(E)-2-Benzylidenecyclanones: Part XIX. Reaction of (E)-2-(4'-X-Benzylidene)-1-tetralones with Cellular Thiols: Comparison of Thiol Reactivities of Open-Chain Chalcones and Their Six- and Seven-Membered Cyclic Analogs.

Non-enzyme-catalyzed thiol addition onto the α,ß-unsaturated carbonyl system is associated with several biological effects. Kinetics and diastereoselectivity of non-enzyme catalyzed nucleophilic addition of reduced glutathione (GSH) and N-acetylcysteine (NAC) to the six-membered cyclic chalcone analogs 2a and 2b were investigated at different pH values (pH 3.2, 7.4 and 8.0). The selected compounds displayed in vitro cancer cell cytotoxicity (IC50) of different orders of magnitude. The chalcones intrinsically reacted with both thiols under all incubation conditions. The initial rates and compositions of the final mixtures depended both on the substitution and the pH. The stereochemical outcome of the reactions was evaluated using high-pressure liquid chromatography with UV detection (HPLC-UV). The structures of the formed thiol-conjugates and the retro-Michael products (Z)-2a and (Z)-2b were confirmed by high-pressure liquid chromatography-mass spectrometry (HPLC-MS). Frontier molecular orbitals and the Fukui function calculations were carried out to investigate their effects on the six-membered cyclic analogs. Data were compared with those obtained with the open-chain (1) and the seven-membered (3) analogs. The observed reactivities do not directly relate to the difference in in vitro cancer cell cytotoxicity of the compounds.

Molecular basis of two pyrimidine-sulfonylurea herbicides: from supramolecular arrangement to acetolactate synthase inhibition.

CONTEXT: The design and synthesis of safe and highly active sulfonylurea herbicides is still a challenge. Therefore, following some principles of structure-activity relationship (SAR) of sulfonylurea herbicides, this work focuses on evaluating two sulfonylurea derivatives bearing electron-withdrawing substituents, namely, -(CO)OCH3 and -NO2 on the aryl group, on herbicidal activity. To understand the effects caused by the substituent groups, the molecular and electronic structures of the sulfonylureas were evaluated by density functional theory. Likewise, the crystalline supramolecular arrangements of both compounds were analyzed by Hirshfeld surface, QTAIM, and NBO, with the aim of verifying changes in intermolecular interactions caused by substituent groups. Finally, through a toxicophoric analysis, we were able to predict the interacting groups in their biological target, acetolactate synthase, and verify the interactions with the binding site. METHODS: All theoretical calculations were conducted using the highly parameterized empirical exchange-correlation functional M06-2X accompanied by the diffuse and polarized basis set 6-311++G(d,p). The atomic coordinates were obtained directly from the crystalline structures, and from the energies of the frontier molecular orbitals (HOMO and LUMO), chemical descriptors were obtained that indicated the influence of the functional groups in the sulfonylureas on the reactivity of the molecules. The intermolecular interactions in the crystals were analyzed using the Hirshfeld, QTAIM, and NBO surfaces. Toxicophoric modeling was performed by the PharmaGist webserver and molecular docking calculations were performed by the GOLD 2022.1.0 software package so that the ligand was fitted to the binding site in a 10 Å sphere. For this, genetic algorithm parameters were used using the ChemPLP scoring function for docking and ASP for redocking.

Structural basis of antibacterial photodynamic action of curcumin against S. aureus.

Antimicrobial photodynamic therapy (aPDT) is an alternative tool to commercial antibiotics for the inactivation of pathogenic bacteria (e.g., S. aureus). However, there is still a lack of understanding of the molecular modeling of the photosensitizers and their mechanism of action through oxidative pathways. Herein, a combined experimental and computational evaluation of curcumin as a photosensitizer against S. aureus was performed. The radical forms of keto-enol tautomers and the energies of curcumin's frontier molecular orbitals were evaluated by density functional theory (DFT) to point out the photodynamic action as well as the photobleaching process. Furthermore, the electronic transitions of curcumin keto-enol tautomers were undertaken to predict the transitions as a photosensitizer during the antibacterial photodynamic process. Moreover, molecular docking was used to evaluate the binding affinity with the S. aureus tyrosyl-tRNA synthetase as the proposed a target for curcumin. In this regard, the molecular orbital energies show that the curcumin enol form has a character of 4.5% more basic than the keto form - the enol form is a more promising electron donor than its tautomer. Curcumin is a strong electrophile, with the enol form being 4.6% more electrophilic than its keto form. In addition, the regions susceptible to nucleophilic attack and photobleaching were evaluated by the Fukui function. Regarding the docking analysis, the model suggested that four hydrogen bonds contribute to the binding energy of curcumin's interaction with the ligand binding site of S. aureus tyrosyl-tRNA synthetase. Finally, residues Tyr36, Asp40, and Asp177 contact curcumin and may contribute to orienting the curcumin in the active area. Moreover, curcumin presented a photoinactivation of 4.5 log unit corroborating the necessity of the combined action of curcumin, light, and O2 to promote the photooxidation damage of S. aureus. These computational and experimental data suggest insights regarding the mechanism of action of curcumin as a photosensitizer to inactivate S. aureus bacteria.

New Insights on Glutathione's Supramolecular Arrangement and Its In Silico Analysis as an Angiotensin-Converting Enzyme Inhibitor.

Angiotensin-converting enzyme (ACE) inhibitors are one of the most active classes for cardiovascular diseases and hypertension treatment. In this regard, developing active and non-toxic ACE inhibitors is still a continuous challenge. Furthermore, the literature survey shows that oxidative stress plays a significant role in the development of hypertension. Herein, glutathione's molecular structure and supramolecular arrangements are evaluated as a potential ACE inhibitor. The tripeptide molecular modeling by density functional theory, the electronic structure by the frontier molecular orbitals, and the molecular electrostatic potential map to understand the biochemical processes inside the cell were analyzed. The supramolecular arrangements were studied by Hirshfeld surfaces, quantum theory of atoms in molecules, and natural bond orbital analyses. They showed distinct patterns of intermolecular interactions in each polymorph, as well as distinct stabilizations of these. Additionally, the molecular docking study presented the interactions between the active site residues of the ACE and glutathione via seven hydrogen bonds. The pharmacophore design indicated that the hydrogen bond acceptors are necessary for the interaction of this ligand with the binding site. The results provide useful information for the development of GSH analogs with higher ACE inhibitor activity.

Theoretical analysis of the effects of counterions on the supramolecular arrangement of sulfamethoxazole.

Active pharmaceutical ingredients are formulated as the salt form, aiming to modulate their physicochemical properties. In this regard, the optimization and choice of the salt former have a strong influence on toxicity, therapeutic efficiency, and bioavailability. Sulfamethoxazole (SMZ) salts with Na+, Cl-, and Br- counterions influence in the supramolecular arrangement as well as in their thermodynamic and kinetic parameters. Herein, we analyzed the interactions of the Na+, Cl-, and Br- counterions on the supramolecular arrangement of the sulfamethoxazole salts by Hirshfeld surfaces, fingerprint plots, and theoretical methods-quantum theory of atoms in molecules and natural bond orbitals. Moreover, we evaluated their electronic structure by density functional theory using calculation of the frontier molecular orbitals. Molecular electrostatic potential maps were also obtained to predict the interactions of the counterions along crystalline arrangements. We observed that the structures of [SMZ]+ and [SMZ]- ions differ slightly from the SMZ. The chemical reactivity indices show that the SMZ is kinetically more stable than its respective ions, while its anion is more polarizable, and its cation has a higher global electrophilicity index. The molecular electrostatic potential maps show high charge density in the sulfonyl group (nucleophilic region) and the heterocyclic amino group (electrophilic region). Although the molecular skeleton is identical among the three SMZ species and the presence of different counterions in the formation of the crystalline structure of the salts results in supramolecular arrangements with different patterns of intermolecular interactions, despite being very similar in terms of intensities.

Cyclohexanone-Based Chalcones as Alternatives for Fuel Additives.

The use of small molecules, such as chalcones and their derivatives, for more efficient fuels is in increasing demand due to environmental factors. Here, three crystal structures (BH I, II, and III) of cyclohexanone-based chalcones were synthesized and described by single-crystal X-ray diffraction and Hirshfeld surface analysis. The supramolecular modeling analysis on the hyperconjugative interaction energies and QTAIM analysis at the ωB97XD/6-311++G(d,p) level of theory were carried out to analyze the intermolecular interactions in the solid-state. The structure-property relationship, frontier molecular orbital, molecular electrostatic potential, and the experimental calorific value analysis show that the three compounds are a good alternative to be used as an additive for some fuels. Our findings represent a further step forward in the development of cheaper and more efficient fuel additives and pose an opportunity for further investigation on similar analogues.

Effect of ortho- and para-chlorine substitution on hydroxychlorochalcone.

This work describes a comparative molecular structure of two hydroxychlorochalcones with an emphasis on their planarity. Hirshfeld surface analysis investigates the effect of ortho- and para-chlorine substitution on supramolecular arrangement and physical chemical properties. The molecular conformation of 2'-hydroxy-4',6'-dimethyl-2-chlorochalcone and 2'-hydroxy-4',6'-dimethyl-4-chlorochalcone chalcones was obtained through DFT with the exchange-correlation functional M06-2X and the 6-311++G(2d,2p) basis set, and the results were compared with the experimental X-ray data in order to get insights on the effect of ortho- and para-chlorine substitution. The charge transfer into entire main carbon chain was also investigated using frontier molecular orbitals (HOMO and LUMO), NBO, and MEP map in order to describe the comparative conformational stability due to the resonance effect produced by π electron displacements. Finally, the intermolecular observed interactions were analyzed by QTAIM, with the M06-2X/6-311G++(d,p) theory level.

A new isostructural halogenated chalcone with optical properties.

Chalcones are organic compounds that present a number of properties. This study presents a comprehensive structural description of a new derivative of a chlorine-substituted chalcone in comparison with a bromine chalcone. Also, supermolecule and sum-over-state approach were used to describe the optical properties of these structures regarding the substitution of the bromine by the chlorine atom. In addition, the electrical properties, dipole moment, linear polarizability, and second IDRI hyperpolarizability were calculated. The linear refractive index and the third-order nonlinear macroscopic susceptibility were evaluated as a function of the applied electric field frequency. Furthermore, the quantum mechanics calculations that were implemented at the M06-2X/6-311++G(d,p) level of the theory for these isostructural chalcones indicate that the change in halogen atoms does not cause meaningful changes in their conformation. Finally, we can postulate that side-to-side and the antiparallel interactions are the interaction forces that drive the crystal growth for new isostructural chalcones. The NLO properties showed title compounds that are good candidates for use as NLO materials.

Halogen bonds on substituted dibromonitrobenzene derivatives.

Halogen bonding is a noncovalent interaction that has attracted great attention because of its importance in several areas, such as photonics, nonlinear optics, pharmaceutical products, supramolecular engineering, biochemistry, protein-ligand complexes, and polymer interactions. In this context, we describe the synthesis, molecular structure, supramolecular arrangement, and theoretical calculations of five dibromonitrobenzene derivatives, which present different halogen atoms substituted. The solid-state characterization was carried out by X-ray diffraction with the contribution of Hirshfeld surfaces for analysis of molecular interactions. The frontier molecular orbital, molecular electrostatic potential, and quantum theory of atoms in molecules were carried out at the M06-2X/6-311+G(d,p) level of theory. Those observed halogen interactions indicate the crystalline solid-state stabilization for the dibromonitrobenzene derivatives.

Synthesis, characterization, and computational study of a new heteroaryl chalcone.

This work presents the synthesis of the chalcone (E)-3-(2,6-difluorophenyl)-1-(furan-2-yl)-prop-2-en-1-one molecule through the equimolar reaction between 1-(furan-2-yl)-ethenone and 2,6-difluorobenzaldehyde. The crystallographic characterization and the extensive theoretical study regarding electronic properties were obtained. The supramolecular arrangement was described by X-ray diffraction and Hirshfeld surfaces. Optimized geometrical structure was obtained by density functional theory, and the electronic study for differences between the solid and gas phases was carried out with M062-X at 6-311++G(2d,2p) basis set. Natural bond orbital, frontier molecular orbitals (HOMO-LUMO), and molecular electrostatic potential map were determined to elucidate the information related to the charge transfer in the molecule. The theoretical and experimental vibrational spectra were plotted, which included the IR intensities, the calculated and experimental vibrational frequencies, and the assigned vibrational modes for the main groups of DTP.

Ab Initio Molecular Dynamics Simulations of Aqueous Glucosamine Solutions: Solvation Structure and Mechanism of Proton Transfer from Water to Amino Group.

Glucosamine is a component of many cellular glycoproteins that constitutes the cartilage, and it has several biological activities, such as anti-inflammatory, antioxidant, antifibrotic, and anticancer, and has been used in arthritis and dermatological treatments. Considering that the biological activities of glucosamine occur mainly in an aqueous environment, it is essential to understand the effects of an aqueous solvent on its geometric and electronic parameters using ab initio molecular dynamics. The Car-Parrinello molecular dynamics results show that the hydroxyl groups form stable hydrogen bonds with the water molecules with intensities ranging from weak (closed-shell interaction) to intermediate (partially covalent interactions). The H bonds formed between the amino group and the water molecule range from weak (closed-shell) to strong (covalent), and it shows an infinity residence time. The natural bonding orbital (NBO) approach was applied to analyze the effects of charge-transfer interactions on the behavior of the hydrogen bonds. The main contribution to stabilizing energies comes from n → σ* hyperconjugation and explains the stability of the H bonds. The energy barrier for the proton transfer from water to the amino group is 0.88 kcal/mol, and the van der Waals complex energy is 0.3 kcal/mol. The low protonation energy barrier shows that glucosamine can be protonated in an aqueous environment at room temperature, which helps to explain many of its biological activities.

Structure-activity relationship of tacrine and its analogues in relation to inhibitory activity against Alzheimer's disease.

Alzheimer's disease is a widespread type of neurodegenerative dementia that mainly affects the elderly. Currently, this disease can only be treated palliatively. Existing drugs can only improve patients' symptoms. The search for new drugs that can effectively treat this disease is an important field of research in medicinal chemistry. Here we report a structure-activity relationship study of tacrine and some of its analogues in relation to their inhibitory activities against Alzheimer's disease. All of the molecular descriptors were calculated at the M062X/6-311++G(d,p) level of theory. Principal component analysis of the molecular descriptors showed that the compounds could be categorized into active and inactive compounds using just two descriptors: the HOMO and LUMO energies. These results should help us to explain the activities of tacrine derivatives and to model new tacrine analogues that are active against Alzheimer's disease. Graphical abstract PCA score plot for tacrine and its analogues.

Explicit Aqueous Solvation Treatment of Epinephrine from Car-Parrinello Molecular Dynamics: Effect of Hydrogen Bonding on the Electronic Absorption Spectrum.

The electronic absorption spectrum of the neurotransmitter epinephrine (EPN) in water solution is studied, combining ab initio Car-Parrinello molecular dynamics (CPMD) with a quantum mechanical approach within the framework of the time-dependent density functional theory (TDDFT) scheme. By selecting 52 uncorrelated snapshots, the excitation modes were calculated at the LC-ωPBE/6-31+G(d) level of theory, using an optimal range-separation parameter ω, determined by means of the gap-tuning scheme in the presence of the solvent molecules. By comparing with static approaches (vacuum and implicit solvation), we show here that explicit solvation treatment dramatically enhances the photophysical properties of the EPN, especially because of the more realistic dynamic description of the molecular geometry. The agreement between the simulated and experimental spectra is demonstrated when TDDFT calculations are performed with the optimally tuned version of the DFT hybrid, not only improving the relative intensities of the absorption bands but also the λmax position. These results highlight that accounting for the nuclear motions, that is, thermal effects (of both chromophore and solvent molecules), is imperative to predict experimental absorption spectra. In this paper, we have addressed the critical importance of explicit solvation effects on the photophysics of the EPN, raking in performance when the simulation is performed based on first-principles molecular dynamics such as CPMD.

Conformation analysis of a novel fluorinated chalcone.

Chalcones are an important class of natural compounds that exhibit numerous biological activities. In this paper, we report the synthesis and characterization of new fluorinated chalcone (FCH). The molecular geometry was determined by means of single crystal X-ray diffraction, and density functional theory (DFT) at B3LYP, M06-2X functionals and MP2 method, with the 6-311++G(d,p) basis set, was applied to optimize the ground state geometry and to study the molecular conformational stability. The molecular electrostatic potential (MEP) was also investigated at the same level of theory in order to identify and quantify the possible reactive sites. The FCH crystallizes in the centrossymmetric space group [Formula: see text] with two independent conformers (α and ß) in the asymmetric unit cell. The α conformer is arranged in planar layer whereas the ß creates a layer of non-classical dimer along c axis, that differ from α in about 11° in the orientation of phenyl groups. The stabilization of the ß conformer is achieved by C-H···π arrangement. The small energy difference between the conformers (0.086 kcal mol-1) and the absence of activation energy indicates that the conversion between them can takes place at room temperature and the ß isomer is stable only in solid state. The FCH most electrophilic site occurs on the oxygen atom from the carboxyl group with absolute MEP value of about -52 kcal mol-1 whereas the MEP value calculated for F site is about -23 kcal mol-1.

Structural and Theoretical Investigation of Anhydrous 3,4,5-Triacetoxybenzoic Acid.

A comprehensive investigation of anhydrous form of 3,4,5-Triacetoxybenzoic acid (TABA) is reported. Single crystal X-ray diffraction, Thermal analysis, Fourier Transform Infrared spectroscopy (FTIR) and DFT calculations were applied for TABA characterization. This anhydrous phase crystallizes in the triclinic [Formula: see text] space group (Z' = 1) and its packing shows a supramolecular motif in a classical [Formula: see text] ring formed by acid-acid groups association. The phase stability is accounted in terms of supramolecular architecture and its thermal behaviour. Conformation search at B3LYP/6-311++G(2d,p) level of theory shows the existence of three stable conformers and the most stable conformation was found experimentally. The reactivity of TABA was investigated using the molecular orbital theory and molecular electrostatic potential. The calculation results were used to simulate the infrared spectrum. There is a good agreement between calculated and experimental IR spectrum, which allowed the assignment of the normal vibrational modes.

Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr.

Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic sampling of the canonical ensemble is indicated as needed for quantitative comparison with the kinetic experiments.

Stereodynamical Origin of Anti-Arrhenius Kinetics: Negative Activation Energy and Roaming for a Four-Atom Reaction.

The OH + HBr → H2O + Br reaction, prototypical of halogen-atom liberating processes relevant to mechanisms for atmospheric ozone destruction, attracted frequent attention of experimental chemical kinetics: the nature of the unusual reactivity drop from low to high temperatures eluded a variety of theoretical efforts, ranking this one among the most studied four-atom reactions. Here, inspired by oriented molecular-beams experiments, we develop a first-principles stereodynamical approach. Thermalized sets of trajectories, evolving on a multidimensional potential energy surface quantum mechanically generated on-the-fly, provide a map of most visited regions at each temperature. Visualizations of rearrangements of bonds along trajectories and of the role of specific angles of reactants' mutual approach elucidate the mechanistic change from the low kinetic energy regime (where incident reactants reorient to find the propitious alignment leading to reaction) to high temperature (where speed hinders adjustment of directionality and roaming delays reactivity).

Synthesis, characterization, and computational study of a new dimethoxy-chalcone.

Chalcones are an important class of medicinal compounds and are known for taking part in various biological activities as in anti-inflammatory, anti-leishmania, antimitotic, and antiviral. Chemically, chalcones consist of open-chain flavonoids in which the two aromatic rings are joined by a three-carbon α,ß-unsaturated carbonyl system. The wide action spectrum has attracted our attention to synthesize, crystallize, and characterize the dimethoxy-chalcone C18H18O3. Aiming to understand the process of crystal lattice stabilization, a combination of technique has been used including X-ray diffraction, infrared spectroscopy and computational molecular modeling. The theoretical calculations were carried out by the density functional method (DFT) with the M06-2X functional, with the 6-311+G(d,p) basis set. The vibrational wavenumbers were calculated and the scaled values were compared with experimental FT-IR spectrum. The intermolecular interactions were quantified and intercontacts in the crystal structure were analyzed using Hirshfeld surfaces. Bond distances and angles described by the X-ray diffraction and theoretical calculation are very similar. The C-H….O contacts contributing to assemble the supramolecular architecture are also responsible for the molecular structure assembly.

Effect of the methanol molecule on the stabilization of C18H18O4 crystal: combined theoretical and structural investigation.

The ability of the chalcone, C18H18O4, to form solvates was theoretically and experimentally investigated. The unit cell with Z' > 1, composed of two independent chalcone molecules (α and ß), shows the formation of a stable molecular complex which is related with the presence of methanol in this crystal lattice. Aiming to understand the process of crystal lattice stabilization, a combination of techniques was used, including X-ray diffraction (XRD), computational molecular modeling, and an ab initio molecular dynamic. The results show that α and ß molecules are sterically barred from forming a direct hydrogen bond with one other. In addition, the presence of the methanol molecule stabilizes the crystal structure by a bifurcated O-H···O interaction acting as a bridge between them. The theoretical thermodynamic parameter and the rigid potential energy surface scan describe the role of methanol in the energy stabilization of the crystal. The absence of the methanol compound in the asymmetric unit destabilizes the crystalline structure, making the formation process of the asymmetric unit nonspontaneous. The energy difference between α and ß molecules is around 0.80 kcal·mol(-1), indicating that both are stable and equally possible in the crystal lattice. The analysis of the energy profile of the C14-O2···H1-O3 and O2-H1···O3-C17 torsion angles in the crystal packing shows that the α and ß molecules are confined in the stable potential region, in agreement with the two conformers in the asymmetric unit. The Molecular Electrostatic Potential (MEP) shows that the methanol has no steric effects, which prevents small motion around the torsion angles.

Theoretical investigation on ruthenium tetraazaporphyrin as potential nitric oxide carrier in biological systems.

Nitric oxide (NO) is an important chemical compound involved in many physiological and pathological processes in living organisms. However, nitric oxide is a very reactive radical that needs to be carried through organisms to reach the desired biological target. With the aim of developing new compounds that can be used as biomedical NO carrier agents we carried out a theoretical investigation at B3LYP/6-31+G(d)/LANL2DZ level on the interaction of NO with RuTAP (Ruthenium tetraazaporphyrin) and Ru(L)TAP, where L=Cl-, NH3, and Pyridine (Py)) and the oxidation state of Ru ranging from +1 to +3. The theoretical calculation results show that the geometric and electronic parameters of the Ru-NO bond are highly dependent on the oxidation state of Ru and of the chemical nature of ligand L at axial position. The results also show clearly that RuTAP and Ru(L)TAP are good potential candidates to be used as NO carriers in living organisms.