Molecular insight into endosulfan degradation by Ese protein from Arthrobacter: Evidence-based structural bioinformatics and quantum mechanical calculations.

Endosulfan is an organochlorine insecticide widely used for agricultural pest control. Many nations worldwide have restricted or completely banned it due to its extreme toxicity to fish and aquatic invertebrates. Arthrobacter sp. strain KW has the ability to degrade α, ß endosulfan and its intermediate metabolite endosulfate; this degradation is associated with Ese protein, a two-component flavin-dependent monooxygenase (TC-FDM). Employing in silico tools, we obtained the 3D model of Ese protein, and our results suggest that it belongs to the Luciferase Like Monooxygenase family (LLM). Docking studies showed that the residues V59, V315, D316, and T335 interact with α-endosulfan. The residues: V59, T60, V315, D316, and T335 are implicated in the interacting site with ß-endosulfan, and the residues: H17, V315, D316, T335, N364, and Q363 participate in the interaction with endosulfate. Topological analysis of the electron density by means of the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction (NCI) index reveals that the Ese-ligands complexes are formed mainly by dispersive forces, where Cl atoms have a predominant role. As Ese is a monooxygenase member, we predict the homodimer formation. However, enzymatic studies must be developed to investigate the Ese protein's enzymatic and catalytic activity.

SERS-based detection of 5-S-cysteinyl-dopamine as a novel biomarker of Parkinson's disease in artificial biofluids.

The early detection of Parkinson's disease (PD) can significantly improve treatment and quality of life in patients. 5-S-Cysteinyl-dopamine (CDA) is a key metabolite of high relevance for the early detection of PD. Therefore, its sensitive detection with fast and robust methods can improve its use as a biomarker. In this work we show the potentialities of label-free SERS spectroscopy in detecting CDA in aqueous solutions and artificial biofluids, with a simple, fast and sensitive approach. We present a detailed experimental SERS band assignment of CDA employing silver nanoparticle (AgNP) substrates in aqueous media, which was supported by theoretical calculations and simulated Raman and SERS spectra. The tentative orientation of CDA over the AgNP was also studied, indicating that catechol and carboxylic acid play a key role in the metallic surface adsorption. Moreover, we showed that SERS can allow us to identify CDA in aqueous media at low concentration, leading to the identification of some of its characteristic bands in pure water and in synthetic cerebrospinal fluid (SCSF) below 1 × 10-8 M, while its band identification in simulated urine (SUR) can be reached at 1 × 10-7 M. In conclusion, we show that CDA can be suitably detected by means of label-free SERS spectroscopy, which can significantly improve its sensitive detection for further analytical studies as a novel biomarker and further clinical diagnosis in PD patients.

How do density functionals affect the Hirshfeld atom refinement?

In this work, the effect of mixing different amounts of Hartree-Fock (HF) exchange with hybrid density functionals applied to the Hirshfeld atom refinement (HAR) of urea and oxalic acid dihydrate is explored. Together, the influence of using different basis sets, methods (including MP2 and HF) and cluster sizes (to model bulk effects) is studied. The results show that changing the amount of HF exchange, no matter the level of theory, has an impact almost exclusively on the H atom refinement parameters. Contrary to pure quantum mechanical calculations where good geometries are obtained with intermediate HF exchange mixtures, in the HAR the best match with neutron diffraction reference values is not necessarily found for these admixtures. While the non-hydrogen covalent bond lengths are insensitive to the combination of method or basis set employed, the X-H bond lengths always increase proportionally to the HF exchange for the analysed systems. This outcome is opposite to what is normally observed from geometry optimisations, i.e., shorter bonds are obtained with greater HF exchange. Additionally, the thermal ellipsoids tend to shrink with larger HF exchange, especially for the H atoms involved in strong hydrogen bonding. Thus, it may be the case that the development of density functionals or basis sets suitable for quantum crystallography should take a different path than those fitted for quantum chemistry calculations.

New venues in electron density analysis.

We provide a comprehensive overview of the chemical information from electron density: not only how to extract information, but also how to obtain and how to assess the quality of the electron density itself. After introducing several indexes derived from electron density, which allow bonding to be revealed, we focus on the various potential sources of electron density, and also explain the error trends they show so that a judicious choice of methods and limitations are clearly laid on the table. Computational, experimental-computational combinations, and machine learning efforts are covered in this work.

Benzene and Borazine, so Different, yet so Similar: Insight from Experimental Charge Density Analysis.

Although benzene and borazine are isoelectronic and isostructural, they have very different electronic structures, mainly due to the polar nature of the B-N bond. Herein, we present an experimental study of the charge density distribution obtained from the multipole model formalism and Hirshfeld atom refinement (HAR) based on high-resolution X-ray diffraction data of borazine B3N3H6 (1) and B,B',B″-trichloroborazine (2) crystals. These data are compared to those obtained from HAR for benzene (4) and 1,3,5-trichlorobenzene (5) and further compared with values obtained from density functional theory calculations in the gas phase, where N,N',N″-trichloroborazine (3) was also included. The results confirm that, unlike benzene, borazines are only weakly aromatic with an island-like electronic delocalization within the B3N3 ring involving only the nitrogen atoms. Furthermore, delocalization indices and interacting quantum atom energy for bonded and non-bonded atoms were found to be highly suitable indicators capable of describing the origin of the discrepancies observed when the degree of aromaticity in 2 and 3 is evaluated using common aromaticity indices. Additionally, analysis of intermolecular interactions in the crystals brings further evidence of a weakly aromatic character of the borazines as it reveals surprising similarities between the crystal packing of borazine and benzene and also between B,B',B″-trichloroborazine and 1,3,5-trichlorobenzene.

Control of Molecular Conformation and Crystal Packing of Biphenyl Derivatives.

This Review presents a discussion of the conformation of biphenyl derivatives in different chemical environments. The interplay between aromatic stabilization and steric repulsion, normally considered to explain the conformation of the molecule, is contrasted with the interpretation provided by models not based on molecular orbitals. The electronic control of conformation by means of appropriate hydrogen substitution is discussed by examples taken from chemistry and molecular electronics. Supramolecular synthons involving biphenyl are critically analyzed in terms of the molecular conformation, crystal packing and intermolecular forces. Some directions for future research on the control of the conformation of biphenyls are also presented.

Non-Covalent Interactions in the Biphenyl Crystal: Is the Planar Conformer a Transition State?

A combined experimental and theoretical study of the biphenyl (BP) crystal is presented. The X-ray diffraction data collected at 100 K were subjected to Hirshfeld atom and multipole refinements of the electron density, ρ(r). A theoretical exploration of the potential energy surface (PES) of the crystal was also carried out. This investigation challenges the common assumption that the planar structure of BP in the phase I crystal is an average of two twisted configurations in a double-well potential. The theoretical computations provide compelling evidence that this structure corresponds to a minimum on the PES hence to a stable molecular arrangement. Consistently, the experiment showed no evidence of positional or dynamic disorder. The intramolecular hydrogen-hydrogen bonds detected are not repulsive. The topological analysis of the experimental and theoretical ρ(r) reveals that both the intra- and intermolecular H⋅⋅⋅H and the C-H⋅⋅⋅π contacts stabilize the BP crystal.

Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus responsible for coronavirus disease 2019 (COVID-19); it become a pandemic since March 2020. To date, there have been described three lineages of SARS-CoV-2 circulating worldwide, two of them are found among Mexican population, within these, we observed three mutations of spike (S) protein located at amino acids H49Y, D614G, and T573I. To understand if these mutations could affect the structural behavior of S protein of SARS-CoV-2, as well as the binding with S protein inhibitors (cepharanthine, nelfinavir, and hydroxychloroquine), molecular dynamic simulations and molecular docking were employed. It was found that these punctual mutations affect considerably the structural behavior of the S protein compared to wild type, which also affect the binding of its inhibitors into their respective binding site. Thus, further experimental studies are needed to explore if these affectations have an impact on drug-S protein binding and its possible clinical effect.

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.

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.

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.

Unveiling the role of intra and interatomic interactions in the energetics of reaction schemes: a quantum chemical topology analysis.

In this work we present a detailed analysis of selected reaction schemes in terms of the atomic components of the electronic energy defined by the quantum theory of atoms in molecules and the interacting quantum atoms method. The aim is to provide an interpretation tool for the energy change involved in a chemical reaction by means of the atomic and interaction contributions to the energies of the molecules involved. Ring strain in cyclic alkanes, the resonance energy of aromatic and antiaromatic molecules, local aromaticity in polycyclic aromatic hydrocarbons, intermolecular bonding in hydrogen fluoride clusters, and hydration of d-block metal dications were selected for the study. It was found that in addition to the changes in the strong C-C interactions in the carbon skeleton of the organic molecular rings, other contributions not usually considered to be important such as those between C and H atoms (either bonded or not) need to be considered in order to account for the net energy changes. The analysis unveils the role of the ionic and covalent contributions to the hydrogen bonding in HF clusters and the energetic origin and extent of cooperative effects involved. Moreover, the "double-hump" behavior observed for the hydration energy trend of [M(H2O)6]2+ complexes is explained in terms of the deformation energy of the metal cation and the increasingly covalent metal-water interactions. In addition, proper comparisons with the description provided by other methodologies are briefly discussed. The topological approach proposed in this contribution proves to be useful for the description of energy changes of apposite reaction schemes in chemically meaningful terms.