readability and reusability. We employed this new implementation to investigate the stability of the time-propagation procedure, which is based on an efficient predictor/corrector second-order midpoint Magnus propagator employing an exact diagonalization, in combination with the FDE scheme. We demonstrate that the inclusion of the FDE potential does not introduce any numerical instability in time propagation of the density matrix of the active subsystem, and in the limit of the weak external field, the numerical results for low-lying transition energies are consistent with those obtained using the reference FDE calculations based on the linear-response TDDFT. The method is found to give stable numerical results also in the presence of a strong external field inducing nonlinear effects. Preliminary results are reported for high harmonic generation (HHG) of a water molecule embedded in a small water cluster. The effect of the embedding potential is evident in the HHG spectrum reducing the number of the well-resolved high harmonics at high energy with respect to the free water. This is consistent with a shift toward lower ionization energy passing from an isolated water molecule to a small water cluster. The computational burden for the propagation step increases approximately linearly with the size of the surrounding frozen environment. Furthermore, we have also shown that the updating frequency of the embedding potential may be significantly reduced, much less than one per time step, without jeopardizing the accuracy of the transition energies.

BERTHA: Implementation of a four-component Dirac-Kohn-Sham relativistic framework.

In this paper, we present and review the most recent computational advances in the BERTHA code. BERTHA can be regarded as the state of the art in fully relativistic four-component Dirac-Kohn-Sham (DKS) software. Thanks to the implementation of various parallelization and memory open-ended distribution schemes in combination with efficient "density fitting" algorithms, it greatly reduces the computational burden of four-component DKS calculations. We also report the newly developed OpenMP version of the code, that, together with the berthmod Python module, provides a significant leap forward in terms of usability and applicability of the BERTHA software. Some applications of the recently developed natural orbitals for chemical valence/charge displacement bonding analysis and the real-time time dependent DKS implementation are also reported.

PyBERTHART: A Relativistic Real-Time Four-Component TDDFT Implementation Using Prototyping Techniques Based on Python.

We present a real-time time-dependent four-component Dirac-Kohn-Sham (RT-TDDKS) implementation based on the BERTHA code. This new implementation takes advantage of modern software engineering, including the prototyping techniques. The software design follows a three step approach: (i) the prototype implementation of a time-propagation algorithm in nonrelativistic real-time TDDFT within the Psi4NumPy framework, which provides a suitable environment for the creation of a clear, readable, and easy to test reference code in Python, (ii) the design of an original Python application programming interface for the relativistic four-component code BERTHA (PyBERTHA), which has an efficient computational kernel for relativistic integrals written in FORTRAN, and (iii) the porting of the time-propagation scheme enveloped within the Psi4NumPy framework to PyBERTHA. The propagation scheme consequently resides in a single readable Python computer code that is easy to maintain and in which the key quantities, such as the Dirac-Kohn-Sham and dipole matrices, can be accessed directly from the PyBERTHA module. For linear algebra operations (matrix-matrix multiplications and diagonalization) we use the highly optimized procedures implemented in the popular NumPy library. The overhead introduced by the Python interface to BERTHA is almost negligible (less than 1% evaluated on the SCF procedure), and the interoperability between different programming languages (FORTRAN, C, and Python) does not affect the numerical stability of the time-propagation scheme. Our new RT-TDDKS implementation has been employed to investigate the stability of the time-propagation procedure in combination with a density-fitting algorithm (both for the Coulomb and for the exchange-correlation matrix construction), which are employed in BERTHA to speed up the Dirac-Kohn-Sham matrix evaluation. On the basis of systematic calculations, employing several density-fitting basis sets of increasing accuracy, we showed that quantitative agreement can be achieved in combination with extended-fitting basis sets, with an error in the Coulomb energy below 1 µ-hartree. Convergence of the transition energies increasing of quality of the fitting basis sets has been also observed. Our data suggest that the error in the Coulomb energy may also represent a good estimate of the fitting basis set quality for real-time electron dynamics simulations. Further, we study the applicability of the RT-TDDKS method in combination with both weak- and extreme strong-field regime. Numerical results of excited-state transitions for the Group 12 atoms are reported and compared with a previous real-time Dirac-Kohn-Sham implementation (Repisky et al. J. Chem. Theory Comput. 2015, 11, 980-991). Finally, calculations of high harmonic generation in the hydrogen molecule and Au dimer have been also carried out. We were able to generate high harmonics with relatively well-defined peaks up to the 21st and 13th order in the case of H2 and Au2, respectively. Our findings show that the four-component structure of the Dirac-Kohn-Sham Hamiltonian provides a suitable theoretical framework, with no intrinsic unfavorable features, to study molecules in the strong-field regime.

Spin-orbit coupling is the key to unraveling intriguing features of the halogen bond involving astatine.

The effect of spin-orbit coupling (SOC) on the halogen bond involving astatine has been investigated using state-of-the-art two- and four-component relativistic calculations. Adducts between Cl-X (X = Cl, Br, I and At) and ammonia have been selected to establish a trend on going down the periodic table. The SOC influence has been explored not only on the geometric and energetic features that can be used to characterize the halogen bond strength but also on the three main contributions to it that are the charge transfer, the "σ-hole" (i.e. the localized region with a net positive electrostatic potential at the halogen site) and the "polar flattening" (which is related to the effective shape of the halogen site). A surprisingly large increase of the Cl-At dipole moment, due to the inclusion of SOC, has been worked out using four-component CCSD(T) reference calculations, indicating that this bond is significantly more ionic than one may predict. Due to the SOC effect, which induces a peculiar charge accumulation on the At side in the Cl-At dimer, a weakening of the astatine-mediated halogen bond occurs arising from the (i) reduced amount of charge transfer, (ii) decrease of the polar flattening and (iii) lowering of the short-range Coulomb potential. The analysis of the electronic structure of the Cl-At moiety allows for a rationalization of the SOC effects on all the considered features of the halogen bond, including an unprecedented unsymmetrical charge back-donation from Cl-At to ammonia.

The Chemical Bond and s-d Hybridization in Coinage Metal(I) Cyanides.

We present a four-component relativistic density functional theory study of the chemical bond and s-d hybridization in the group 11 cyanides M-CN (M = Cu, Ag, and Au). The analysis is carried out within the charge-displacement/natural orbital for chemical valence (CD-NOCV) scheme, which allows us to single out meaningful contributions to the total charge rearrangement that arises upon bond formation and to quantify the components of the Dewar-Chatt-Duncanson bonding model (the ligand-to-metal donation and metal-to-ligand back-donation). The M-CN bond is characterized by a large donation from the cyanide ion to the metal cation and by two small back-donation components from the metal toward the cyanide anion. The case of gold cyanide elucidates the peculiar role of the relativistic effects in determining the characteristics of the Au-C bond with respect to the copper and silver homologues. In AuCN, the donation and back-donation components are significantly enhanced, and the spin-orbit coupling, removing the degeneracy of the 5d atomic orbitals, induces a substantial split in the back-donation components. A simple spatial analysis of the NOCV-pair density, related to the ligand-to-metal donation component, allows us to quantify, with unprecedented accuracy, the charge rearrangement due to the s-d hybridization occurring at the metal site. The s-d hybridization plays a key role in determining the shape and size of the metal; it removes electron density from the bond axis and induces a significant flattening at the metal site in the position trans to the ligand. The s-d hybridization is present in all noble metal complexes, influencing the bond distances, and its effect is enhanced for Au, which is consistent with the preference of gold to form linear complexes. A comparative investigation of simple complexes [AuL]+/0 of Au+ with different ligands (L = F-, N-heterocyclic carbene, CO, and PH3) shows that the s-d hybridization mechanism is also influenced by the nature of the ligand.

Charge-Displacement Analysis via Natural Orbitals for Chemical Valence in the Four-Component Relativistic Framework.

We have recently introduced a simple yet powerful tool for analyzing quantitatively the coordination bond in terms of the donation and back-donation constituents of the Dewar-Chatt-Duncanson model. Our approach is based on the decomposition, via natural orbitals for chemical valence (NOCV), of the so-called charge-displacement (CD) function into additive chemically meaningful components (Bistoni et al. J. Chem. Phys. 2015, 142, 084112 ). The method, referred to as NOCV/CD, provides clear-cut measures of donation and back-donation charge flows following bond formation, and its robustness has been demonstrated by a tight correlation of the related charge-transfer estimates with experimental observables. In this paper we extend the NOCV/CD analysis scheme to the four-component relativistic framework, which includes spin-orbit coupling variationally. This formalism is incorporated into a recently developed, highly efficient parallel version of the relativistic Dirac-Kohn-Sham (DKS) program BERTHA (Rampino et al. J. Chem. Theory Comput. 2014, 10, 3766-3776 ). We test the accuracy and numerical stability of this new implementation through the analysis of the convergence properties of the basis sets employed to expand the DKS spinor solution and those used to linearize the electronic density in the density-fitting algorithm speeding up the evaluation of the DKS matrix. An illustration of NOCV/CD analysis in the relativistic framework is also given through a study of the metal-carbonyl coordination bond in a series of [M-CO]+ (M = Cu, Ag, Au) complexes of group 11 metals, where relativistic effects, including spin-orbit coupling, are found to play an important role.