CO2 Capture by Diamines in Dry and Humid Conditions: A Theoretical Approach

This work is a mechanistic study of the CO2 reaction with diamines under both dry and wet conditions. All protic α,ω-diamines R1H1N1-(CH2)n-N2H2R2, with n = 1-5 and R1 and R2 = H and/or CH3, were investigated. Depending on the nature of the diamine, the reaction was found to follow one of two concerted asynchronous reaction mechanisms with a zwitterion hidden intermediate. Both mechanisms involved two processes. The first process consisted of a nucleophilic attack of the nitrogen N1 of the first amine group on the carbon of CO2, accompanied by the transfer of a hydrogen atom H1 from N1 to the nitrogen N2 of the second amine group, leading to the formation of a carbamate zwitterion. The subsequent process corresponds to the transfer of a hydrogen atom H2 from the second amine group N2 to an oxygen atom of CO2, thus ending the reaction by the formation of carbamic acid. The structure of the zwitterion hidden intermediate was determined using the reactive internal reaction coordinates (RIRC), a reaction pathway visualization tool, consisting of a 3D representation of the potential energy versus the internuclear distances N2-H1 and N2-H2, which correspond to the bond being formed and the bond being broken, respectively. The life span of the transitory species, i.e., the zwitterion, was found to depend on the nature of the second amine group. For primary amines, the life span of the zwitterion was "short", whereas for secondary amines, it was "long". The corresponding mechanisms were termed the "early" and "late" asynchronous mechanism, respectively. Regardless of the mechanism, the activation barriers were found to decrease with the length of the carbon chain linking the two amine groups, with an asymptotic behavior from n = 4. Involvement of a water molecule generates a significant catalytic effect for diamines with short carbon chains (n < 4), whereas for longer chain diamines, water has a slightly adverse effect.

Fingerprinting of two an acylated polyoxypregnane glycosides from Caralluma quadrangula (Forssk.) N.E.Br. using UPLC-ESI-Q-TOF and computational study

The present study has tentatively elucidated the structure of two acylated polyoxypregnane glycosides from Caralluma quadrangula (Forssk.) N.E.Br. (CQ). The analyses were performed using an electrospray-ionization quadrupole time-of-flight (ESI-Q-TOF) mass spectrometer in positive ionization modes to explore fragmentation pathways. The used ionization mode provided consistent and/or complementary information for most of the pregnane glycosides, their fragmentation sequences, and their aglycones. Presumably, this is due to higher efficiency, sensitivity, and better selectivity of the mass spectrometry-based method. The present experimental and theoretical report deals with the characteristic fragmentation behaviors of two acylated polyoxypregnane glycosides CQ1 and CQ2 from the aerial parts of C. quadrangular. A DFT Study was performed to elucidate the position of ikemoyl, and benzoyl residues in compounds CQ1 and CQ2, respectively.

Evaluation of a new series of pyrazole derivatives as a potent epidermal growth factor receptor inhibitory activity: QSAR modeling using quantum-chemical descriptors

Pyrazole derivatives correspond to a family of heterocycle molecules with important pharmacological and physiological applications. At present, we perform a density functional theory (DFT) calculations and a quantitative structure-activity relationship (QSAR) evaluation on a series of 1-(4,5-dihydro-1H-pyrazol-1-yl) ethan-1-one and 4,5-dihydro-1H-pyrazole-1-carbothioamide derivatives as an epidermal growth factor receptor (EGFR) inhibitory activity. We thus propose a virtual screening protocol based on a machine-learning study. This theoretical model relates the studied compounds' biological activity to their calculated physicochemical descriptors. Moreover, the linear regression function is used to validate the model via the evaluation of Q² _ext and Q² _cv parameters for external and internal validations, respectively. Our QSAR model shows a good correlation between observed activities IC₅₀ and predicted ones. Our model allows us to mitigate time-consuming problems and waste chemical and biological products in the preclinical phases.

p-Trifluoromethyl- and p-pentafluorothio-substituted curcuminoids of the 2,6-di[(E)-benzylidene)]cycloalkanone type: Syntheses and activities against Leishmania major and Toxoplasma gondii parasites

A series of the title curcuminoids with structural variance in the heteroatom of the cycloalkanone and the p-substituents of the phenyl rings were tested for their activities against Leishmania major and Toxoplasma gondii parasites. The majority of them showed high activities against both parasite forms with EC₅₀ values in the sub-micromolar concentration range. Bis(p-pentafluorothio)-substituted 3,5-di[(E)-benzylidene]piperidin-4-one 1b was not just noticeable antiparasitic, but also exhibited a considerable selectivity for L. major promastigotes over normal Vero cells. While derivatives differing only in the p-phenyl substituents being CF₃ or SF₅ showed similar antiparasitic activities, the cyclic ketone hub was more decisive both for the anti-parasitic activities and the selectivities for the parasites vs. normal cells. QSAR calculations confirmed the observed structure-activity relations and suggested structural variations for a further improvement of the antiparasitic activity. Docking studies based on DFT calculations revealed L. major pteridine reductase 1 as a likely molecular target protein of the title compounds.

Structural, QSAR, machine learning and molecular docking studies of 5-thiophen-2-yl pyrazole derivatives as potent and selective cannabinoid-1 receptor antagonists

We performed a structural study followed by theoretical analysis of the chemical descriptors and biological activity of a series of 5-thiophen-2-yl pyrazole derivatives as potent and selective cannabinoid-1 (CB1) receptor antagonists.

A Unified Approach to CO2-Amine Reaction Mechanisms

A unified CO₂-amine reaction mechanism applicable to absorption in aqueous or nonaqueous solutions and to adsorption on immobilized amines in the presence of both dry and humid conditions is proposed. Key findings supported by theoretical calculations and experimental evidence are as follows: (1) The formation of the 1,3-zwitterion, RH₂N⁺-COO^-, is highly unlikely because not only the associated four-membered mechanism has a high energy barrier, but also it is not consistent with the orbital symmetry requirements for chemical reactions. (2) The nucleophilic attack of CO₂ by amines requires the catalytic assistance of a Bro̷nsted base through a six-membered mechanism to achieve proton transfer/exchange. An important consequence of this concerted mechanism is that the N and H atoms added to the C=O double bond do not originate from a single amine group. Using ethylenediamine for illustration, detailed description of the reaction pathway is reported using the reactive internal reaction coordinate as a new tool to visualize the reaction path. (3) In the presence of protic amines, the formation of ammonium bicarbonate/carbonate does not take place through the widely accepted hydration of carbamate/carbamic acid. Instead, water behaves as a nucleophile that attacks CO₂ with catalytic assistance by amine groups, and carbamate/carbamic acid decomposes back to amine and CO₂. (4) Generalization of the catalytic assistance concept to any Bro̷nsted base established through theoretical calculations was supported by infrared measurements. A unified six-membered mechanism was proposed to describe all possible interactions of CO₂ with amines and water, each playing the role of a nucleophile and/or Bro̷nsted base, depending on the actual conditions.

Encapsulation of anticancer drug doxorubicin inside dendritic macromolecular cavities: First-principles benchmarks

By using first-principles approaches based on Density Functional Theory, we explore the possibility of using dendritic macromolecular structures as carriers of the doxorubicin anticancer drug. In particular, we consider macromolecular cavities of different sizes composed of phenylene-, thiophene-, phenyl-cored thiophen- and thioazole-based dendrimers. The comparison between the optimized molecular geometries of the monomers and of the host-guest complexes reveals that only slight structural changes are observed in doxorubicin upon complexation. Also, the encapsulation energies for the host-guest complexes suggest that these systems are of potential use for pharmacology applications in vivo. The interaction of the guest doxorubicin with the macromolecular cavities exploits different types of weak intermolecular forces including σ, π and hydrogen bond interactions. The electronic structure of these complexes is discussed, with particular emphasis placed on the role of the charge distribution and the nature of the frontier molecular orbitals in the encapsulation process. Spectroscopic properties of these complexes are derived to facilitate their detection in laboratory and in vivo. These include IR vibrational frequencies, absorption wavelengths and relative oscillator strengths for the main transitions in the UV-Vis spectrum.

Proton transfer in the benzimidazolone and benzimidazolthione tautomerism process catalyzed by polar protic solvents

The tautomeric equilibrium of benzimidazolone and benzimidazolthione have been studied by the density functional theory method using the CAM-B3LYP functional together with the 6-311G(d,p) basis set. Two separate mechanisms have been investigated: a direct intramolecular transfer using the polarizable continuum model and an indirect proton transfer assisted by a molecule of solvent (C6H12, H2O, CH3OH, and H2O2). In both cases, the results obtained indicate that ketone and thione are the most stable forms. However, the enhanced height of the activation barrier for the four-center mechanisms describing the tautomerism reaction as a direct intramolecular transfer implicates a relatively disadvantaged process. The participation of a polar protic solvent molecule allows the lowering of the activation energy barrier. Potential energy profiles of keto-enol and thio-enol tautomerism assisted by methanol and water are very different. The former one describes a concerted mechanism but the latter does not because it is associated with asynchronous processes that take place during the thio-enol tautomerism.

Intramolecular Path Determination of Active Electrons on Push-Pull Oligocarbazole Dyes-Sensitized Solar Cells

Several push‐pull oligocarbazole dye‐sensitizers have been studied using theoretical methods in order to better understand the relationship between structural electronic or optical properties and intramolecular path of active electrons during the ionization and injection processes. DFT/TD‐DFT calculations were performed on a series of five dye sensitizers. They differ by the presence of electron donating group (EDG) by inductive effect (noted+I) or electron releasing group (ERG) by mesomeric effect (noted+M) or electron withdrawing group by inductive effect (noted‐I) on the pushed part of the dyes studied. Our work focused on the internal distribution of electrons in the different parts of dye that are the push/pull moieties and the π‐bridge. The study concerned the ground state, the electronic transition process and the excited state. In each situation, the fragment acting in the ionization or transition phenomena were identified. In the ground state, the electrons of the push part appear to be the least bound because they have the highest probabilities of ionization. In the excited state, the ionized atoms are essentially positioned in the pushing part and some neighboring atoms of the bridge. In the electronic transition, the active atoms are located in the π‐conjugated part but only on the side adjacent to the acceptor group. To arrive to this conclusion, we optimized the structures of the five dyes in their ground and excited states. We calculated the atomic charges, the wavelengths and intensities of electronic transitions in the visible domain, the reorganization energies as well as the oxidation potential. It appears that +M donor ligands improve the performance of a dye because the great distribution of atoms to be ionized in the push parts.

Interaction of HF, HBr, HCl and HI Molecules with Carbon Nanotubes

The present work applies the density functional theory (DFT) to study the interactions between armchair (n,n) single walled carbon nanotubes (SWCNTs) and hydrogen halides confined along the nanotube axis and perpendicular to it. Calculations are performed using the CAM-B3LYP functional. According to the hydrogen halides orientation and the internal diameter of CNTs hollow space, HF, HCl, HBr and HI behave differently. The nanoconfinement alters the charge distribution and the dipolar moment. The encapsulated hydrogen fluoride (HF) molecule is stable along and perpendicular to the nanotubes (5,5) and (6,6) axis. The hydrogen chloride (HCl), hydrogen bromide (HBr) and hydrogen iodide (HI) form stable systems inside the nanotube (6,6) only at the perpendicular orientation. In addition, other phenomena are observed such as leaving the nanotube or decreasing the bond length of the molecule and even the creation of covalent bind between the guest molecule and the host nanotube.

The Cytochrome P450 3A4 has three Major Conformations: New Clues to Drug Recognition by this Promiscuous Enzyme

We computed the channels of the 3A4 isoform of the cytochrome P450 3A4 (CYP) on the basis of 24 crystal structures extracted from the Protein Data Bank (PDB). We identified three major conformations (denoted C, O1 and O2) using an enhanced version of the CCCPP software that we developed for the present work, while only two conformations (C and O² ) are considered in the literature. We established the flowchart of definition of these three conformations in function of the structural and physicochemical parameters of the ligand. The channels are characterized with qualitative and quantitative parameters, and not only with their surrounding secondary structures as it is usually done in the literature.

Theoretical investigation of methoxide ion reaction on the 7-methyl-4,6-dinitrobenzofuroxan

Reaction of the methoxide ion on the 7-methyl-4,6-dinitrobenzofuroxan (DNBF) 1 has been studied theoretically by means of DFT/B3LYP technique to interpret the kinetic–thermodynamic competition between the three possible compounds that are carbanion DNBF− 4 and the two complexed forms (2, 3) of the methoxide group in positions 5 and 7, respectively. Optimized geometry, nbo atomic charge distribution, thermodynamic/kinetic parameters (ΔrH°T, ΔrS°T, ΔrG°T, ΔH*, ΔS*, and ΔG*) and IRC path have been calculated for possible products and their transitional states using water as solvent. All obtained ΔrG°T are negative, ranging from −19.16 to −42.87 kcal mol−1 (1 cal = 4.184 J), indicating the possible observation of all products, but the experimenters only detected the anionic form DNBF−. Fukui indices, which were calculated by means of NBO atomic charge distribution, confirm the electrophilicity of the sites C5 and C7. Transition states barriers, ΔG*, are 14.97, 15.16, and 21.94 kcal mol−1 for the three possible products 2, 3, and 4, respectively, in water. As expected, the most stable compound is carbanion, but it also exhibits the highest activation barrier. If this situation formally engenders a double kinetic–thermodynamic competition, the very weak activation energy of the two complexes in C5 and C7 makes improbable the simultaneous detection of the three expected compounds.

Theoretical and experimental reinvestigation of methoxide ion reaction with 7-methyl 4-nitro benzofuroxan

DFT/B3LYP theoretical study has been performed in order to interpret the kinetic-thermodynamic competition between compounds obtained by reaction of the methoxide ion on the 7-methyl 4-nitro benzofuroxan. Geometry, atomic charge distribution, transition states, IRC path, thermodynamic, and kinetic parameters ([Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text]*, [Formula: see text]*, and [Formula: see text]*) have been calculated for all possible products. In gaseous state or in the presence of water as solvent, all [Formula: see text] values were found to be negative, ranging from [Formula: see text]12.54[Formula: see text]kcal mol[Formula: see text] to [Formula: see text]29.85[Formula: see text]kcal mol[Formula: see text] in water, indicating that all possible products should form spontaneously. Those values indicated the possible observation of all products but experimenters only detect simultaneously two [Formula: see text]-complexes in C5 and C7 among three possibilities. The Fukui indices obtained by NBO atomic charge distribution confirm the super electrophilicity of those two sites. For transition states barriers, [Formula: see text]* ranged from 18.98[Formula: see text]kcal mol[Formula: see text] to 42.12[Formula: see text]kcal mol[Formula: see text] in gaseous state and from 18.59[Formula: see text]kcal mol[Formula: see text] to 24.22[Formula: see text]kcal mol[Formula: see text] in water. The unexpected result of our calculations is that the most stable compound is the unobserved carbanion but it also exhibits the highest activation barrier. Our results indicated the existence of two consecutive kinetic/thermodynamic competitions that occur in separate periods. The simultaneous observation of the three compounds is impossible because compound 4 occurs as a trace at the time compound 2 disappears completely. Experimental reinvestigation of the studied reaction leads by a very slow process to the earlier unobserved carbanion. Reaction mechanisms were also discussed on the basis of IRC calculations.

F2 storage by confinement inside carbon nanotubes

Theoretical calculations have been achieved to study the interaction between the confined F2 molecule along the nanotube axis and perpendicular to it and armchair (n,n) single-walled carbon nanotubes with n = 4, 5, 6, 7, and 8 and the zig-ag nanotube (9,0) using the density functional theory method with the CAM-B3LYP functional and both cc-pVQZ and STO-3G basis sets. The interaction of the F2 molecule with the nanotube is different according to the molecular orientation, the chirality of the carbon nanotube, and the confinement space extension. These results interpreted by means of van der Waals interactions reveal anisotropic and competitive behavior at the nanometric level. The π electrons of the nanotube interact with the lone pairs of F2 highlighting its lateral polarizability. The encapsulated F2 molecule is stable along and perpendicular to the nanotube (5,5) and (6,6) axis. The best stabilization energy is obtained fornanotube (5,5) at the perpendicular position using the cc-pVQZ basis set.

Stabilizing of the Transitory Species (TiO2)2 by Encapsulation Into Carbon Nanotubes

The aim of this paper is studying the encapsulation effect of carbon nanotubes (CNTs ) on the stabilizing process of titanium dioxide molecule dimers (TiO2)2. First, a theoretical study was performed concerning the guest species that are various titanium dioxide dimers. Five structures were treated as following: i) Cis (C) or ii)Trans (T) relatively to a square shaped fragment Ti2O2, iii) a mixed Tetrahedral/Pyramidal (T/P) disposition while two titanium atoms are sharing three oxygen atoms, and finally not bonded dimers in iv) parallel (P) and v) orthogonal (O) positions respectively. Only the (T), (C) and (T/P) isomers may be considered as stable compounds. The structure of the T-dimer is more stable than the Cis one by only 6.5 kcal mol-1. Typically, intra and extracyclic Ti-O bond lengths are 1.84Å and 1.61Å respectively. (T/P) dimer can be described as a metastable structure since its energy is higher than (T) one by 19 kcal mol-1. NBO analysis highlights the participation of dative bonding between oxygen lone pair and vacant titanium 3d orbitals. (P) and (O) structures represent transitory species that transform into the more stable structure which is the T-dimer. The second and principal part of this work concerns the re-optimization of the studied structures placed inside the CNT (12,0). Only (T), (C) and (P) dimers are stabilized by encapsulation through the establishment of strong interactions with the CNT wall. The (T / P) and (O) isomers which are converted into (T) and (P) dimers respectively, are leaving the nanotube while they still interacting with its edge. These favorable results are indicating in one hand the possibly detection of (T) and (C) isomers, and in another hand that the process of polymerization of the TiO2 molecule which is leading to nanostructured materials could be controlled by encapsulation within the CNTs.