Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator.

The reactivity of 22 unsaturated molecules undergoing attack by a methyl radical (⋅CH3) have been elucidated using the condensed radical general-purpose reactivity indicator (condensed radical GPRI) appropriate for relatively nucleophilic or electrophilic molecules. Using the appropriate radical GPRI equation for electrophilic attack or nucleophilic radical attack, seven different population schemes were used to assign the most reactive atoms in each of the 22 molecules. The results show that the condensed radical GPRI is sensitive to the population scheme chosen, but less sensitive than the radical Fukui function. Therefore, the reliability of these methods depends on the population scheme. Our investigation indicates that the condensed radical GPRI is most accurate in predicting the dominant products of the methyl radical addition reactions on a variety of unsaturated molecules when the Hirshfeld, Merz-Singh-Kollman, or Voronoi deformation density population schemes are used. Furthermore, for all populations schemes in the majority of instances where the radical Fukui function failed the radical GPRI was able to identify the most reactive atom under certain reactivity conditions.

Synergistic topological and supramolecular control of Diels-Alder reactivity based on a tunable self-complexing host-guest molecular switch.

Compartmentalization and binding-triggered conformational change regulate many metabolic processes in living matter. Here, we have synergistically combined these two biorelevant processes to tune the Diels-Alder (DA) reactivity of a synthetic self-complexing host-guest molecular switch CBPQT4+ -Fu, consisting of an electron-rich furan unit covalently attached to the electron-deficient cyclobis(paraquat-p-phenylene) tetrachloride (CBPQT4+ , 4Cl- ) host. This design allows CBPQT4+ -Fu to efficiently compartmentalize the furan ring inside its host cavity in water, thereby protecting it from the DA reaction with maleimide. Remarkably, the self-complexed CBPQT4+ -Fu can undergo a conformational change through intramolecular decomplexation upon the addition of a stronger binding molecular naphthalene derivative as a competitive guest, triggering the DA reaction upon addition of a chemical regulator. Remarkably, connecting the guest to a thermoresponsive lower critical solution temperature (LCST) copolymer regulator controls the DA reaction on command upon heating and cooling the reaction media beyond and below the cloud point temperature of the copolymer, representing a rare example of decreased reactivity upon increasing temperature. Altogether, this work opens up new avenues towards combined topological and supramolecular control over reactivity in synthetic constructs, enabling control over reactivity through molecular regulators or even mild temperature variations.

Investigation on the Influence of Solvents Environment on the Optoelectronic Properties of the Fluorescent Probe 1,3,4-Oxadiazole Analogues: A Combined Theoretical and Experimental Study.

This study investigates the photophysical properties of a nitrobenzene-substituted 1,3,4-oxadiazole derivative (OX-NO) using both theoretical and experimental methods. The impact of the solvent on OX-NO absorption and fluorescence spectra, as well as its fluorescence quantum yield, was initially studied. A noticeable bathochromic shift in the Stokes shift indicated a π→ π* transition within the molecules. Solute-solvent interactions were analysed using Catalan parameters, distinguishing between specific and nonspecific interactions. Excited state dipole moments were derived from Lippert's, Bakshiev's, and Chamma Viallet's equations, showing increased polarity in the excited state compared to the ground state. Ground state dipole moments were determined via solvatochromic shift methods and ab initio techniques. Additionally, detailed analyses of bond length, angles, dihedral angles, Mulliken charge distribution, and HOMO-LUMO energy gap were conducted using the DFT-B3LYP-6-311G basis set in Gaussian-09 W. The energy band gap values obtained from theoretical calculations and experimental methods (cyclic voltammetry and UV-Visible spectroscopy) exhibited excellent agreement. Reactive sites such as electrophilic and nucleophilic regions were identified through total electron density, electrostatic maps, molecular electrostatic potential, and 3D plots using DFT computational analysis. Global descriptors were employed to characterize the compounds' chemical reactivity comprehensively. The observed photophysical attributes underscore the potential of these fluorophores in various applications like organic light-emitting diodes, solar cells, and chemosensors. This study contributes crucial insights into the optoelectronic properties of nitrobenzene-substituted 1,3,4-oxadiazole derivatives, paving the way for their future integration in advanced technological domains.

Reactivity of amino acids and short peptide sequences: identifying bioactive compounds via DFT calculations.

Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds.

Marine Toxins as Pharmaceutical Treasure Troves: A Focus on Saxitoxin Derivatives from a Computational Point of View.

This work highlights the significant potential of marine toxins, particularly saxitoxin (STX) and its derivatives, in the exploration of novel pharmaceuticals. These toxins, produced by aquatic microorganisms and collected by bivalve mollusks and other filter-feeding organisms, offer a vast reservoir of chemical and biological diversity. They interact with sodium channels in physiological processes, affecting various functions in organisms. Exposure to these toxins can lead to symptoms ranging from tingling sensations to respiratory failure and cardiovascular shock, with STX being one of the most potent. The structural diversity of STX derivatives, categorized into carbamate, N-sulfocarbamoyl, decarbamoyl, and deoxydecarbamoyl toxins, offers potential for drug development. The research described in this work aimed to computationally characterize 18 STX derivatives, exploring their reactivity properties within marine sponges using conceptual density functional theory (CDFT) techniques. Additionally, their pharmacokinetic properties, bioavailability, and drug-likeness scores were assessed. The outcomes of this research were the chemical reactivity parameters calculated via CDFT as well as the estimated pharmacokinetic and ADME properties derived using computational tools. While they may not align directly, the integration of these distinct datasets enriches our comprehensive understanding of the compound's properties and potential applications. Thus, this study holds promise for uncovering new pharmaceutical candidates from the considered marine toxins.

Combining Molecular Quantum Mechanical Modeling and Machine Learning for Accelerated Reaction Screening and Discovery.

Molecular quantum mechanical modeling, accelerated by machine learning, has opened the door to high-throughput screening campaigns of complex properties, such as the activation energies of chemical reactions and absorption/emission spectra of materials and molecules; in silico. Here, we present an overview of the main principles, concepts, and design considerations involved in such hybrid computational quantum chemistry/machine learning screening workflows, with a special emphasis on some recent examples of their successful application. We end with a brief outlook of further advances that will benefit the field.

Deeper Defluorination and Mineralization of a Novel PFECA (C7 HFPO-TA) in Vacuum UV/Sulfite: Unique Mechanism of H/OCF3 Exchange.

C7 HFPO-TA is a newly identified alternative to PFOA, which possesses a unique structure fragment (CF3O-CF(CF3)-). In this study, we evaluated the chemical reactivity of C7 HFPO-TA in advanced oxidation and reduction processes for the first time, which revealed a series of unexpected transformation mechanisms. The results showed that reductive degradation based on hydrated electrons (eaq-) was more feasible for the degradation of C7 HFPO-TA. For oxidative degradation, the branched -CF3 at the α-position carbon posed as the spatial hindrance, shielding the attack of SO4•- to -COO-. The synergistic effects of HO•/eaq- and direct photolysis led to deeper defluorination and mineralization of C7 HFPO-TA in the vacuum UV/sulfite (VUV/SF) process. We identified a unique H/OCF3 exchange that converted the CF3O-CF(CF3)- into H-CF(CF3)- directly, and the SO3•- involved mechanism of C7 HFPO-TA for the first time. We revealed the branched -CF3 connected to the same carbon next to the CF3O- group affected the C-O bond cleavage site, preferring the H/OCF3 exchange pathway. The defluorination of C7 HFPO-TA was compared with PFOA and three PFECAs in the VUV/SF process, which was highly dependent on structures. Degradation kinetics, theoretical calculations, and products' analysis provided an in-depth perspective on the degradation mechanisms and pathways of C7 HFPO-TA.

Ultrasound-promoted convenient and ionic liquid [BMIM]BF4 assisted green synthesis of diversely functionalized pyrazolo quinoline core via one-pot multicomponent reaction, DFT study and pharmacological evaluation.

An ultrasound-assisted green protocol for one-pot synthesis of a new series of pharmaceutically relevant pyrazolo quinoline derivatives (4a-t) were synthesized, characterized, and evaluated using DFT and biological activities. Pyrazolo quinoline derivatives (4a-t) were synthesized via a three-component tandem reaction of 1,3-dicarbonyl compound (1a-b), substituted aromatic aldehyde (2a-o), and 5-amino indazole (3a) in the presence of 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM]BF4 ionic liquid in ethanol at ambient conditions. The main purpose of the present work is selective functionalization of pyrazolo quinoline (4a-t) core excluding another potential parallel reaction under environmentally benign reaction conditions. The present protocol shows features such as amphiphilic behavior of ionic liquid during reaction transformation, and reusability of the [BMIM]BF4 ionic liquid under mild reaction condition. All newly derived compounds were evaluated for their in vitro anti-inflammatory and antioxidant activity. Among them, compound 4c showed encouraging antioxidant activity compared with standard antioxidant ascorbic acid, and compounds 4n and 4r displayed very good anti-inflammatory activity compared with a standard drug. In this study, a theoretical computational density functional study was also executed to perform the geometry optimizations, frontier molecular orbital approach, and molecular electrostatic potential (MESP). The DFT study was carried out with the basis set DFT/B3LYP/6-31+G (d, p) level of theory. The quantum chemical descriptors (QCDS) and MESP diagrams were plotted to examine the biological reactivities of representative pyrazolo quinolines (4a-t).

A real space picture of the role of steric effects in SN 2 reactions.

Within substitution reactions, the Bimolecular Nucleophilic Substitution (SN 2) reaction mechanism is one of the most frequently found and studied ones. Among other factors, the easiness of the SN 2 pathway is classically considered to be determined by steric hindrance. However, the diffuse nature of the latter inevitably darkens these and other arguments holding the pillars of chemical intuition. In this work, we employ the steric energy (EST ) descriptor, formulated within the Interacting Quantum Atoms approach, to offer insights regarding this problem. The steric demands of the substrate, nucleophile and leaving group were studied using the gas-phase SN 2 reaction with different organic skeletons (CH3 , CH3 CH2 , (CH3 )2 CH, (CH3 )3 C, (CH3 )3 CCH2 ) and halogens (F, Cl, and Br) as test-bed systems. Our results show that, according to EST , the SH experienced along these simple reactions fits, in the general case, the trends predicted by a meticulous and rigorous application of chemical intuition. However, steric clash alone should not be considered as the only argument used to explain the easiness of the SN 2 reaction over different electrophiles.

New Organic-Inorganic Salt Based on Fluconazole Drug: TD-DFT Benchmark and Computational Insights into Halogen Substitution.

In this study, we report the synthesis of a new organic-inorganic molecular salt of the clinically used antifungal drug fluconazole, (H2Fluconazole).SnCl6.2H2O. By detailed investigation and analysis of its structural properties, we show that the structure represents a 0D structure built of alternating organic and inorganic zig-zag layers along the crystallographic c-axis and the primary supramolecular synthons in this salt are hydrogen bonding, F···π and halogen bonding interactions. Magnetic measurements reveal the co-existence of weak ferromagnetic behavior at low magnetic field and large diamagnetic contributions, indicating that the synthesized material behaves mainly as a diamagnetic material, with very low magnetic susceptibility and with a band gap energy of 3.6 eV, and the salt is suitable for semiconducting applications. Extensive theoretical study is performed to explain the acceptor donor reactivity of this compound and to predict the Cl-substitution effect by F, Br and I. The energy gap, frontier molecular orbitals (FMOs) and the different chemical reactivity descriptors were evaluated at a high theoretical level. Calculations show that Cl substitution by Br and I generates compounds with more important antioxidant ability and the intramolecular charge transfer linked to the inorganic anion.

Atoms-In-Molecules' Faces of Chemical Hardness by Conceptual Density Functional Theory.

The chemical hardness concept and its realization within the conceptual density functional theory is approached with innovative perspectives, such as the electronegativity and hardness equalization of atoms in molecules connected with the softness kernel, in order to examine the structure-reactivity equalization ansatz between the electronic sharing index and the charge transfer either in the additive or geometrical mean picture of bonding. On the other hand, the maximum hardness principle presents a relation with the chemical stability of the hardness concept. In light of the inverse relation between hardness and polarizability, the minimum polarizability principle has been proposed. Additionally, this review includes important applications of the chemical hardness concept to solid-state chemistry. The mentioned applications support the validity of the electronic structure principles regarding chemical hardness and polarizability in solid-state chemistry.

Theoretical Study of the Structural Stability, Chemical Reactivity, and Protein Interaction for NMP Compounds as Modulators of the Endocannabinoid System.

The cannabinoid receptors (CB1/CB2) and the T-type calcium channels are involved in disorders associated with both physiological pain and depressive behaviors. Valuable pharmacological species carbazole derivatives such as the NMP-4, NMP-7, and NMP-181 (Neuro Molecular Production) regulate both biological entities. In this work, DFT calculations were performed to characterize theoretically their structural and chemical reactivity properties using the BP86/cc-pVTZ level of theory. The molecular orbital contributions and the chemical reactivity analysis reveal that a major participation of the carbazole group is in the donor-acceptor interactions of the NMP compounds. The DFT analysis on the NMP compounds provides insights into the relevant functional groups involved during the ligand-receptor interactions. Molecular docking analysis is used to reveal possible sites of interaction of the NMP compounds with the Cav3.2 calcium channel. The interaction energy values and reported experimental evidence indicate that the site denominated as "Pore-blocking", which is formed mainly by hydrophobic residues and the T586 residue, is a probable binding site for the NMP compounds.

Reactivity of Waterlogged Archeological Elm Wood with Organosilicon Compounds Applied as Wood Consolidants: 2D 1H-13C Solution-State NMR Studies.

Some organosilicon compounds, including alkoxysilanes and siloxanes, proved effective in stabilizing the dimensions of waterlogged archaeological wood during drying, which is essential in the conservation process of ancient artifacts. However, it was difficult to determine a strong correlation between the wood stabilizing effect and the properties of organosilicon compounds, such as molecular weight and size, weight percent gain, and the presence of other potentially reactive groups. Therefore, to better understand the mechanism behind the stabilization effectiveness, the reactivity of organosilicons with wood polymers was studied using a 2D 1H-13C solution-state NMR technique. The results showed an extensive modification of lignin through its demethoxylation and decarbonylation and also the absence of the native cellulose anomeric peak in siloxane-treated wood. The most substantial reactivity between wood polymers and organosilicon was observed with the (3-mercaptopropyl)trimethoxysilane treatment, showing complete removal of lignin side chains, the lowest syringyl/guaiacyl ratio, depolymerization of cellulose and xylan, and reactivity with the C6 primary hydroxyls in cellulose. This may explain the outstanding stabilizing effectiveness of this silane and supports the conclusion that extensive chemical interactions are essential in this process. It also indicates the vital role of a mercapto group in wood stabilization by organosilicons. This 2D NMR technique sheds new light on the chemical mechanisms involved in organosilicon consolidation of wood and reveals what chemical characteristics are essential in developing future conservation treatments.

Why Ortho- and Para-Hydroxy Metabolites Can Scavenge Free Radicals That the Parent Atorvastatin Cannot? Important Pharmacologic Insight from Quantum Chemistry.

The pharmaceutical success of atorvastatin (ATV), a widely employed drug against the "bad" cholesterol (LDL) and cardiovascular diseases, traces back to its ability to scavenge free radicals. Unfortunately, information on its antioxidant properties is missing or unreliable. Here, we report detailed quantum chemical results for ATV and its ortho- and para-hydroxy metabolites (o-ATV, p-ATV) in the methanolic phase. They comprise global reactivity indices, bond order indices, and spin densities as well as all relevant enthalpies of reaction (bond dissociation BDE, ionization IP and electron attachment EA, proton detachment PDE and proton affinity PA, and electron transfer ETE). With these properties in hand, we can provide the first theoretical explanation of the experimental finding that, due to their free radical scavenging activity, ATV hydroxy metabolites rather than the parent ATV, have substantial inhibitory effect on LDL and the like. Surprisingly (because it is contrary to the most cases currently known), we unambiguously found that HAT (direct hydrogen atom transfer) rather than SPLET (sequential proton loss electron transfer) or SET-PT (stepwise electron transfer proton transfer) is the thermodynamically preferred pathway by which o-ATV and p-ATV in methanolic phase can scavenge DPPH• (1,1-diphenyl-2-picrylhydrazyl) radicals. From a quantum chemical perspective, the ATV's species investigated are surprising because of the nontrivial correlations between bond dissociation energies, bond lengths, bond order indices and pertaining stretching frequencies, which do not fit the framework of naive chemical intuition.

A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction.

Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the 'inhibitor' and 'catalyst' mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile-Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes.

Rényi's divergence as a chemical similarity criterion.

In this work, a new version of Rényi's divergence is presented. The expression obtained is used as a tool to identify molecules that could share some chemical or structural properties, and a data basis set of 1641 molecules is used in this study. Our results suggest that this new form of Rényi divergence could be a useful tool that will eventually permit complementary studies in which the main goal is to obtain molecules with similar properties.

Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule.

This paper presents a brief summary of the difficulty that resides in the definition of the elusive concept of local chemical hardness. We argue that a definition of local hardness should be useful to a reactivity principle and not just as a mere definition. We then continue with a formal discussion about the benefits and difficulties of using the Fukui potential, which is interpreted as an alchemical derivative (alchemical hardness), as descriptor of local hardness of molecules. Computational evidence shows that the alchemical hardness is at least as good a descriptor as the combination of other two well-stabilized descriptors of local hardness, such as the Fukui function and grand canonical local hardness. Although our results are auspicious for the alchemical hardness as descriptor of local hardness, we finish by calling the attention of the community on the importance of discussing the raison d'être of a local hardness function and its main characteristics. We suggest that an axiomatic construction of local hardness could be they way of constructing a local hardness which is both useful and free of arbitrariness.

New insights in chemical reactivity from quantum chemical topology.

Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.

Towards a converged strategy for including microsolvation in reaction mechanism calculations.

A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pKa values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.

New Findings of Ferrate(VI) Oxidation Mechanism from Its Degradation of Alkene Imidazole Ionic Liquids.

Chemical reactivity, kinetics, degradation pathways and mechanisms, and ecotoxicity of the oxidation of 1-vinyl-3-ethylimidazolium bromide ([VEIm]Br), the most common alternative to organic solvents, by Fe(VI) (HFeO4-) were studied by lab experiments and theoretical calculations. Results show that Fe(VI) can efficiently remove VEIm through the dioxygen transfer-hydrolysis mechanism, which has not been reported yet. The reactivity of VEIm toward Fe(VI) mainly depends on the double bonds in the side chain of VEIm. The second-order rate constant for VEIm was 629.45 M-1 s-1 at pH 7.0 and 25 °C. Typical water constituents, except for SO32-, Cl-, and Cu2+, had no obvious effects on the oxidation. The oxidation products were determined by high-performance liquid chromatography hybrid quadrupole time-of-flight mass spectrometry, which proves that there were interactions between the oxidation intermediates of the anion and cation parts of [VEIm]Br during the degradation process. The structures of related products and oxidation mechanisms were further rationalized by theoretical calculations. The ecotoxicity of products from the three oxidation pathways all showed a trend of increase after the initial decrease. We hope that the findings of this work can give researchers some new inspirations on Fe(VI) degradation of other alkene-containing contaminants.