Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions.

Today's demand for precisely predicting chemical reactions from first principles requires research to go beyond Gibbs' free energy diagrams and consider other effects such as concentrations and quantum tunneling. The present work introduces overreact, a novel Python package for propagating chemical reactions over time using data from computational chemistry only. The overreact code infers all differential equations and parameters from a simple input that consists of a set of chemical equations and quantum chemistry package outputs for each chemical species. We evaluate some applications from the literature: gas-phase eclipsed-staggered isomerization of ethane, gas-phase umbrella inversion of ammonia, gas-phase degradation of methane by chlorine radical, and three solvation-phase reactions. Furthermore, we comment on a simple solvation-phase acid-base equilibrium. We show how it is possible to achieve reaction profiles and information matching experiments.

Shedding light on the physical nature of ion pair interactions involving carba-closo-dodecaborate anions. Insights from computation.

closo-Carboranes are structures that have been studied for many decades due to their vast applicability in medicine, catalysis, and energy storage. In order to go deeper into the physics behind the interactions of oppositely charged ions, which have potential applications in electrical energy storage and conversion devices, the present work aims to shed light on the physical nature of the interactions involving (R-CB11H11-, R = H, F, CH3, CF3) and Mq+ = Li+, Na+, Mg2+, Zn2+ ions. The bonding situations are evaluated in light of both canonical Kohn-Sham energy decomposition, EDA-NOCV, and local energy decomposition, LED, analyses. Electron and hole transports are also evaluated through charge transfer integrals. The findings reveal that such complexes present not only more significant electrostatic, but also non-negligible orbital contributions. Both energy decomposition analyses EDA-NOCV and DLPNO-LED confirm that the strength of ionic pair interactions (R-CB11H11- ↔ Mq+) is much more dependent on the nature of the cation employed than on the substituent R used. The results also reveal that charge transfers are not significant in such interacting systems.

Spectroscopical and Molecular Studies of Four Manganese(I) PhotoCORMs with Bioinspired Ligands Containing Non-Coordinated Phenol Groups.

Carbonyl compounds are widely explored in medicinal inorganic chemistry and have drawn attention due to their signaling functions in homeostasis. Carbon-monoxide-releasing molecules (CORMs) were developed with the purpose of keeping the CO inactive until its release in the intracellular environment, considering its biological relevance. However, for therapeutic applications, the mechanisms of photorelease and which electronic and structural variations influence its rates must be fully understood. In this work, four ligands containing a pyridine, a secondary amine, and a phenolic group with different substituents were used to prepare new Mn(I) carbonyl compounds. Structural and physicochemical characterization of these complexes was carried out and confirmed the proposed structures. X-ray diffractometry structures obtained for the four organometallic compounds revealed that the substituents in the phenolic ring promote only negligible distortions in their geometry. Furthermore, UV-Vis and IR kinetics showed the direct dependence of the electron-withdrawing or donating ability of the substituent group, indicating an influence of the phenol ring on the CO release mechanism. These differences in properties were also supported by theoretical studies at the DFT, TD-DFT, and bonding situation analyses (EDA-NOCV). Two methods were used to determine the CO release constants (kCO,old and kCO,new), where Mn-HbpaBr (1) had the greatest kCO by both methods (Kco,old = 2.36 × 10-3 s-1 and kCO,new = 2.37 × 10-3 s-1). Carbon monoxide release was also evaluated using the myoglobin assay, indicating the release of 1.248 to 1.827 carbon monoxides upon light irradiation.

Nature of hydride and halide encapsulation in Ag8 cages: insights from the structure and interaction energy of [Ag8(X){S2P(OiPr)2}6]+ (X = H-, F-, Cl-, Br-, I-) from relativistic DFT calculations.

Unraveling the different contributing terms to an efficient anion encapsulation is a relevant issue for further understanding of the underlying factors governing the formation of endohedral species. Herein, we explore the favorable encapsulation of hydride and halide anions in the [Ag8(X){S2P(OPr)2}6]+ (X- = H, 1, F, 2, Cl, 3, Br, 4, and, I, 5) series on the basis of relativistic DFT-D level of theory. The resulting Ag8-X interaction is sizable, which decreases along the series: -232.2 (1) > -192.1 (2) > -165.5 (3) > -158.0 (4) > -144.2 kcal mol-1 (5), denoting a more favorable inclusion of hydride and fluoride anions within the silver cage. Such interaction is mainly stabilized by the high contribution from electrostatic type interactions (80.9 av%), with a lesser contribution from charge-transfer (17.4 av%) and London type interactions (1.7 av%). Moreover, the ionic character of the electrostatic contributions decreases from 90.7% for hydride to 68.6% for the iodide counterpart, in line with the decrease in hardness according to the Pearson's acid-base concept (HSAB) owing to the major role of higher electrostatic interaction terms related to the softer (Lewis) bases. Lastly, the [Ag8{S2P(OPr)2}6]2+ cluster is able to adapt its geometry in order to maximize the interaction towards respective monoatomic anion, exhibiting structural flexibility. Such insights shed light on the physical reasoning necessary for a better understanding of the different stabilizing and destabilizing contributions related to metal-based cavities towards favorable incorporation of different monoatomic anions.

Platinum-Triggered Bond-Cleavage of Pentynoyl Amide and N-Propargyl Handles for Drug-Activation.

The ability to create ways to control drug activation at specific tissues while sparing healthy tissues remains a major challenge. The administration of exogenous target-specific triggers offers the potential for traceless release of active drugs on tumor sites from antibody-drug conjugates (ADCs) and caged prodrugs. We have developed a metal-mediated bond-cleavage reaction that uses platinum complexes [K2PtCl4 or Cisplatin (CisPt)] for drug activation. Key to the success of the reaction is a water-promoted activation process that triggers the reactivity of the platinum complexes. Under these conditions, the decaging of pentynoyl tertiary amides and N-propargyls occurs rapidly in aqueous systems. In cells, the protected analogues of cytotoxic drugs 5-fluorouracil (5-FU) and monomethyl auristatin E (MMAE) are partially activated by nontoxic amounts of platinum salts. Additionally, a noninternalizing ADC built with a pentynoyl traceless linker that features a tertiary amide protected MMAE was also decaged in the presence of platinum salts for extracellular drug release in cancer cells. Finally, CisPt-mediated prodrug activation of a propargyl derivative of 5-FU was shown in a colorectal zebrafish xenograft model that led to significant reductions in tumor size. Overall, our results reveal a new metal-based cleavable reaction that expands the application of platinum complexes beyond those in catalysis and cancer therapy.

In Silico Design of Cylindrophanes: The Role of Functional Groups in a Fluoride Selective Host.

Molecular recognition is the key driver in the formation of supramolecular complexes, enabling the selective encapsulation of specific guests. Here, we explore the delicate balance between different energetic terms in the formation of an efficient host for fluoride anions based on a cylindrophane structure, which can be achieved by the incorporation of ligand sites into a cyanuric acid based cyclophane framework, resulting a close proximity between the ammonium hydrogens and the anion. This study describes the character and contribution of different energetic and repulsive terms that favor the efficient inclusion of fluoride. Our findings are useful for further rational design and synthesis of efficient and highly selective fluoride hosts, which have been generally less well described than complexing agents for other halides.

Coordination among Bond Formation/Cleavage in a Bifunctional-Catalyzed Fast Amide Hydrolysis: Evidence for an Optimized Intramolecular N-Protonation Event.

A density functional theory (DFT) computational analysis, using the ωB97X-D functional, of a rapid amide cleavage in 2-carboxyphthalanilic acid (2CPA), where the amide group is flanked by two catalytic carboxyls, reveals key mechanistic information: (a) General base catalysis by a carboxylate coupled to general acid catalysis by a carboxyl is not operative. (b) Nucleophilic attack by a carboxylate on the amide carbonyl coupled to general acid catalysis at the amide oxygen can also be ruled out. (c) A mechanistic pathway that remains viable involves general acid proton delivery to the amide nitrogen by a carboxyl, while the other carboxylate engages in nucleophilic attack upon the amide carbonyl; a substantially unchanged amide carbonyl in the transition state; two concurrent bond-forming events; and a spatiotemporal-base rate acceleration. This mechanism is supported by molecular dynamic simulations which confirm a persistent key intramolecular hydrogen bonding. These theoretical conclusions, although not easily verified by experiment, are consistent with a bell-shaped pH/rate profile but are at odds with hydrolysis mechanisms in the classic literature.

What is the driving force behind molecular triangles and their guests? A quantum chemical perspective about host-guest interactions.

The physical nature of host-guest (HG) interactions occurring between molecular triangles and linear anions was explored using density functional theory (DFT) calculations combined with energy decomposition analyses (EDA), nuclear independent chemical shift (NICS), and non-covalent interaction index (NCI). We demonstrate that: (i) in addition to the host being significantly rigid, the strain energies are not negligible, especially for host 2; (ii) halogen anions interact mainly by electrostatic forces (ΔEelst > ΔE > ΔEdisp), meanwhile; (iii) trihalogen anions interact mostly by dispersion forces (ΔEdisp > ΔEelst≈ΔE). The NICS and NCI calculations corroborate the idea that HG interactions are considerably mediated through dispersion terms, and also indicate an antiaromatic character inside the host walls.

Are DFT Methods Able to Predict Reduction Potentials of Ruthenium Nitrosyl Complexes Accurately?

The nitric oxide (NO) molecule is directly related to important physiological and physiopathological processes. Ruthenium tetraammine nitrosyl complexes can release NO from the [RuIINO+]3+/[RuIINO0]2+ reduction potential. Experimentally, well established is the practice of determining the redox potential with relation to a reference redox pair. However, there is no agreement on the best methodology that allows the minimization of uncertainties, both experimental and theoretical results. Here, the reduction potential relative to a reference redox pair is obtained from calculated absolute potentials for the target complex: trans-[Ru(NO)(L)(NH3)4]3+/2+ and reference pair: [Ru(bpy)3]3+/2+. The correlation between the calculated and experimental reduction potentials strongly depend on the DFT functional chosen. The best results were obtained with the GGA functional BP86, which showed deviations lower than 200 mV. The assignment of explicit solvent, in addition to continuum solvent influence, also appears as a relevant factor.

Evaluation of Lignans from Piper cubeba against Schistosoma mansoni Adult Worms: A Combined Experimental and Theoretical Study.

Six dibenzylbutyrolactonic lignans ((-)-hinokinin (1), (-)-cubebin (2), (-)-yatein (3), (-)-5-methoxyyatein (4), dihydrocubebin (5) and dihydroclusin (6)) were isolated from Piper cubeba seed extract and evaluated against Schistosoma mansoni. All lignans, except 5, were able to separate the adult worm pairs and reduce the egg numbers during 24 h of incubation. Lignans 1, 3 and 4 (containing a lactone ring) were the most efficient concerning antiparasitary activity. Comparing structures 3 and 4, the presence of the methoxy group at position 5 appears to be important for this activity. Considering 1 and 3, it is possible to see that the substitution pattern change (methylenedioxy or methoxy groups) in positions 3' and 4' alter the biological response, with 1 being the second most active compound. Computational calculations suggest that the activity of compound 4 can be correlated with the largest lipophilicity value.

Reverse Solvatochromism of Imine Dyes Comprised of 5-Nitrofuran-2-yl or 5-Nitrothiophen-2-yl as Electron Acceptor and Phenolate as Electron Donor.

Eight compounds with phenols as electron-donating groups and 5-nitrothiophen-2-yl or 5-nitrofuran-2-yl acceptor moieties in their molecular structures were synthesized. The crystalline structures of six compounds were obtained. Their corresponding phenolate dyes were studied in 29 solvents and the data showed that in all cases a reverse solvatochromism occurred. The results are explained in terms of the ability of the medium to stabilize the electronic ground and excited states of the probes to different extents. The frontier molecular orbitals were analyzed for the protonated and deprotonated forms of the compounds. The calculated geometries are in agreement with the X-ray structures determined for the compounds and it was verified that after their deprotonation an increase in the electron delocalization occurs. Radial distribution functions were calculated for the dyes in water and n-hexane to analyze different solvation patterns resulting from the interaction of the solvents with the dyes. Data obtained by using the Catalán multiparameter equation revealed that the medium acidity is responsible for hypsochromic shifts, whereas the solvent basicity, polarizability, and dipolarity contributed to bathochromic shifts of the solvatochromic band of these dyes. Two model "hybrid cyanine" dyes were used in the design of simple experiments to demonstrate that the solvatochromic behavior of these dyes in solution can be tuned with careful consideration of the properties of the medium.

Helicenes as Molecular Tweezers in the Formation of Cation-π Complexes. Bonding and Circular Dichroism Properties from Relativistic DFT Calculations.

Helicene ligands possess a unique helicoidal π-conjugated framework providing high optical rotation values. This has stimulated a growing interest in helicene derivatives as building blocks, which has triggered the development of simple strategies to tune their properties. In this context, we evaluated the formation of cation-π complexes derived from [6]- and [7]helicene, involving Sn2+ , Cd2+ , and In+ in addition of Ag+ , which appears as a plausible modification of such helicoidal structure. The nature of the cation-π interaction in the studied helicene complexes exhibits a covalent character, accounting for ligand π-donation to 5 s and 5p empty orbitals of the involved cations. Furthermore, the evaluation of their optical activity exhibits notorious modification patterns in the circular dichroism spectrum, suggesting that the modifications of the optical activity are dependent on the nature of the cation and its related charge state. Thus, the plausible formation of new cation-π complexes derived from helicene ligands, as discussed here, may lead to the characterization of novel species expanding the chemistry of helicene metal complexes to even to larger helicene units. We believe that the present study may open new avenues in the formation of cation-π helicene complexes.

Quest for Insight into Ultrashort C-H···π Proximities in Molecular "Iron Maidens".

Molecular iron maidens are a strained type of cyclophane in which a methine hydrogen, by the action of the bridges, is placed closer to the center of an aromatic ring. Such constrained molecular frameworks are in fact a noteworthy synthetic challenge. The present study provides a comprehensible theoretical analysis that elucidates unique structural and energetic aspects of this class of molecules, evaluating, in the light of quantum chemistry, both the influence of the aromatic moiety, from π-basic to π-acid, and the nature of the heteroatoms located at the bridges. Our results not only propose the shortest intramolecular centered C-H···π distance to date, which is supported by calculated 1H chemical shifts, but also shed light on the main factors that rationalize and justify such proximity. QTAIM, NBO, and NCI analyses allow us prematurely to conclude that the ultrashort C-H···π distance is sustained by an interplay between a large stabilizing electrostatic component with a non-negligible covalent character. However, the energetics involving such strained molecular scaffolds, addressed by means of isodesmic reactions, revealed that the C-H···π proximity is modulated mainly by the capacity of the bridges to support the strain imposed by the whole structure, hence compressing the C-H bond against the π-system.

Tuning Heterocalixarenes to Improve Their Anion Recognition: A Computational Approach.

We have explored and analyzed the physical factors through which noncovalent interactions in anion sensing based on calixarene-type hosts can be tuned, using dispersion-corrected DFT and Kohn-Sham molecular orbital (KS-MO) theory in conjunction with a canonical energy decomposition analysis (EDA). We find that the host-guest interaction can be enhanced through the introduction of strongly electron-withdrawing groups at particular positions of the arene and triazine units in the host molecule as well as by coordination of a metal complex to the arene and triazine rings. Our analyses reveal that the enhanced anion affinity is caused by increasing the electrostatic potential in the heterocalixarene cavities. This insight can be employed to further tune and improve their selectivity for chloride ions.

In vivo and in silico anti-inflammatory mechanism of action of the semisynthetic (-)-cubebin derivatives (-)-hinokinin and (-)-O-benzylcubebin.

(-)-Cubebin (CUB), isolated from seeds of Piper cubeba, was used as starting material to obtain the derivatives (-)-hinokinin (HK) and (-)-O-benzyl cubebin (OBZ). Using paw edema as the experimental model and different chemical mediators (prostaglandin and dextran), it was observed that both derivatives were active in comparison with both negative (5% Tween® 80 in saline) and positive (indomethacin) controls. The highest reduction in the prostaglandin-induced edema was achieved by OBZ (66.0%), while HK caused a 59.2% reduction. Nonetheless, the dextran-induced paw edema was not significantly reduced by either of the derivatives (HK or OBZ), which inhibited edema formation by 18.3% and 3.5%, respectively, in contrast with the positive control, cyproheptadine, which reduced the edema by 56.0%. The docking analysis showed that OBZ presented the most stable ligand-receptor (COX-2 - cyclooxygenase-2) interaction in comparison with CUB and HK.

How the electron-deficient cavity of heterocalixarenes recognizes anions: insights from computation.

We have quantum chemically analyzed the bonding mechanism behind the affinity of various heterocalixarenes for anions with a range of geometries and net charges, using modern dispersion-corrected density functional theory (DFT-D3BJ). The purpose is to better understand the physical factors that are responsible for the computed affinities and thus to develop principles for a more rational design of anion receptors. Our model systems comprise heterocalixarenes 1-4 as hosts, which are characterized by different bridging heteroatoms (O, N, S) as well as the anionic guests Cl-, Br-, I-, BF4-, CH3CO2-, H2PO4-, HSO4-, NCS-, NO3-, PF6-, and SO42-. We use various analysis schemes (EDA, NCI, and NBO) to elucidate the interactions between the calixarene cavity and the anions to probe the importance of the different bonding modes (anion-π, lone-pair electron-π, σ-complexes, hydrogen bonds, and others) of the interactions. Electrostatic interactions appear to be dominant for heterocalixarenes with oxygen bridges whereas orbital interactions prevail in the case of nitrogen and sulfur bridges. Dispersion interactions are however in all cases non-negligible.

Evaluation of Electron Donation as a Mechanism for the Stabilisation of Chalcogenate-Protected Gold Nanoclusters.

Models based on Au(111) face have been extensively used to describe self-assembled monolayers, as well nanoparticles and nanoclusters. However, for very small clusters (<2 nm), the chemisorption of ligands leads to surface reconstruction, making necessary the use of a more reliable model that is able to simulate the main electronic and geometrical features of these small systems. In this work, a simple model to describe the geometries and the metal-ligand bonding in chalcogenate-protected gold nanoclusters is proposed. Three different models with Aun+ and [XCH3 ]- (n=10, 15, 19, 22 and X=S, Se, Te) are used in this work. The obtained structures are in close agreement not only with the available crystallographic data, but also with much more expensive computational procedures, confirming that the proposed models are robust enough to describe the metal-ligand bonding. The results reveal that the Au-X distances are dependent on both the nature of the chalcogen and the coordination mode. The shortest Au-X distances are observed in the face-centred cubic mode, indicating that the central gold atom seems to play a role in determining the adsorption strength. The proposed models show unambiguously chalcogen→cluster σ-donation, as supported by energy decomposition analysis coupled with the natural orbitals for chemical valence and natural bond orbital analyses. In all cases, the metal-ligand interactions are characterised as being more covalent than electrostatic.

Copaifera duckei Oleoresin and Its Main Nonvolatile Terpenes: In Vitro Schistosomicidal Properties.

In this article, the in vitro schistosomicidal effects of three Brazilian Copaifera oleoresins (C. duckei, C. langsdorffii, and C. reticulata) are reported. From these botanical sources, the oleoresin of C. duckei (OCd) demonstrated to be the most promising, displaying LC50 values of 75.8, 50.6, and 47.2 µg/ml at 24, 48, and 72 h of incubation, respectively, against adult worms of Schistosoma mansoni, with a selectivity index of 10.26. Therefore, the major compounds from OCd were isolated, and the diterpene, (-)-polyalthic acid (PA), showed to be active (LC50 values of 41.7, 36.2, and 33.4 µg/ml, respectively, at 24, 48, and 72 h of incubation). Moreover, OCd and PA affected the production and development of eggs, and OCd modified the functionality of the tegument of S. mansoni. Possible synergistic and/or additive effects of this balsam were also verified when a mixture of the two of its main compounds (PA and ent-labd-8(17)-en-15,18-dioic acid) in the specific proportion of 3:1 (w/w) was tested. The obtained results indicate that PA should be considered for further investigations against S. mansoni, such as, synergistic (combination with praziquantel (PZQ)) and in vivo studies. It also shows that diterpenes are an important class of natural compounds for the investigation of agents capable of fighting the parasite responsible for human schistosomiasis.

Proton-induced generation of remote N-heterocyclic carbene-Ru complexes.

The proton-induced Ru-C bond variation, which was previously found to be relevant in the water oxidation, has been investigated by using cyclometalated ruthenium complexes with three phenanthroline (phen) isomers. The designed complexes, [Ru(bpy)2 (1,5-phen)](+) ([2](+)), [Ru(bpy)2 (1,6-phen)](+) ([3](+)), and [Ru(bpy)2 (1,7-phen)](+) ([4](+)) were newly synthesized and their structural and electronic properties were analyzed by various spectroscopy and theoretical protocols. Protonation of [4](+) triggered profound electronic structural change to form remote N-heterocyclic carbene (rNHC), whereas protonation of [2](+) and [3](+) did not affect their structures. It was found that changes in the electronic structure of phen beyond classical resonance forms control the rNHC behavior. The present study provides new insights into the ligand design of related ruthenium catalysts.

Synthesis and Solvatochromism of Substituted 4-(Nitrostyryl)phenolate Dyes.

4-(Nitrostyryl)phenols 2a-9a were synthesized, and by deprotonation in solution, the solvatochromic phenolates 2b-9b were formed. Their absorption bands in the vis region of the spectra are due to π-π* electronic transitions, of an intramolecular charge-transfer nature, from the electron-donor phenolate toward the electron-acceptor nitroarene moiety. The frontier molecular orbitals and natural bond orbitals were analyzed for the protonated and deprotonated forms. The calculated geometries are in agreement with X-ray structures observed for 4a, 6a, and 8a. The HOMO-LUMO energy gaps suggest that, after their deprotonation, an increase in the electron delocalization is observed. In the protonated compounds, the HOMO is primarily localized over the phenol ring and the C═C bridge. After deprotonation, it extends toward the entire molecule, including the NO2 groups. The solvatochromism of each dye was studied in 28 organic solvents, and it was found that all compounds exhibit a reversal in solvatochromism, which is interpreted in terms of the ability of the media to stabilize their electronic ground and excited states to different extents. The Catalán multiparameter equation is used in the interpretation of the solvatochromic data, revealing that the most important contribution to the solute/solvent interaction is the hydrogen-bond donor acidity of the solvent.