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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Three systems with different hydrogen bond strengths were examined by using the Hartree-Fock (HF), Kohn-Sham (KS) methods as well as the second-order Mollet-Plesset perturbation theory (MP2). Since the MP2 method used both, occupied and unoccupied HF orbitals, to compute the total energy, the contribution of the basis set superposition error (BSSE) was found to be bigger than that obtained with HF or KS methodologies.

It is for the first time that orientational probability distribution function for CO transiently docked in myoglobin (Mb) and Hb is established. The ordered protein structure around the active site of the enzyme has a selectivity even for small ligands.

Peptide nano-doughnuts were treated from synthetic peptides and organic Au salts through self-assembly. This may allow them to be applied on the fields of controlled release systems and during delivery.

A versatile procedure to synthesize mono disperse hollow polymer colloid particles which can self-assemble into a crystalline colloidal array (CCA) is developed. These help in confining the reaction inside the hollow particles to fabricate.

The existence of a set of structural criteria for the rational design of molecular receptors which complex NO(sub 3)(super -) anion due to hydrogen bonding interactions. recent research shows that it is possible to chelate three nonconnected urea groups to NO(sub 3)(super -), without any steric effects.

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]

The ab initio electronic structure theory level and the second-order Moller-Plesset perturbation theory (MP2) with augmented correlation consistent basis sets are utilized to evaluate the structures of the dimers of formamide and N-methylacetamide. The differences in the hydrogen bond strengths of both dimers are attributed to differences in basicity at the carbonyl oxygen receptor site.

In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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)-TDC⋯I2 configuration, the I2 molecule is bonded mainly by an O–H⋯I hydrogen bond. The QTAIM showed that other non-covalent interactions also provided stability to MIL-53(Al)-TDC⋯I2. 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. [ABSTRACT FROM AUTHOR]

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–H⋯O hydrogen bonds, and C⋯π interactions by the biphenyl rings of the MOF. These results provide useful information on the CO adsorption mechanisms in InOF-1. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this report, it is shown that the Kohn-Sham (KS) kinetic energy density (KED) contains the average local electrostatic potential (ALEP) and the average local ionization energy (ALIE); the shell structure in atomic systems is presented as one application of the KS-KED. By writing the KS-KED from the KS equations, this quantity was divided in three contributions: orbital, Coulomb, and exchange correlation. By studying several closed and open shell atoms, the shell structure was established by the maxima presented by the Coulomb contribution and the minima in the orbital contribution of the KS-KED. The exchange-correlation contribution to the KS-KED does not show maxima or minima, but this quantity shows bumps where the division between shells is expected. The results obtained in this work were compared with other shell structure indicators such as the electron localization function, the ALEP, the ALIE, and the radial distribution function. The most important result in this work is related to the fact that even when the ALEP and the ALIE functions were built with different arguments to each other, they are contained in the KS-KED. In this way, the KS-KED shows its importance to reveal the electron localization in atomic systems. [ABSTRACT FROM AUTHOR]

Calculations of mean excitation energy, I[sub m], static polarizability, α, and hyperpolarizability, γ, using the variation perturbation procedure are reported for the spherically confined hydrogen atom. The electric response properties α and γ have been found to strongly depend upon the radius of confinement. The hyperpolarizabilty changes sign and becomes negative under strong confinement. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]