Perovskenes: two-dimensional perovskite-type monolayer materials predicted by first-principles calculations.

Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3 onto various substrates without any thickness limitation, in this study, using density functional theory (DFT), we assessed the structural stability of a group of two-dimensional perovskite-type materials which we call perovskenes. Specifically, we analyzed the stability of 2D SrTiO3, SrZrO3, BaTiO3, and BaZrO3 monolayers. Our simulations revealed that the 2D monolayers of SrTiO3, BaTiO3, and BaZrO3 are at least meta-stable, as confirmed by cohesive energy calculations, evaluation of elastic constants, and simulation of phonon dispersion modes. With this information, we proceeded to investigate the electronic, optical, and thermoelectric properties of these perovskenes. To gain insight into their promising applications, we investigated the electronic and optical properties of these 2D materials and found that they are wide bandgap semiconductors with significant absorption and reflection in the ultraviolet (UV) region of the electromagnetic field, suggesting them as promising materials for use in UV shielding applications. In addition, evaluating their thermoelectric factors revealed that these materials become better conductors of electricity and heat as the temperature rises. They can, hence, convert temperature gradients into electrical energy and transport electrical charges, which is beneficial for efficient power generation in thermoelectric devices. This work opens a new window for designing a novel family of 2D perovskite type materials termed perovskenes. The vast variety of different perovskite compounds and their variety of applications suggest deeper studies on the perovskenes materials for use in innovative technologies.

Ni on the CeO2(110) and (100) surfaces: adsorption vs. substitution effects on the electronic and geometric structures and oxygen vacancies.

We report density functional theory (DFT) calculations of the interactions of both Ni adsorbate and substitutional dopant with the ceria (110) and (100) surfaces to explain the origin of the activity of Ni/ceria catalysts. Our results indicate that the Ni adatom on the (110) surface prefers to adsorb on a two-fold bridge site over a hollow site up to 0.25 ML coverage, and the most stable position of a Ni adsorbate on the (100) surface was found to be the bridge site where the Ni atom is coordinated to two surface O atoms. The Ni(+) oxidation state for the Ni adatom on the (110) surface was found to be more favorable than the Ni(2+) state on the two-fold bridge site while on the (100) surface, a Ni adatom prefers its Ni(2+) oxidation state over the Ni(+) oxidation state. With increasing coverage, the binding energy of a Ni adatom on the (110) surface was found to decrease from -0.45 eV at 0.083 ML coverage to -0.32 eV at 0.25 ML coverage. Oxidation of the Ni adatom to Ni(+) reduces one Ce(4+) ion on the ceria surface to Ce(3+) which preferred to be located next to the Ni(+) ion in the nearest neighbor location. The Ce(3+) ions on the (100) surface also prefer to stay in the vicinity of the adsorbed Ni atom, while they prefer to be located away from the Ni adatom on the (111) surface. No reduction of Ce(4+) ions was observed upon substitution of Ce atoms by Ni atoms. Two Ni substituents preferred to be distributed on adjacent metal ion sites on the (110) surface. Ni adsorbate and substituent on the (110) surface were both found to induce significant structural distortions. In comparison to the pure ceria (110) and (100) surfaces, we show that a Ni adsorbate increases the energy required to create an oxygen vacancy while a Ni dopant reduces it. While multiple dopants on the (110) surface do reduce the vacancy formation energy, the degree of reduction is smaller compared to a single dopant indicating the presence of an optimum level of doping to obtain enhanced catalytic activity.

Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study.

This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, transition states have been identified. The three (13)C NMR chemical shifts of the molecule were estimated by averaging their calculated values over a large set of BOMD snapshots. The simulation time needed to obtain a good agreement with the two signals present in the experimental spectrum is shown to be dependent on the atomic orbital basis set used for the dynamics, with a necessary longer trajectory for the most extended basis sets. The large structural deformations with respect to the optimized conformer geometries that occur along the dynamics are related to a kinetically driven conformer distribution. Calculated conformer type populations are in good agreement with experimental gas phase microwave results.

Quantum Machine Learning in Materials Prediction: A Case Study on ABO3 Perovskite Structures.

Quantum machine learning (QML), ML on quantum computers, offers a promising approach for discovering and screening novel materials. This study introduces a hybrid classical-quantum ML method using a variational quantum classifier to identify simple perovskite structures within a data set of ABO3 compounds. The model is trained using a data set of 397 known ABO3 compounds, with 254 perovskites and 143 non-perovskite structures labeled as +1 and -1, respectively. By considering feature correlation and eliminating less important features, the QML system achieves an optimal accuracy of 88% for training data and 87% for unseen test data. These results demonstrate the potential of QML in materials science classification tasks, even with limited training data, leveraging the intrinsic properties of quantum computation to enhance the investigation of materials. In addition, perspectives on QML applications in materials science are discussed.

Density functional theory-based conformational analysis of a phospholipid molecule (dimyristoyl phosphatidylcholine).

The conformational space of the dimyristoyl phosphatidylcholine (DMPC) molecule has been studied using density functional theory (DFT), augmented with a damped empirical dispersion energy term (DFT-D). Fourteen ground-state isomers have been found with total energies within less than 1 kcal/mol. Despite differences in combinations of their torsion angles, all these conformers share a common geometric profile, which includes a balance of attractive, repulsive, and constraint forces between and within specific groups of atoms. The definition of this profile fits with most of the structural characteristics deduced from measured NMR properties of DMPC solutions. The calculated vibrational spectrum of the molecule is in good agreement with experimental data obtained for DMPC bilayers. These results support the idea that DMPC molecules preserve their individual molecular structures in the various assemblies.

Conformational dynamics of an alanine dipeptide analog: an ab initio molecular dynamics study.

An ab initio molecular dynamics (MD) simulation technique employing the Born-Oppenheimer approach in the framework of a Gaussian implementation of Kohn-Sham density functional theory is used to study the gas-phase conformational dynamics of an alanine dipeptide analog. It is found that conformational transformation between C5 and C7(eq) occurs on the picosecond time scale. Classical MD simulations using most of the popular force fields do not yield a transition even after nanoseconds. An analysis is given of the difference, for this small gas-phase system, between ab initio MD and traditional MD simulation using force fields.

Structure, dynamics, and energetics of lysobisphosphatidic acid (LBPA) isomers.

Lysobisphosphatidic acid (LBPA), or bis(monoacylglycerol)phosphate, is a very interesting lipid, that is mainly found in late endosomes. It has several intriguing characteristics, which differ from those of other animal glycerophospholipids, that may be related to its specific functions, particularly in the metabolism of cholesterol. Its phosphodiester group is bonded at the sn-1 (sn-1') positions of the glycerols rather than at sn-3 (sn-3'); the position of the two fatty acid chains is still under debate but, increasingly, arguments favor the sn-2, sn-2' position in the native molecule, whereas isolation procedures or acidic conditions lead to the thermodynamically more stable sn-3, sn-3' structure. Because of these peculiar features, it can be expected that LBPA shape and interactions with membrane lipids and proteins are related to its structure at the molecular level. We applied quantum mechanical methods to study the structures and stabilities of the 2,2' and 3,3' LBPA isomers, using a step-by-step procedure from glycerol to precursors (in vitro syntheses) and to the final isoforms. The structures of the two positional LBPA isomers are substantially different, showing that the binding positions of the fatty acid chains on the glycerol backbone determine the shape of the LBPA molecule and thus, possibly, its functions. The 3,3' LBPA structures obtained are more stable with respect to the 2,2' form, as expected from experiment. If one argues that the in vivo synthesis starts from the present glycerol conformers and considering the most stable bis(glycero)phosphate structures, the 2,2' isoform should be the most probable isomer.

Towards a density functional treatment of chemical reactions in complex media.

We discuss two techniques involving density functional theory (i.e., ab initio molecular dynamics simulations and frozen density functional theory) which show promise for applications directed towards understanding reactions in complex media. Preliminary results for the simulation of the conformational dynamics of an isolated analogue of alanine dipeptide and for the interaction between F- and H2O are included. These results represent the first steps towards a combined theoretical approach of reactions in complex media.

A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft.

The relative energy between two different protonation sites of the Asp25' catalytic site residue is computed and analyzed for various HIV-1 Protease/inhibitor complexes and compared to the wild-type structure. By comparing calculations of negatively charged fragments of gradually increasing size up to 105 atoms we show that correct modeling of the HIV-1 Protease active site requires much larger models than the commonly used acetic acid/acetate moieties. The energy difference between the two proposed protonation sites decreases as the size of the system increases and tends to converge only when the entire catalytic triad of both monomers is taken into account. The importance of the Gly27 backbone amine groups in the stabilization of the negative charge within the catalytic site cleft is revealed. Comparison of the wild-type structure with the structures from various Pr/drug complexes indicates that the HIV-1 protease has a particular catalytic site flexibility.