The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (P<Superscript>III</Superscript>)

Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus–carbon bond cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (P^III). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that decomposition to P^III derivatives proceeds via an elimination reaction. Figure The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (P^III)     

CHIH-DFT determination of the molecular structure and IR and UV spectra of solanidine

Solanidine is the steroidal aglycon of some potato glycoalkaloids and a very important precursor for the synthesis of hormones and some pharmacologically active compounds. In this work, we make use of a new chemistry model within Density Functional Theory, called CHIH-DFT, to calculate the molecular structure of solanidine, as well to predict its infrared and ultraviolet spectra. The calculated values are compared with the experimental data available for this molecule as a means of validation of our proposed chemistry model. Figure Molecular structure of solanidine calculated with the CHIH(small) model chemistry     

Molecular model for host–guest interaction of tetraamino-<Emphasis Type="Italic">tert</Emphasis>-butylthiacalix[4]arene and tetraamino-<Emphasis Type="Italic">tert</Emphasis>-butylcalix[4]arene receptors with carboxylate and dicarboxylate guests: an ONIOM study

Geometry optimizations of tetraamino-tert-butylthiacalix[4]arene (tatbtc4a) and tetraamino-tert-butylcalix[4]arene (tatbc4a) complexes with acetate, oxalate, malonate, succinate, glutarate, adipate, and pimelate were carried out using the integrated MO:MO method. Thermodynamic quantities, preorganization energies and complexation energies of these complexes were obtained at the ONIOM(B3LYP/6-31G(d):AM1) level of theory. The relative stabilities of the tatbtc4a and tatbc4a complexes with carboxylate guests are reported. The complexes tatbtc4a/malonate and tatbc4a/oxalate were found to be the most stable species. The selectivity of the tatbtc4a receptor toward to malonate with respect to oxalate, in terms of selectivity coefficient, is 9.90×10². Figure Atom labeling of tatbtc4a/oxalate complex as a representative of host-guest system.     

SOMMER: self-organising maps for education and research

SOMMER is a publicly available, Java-based toolbox for training and visualizing two- and three-dimensional unsupervised self-organizing maps (SOMs). Various map topologies are implemented for planar rectangular, toroidal, cubic-surface and spherical projections. The software allows for visualization of the training process, which has been shown to be particularly valuable for teaching purposes. Spread of a spherical self-organizing map (SOM) in a three-dimensional data space     

Structure-based 3D-QSAR studies on thiazoles as 5-HT<Subscript>3</Subscript> receptor antagonists

Structure-based 3D-QSAR studies were performed on 20 thiazoles against their binding affinities to the 5-HT₃ receptor with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The thiazoles were initially docked into the binding pocket of a human 5-HT_3A receptor homology model, constructed on the basis of the crystal structure of the snail acetylcholine binding protein (AChBP), using the GOLD program. The docked conformations were then extracted and used to build the 3D-QSAR models, with cross-validated values 0.785 and 0.744 for CoMFA and CoMSIA, respectively. An additional five molecules were used to validate the models further, giving satisfactory predictive values of 0.582 and 0.804 for CoMFA and CoMSIA, respectively. The results would be helpful for the discovery of new potent and selective 5-HT₃ receptor antagonists.      

EMPIRE: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions

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Docking studies suggest ligand-specific δ-opioid receptor conformations

An automated docking procedure was used to study binding of a series of δ-selective ligands to three models of the δ-opioid receptor. These models are thought to represent the three ligand-specific receptor conformations. Docking results are in agreement with point mutation studies and suggest that different ligands—agonists and antagonists—may bind to the same binding site under different receptor conformations. Docking to different receptor models (conformations) also suggests that by changing to a receptor-specific conformation, the receptor may open or close different binding sites to other ligands. Figure  Ligands 5 (green) and 6 (orange) in bindingpocket BP1 of the R1 δ-opioid receptor model     

Rotational model for nematic phase stability of fluorinated phenylbicyclohexane liquid crystals

A mechanical molecular rotation model for liquid crystal (LC) systems is employed to evaluate phase transition temperature of fluorinated phenylbicyclohexane isomeric LC compounds. Results show that when a fluorine atom is substituted along the molecular long axis, an LC molecule acquires high rotational speed and its rotation becomes stable, thereby resulting in a better thermal stability of the nematic phase. A novel explanation is proposed for the behavior of the nematic-isotropic phase of the LC system when a heavy atom is substituted along the molecular long axis. Figure Molecular conformation of fluorinated bicyclohexylphenyl compounds. . The fluorine atoms are substituted in different positions 2, 3, 4, and 5 of the phenyl ring, respectively. The axis expresses molecular long rotation axis.     

Molecular dynamics study of the initial stages of catalyzed single-wall carbon nanotubes growth: force field development

Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are modified to simulate the catalyzed growth of single-wall carbon nanotubes on Ni_n clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of the metal atoms on such interactions. Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters.     

Influence of different transition metals in phthalocyanines on their interaction energies with volatile organic compounds: an experimental and computational study

Experimental partition coefficients were determined for a series of volatile organic compounds (VOCs) (acetonitrile, n-butylamine, n-octane tetrachloroethene, and toluene) for the interaction with 2,3,9,10,16,17,23,24-octakis(octyloxy)-phthalocyaninato complexes, PcM(OR)₈, with varying central metal atoms [M=H₂ (metal-free), Ni, Pd, Cu, Zn]. Large partition coefficients for toluene were observed in the case of the nickel and palladium phthalocyanines, whereas for the corresponding zinc-containing compound, interaction with n-butylamine resulted in a high value for the partition coefficient. Interaction energies for model coordination complexes were obtained at the ab initio LMP2/ LACVP* level of theory. The interaction of various small volatiles with the various PcM(OR)₈ compounds was studied using the PM3 semiempirical Hamiltonian. Large values for interaction energies correspond to particularly strong partition coefficients, suggesting that coordination of the volatiles to the central metal dominates over the often discussed π-system stacking at the PcM(OR)₈’s. Figure: Chemical structure of the phthalocyanines investigated.     

Mechanistic study of palladium-catalyzed telomerization of 1,3-butadiene with methanol

The Pd-catalyzed telomerization in the presence of phosphine and carbene ligands has been computed. It is shown that the C–C coupling of the less stable complex A with one trans- and one cis-butadiene in syn orientation forms the most stable intermediate B and is favorable both kinetically and thermodynamically. Protonation of B leads to equilibrium of the two most stable isomers of intermediate C. The overall regioselectivity is favored thermodynamically.      

Experimental and theoretical investigations of spectroscopic properties of azobenzene derivatives in solution

The UV-Vis spectra of series of polymethylmethacrylate (PMMA) copolymers with attached trans-azobenzene derivatives were measured in 1,1,2-trichloroethane. In order to gain some insight into the recorded spectra, the quantum chemical calculations were performed for the substituted azobenzenes using both configuration interaction with single excitations method (CIS) as well as density functional theory (DFT) with B3LYP and PBE0 functionals. The calculations were performed in solvent. In particular, we found that the PBE0 excitation energies are in very good agreement with the experimental data. Figure The plots of orbital contour surfaces for molecule II. The molecular orbitals were calculated at the PBE0/6-311++G(d,p) level of theory. The upper plot presents contour surface of HOMO and the lower presents contour surface of LUMO. Shown are the contour surfaces of orbital amplitude 0.04 (red) and -0.04 (blue)     

A theoretical investigation of cytotoxic activity of celastroid triterpenoids

Quantum chemical calculations at the B3LYP/6-31G* level of theory have been carried out on 20 celastroid triterpenoids to obtain a set of molecular electronic properties and to correlate these with cytotoxic activities. The cytotoxic activities of these compounds can be roughly correlated with electronic effects related to nucleophilic addition to C(6) of the compounds: The energies of the frontier molecular orbitals (E _HOMO and E _LUMO), the HOMO-LUMO energy gap, the dipole moment, the charge on C(6), and the electrophilicity on C(6). Figure LUMO of Pristimerin.     

Molecular models of protein kinase 6 from Plasmodium falciparum

Cyclin-dependent kinases (CDKs) have been identified as potential targets for development of drugs, mainly against cancer. These studies generated a vast library of chemical inhibitors of CDKs, and some of these molecules can also inhibit kinases identified in the Plasmodium falciparum genome. Here we describe structural models for Protein Kinase 6 from P. falciparum (PfPK6) complexed with Roscovitine and Olomoucine. These models show clear structural evidence for differences observed in the inhibition, and may help designing inhibitors for PfPK6 generating new potential drugs against malaria. Figure Ribbon diagram of PfPK6 complexed with a roscovitine and b olomoucine     

Localized and delocalized perfluorosemibullvalenes

On the basis of the experimental Gibbs free-energy barrier of the degenerate Cope arrangement in semibullvalene, B3P86 shows the best agreement, while B3LYP and MP2 underestimate and CCSD(T) overestimates the barrier. The substituent effect proposal by Hoffmann has been verified. In contrast to semibullvalenes with either localized energy-minimum structures or delocalized transition-state structures, perfluorosemibullvalene has both localized and delocalized energy-minimum structures that are very close in energy. Localized and delocalized perfluorosemibullvalenes Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users.     

Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-β-glucanase by molecular dynamics simulations

The dependence of some molecular motions in the enzyme 1,3-1,4-β-glucanase from Bacillus licheniformis on temperature changes and the role of the calcium ion in them were explored. For this purpose, two molecular dynamics simulated trajectories along 4 ns at low (300 K) and high (325 K) temperatures were generated by the GROMOS96 package. Several structural and thermodynamic parameters were calculated, including entropy values, solvation energies, and essential dynamics (ED). In addition, thermoinactivation experiments to study the influence of the calcium ion and some residues on the activity were conducted. The results showed the release of the calcium ion, which, in turn, significantly affected the movements of loops 1, 2, and 3, as shown by essential dynamics. These movements differ at low and high temperatures and affect dramatically the activity of the enzyme, as observed by thermoinactivation studies. The first two authors contributed equally to this work     

DFT investigation of the 1-octene metathesis reaction mechanism with the Phobcat precatalyst

The productive self-metathesis reaction of 1-octene in the presence of the Phobcat precatalyst [RuCl₂(Phoban-Cy)₂(=CHPh)] using density functional theory was investigated and compared to the Grubbs 1 precatalyst [RuCl₂(PCy₃)₂(=CHPh)]. At the GGA-PW91/DNP level, the geometry optimization of all the participating species and the PES scans of the various activation and catalytic cycles in the dissociative mechanism were performed. The formation of the catalytically active heptylidene species is kinetically and thermodynamically favored, while the formation of trans-tetradecene is thermodynamically favored.      

A molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface

Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid–liquid interface. Furthermore, we have studied the relation between the mean-square gyration radius and N. Figure Log–log plot of the self-diffusion coefficient D versus the chain length N. The error bars are the standard deviation measured in three repeated simulations     

Quantitative trait loci identified for sugar related traits in a sugarcane (<Emphasis Type="Italic">Saccharum</Emphasis> spp.) cultivar × <Emphasis Type="Italic">Saccharum officinarum</Emphasis> population

The identification of markers linked to quantitative trait loci (QTLs) for increased sugar accumulation could improve the effectiveness of current breeding strategies in sugarcane. Progeny from a cross between a high sucrose producing cultivar, (denotes Australian plant breeding rights), and a Saccharum officinarum clone, IJ76-514 were grown in two field experiments in different years, and evaluated in the early and mid-season phases of crop maturity, to identify robust QTLs in affecting sucrose content in cane. Using an extensive genetic map constructed for with over 1,000 AFLP and SSR markers, a total of 37 QTLs were identified for brix and pol of which, 16 were detected in both experiments. Of these 37 QTL, 30 were clustered into 12 genomic regions in six of the eight homo(eo)logous groups. Each QTL explained from 3 to 9% of the phenotypic variation observed. Both positive and negative effects were identified and the location of the QTLs on linkage groups belonging to the same homo(eo)logy group suggested that a number of the QTLs were allelic forms of the same genes. Of the 37 QTLs identified, the majority were significant in both early and mature cane, but 8 were identified as early specific QTLs and 9 as mature cane QTLs. In total, 97 interactions were significant (P<10⁻⁵) and these were localised to 32 genomic regions of which 6 were detected with both years’ data. Models including all the QTLs explained from 37 to 66% of the total phenotypic variation, depending on the trait. The results will be subsequently applied in marker assisted breeding. denotes variety covered by Australian plant breeding rights.     

Molecular modeling of the three-dimensional structure of GLP-1R and its interactions with several agonists

Glucagon-like peptide-1 receptor (GLP-1R) is a promising molecular target for developing drugs treating type 2 diabetes. We have predicted the complete three-dimensional structure of GLP-1R and the binding modes of several GLP-1R agonists, including GLP-1, Boc5, and Cpd1, through a combination of homology modeling, molecular docking, and long-time molecular dynamics simulation on a lipid bilayer. Our model can reasonably interpret the results of a number of mutation experiments regarding GLP-1R as well as the successful modification to GLP-1 by Liraglutide. Our model is also validated by a recently revealed crystal structure of the extracellular domain of GLP-1R. An activation mechanism of GLP-1R agonists is proposed based on the principal component analysis and normal mode analysis on our predicted GLP-1R structure. Before the complete structure of GLP-1R is determined through experimental means, our model may serve as a valuable reference for characterizing the interactions between GLP-1R and its agonists. Figure Comparison of our predicted model of rGLP-1R (left) with the recently revealed crystal structure of hGLP-1R (right)