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Deformations of the three most common cyclodextrins (α, β, and γ) were induced to form inclusion compounds with sertraline and abacavir. The deformations were obtained from classical molecular dynamics (CMD) using as starting point X‐ray structures. The molecular dynamics were performed in two ways, over the cyclodextrins with and without the presence of a guest. Two characteristic rings within these cyclodextrins were used to measure the distortions observed along with the molecular dynamics. A docking approach was used to build inclusion compounds over the structures obtained from CMD without the presence of sertraline or abacavir. Thus, we compared structures of inclusion compounds obtained from deformations induced by the presence of a guest or with intrinsic deformations exhibited by each cyclodextrin. After this step, each structure was optimized by the PBE0‐D3/6‐31G(d,p) method, and the electron density delivered by this method was used to perform the quantum theory of atoms in molecules approach to analyze intermolecular contacts between sertraline, or abacavir, and three cyclodextrins. From this procedure, we found that inclusion compounds obtained from X‐ray structures present the highest energies over the potential energy surface. Thus, for getting low‐lying energy structures of inclusion compounds, deformations on cyclodextrins are necessary. [ABSTRACT FROM AUTHOR]

Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g., molecular properties), with a strong emphasis on facilitating these operations in computational chemistry and conceptual density functional theory. Although designed, maintained, and released as a stand-alone Python library, Grid was originally developed for molecular integration, interpolation, and solving the Poisson equation in the HORTON and ChemTools packages. Grid is designed to be easy to use, extend, and maintain; this is why we use Python and adopt many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. We leverage popular scientific packages, such as NumPy and SciPy, to ensure high efficiency and optimized performance in grid development. This article is the official release note of the Grid library showcasing its unique functionality and scope. [ABSTRACT FROM AUTHOR]

Isomers of (NaCl)n(H2O)2n clusters, with n = 1, 2 and 4, were investigated using an implementation of the simulated annealing method that imposes a virtual confinement on each isomer to stay within a sphere with an arbitrary radius. By using several confinement radii, we reported 2, 56 and 38 isomers for n = 1, 2 and 4, respectively. For n = 1, the CCSD(T)/aug-cc-pVTZ method was used as a reference by optimizing the corresponding isomers. These results were contrasted with those obtained by the MP2 method and eight exchange–correlation functionals: PBE, PBE0, B3LYP, PBE-D3, PBE0-D3, B3LYP-D3, LC-̉PBE and M06-2X. From this analysis we conclude that the M06-2X method gives reliable results and then, isomers with n = 2 and 4 were analyzed with this exchange–correlation functional. From the analysis of these two systems, the resulting isomers with the lowest energy showed cuboid structures and no breaking bond was present for NaCl molecules. Thus, in the nucleation process of the NaCl dihydrate our results suggest that the Na–Cl bond is present. Besides, bond length and electron density evaluated at bond critical points for the biggest system delivered values close to those found in the crystal structure. [ABSTRACT FROM AUTHOR]

Using a grid-based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for highperformance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single-precision is used. [ABSTRACT FROM AUTHOR]

For the first time, the electron density of the H2+ molecule is analyzed when this system is confined by spheroidal walls with an infinite potential. Typically, this system is studied to obtain information of the total energy and its components or to gain insight of some expected values when such a system is squeezed by this kind of confinement. However, this is the first report where the electron density and its derivatives, under the quantum theory of atoms in molecules (QTAIM), are analyzed to study the chemical bond involved with this molecule. This confinement induces an unexpected behavior of the chemical bond and gives an idea about atomic interactions under high pressures, where the QTAIM approach indicates that the chemical bond disappears. For strong confinements, there is a significant contribution of the electron kinetic energy and the nuclear‐electron energy contribution can be neglected. Under this situation, the confined H2+ system is another example where the notion of the topological atom given by the QTAIM is no longer suitable. [ABSTRACT FROM AUTHOR]

The analysis of scalar and vector fields in quantum chemistry is an essential task for the computational chemistry community, where such quantities must be evaluated rapidly to perform a particular study. For example, the atoms in molecules approach proposed by Bader has become popular; however, this method demands significant computational resources to compute the involved tasks in short times. In this article, we discuss the importance of graphics processing units (GPU) to analyze electron density, and related fields, implementing several scalar, and vector fields within the graphics processing units for atoms and molecules (GPUAM) code developed by a group of the Universidad Autónoma Metropolitana in México City. With this application, the quantum chemistry community can perform demanding computational tasks on a desktop, where CPUs and GPUs are used to their maximum capabilities. The performance of GPUAM is tested in several systems and over different GPUs, where a GPU installed in a workstation converts it to a robust high‐performance computing system. The Graphics Processing Units for Atoms in Molecules (GPUAM) project is benchmarked in several systems and over different GPUs, where a GPU installed in a workstation converts it to a robust high‐performance computing system. Developed at the Universidad Autónoma Metropolitana in México City, GPUAM can evaluate electron density, or related scalar or vector quantum chemistry fields, using CPUs and GPUs over desktops, or high‐performance computing hardware. [ABSTRACT FROM AUTHOR]

The phase change energetics of adamantane, 1-adamantanemethanol, 1-adamantanethanol, 1-adamantanecarboxylic acid, and 1-adamantaneacetic acid is reported. To conduct the study of the compounds' phase changes, calorimetric techniques and theoretical methodologies were applied. Mole fraction purities, enthalpies, fusion temperatures, and solid phase heat capacities were obtained using differential scanning calorimetry. Enthalpies of sublimation were determined from measurements of mass loss rate and the Clausius-Clapeyron and Langmuir equations, i.e., through thermogravimetric analysis. The gas-phase heat capacities of all stable conformers of the adamantane derivatives at different temperatures were estimated using harmonic oscillator approximation. Finally, the molecular interactions of the adamantane derivatives are discussed. [ABSTRACT FROM AUTHOR]

The off-diagonal regions of the one-electron density matrix (ODM) are characterized according to their contributions to the chemical bond. In particular, these regions of the ODM difference maps were used to characterize the chemical bond in various diatomic molecules. The nature of a critical point, core interaction critical point, in the off-diagonal part of ODM reveals the chemical bond type: maximum for covalent bond, minimum for closed-shell interaction, and saddle point for a charge-shift bond. [ABSTRACT FROM AUTHOR]

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library. [ABSTRACT FROM AUTHOR]

The potential energy surface of ZnnOn clusters (n = 2, 4, 6, 8) has been explored by using a simulated annealing method. For n = 2, 4, and 6, the CCSD(T)/TZP method was used as the reference, and from here it is shown that the M06-2X/TZP method gives the lowest deviations over PBE, PBE0, B3LYP, M06, and MP2 methods. Thus, with the M06-2X method we predict isomers of ZnnOn clusters, which coincide with some isomers reported previously. By using the atoms in molecules analysis, possible contacts between Zn and O atoms were found for all structures studied in this article. The bond paths involved in several clusters suggest that ZnnOn clusters can be obtained from the zincite (ZnO crystal), such an observation was confirmed for clusters with n = 2 − 9,18 and 20. The structure with n = 23 was obtained by the procedure presented here, from crystal information, which could be important to confirm experimental data delivered for n = 18 and 23. [ABSTRACT FROM AUTHOR]

Adhesive formulations based on depolymerized lignins were studied to investigate the contribution of their oligolignols content in the determination of its Young's modulus towards the contact with a cellulose surface. Four lignins with low molar mass, tested and reported in an earlier study, were employed to model oligolignol molecular sub-structures. Over these oligolignols, several Reactive Force Field (ReaxFF) molecular dynamic simulations were considered to elucidate the contribution of each molecular structure to the adhesive capacity of the lignin mixture, modelling the interaction of each oligolignol over one model of cellulose I-β. One important result obtained from these simulations is, that coupling energies obtained for the oligolignol-cellulose complexes correlate quite well with experimental values of Young's modulus, yielding the insight to describe how oligolignols within lignin-adhesive formulations drive their Young's modulus from an atomistic point of view. This study opens a new perspective to design novel wood adhesive formulations based on lignins, considering the oligolignols present in their composition. [ABSTRACT FROM AUTHOR]