Reactions of ketones with aromatics in acid media. The effect of trifluoromethyl groups and the acidity media. A theoretical study

The reactions of acetone, 2,2,2-trifluoroacetone and hexafluoroacetone in methanesulfonic (MSA) and triflic acids (TFSA) with benzene have been studied at M06-2X/6-311+G(d,p) level using cluster-continuum model, where the carbonyl group is explicitly solvated by acid molecules. The introduction of a trifluoromethyl group into the ketone structure reduces the activation energy of the tetrahedral intermediates formation due to an increase of the electrophilicity of the carbonyl group and raises the activation and the reaction energies of the C-O bond cleavage in formed carbinol due to the destabilization of the corresponding carbocation. The introduction of the second trifluoromethyl group inhibits the hydroxyalkylation reaction due to a very strong increase of the reaction and activation energies of the C-O bond cleavage which becomes the rate determining step. The most important catalytic effect of TFSA compared to MSA is not the protonation of the ketone carbonyl, but the reduction of the activation and reaction energies of the carbinol C-O bond cleavage due to better protosolvation properties. Even for TFSA no complete proton transfer to carbonyl oxygen has been observed for free ketones. Therefore, the protonation energies of free ketones cannot be considered as a measure of ketone reactivity in the hydroxyalkylation reaction.

Theoretical study of the solvatochromism of a donor-acceptor bithiophene

The solvation and the solvatochromic behavior of the 5-(methylthio)-5′-nitro-2,2′-bithiophene 1 in diethyl ether, dichloromethane, acetonitrile, methanol and formamide was theoretically investigated with an iterative molecular and quantum mechanics (QM/MM) approach. Calculated longest-wavelength solvatochromic absorption band of 1, obtained as averages of statistically uncorrelated configurations, including the solute and explicit solvent molecules of the first and second solvation layer, were in excellent agreement with the experimental results.

Zinc-, cadmium-, and mercury-containing one-dimensional tetraphenylporphyrin arrays: a DFT study

This work describes theoretical and experimental studies on glycerol esterification to obtain acetins focusing on the obtained isomers. The reaction of glycerol with acetic acid was carried out on Amberlyst 36 wet. Density functional theory calculations on the level of M06-2X functional and 6-311+G(d,p) basis set are carried out and the most stable structures of the reactants and products are located by considering a large number of conformers. The thermodynamics is discussed in terms of the calculated reaction Gibbs free energy. The AIM theory was used to characterize reactants and products. The glycerol esterification with acetic acid is found to be thermodynamically favored, with exothermal property. These agree well with experiments and allow us to explain the relative selectivity of products.

Modeling the activity of glutathione as a hydroxyl radical scavenger considering its neutral non-zwitterionic form

Glutathione is an immensely important antioxidant, particularly in the central nervous system. The scavenging mechanism of glutathione towards the OH radical was studied theoretically, considering its neutral, non-zwitterionic form relevant to acidic media. Gibbs free barrier and released energies involved in hydrogen abstraction from the different sites of glutathione by an OH radical were studied at the B3LYP/6-31G(d,p), B3LYP/AUG-cc-pVDZ, M06/AUG-cc-pVDZ, M06-2X/AUG-cc-pVDZ levels of density functional theory. Solvation in bulk aqueous media was also studied at all these levels of theory employing the polarizable continuum model. Our study shows that a hydroxyl radical can abstract a hydrogen atom easily from glutathione. Thus, glutathione is shown to be an efficient scavenger of OH radicals, which is in agreement with the results of previous studies.

A theoretical study on the hydrogen adducts of diamidocarbenes and diaminocarbenes

The hybrid-meta GGA DFT functional M06-2X was used to examine the potential of N,N′-diamidocarbenes for use as hydrogen storage materials. We previously discovered that borylene, which is isoelectronic with an Arduengo-type carbene, was a suitable candidate for a hydrogen storage material. We compared the capabilities of N,N′-diamidocarbenes and N-heterocyclic carbenes as hydrogen storage materials. The results indicate that diamidocarbenes are not suitable hydrogen storage materials because the removal of H₂ is more endothermic for diamidocarbenes than for diaminocarbenes.

Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes

This paper presents an ab initio quantum chemical investigation of the geometrical structures and the non-linear optical properties (NLO) of three structural isomers of pyridinium N-phenolate betaine dye. The ground state geometrical parameters and the first-order hyperpolarizabilities were calculated using the Hartree-Fock (HF) as well as the second-order perturbation Møller-Pleset (MP2) method with the 6–31G, 6–31G(d), 6–31G(d,p), 6–31+G(d), 6–31++G(d,p), 6–311+G(d), aug-cc-PVDZ and the recently developed Z3PolX basis sets. Moreover, the first-order hyperpolarizability was calculated at the coupled cluster singles and doubles (CCSD/6–31+G(d)) level of theory. The analysis of the results of calculations for the investigated isomers indicates that there are important differences in their NLO activities. Additionally, it was shown that Z3PolX basis set works reasonable well for betaine dyes.

Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bond networks

A stochastic exploration of the quantum conformational spaces in the microsolvation of divalent cations with explicit consideration of up to six solvent molecules [Mg (H ₂ O) _n )]²⁺, (n?=?3, 4, 5, 6) at the B3LYP, MP2, CCSD(T) levels is presented. We find several cases in which the formal charge in Mg²⁺ causes dissociation of water molecules in the first solvation shell, leaving a hydroxide ion available to interact with the central cation, the released proton being transferred to outer solvation shells in a Grotthus type mechanism; this particular finding sheds light on the capacity of Mg²⁺ to promote formation of hydroxide anions, a process necessary to regulate proton transfer in enzymes with exonuclease activity. Two distinct types of hydrogen bonds, scattered over a wide range of distances (1.35–2.15 Å) were identified. We find that in inner solvation shells, where hydrogen bond networks are severely disturbed, most of the interaction energies come from electrostatic and polarization+charge transfer, while in outer solvation shells the situation approximates that of pure water clusters.

Entropy versus aromaticity in the conformational dynamics of aromatic rings

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

Nickel/zinc-catalyzed decarbonylative addition of anhydrides to alkynes: A DFT study

Density functional theory (DFT) was used to investigate the nickel- or nickel(0)/zinc- catalyzed decarbonylative addition of phthalic anhydrides to alkynes. All intermediates and transition states were optimized completely at the B3LYP/6-31+G(d,p) level. Calculated results indicated that the decarbonylative addition of phthalic anhydrides to alkynes was exergonic, and the total free energy released was ?87.6 kJ mol^?1. In the five-coordinated complexes M4a and M4b, the insertion reaction of alkynes into the Ni-C bond occurred prior to that into the Ni-O bond. The nickel(0)/zinc-catalyzed decarbonylative addition was much more dominant than the nickel-catalyzed one in whole catalytic decarbonylative addition. The reaction channel CA→M1'→T1'→M2'→T2'→M3a'→M4a'→T3a1'→M5a1' →T4a1'→M6a'→P was the most favorable among all reaction pathways of the nickel- or nickel(0)/zinc- catalyzed decarbonylative addition of phthalic anhydrides to alkynes. And the alkyne insertion reaction was the rate-determining step for this channel. The additive ZnCl₂ had a significant effect, and it might change greatly the electron and geometry structures of those intermediates and transition states. On the whole, the solvent effect decreased the free energy barriers.

Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: a molecular dynamics simulation approach

Articaine, as a local anesthetic drug has been simulated in neutral and charged forms, and its interaction with the dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane is investigated by molecular dynamics simulation using GROMACS software. In order to obtain the optimum location of the drug molecules, as they penetrate into the membrane, umbrella sampling is applied and the free energy is calculated. The effect of protein binding to DMPC membrane on the process of drug diffusion through the membrane is considered. Five simulation systems are designed and by applying the potential of mean force, the molecular dynamics simulation on the system is performed. In light of the obtained results, the electrostatic potential, variation of lipid bilayer’s order parameter and the diffusion coefficient of drug are discussed.

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

Coarse-grained studies of CH₃SH, CH₃CHO and CHCl₃ liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

Spectroscopic investigations and hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine: a theoretical study

The structure, spectral properties and the hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine have been studied by using quantum chemical methods. The time-dependent density functional theory (TD-DFT) and the singly excited configuration interaction (CIS) methods are employed to optimize the excited state geometries of isolated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine in both the gas and solvent phases. The solvent phase calculations are performed using the polarizable continuum model (PCM). The absorption and emission spectra are calculated using the time-dependent density functional theory (TD-DFT) method. The results from the TD-DFT calculations reveal that the excitation spectra are red shifted relative to absorption in aqueous medium. These changes in the transition energies are qualitatively comparable to the experimental data. The examination of molecular orbital reveals that the molecules with a small H→L energy gap possess maximum absorption and emission wavelength. The relative stability and hydrogen bonded interactions of mono and heptahydrated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine have been studied using the density functional theory (DFT) and Møller Plesset perturbation theory (MP2) implementing the 6-311++G(d,p) basis set. The formation of strong N-H…O bond has resulted in the highest interaction energy among the monohydrates. Hydration does not show any significant impact on the stability of heptahydrated complexes. The atoms in molecule (AIM) and natural bonding orbital (NBO) analyses have been performed to elucidate the nature of the hydrogen bond interactions in these complexes.

Theoretical study of photophysical properties of 1,4-dihydropyrrolo[3,2-b]pyrrole-cored branched molecules with thienylenevinylene arms toward broad absorption spectra for solar cells

A series of oligo(thienylenevinylene) derivatives with 1,4-dihydropyrrolo[3,2-b]pyrrole as core has been investigated at the PBE0/6-31G(d) and the TD-PBE0/6-31+G(d,p) levels to design materials with high performances such as broad absorption spectra and higher balance transfer property. The results show that position and amount of arm affect the electronic density contours of frontier molecular orbitals significantly. The molecule with four arms owns the narrowest energy gap and the largest maximum absorption wavelength, and the molecule with two arms in positions a and c has the broadest absorption region among the designed molecules. Calculated reorganization energies of the designed molecules indicate that the molecules with two arms can be good potential ambipolar transport materials under proper operating conditions.

A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes

The potential energy surfaces of the reactions of organometallic arene complexes of the type [(η ⁶-arene)M^II(pic)Cl] (where pic = 2-picolinic acid, M = Ru or Os) were examined by a DFT computational study. Among the seven density functional methods, hybrid exchange functional B3LYP outperforms the others to explain the aquation of the complexes. The reactions and binding energies of Ru^II and Os^II arene complexes with both 9EtG and 9EtA were studied to gain insight into the reactivity of these types of organometallic complexes with DNA. The obtained data rationalize experimental observation, contributing to partly understanding the potential biological and medical applications of organometallic complexes.

Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies

We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

Structural elucidation of supramolecular alpha-cyclodextrin dimer/aliphatic monofunctional molecules complexes

The structural elucidation of 2α-cyclodextrin/1-octanethiol, 2α-cyclodextrin/1-octylamine and 2α-cyclodextrin/1-nonanoic acid inclusion complexes by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling has been achieved. The detailed spatial configurations are proposed for the three inclusion complexes based on 2D NMR method. ROESY experiments confirm the inclusion of guest molecules inside the α-cyclodextrin (α-CD) cavity. On the other hand, the host-guest ratio observed was 2:1 for three complexes. The detailed spatial configuration proposed based on 2D NMR methods were further interpreted using molecular modeling studies. The theoretical calculations are in good agreement with the experimental data.

Can cyclic HIV protease inhibitors bind in a non-preferred form? An ab initio, DFT and MM-PB(GB)SA study

X-ray crystallography studies have identified that most cyclic inhibitors of HIV protease (including cyclic ureas) bind in a symmetric manner, however some cyclic inhibitors, such as cyclic sulfamides, bind in a non-symmetric manner. This raises the question as to whether it is possible for cyclic sulfamides to bind symmetrically and conversely for cyclic ureas to bind non-symmetrically. Herein we report an analysis of the conformational preference of cyclic ureas and sulfamides both free in solution and bound to HIV protease, including an investigation of the effect of branching. Quantum chemical calculations (B3LYP, M06-2X, MP2, CCSD(T)) predict the cyclic urea to prefer a symmetric conformation in solution, with a large activation barrier towards inter-conversion to the non-symmetric conformation. This differs from the cyclic sulfamides, which marginally prefer a non-symmetric conformation with a much smaller barrier to inter-conversion making it more likely for a non-preferred conformation to be observed. It is predicted that the cyclic scaffold itself favours a symmetric form, while branching induces a preference for a non-symmetric form. MD simulations on the free inhibitors identified inter-conversion with the cyclic sulfamides but not the cyclic ureas, in support of the quantum chemical results. MM-PB(GB)SA calculations on the cyclic inhibitors bound to HIV protease corroborate the X-ray crystallography studies, identifying the cyclic ureas to bind symmetrically and the cyclic sulfamides in a non-symmetrical manner. While the non-preferred form of the sulfamide may well be present as a free molecule in solution, our results suggest that it is unlikely to bind to HIV protease in a symmetric manner.

First-principles study of ammonium ions and their hydration in montmorillonites

Density functional theory calculations were performed to investigate the adsorption and hydration of an ammonium ion (NH₄ ⁺) confined in the interlayer space of montmorillonites (MMT). NH₄ ⁺ is trapped in the six-oxygen-ring on the internal surface and forms a strong binding with the surface O atoms. The hydration of NH₄ ⁺ is affected significantly by the surface. Water molecules prefer the surface sites, and do not bind with the NH₄ ⁺ unless enough water molecules are supplied. Moreover, the water molecules involved in NH₄ ⁺ hydration tend to bind with the surface simultaneously. The hydration energy increases with the intercalated water molecules, in contrast to that in gas phase. In addition, the hydration leads to the extension of MMT basal spacing.