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.

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 Q2ext and Q2cv 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.

Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity.

We computed the network of channels of the 3A4 isoform of the cytochrome P450 (CYP) on the basis of 16 crystal structures extracted from the Protein Data Bank (PDB). The calculations were performed with version 2 of the CCCPP software that we developed for this research project. We identified the minimal cost paths (MCPs) output by CCCPP as probable ways to access to the buried active site. The algorithm of calculation of the MCPs is presented in this paper, with its original method of visualization of the channels. We found that these MCPs constitute four major channels in CYP3A4. Among the many channels proposed by Cojocaru et al. in 2007, we found that only four of them open in 3A4. We provide a refined description of these channels together with associated quantitative data.

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.

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.

Hexene hydrogenation catalysed by the complex monohydrid complexes: A DFT study of associated vs dissociated pathways.

A DFT study was conducted to elucidate the mechanism of hexene hydrogenation catalysed by a series of ruthenium (II) monohydride catalysts: RuH(CO)(Cl)(LL') where L and L' represent C(cyclohexyl), Me (methyl) and IMe (N, N '-bis (mesityl) imidazole-2-ylidene). This investigation explores the feasibility of two different proposed mechanisms: the first describes the dissociated pathway and exploits a single phosphine complex. The second is the associative one and uses a two phosphines complex. The detailed pathways have been explored for the catalyst model with L = L' = Me. Three possibilities have been supported for the dissociative route. Pathway (A) begins with a phosphine release. The initial addition of hexane or a dihydrogen molecule on the ruthenium catalyst generates the pathways (B) and (C), respectively. Pathways (B) and (C) merge with the pathway (A) before and after the first proton transfer, respectively. Activation energies in the first hydrogen migration (the key-step of the mechanism) are close. Therefore, both mechanisms (A) and (B) are possible but the former is more probable. The substitution of the catalyst model RuHCl(CO)(PMe3)2 by the real catalysts RuHCl(CO)(PCy3)2 or RuHCl(CO)(IMes)(PMe3) shows no significant influence on the energetic barriers of hexene hydrogenation mechanism. The energy profile of the first hydrogen migration for the catalyst RuHCl(CO)(PCy3)2 is characteristic of a concerted asynchronous mechanism while our calculation led to two separated synchronous steps when the model catalyst is used. The associative pathway (D) integrates the two experimentally detected intermediates and generates activation energies close to those of dissociative pathways (A) and (B). The rationale to explain the experimentally detected species is achieved by considering the four proposed mechanisms where they occur simultaneously and with different rates (ie. The dissociative mechanism has the highest rate).

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 BroÌ·nsted 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 BroÌ·nsted 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 BroÌ·nsted 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.

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.

The encapsulation of the gemcitabine anticancer drug into grapheme nest: a theoretical study.

The efficient transport of a drug molecule until its target cell constitutes a significant challenge for delivery processes. To achieve such objectives, solid nanocapsules that protect the immune system during the transport should be developed and controlled at the nanoscale level. From this point of view, nanostructures based on graphene sheets could present some promising properties due to their ultimate size and dimension. In this work, we present theoretical results using DFT calculations, dealing with a graphene-based delivery system. Indeed, we demonstrate the stability of the gemcitabine anticancer molecule when it is encapsulated into two concave graphene sheets organized as a nest. Quantum calculations showed that the most stable state is located inside the nest, which is then formed by two layers distanced 6 Å from each other. For all the optimized systems, we focused on the dependence of the interaction energy on the molecule displacements during its entrance in the graphene nest and its exit from it. We also analyzed their consequence on the local morphological and electronic charge properties. Graphical Abstract Adsorption energy (in eV) of gemcitabine drug during its encapsulation inside the nest of grapheneand its release from it.

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.

Controlling activation barrier by carbon nanotubes as nano-chemical reactors.

The oxidative addition of primary amine on a monocyclic phospholane was studied in confined conditions. This one-step chemical reaction has been investigated using the DFT technique to elucidate the role of confinement in carbon nanotubes on the reaction. Calculations were carried out by a progressive increase of the nanotube diameters from 10 Å to 15 Å in order to highlight the dependence of the reactivity on the nanotube diameter. First, single point investigations were dedicated to the study of reactants, transition states, and products placed in the different nanotubes while keeping their optimized structure as free compounds. Second, all studied compounds were relaxed inside nanotubes and their geometries were fully optimized. Within these approaches, we proved that the activation barrier could be controlled depending on the confinement, generating a well-controlled catalysis process.

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.

Encapsulation into carbon nanotubes and release of anticancer Cisplatin drug molecule.

Molecular dynamics simulations have been investigated to study the interactions between single-wall carbon nanotubes and an anticancer agent Pt complex (Cisplatin). The optimized diameter of the vector system has been determined to encapsulate in the best conditions the drug molecules. The simulation results show also that several drug molecules can be adsorbed inside the nanotubes, leading to an increased confinement time. Moreover, our simulations show that the release of the drug near a cell membrane model is favored, opening the way to a natural drug nanocapsule.