Computational tools to study non-covalent interactions and confinement effects in chemical systems.

Confinement is a very common phenomenon in chemistry, for example, when molecules are located inside cavities. In these conditions, the electronic structure of atoms and molecules is modified. These changes could be mapped through the interaction with other molecules since non-covalent interactions between molecules are also influenced by confinement. In this work we address both topics, non-covalent interactions, and confined systems, using quantum chemistry tools with new software, emphasizing the importance of analyzing both fields simultaneously.

Revealing the Role of Noncovalent Interactions on the Conformation of the Methyl Group in Tricyclic Orthoamide.

Tricyclic orthoamides are valuable molecules with wide-ranging applications, including organic synthesis and molecular recognition. Their structural properties make them intriguing, particularly the eclipsed all-trans conformer, which is typically less stable than the alternated conformation and is a rare phenomenon in organic chemistry. However, it gains stability in crystalline and hydrated settings, challenging the existing theoretical explanations. This study investigates which factors make eclipsed conformers more stable using experimentally reported anhydrous (ATO) and hydrated (HTO) crystal structures. Employing the quantum theory of atoms in molecules, noncovalent interaction index, and pairwise energy decomposition analysis, we delve into the noncovalent interaction environment surrounding the molecule of interest. In ATO, dispersive interactions dominate, whereas in HTO, both dispersive and electrostatic contributions are observed due to the presence of water molecules. Anchored to the lone pairs of the nitrogen atom in the orthoamide tricycle, water molecules prompt the methyl group's eclipsing through intermolecular and intramolecular interactions. This work resolves the long-standing conflict behind why tricyclic orthoamide has an eclipsed conformation by establishing the stabilization factors. These insights have implications for crystal engineering and design, enhancing our understanding of structural behavior in both crystalline and hydrated environments.

Finite element method as an alternative to study the electronic structure of confined atoms.

The finite element method (FEM) based on a nonregular mesh is used to solve Hartree-Fock and Kohn-Sham equations for three atoms (hydrogen, helium, and beryllium) confined by finite and infinite potentials, defined in terms of piecewise functions or functions with a well-defined first derivative. This approach's reliability is shown when contrasted with Roothaan's approach, which depends on a basis set. Therefore, its exponents must be optimized for each confinement imposed over each atom, which is a monumental task. The comparison between our numerical approach and Roothaan's approach is made by using total and orbitals energies from the Hartree-Fock method, where there are several comparison sources. Regarding the Kohn-Sham method, there are few published data and consequently the results reported here can be used as a benchmark for future comparisons. The way to solve Hartree-Fock or Kohn-Sham equations by the FEM is entirely appropriate to study confined atoms with any form of confinement potential. This article represents a step toward developing a fully numerical quantum chemistry code free of basis sets to obtain the electronic structure of many-electron atoms confined by arbitrary confinement.

Encapsulation of dopamine within SU-101: insights by computational chemistry.

Encapsulating and protecting dopamine from oxidation is a difficult challenge. We propose to use SU-101 BioMOF as a dopamine host, where we study different adsorption scenarios by a robust computational approach. Our results show that dopamine encapsulation is feasible with the formation of non-covalent interactions within the SU-101 pores. These computational results have been corroborated experimentally.

Non-conventional interactions of N3 inhibitor with the main protease of SARS-CoV and SARS-CoV-2.

The extensive spread of COVID-19 in every continent shows that SARS-CoV-2 virus has a higher transmission rate than SARS-CoV virus which emerged in 2002. This results in a global pandemic that is difficult to control. In this investigation, we analyze the interaction of N3 inhibitor and the main protease of SARS-CoV and SARS-CoV-2 by quantum chemistry calculations. Non-covalent interactions involved in these systems were studied using a model of 469 atoms. Density Functional Theory and Quantum Theory of Atoms in Molecules calculations lead us to the conclusion that non-conventional hydrogen bonds are important to describe attractive interactions in these complexes. The energy of these non-conventional hydrogen bonds represents more than a half of the estimated interaction energy for non-covalent contacts. This means that hydrogen bonds are crucial to correctly describe the bonds between inhibitors and the main proteases. These results could be useful for the design of new drugs, since non-covalent interactions are related to possible mechanisms of action of molecules used against these viruses.

Main interactions of dopamine and risperidone with the dopamine D2 receptor.

Psychosis is one of the psychiatric disorders that is controlled by dopaminergic drugs such as antipsychotics that have affinity for the dopamine D2 receptor (DRD2). In this investigation we perform quantum chemical calculations of two molecules [dopamine and risperidone] within a large cavity of DRD2 that represents the binding site of the receptor. Dopamine is an endogenous neurotransmitter and risperidone is a second-generation antipsychotic. Non-covalent interactions of dopamine and risperidone with DRD2 are analyzed using the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction index (NCI). The QTAIM results show that these molecules strongly interact with the receptor. There are 22 non-covalent interactions for dopamine and 54 for risperidone. The electron density evaluated at each critical binding point is small in both systems but it is higher for dopamine than for risperidone, indicating that the interactions of DRD2 with the first are stronger than with the second molecule. However, the binding energy is higher for risperidone (-72.6 kcal mol-1) than for dopamine (-22.8 kcal mol-1). Thus, the strength of the binding energy is due to the number of contacts rather than the strength of the interactions themselves. This could be related to the ability of risperidone to block DRD2 and may explain the efficacy of this drug for controlling the symptoms of schizophrenia, but likewise its secondary effects.

Ionization of many-electron atoms by the action of two plasma models.

The Hartree-Fock equations for many-electron atoms embedded in a plasma medium are solved using two different plasma models: (a) Debye-Hückel screening (DHS) potential and (b) exponential cosine screened Coulomb (ECSC) potential. Roothaan's approach is implemented for these models after solving the inherent difficulties to evaluate integrals where screening appears explicitly. A corresponding computer code was developed using the method of global basis sets (GBS). The reliability of this approach was verified by solving the Hartree-Fock equations through implementation of the finite-differences and finite-element grid methods and applied to two-electron atoms, yielding excellent agreement with the Roothaan-GBS (RGBS) method. The RGBS method was used to study the energy evolution and ionization threshold of several closed- and open-shell many-electron atoms embedded either in weak or strong DHS or ECSC plasma conditions. In all cases, a critical value of the screening length is obtained for which ionization is achieved, being systematically larger for DHS conditions, indicating the effect of a more repulsive ECSC potential. For He-like atoms in the ground state, we report a comprehensive set of accurate total energy data as a function of the screening constant using the Lagrange mesh method, which includes the electron correlation effects. The electron correlation energy is estimated using this data with reference to the RGBS estimates of energy as the Hartree-Fock energy. The variation of correlation energy as a function of screening constant under the different plasma potentials is rationalized in terms of a conjectured comparison theorem. Finally, a discussion on the effect of plasma strength on localization or delocalization of the electronic density derived from the RGBS method is presented in terms of changes in the Shannon entropy, yielding consistent results for delocalization close to the ionization threshold.

Identification of the preferential CO and SO2 adsorption sites within NOTT-401.

NOTT-401 was found to be a highly stable adsorbent for SO2 and CO with excellent cyclability and a straightforward regeneration at room temperature. Moreover, the preferential CO binding sites within the MOF material have been identified by experimental in situ DRIFT spectroscopy coupled with DFT and QTAIM calculations. Such preferential CO adsorption sites were correlated to identify the most significant SO2 interactions within NOTT-401. This study sheds light on the role of the thiophene and hydroxo functionality, for a MOF material, in the binding of SO2 or CO.

New information of dopaminergic agents based on quantum chemistry calculations.

Dopamine is an important neurotransmitter that plays a key role in a wide range of both locomotive and cognitive functions in humans. Disturbances on the dopaminergic system cause, among others, psychosis, Parkinson's disease and Huntington's disease. Antipsychotics are drugs that interact primarily with the dopamine receptors and are thus important for the control of psychosis and related disorders. These drugs function as agonists or antagonists and are classified as such in the literature. However, there is still much to learn about the underlying mechanism of action of these drugs. The goal of this investigation is to analyze the intrinsic chemical reactivity, more specifically, the electron donor-acceptor capacity of 217 molecules used as dopaminergic substances, particularly focusing on drugs used to treat psychosis. We analyzed 86 molecules categorized as agonists and 131 molecules classified as antagonists, applying Density Functional Theory calculations. Results show that most of the agonists are electron donors, as is dopamine, whereas most of the antagonists are electron acceptors. Therefore, a new characterization based on the electron transfer capacity is proposed in this study. This new classification can guide the clinical decision-making process based on the physiopathological knowledge of the dopaminergic diseases.

Fluorometric detection of iodine by MIL-53(Al)-TDC.

The fluorescent properties of MIL-53(Al)-TDC are drastically changed due to the presence of iodine, even in small quantities, as a result of an energy transfer process from the host material (MIL-53(Al)-TDC) to the guest molecule (I2). While MIL-53(Al)-TDC's emission spectrum shows a weak and broad band, after I2 adsorption, it exhibits well-resolved and long-lasting emission lines, which could be exploited for iodine detection. Density Functional Theory periodical calculations demonstrated that in the most stable MIL-53(Al)-TDCI2 configuration, the I2 molecule is bonded mainly by an O-HI hydrogen bond. The QTAIM showed that other non-covalent interactions also provided stability to MIL-53(Al)-TDCI2. The electrostatic potential analysis indicated that the I2 molecule adsorption occurs by a combination of specific interactions with a strong electrostatic contribution and weak interactions. These results postulate fluorescent MIL-53(Al)-TDC as an efficient I2 detector (potentially for radioactive I2), using a simple fluorimetric test.

A detailed description of the CO molecule adsorbed in InOF-1.

CO is extremely toxic to humans since it can combine with haemoglobin to form carboxy-haemoglobin that reduces the oxygen-carrying capacity of blood. Metal-organic frameworks (MOFs), in particular InOF-1, are currently receiving preferential attention for the separation and capture of CO. In this investigation we report a theoretical study based on periodic density-functional-theory (DFT) analysis and matching experimental results (in situ DRIFTS). The aim of this article is to describe the non-covalent interactions between the functional groups of InOF-1 and the CO molecule since they are crucial to understand the adsorption mechanism of these materials. Our results show that the CO molecule mainly interacts with the µ2-OH hydroxo groups of InOF-1 through O-HO hydrogen bonds, and Cπ interactions by the biphenyl rings of the MOF. These results provide useful information on the CO adsorption mechanisms in InOF-1.

Confined benzene within InOF-1: contrasting CO2 and SO2 capture behaviours.

The confinement of small amounts of benzene in InOF-1 (Bz@InOF-1) shows a contradictory behavior in the capture of CO2 and SO2. While the capture of CO2 is increased 1.6 times, compared to the pristine material, the capture of SO2 shows a considerable decrease. To elucidate these behaviors, the interactions of CO2 and SO2 with Bz@InOF-1 were studied by DFT periodical calculations postulating a plausible explanation: (a) in the case of benzene and CO2, these molecules do not compete for the preferential adsorption sites within InOF-1, providing a cooperative CO2 capture enhancement and (b) benzene and SO2 strongly compete for these preferential adsorption sites inside the MOF material, reducing the total SO2 capture.

Non-covalent interactions between sertraline stereoisomers and 2-hydroxypropyl-ß-cyclodextrin: a quantum chemistry analysis.

Inclusion compounds formed between sertraline stereoisomers and ß-cyclodextrin, and 2-hydroxypropyl-ß-cyclodextrin, were analyzed by using quantum chemistry methods. The exploration of the potential energy surface was performed using chemical intuition and classical molecular mechanics. This approach delivered around 200 candidates for low energy adducts, which were optimized through the PBE0/6-31G(d,p) method, and after this process solvent effects were considered by the continuous solvent model. This analysis showed that ß-cyclodextrin and 2-hydroxypropyl-ß-cyclodextrin are good trappers of sertraline, although the isomers suggested by molecular dynamics presented higher binding energies than those obtained by chemical intuition. The role of hydrogen bonds in the formation of adducts was studied using the non-covalent interactions index and the quantum theory of atoms in molecules. In this article we concluded that these interactions are present in all adducts, however, they are not important in the stabilization of these inclusion compounds. The molecular electrostatic potential indicates that Coulomb interactions could be responsible for the formation of these systems, although sophisticated solvent models must be used to confirm this conclusion, which are impractical in this case because of the sizes involved in these systems.

A quantum chemical approach representing a new perspective concerning agonist and antagonist drugs in the context of schizophrenia and Parkinson's disease.

Schizophrenia and Parkinson's disease can be controlled with dopamine antagonists and agonists. In order to improve the understanding of the reaction mechanism of these drugs, in this investigation we present a quantum chemical study of 20 antagonists and 10 agonists. Electron donor acceptor capacity and global hardness are analyzed using Density Functional Theory calculations. Following this theoretical approach, we provide new insights into the intrinsic response of these chemical species. In summary, antagonists generally prove to be better electron acceptors and worse electron donors than dopamine, whereas agonists present an electron donor-acceptor capacity similar to that of dopamine. The chemical hardness is a descriptor that captures the resistance of a chemical compound to change its number of electrons. Within this model, harder molecules are less polarizable and more stable systems. Our results show that the global hardness is similar for dopamine and agonists whilst antagonists present smaller values. Following the Hard and Soft Acid and Bases principle, it is possible to conclude that dopamine and agonists are hard bases while antagonists are soft acids, and this can be related to their activity. From the electronic point of view, we have evolved a new perspective for the classification of agonist and antagonist, which may help to analyze future results of chemical interactions triggered by these drugs.

Relevance of hydrogen bonding in CO2 capture enhancement within InOF-1: an energy and vibrational analysis.

The enhancement of CO2 capture due to the confinement of polar molecules within InOF-1 was previously demonstrated. In particular, the presence of MeOH produced 1.30-fold increase in the total CO2 capture. This was explained before with the presence of hydrogen bonds. However, a detailed analysis of the hydrogen bonds among µ2-OH functional groups, MeOH molecules and CO2 molecules was not elucidated; moreover, the possible mechanisms that could explain the enhancement of the capture were also not explained. In this investigation, the density functional theory (DFT) periodic calculations and experimental in situ DRIFTS results allowed us to postulate four plausible CO2 adsorption mechanisms for MeOH-functionalised InOF-1, which described the hydrogen bonds and rationalised the nature of the CO2 capture enhancement.

Implementation of the Molecular Electrostatic Potential over Graphics Processing Units.

The molecular electrostatic potential (MEP) generated by quantum chemistry methods and Gaussian functions is evaluated over graphics processing units (GPUs). This implementation is based on full-range Rys polynomials with nodes and weights obtained in each thread of a GPU. For high angular moments, the corresponding integral is solved using a one-dimension vertical recurrence relation. Thus, we computed the MEP with minimal approximations. We show that this implementation is stable and very efficient since the time consumed over GPUs is quite small compared with similar implementations over CPUs. The implementation was done by using CUDA-C programming techniques within the Graphics Processing Units for Atoms and Molecules (GPUAM) project, which has been designed to analyze quantum chemistry fields over heterogeneous computational resources. With this new scalar field GPUAM is a useful application for the quantum chemistry community, in particular for people interested in chemical reactivity analysis.

van der Waals exchange-correlation functionals over bulk and surface properties of transition metals.

The correct description of van der Waals (vdW) interaction forces is required for accurately describing dispersion bonded systems. Several approaches have been proposed to include London dispersion in density functional theory exchange-correlation functionals, where the family of so-called van der Waals (vdW-DF) exchange-correlation functionals have shown a better performance than local or semi local exchange-correlation functionals for describing molecular adsorption on metals. Despite the numerous benchmarks performed with these functionals, their performance in predicting bulk properties of transition metals has hitherto not been investigated in detail. We have therefore tested five vdW-DF exchange-correlation functionals, vdW-DF2, optPBE-vdW, BEEF-vdW, optB88-vdW and C09 x -vdW to assess their performance in the prediction of lattice constants, bulk moduli, cohesive energies and surface energies of bulk Ni, Cu, Rh, Pd, Ag, Ir, Pt and Au (in fcc crystal structure). These transition metals are commonly used for benchmarking density functionals because they are important for applications in catalysis. The results are compared with experimental data and the PBE exchange-correlation functional. We found that both the optB88-vdW and the C09 x -vdW exchange-correlation functionals estimate all properties with high accuracy, in better agreement with experimental data than PBE and other considered vdW functionals. The C09 x -vdW functional clearly outperforms all other exchange-correlation functionals for surface energies for the (1 1 1) termination of different metals. We have also evaluated the interatomic electron density emerging from different functionals, and concluded that the observed differences are a result of the predicted lattice parameter, rather than a direct consequence of the functional form. Plane-wave and real-space grid-based expansions of the electron density are also compared, revealing good agreement between the two approaches for lattice parameters, cohesive energies, and surface energies, but more severe differences in bulk moduli. On the basis of our results, we recommend using the C09 x -vdW for studying bulk properties and surface energies of transition metals.

CO2 capture enhancement for InOF-1: confinement of 2-propanol.

The 2-propanol (i-PrOH) adsorption properties of InOF-1 are investigated along with the confinement of small amounts of this alcohol to enhance the CO2 capture for i-PrOH@InOF-1 (1.25-fold improvement compared to pristine InOF-1). InOF-1 exhibited a high affinity towards i-PrOH, experimentally quantified by ΔHads (-55 kJ mol-1), and DFT geometry optimisations showed strong hydrogen bonding between O(i-PrOH) and H(µ2-OH). Quantum chemical models demonstrated that the CO2 capture increase for i-PrOH@InOF-1 was due to a decrease in the void surface of InOF-1 (bottleneck effect), and the formation of essential hydrogen bonds of CO2 with i-PrOH and with the hydroxo functional group (µ2-OH) of InOF-1.

Confined toluene within InOF-1: CO2 capture enhancement.

The toluene adsorption properties of InOF-1 are studied along with the confinement of small amounts of this non-polar molecule revealing a 1.38-fold increase in CO2 capture, from 5.26 wt% under anhydrous conditions to 7.28 wt% with a 1.5 wt% of pre-confined toluene at 298 K. The InOF-1 affinity towards toluene was experimentally quantified by ΔH ads (-46.81 kJ mol-1). InOF-1 is shown to be a promising material for CO2 capture under industrial conditions. Computational calculations (DFT and QTAIM) and DRIFTs in situ experiments provided a possible explanation for the experimental CO2 capture enhancement by showing how the toluene molecule is confined within InOF-1, which constructed a "bottleneck effect".

SBA15-Fluconazole as a Protective Approach Against Mild Steel Corrosion: Synthesis, Characterization, and Computational Studies.

A SBA15-Fluconazole composite (SBA15-Flu) was prepared to formulate a self-healing coating for mild steel. The composite was obtained by dispersing SBA15 in a methanolic solution containing Fluconazole (Flu). The materials were characterized by using different techniques. Electrochemical impedance spectroscopy (EIS) was used for protective behavior evaluation of the coatings on mild steel substrates in an electrolytic solution prepared from sodium chloride and ammonium sulfate. The EIS results indicate that the inhibitor trapped in the SiO2 matrix is released when it comes into contact the aggressive solution, thus protecting the metal. To understand the inhibitor release mechanism, docking studies were used to model the SBA15-Flu complex, which allowed us to further determine polar and non-polar contributions to the binding free energy. An analysis of the electron density within the quantum theory of atoms in molecules and the non-covalent interaction index frameworks were also carried out for the most favorable models of SBA15-Flu. The results indicate that the liberation rate of the Flu molecules is mainly determined by the formation of strong O-H⋅⋅⋅O, O-H⋅⋅⋅N, and O-H⋅⋅⋅F hydrogen bonds.