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.

Computational comparison of the kinetic stabilities of diamino- and diamidocarbenes in the 1,2-H shift reaction

In this study, we performed several DFT, MP2, and BD(T) calculations on the 1,2-H shift reactions of two diaminocarbenes (1, 2) and a diamidocarbene (3) using the Gaussian 09 program. In Gaussian 09, the BD(T) method keyword requests a Brueckner doubles calculation including a perturbative triples contribution. Although N-heterocyclic carbenes (NHC) are typically known for their exceptional σ-donor abilities, recent studies have indicated that π-interactions also play a role in the bonding between NHCs and transition metals or BX₃ (X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br) (Nemcsok et al. Organomet 23:3640–3646, 2004, Esrafili. J Mol Model 18:2003–2011, 2012). In order to study the importance of π-interactions between carbenes and transition metals, Hobbs and co-workers (Hobbs et al. New J Chem 34:1295–1308, 2010) focused on the synthesis of NHCs with reduced-energy lowest unoccupied molecular orbitals. By introducing an oxalamide moiety into the heterocyclic backbone, they found the resulting carbene possessed higher electrophilicity than usual NHCs. According to our results, the N,N'-diamidocarbene should be more stable than the diaminocarbenes with respect to the 1,2-H shift reaction.

Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)

Quantum chemical calculations are performed to study the interplay between halogen?nitrogen and halogen?carbene interactions in NCX?NCX?CH₂ complexes, where X?=?F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that the X?N and X?C_carbene interaction energies in the triads are larger than those in the dyads, indicating that both the halogen bonding interactions are enhanced. The estimated values of cooperative energy E _coop are all negative with much larger E _coop in absolute value for the systems including iodine. The nature of halogen bond interactions of the complexes is analyzed using parameters derived from the quantum theory atoms in molecules methodology and energy decomposition analysis.

Electron density reactivity indexes of the tautomeric/ionization forms of thiamin diphosphate

The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6–31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reactivity. The results allow to conclude that the highly conserved glutamic residue does not protonate the N1′ atom of the pyrimidyl ring, but it participates in a strong hydrogen bonding, stabilizing the eventual negative charge on the nitrogen, in all forms involved in the ylide generation. This condition provides the necessary reactivity on key atoms, N4′ and C2, to carry out the formation of the ylide required to initiate the catalytic cycle of ThDP- dependent enzymes. This study represents a new approach for the ylide formation in ThDP catalysis.

Conformational flexibility of the ErbB2 ectodomain and trastuzumab antibody complex as revealed by molecular dynamics and principal component analysis

Human epidermal growth factor receptor 2 (ErbB2) is a transmembrane oncoprotein that is over expressed in breast cancer. A successful therapeutic treatment is a monoclonal antibody called trastuzumab which interacts with the ErbB2 extracellular domain (ErbB2-ECD). A better understanding of the detailed structure of the receptor-antibody interaction is indeed of prime interest for the design of more effective anticancer therapies. In order to discuss the flexibility of the complex ErbB2-ECD/trastuzumab, we present, in this study, a multi-nanosecond molecular dynamics simulation (MD) together with an analysis of fluctuations, through a principal component analysis (PCA) of this system. Previous to this step and in order to validate the simulations, we have performed a detailed analysis of the variable antibody domain interactions with the extracellular domain IV of ErbB2. This structure has been statically elucidated by x-ray studies. Indeed, the simulation results are in excellent agreement with the available experimental information during the full trajectory. The PCA shows eigenvector fluctuations resulting in a hinge motion in which domain II and C_H domains approach each other. This move is likely stabilized by the formation of H-bonds and salt bridge interactions between residues of the dimerization arm in the domain II and trastuzumab residues located in the C_H domain. Finally, we discuss the flexibility of the MD/PCA model in relation with the static x-ray structure. A movement of the antibody toward the dimerization domain of the ErbB2 receptor is reported for the first time. This finding could have important consequences on the biological action of the monoclonal antibody.

Ion disturbance and clustering in the NaCl water solutions

Ion clustering and the solvation properties in the NaCl solutions are explored by molecular dynamics simulations with several popular force fields. The existence of ions has a negligible disturbance to the hydrogen bond structures and rotational mobility of water beyond the first ion solvation shells, which is suggested by the local hydrogen bond structures and the rotation times of water. The potential of mean force (PMF) of ion pair in the dilute solution presents a consistent view with the populations of ion clusters in the electrolyte solutions. The aggregation level of ions is sensitive to the force field used in the simulations. The ion-ion interaction potential plays an important role in the forming of the contact ion pair. The entropy of water increases as the ion pair approaches each other and the association of ion pair is driven by the increment of water entropy according to the results from the selected force fields. The kinetic transition from the single solvent separated state to the contact ion pair is controlled by the enthalpy loss of solution.

Role of gold in a complex cascade reaction involving two electrocyclization steps

Quantum chemical computations (B3LYP/LACVP**) were applied to assess the impact of Au(I) complexation on activation barriers for sequential electrocyclization reactions (one a 1,2-dihydroazete ring-opening and another a pentadienyl cation ring-closure) proposed to occur during a complex reaction cascade that converts alkynes and imines to cyclopentenimines.

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.

Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the “horse-saddle” conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones’ structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O_C atoms of the CHPs’ backbones and H_w atoms of water molecules. N atoms of the CHPs’ backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D _xy ) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Ruthenium(II) carbonyl chloride complexes containing pyridine-functionalised bidentate N-heterocyclic carbenes: Synthesis, structures, and impact of the carbene ligands on catalytic activities

A series of new ruthenium(II) carbonyl chloride complexes with pyridine-functionalised N-heterocyclic carbenes [Ru(Py-NHC)(CO)₂Cl₂], [Py-NHC = 3-methyl-1-(2-pyridyl)imidazol-2-ylidene, 1 (1a and 1b); 3-methyl-1-(2-picoyl)imidazol-2-ylidene, 2 (2a and 2b); 3-methyl-1-(2-pyridyl)benzimidazolin-2-ylidene, 3 (3b); 3-methyl-1-(2-picoyl)benzimidazolin-2-ylidene, 4 (4a and 4b); 1-methyl-4-(2-pyridyl)-1,2,4-triazoline-5-ylidene, 5 (5a and 5b)] have been prepared by transmetallation from the corresponding silver carbene complexes and characterized by NMR, IR spectroscopy and elemental analysis. In these complexes with bidentate Py-NHC ligands, one CO ligand is trans to the Py ligand. In 1a, 2a, 4a, and 5a, the NHC ligand is trans to the other CO ligand, thus leaving the two Cl⁻ ligands trans to each other. In 1b, 2b, 3b, 4b, and 5b, the NHC ligands are trans to one Cl⁻ ligand, and the two Cl⁻ ligands are cis to each other. The structures for 1b, 2b, 3b and 4b have been determined by single-crystal X-ray diffraction. These complexes are efficient catalysts in the transfer hydrogenation of acetophenone and their catalytic activities are found to be influenced by electronic effect of the N-heterocyclic carbene ligands.     

Molecular simulation study of PAMAM dendrimer composite membranes

Pure polysulfone (PSF) and its composites with chitosan (CST), hyaluronic acid (HA), conventional poly(amidoamine), and hydroxyl poly(amidoamine) dendrimers as the membranes for separation of the gases, methane, carbon dioxide, hydrogen sulfide, nitrogen, and oxygen have been studied by molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. The transport properties (solubility, diffusivity, and permeability) of pure and gas mixtures in the membranes were calculated and the results of the simulations were compared with the available experimental data. The simulated structural properties of the pure and composite PSF membranes including occupied volume, free volume, surface area, fractional free volume (FFV), and radius of gyration (R _g ) were evaluated and their effects on the separability of the gases by the membranes were analyzed and interpreted by the obtained results.

Insights into the strength and nature of carbene···halogen bond interactions: a theoretical perspective

Halogen-bonding, a noncovalent interaction between a halogen atom X in one molecule and a negative site in another, plays critical roles in fields as diverse as molecular biology, drug design and material engineering. In this work, we have examined the strength and origin of halogen bonds between carbene CH₂ and XCCY molecules, where X?=?Cl, Br, I, and Y?=?H, F, COF, COOH, CF₃, NO₂, CN, NH₂, CH₃, OH. These calculations have been carried out using M06-2X, MP2 and CCSD(T) methods, through analyses of surface electrostatic potentials V _S(r) and intermolecular interaction energies. Not surprisingly, the strength of the halogen bonds in the CH₂···XCCY complexes depend on the polarizability of the halogen X and the electron-withdrawing power of the Y group. It is revealed that for a given carbene···X interaction, the electrostatic term is slightly larger (i.e., more negative) than the dispersion term. Comparing the data for the chlorine, bromine and iodine substituted CH₂···XCCY systems, it can be seen that both the polarization and dispersion components of the interaction energy increase with increasing halogen size. One can see that increasing the size and positive nature of a halogen’s σ-hole markedly enhances the electrostatic contribution of the halogen-bonding interaction.

Investigation of the binding network of IGF-I on the cavity surface of IGFBP4

Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employed to study the interaction mechanism of IGFBP4 and IGF-I by molecular dynamics (MD) simulation. In IGF-I, residues Gly7 to Asp12 were found to be the hot spots and they mainly anchored on the N-domain of IGFBP4. The contact area, the shape and size of protein, the surroundings of the binding site, the hydrophobic and electrostatic interaction between the two proteins worked as a complex network to regulate the protein-protein interaction. It was also found that the unfolding of the helix was not inevitable in the mutant, and it could be regulated by careful selection of the substituted amino acid.

Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3)

A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing metathesis of a diene precursor. The nature of the optimal linker and its size was directed by docking. In a kinase panel screen, selected macrocycles were active on other kinase targets, mainly FLT3, JAK2, and CDKs. These compounds then became leads in a CDK/FLT3/JAK2 inhibitor project. Macrocycles with a basic nitrogen in the linker form a salt bridge with Asp86 in CDK2 and Asp698 in FLT3. Interaction with this residue explains the observed selectivity. The Asp86 residue is conserved in most CDKs, resulting in potent pan-CDK inhibition by these compounds. Optimized macrocycles generally have good DMPK properties, and are efficacious in mouse models of cancer. Compound 5 (SB1317/TG02), a pan-CDK/FLT3/JAK2 inhibitor, was selected for preclinical development, and is now in phase 1 clinical trials.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

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.

Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide—a novel topoisomerase II inhibitor

The preliminary cytotoxic effect of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride (1)—a potent topoisomerase II inhibitor—was measured using a MTT assay. It was found that the compound decreased the number of viable cells in both estrogen receptor-positive MCF-7 and estrogen receptor-negative MDA-MB-231breast cancer cells, with IC₅₀ values of 146?±?2 and 132?±?2 μM, respectively. To clarify the molecular basis of the inhibitory action of 1, molecular docking studies were carried out. The results suggest that 1 targets the ATP binding pocket.