Backbone Carbon Atoms Research Articles

Cytotoxicity of Prymnesium parvum extracts and prymnesin analogs on epithelial fish gill cells RTgill-W1 and the human colon cell line HCEC-1CT.

Harmful algal blooms kill fish populations worldwide, as exemplified by the haptophyte microalga Prymnesiumparvum. The suspected causative agents are prymnesins, categorized as A-, B-, and C-types based on backbone carbon atoms. Impacts of P.parvum extracts and purified prymnesins were tested on the epithelial rainbow trout fish gill cell line RTgill-W1 and on the human colon epithelial cells HCEC-1CT. Cytotoxic potencies ranked A > C > B-type with concentrations spanning from low (A- and C-type) to middle (B-type) nM ranges. Although RTgill-W1 cells were about twofold more sensitive than HCEC-1CT, the cytotoxicity of prymnesins is not limited to fish gills. Both cell lines responded rapidly to prymnesins; with EC50 values for B-types in RTgill-W1 cells of 110 ± 11nM and 41.5 ± 0.6nM after incubations times of 3 and 24h. Results of fluorescence imaging and measured lytic effects suggest plasma membrane interactions. Postulating an osmotic imbalance as mechanisms of toxicity, incubations with prymnesins in media lacking either Cl-, Na+, or Ca2+ were performed. Cl- removal reduced morphometric rearrangements observed in RTgill-W1 and cytotoxicity in HCEC-1CT cells. Ca2+-free medium in RTgill-W1 cells exacerbated effects on the cell nuclei. Prymnesin composition of different P.parvum strains showed that analog composition within one type scarcely influenced the cytotoxic potential, while analog type potentially dictate potency. Overall, A-type prymnesins were the most potent ones in both cell lines followed by the C-types, and lastly B-types. Disturbance of Ca2+ and Cl- ionoregulation may be integral to prymnesin toxicity.

Tris(pentafluoroethyl)difluorophosphorane and N‐Heterocyclic Carbenes: Adduct Formation and Frustrated Lewis Pair Reactivity

AbstractThe synthesis and characterization of Lewis acid/base adducts between tris(pentafluoroethyl)difluorophosphorane PF2(C2F5)3 and selected N‐heterocyclic carbenes (NHCs) R2Im (1,3‐di‐organyl‐imidazolin‐2‐ylidene) and phosphines are reported. For NHCs with small alkyl substituents at nitrogen (R=Me, nPr, iPr) the adducts NHC ⋅ PF2(C2F5)3 (2 a–h) were isolated. The reaction with the sterically more demanding NHCs Dipp2Im (1,3‐bis‐(2,6‐di‐iso‐propylphenyl)‐imidazolin‐2‐ylidene) (1 i) and tBu2Im (1,3‐di‐tert‐butyl‐imidazolin‐2‐ylidene) (1 j) afforded the aNHC adducts 3 i and 3 j (a denotes “abnormal” NHC coordination via a backbone carbon atom). The use of tBuMeIm (1‐tert‐butyl‐3‐methyl‐imidazolin‐2‐ylidene) (1 m) led to partial decomposition of the NHC and formation of the salt [tBuMeIm−H][MeIm ⋅ PF2(C2F5)3] (4 m). The phosphorane PF2(C2F5)3 forms adducts with PMe3 but does not react with PPh3 or PCy3. The mer‐cis isomer of literature‐known Me3P ⋅ PF2(C2F5)3 (5 a) was structurally characterized. Mixtures of the phosphorane PF2(C2F5)3 and the sterically encumbered NHCs tBu2Im, Dipp2Im, and Dipp2ImH2 (1,3‐bis‐(2,6‐di‐iso‐propylphenyl)‐imidazolidin‐2‐ylidene) (1 k) showed properties of FLPs (Frustrated Lewis Pairs) as these mixtures were able to open the ring of THF (tetrahydrofuran) to yield NHC−(CH2)4O−PF2(C2F5)3 6 i–k. Furthermore, the deprotonation of the weak C−H acids CH3CN, acetone, and ethyl acetate was achieved, which led to the formation of the corresponding imidazolium salts and the phosphates [PF2(C2F5)3(CH2CN)]− (7), [PF2(C2F5)3(OC(=CH2)CH3)]− (8) and [PF2(C2F5)3(CH2CO2Et)]− (9).

MAS NMR detection of hydrogen bonds for protein secondary structure characterization

Hydrogen bonds are essential for protein structure and function, making experimental access to long-range interactions between amide protons and heteroatoms invaluable. Here we show that measuring distance restraints involving backbone hydrogen atoms and carbonyl- or α-carbons enables the identification of secondary structure elements based on hydrogen bonds, provides long-range contacts and validates spectral assignments. To this end, we apply specifically tailored, proton-detected 3D (H)NCOH and (H)NCAH experiments under fast magic angle spinning (MAS) conditions to microcrystalline samples of SH3 and GB1. We observe through-space, semi-quantitative correlations between protein backbone carbon atoms and multiple amide protons, enabling us to determine hydrogen bonding patterns and thus to identify β-sheet topologies and α-helices in proteins. Our approach shows the value of fast MAS and suggests new routes in probing both secondary structure and the role of functionally-relevant protons in all targets of solid-state MAS NMR.

Single-chain folding of a quenched isotactic polypropylene chain through united atom molecular dynamics simulations

The single-chain folding of an isotactic polypropylene (iPP) chain through united atom (UA) molecular dynamics simulations under quenching was investigated using force fields (FFs) based on TraPPE-UA. We estimated the degree of local rigidity of the folded chain along iPP undergoing single-chain folding. To maintain the tacticity of iPP, we introduced improper torsional angle potentials and/or explicit hydrogen atoms bonded to backbone carbon atoms. In the simulation using modified TraPPE-UA FFs with added hydrogen atoms, folded structures were observed. In the cases using modified TraPPE-UA FFs with only improper torsional potentials, folding of the quenched iPP chain was not observed. Moreover, to clarify the folding behavior of the iPP chain, we studied the chirality of a single iPP chain and subsequently observed spontaneous chirality selection during the quenched folding process. We also examined the effect of the angle and torsional potentials of the added hydrogen on the folding behavior of a single iPP chain into local crystals. Therefore, we confirmed that the strength of the angle and torsional potentials contributed to the acceleration of the folding behavior.

Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers.

Coarse-grained (CG) polymer simulations can access longer times and larger lengths than all-atom (AA) molecular dynamics simulations; however, not all CG models correctly reproduce polymer properties on all length scales. Here we coarse-grain atomistic position data from polyethylene (PE) and polytetrafluoroethylene (PTFE) melt simulations by combining λ backbone carbon atoms in a single CG bead. Resulting CG variables have correlations along the chain backbone that depend on the coarse-graining scale λ and are generally not reproduced by independent bond-length, bond-angle and torsion-angle distributions. By constructing distributions of CG variables equivalent to those from simulated CG potentials we are able to evaluate the bond-orientation correlation for different CG models at reduced computational cost. CG models and potentials that include only nonbonded, bond-length, and bond-angle interactions computed by Boltzmann inversion correctly reproduce the CG variable distributions but do not necessarily reproduce the chain stiffness, overestimating the persistence length Lp and end-to-end distance ⟨ R2⟩1/2 with increasing λ. While CG models that include an independent torsion angle match the bond-orientation correlation and ⟨ R2⟩1/2 better, only approximate models that include correlations between bond and torsion angles match the true bond-orientation correlation.

Stiff and hierarchical chain nature of atactic and stereoregular poly(substituted methylene)s

AbstractIn this study, we estimated the chain nature of atactic and stereoregular poly(substituted methylene)s containing a phenylmethoxy side chain at each main‐chain backbone carbon atom using synchrotron X‐ray scattering to understand the topological and conformational properties of these rigid polymers. The atactic poly(substituted methylene) showed a linear chain nature. Contrastingly, the stereoregular poly(substituted methylene) exhibited a random coil structure. © 2018 Society of Chemical Industry

Selective catalytic reduction of NO in the presence of SO2 and O2: The poisoning effect of SOx under oxygen rich and lean conditions

SOx poisoning has been a critical problem in the chemistry of selective catalytic reduction of NOx, and many fundamental issues surrounding the reactions remain unclear. In this paper, reactions taking place in the 13C2H5OHNO-S18O2O2 system on a platinum single crystal surface were studied. Oxidation of 13C2H5OH by S18O2 proceeds mainly through 18O-H reaction, and oxidation of the backbone carbon atoms can occur at high S18O2 exposures, e.g., 1.6 Ls of S18O2 for 0.4 L of 13C2H5OH. Thus, the presence of S18O2 only slightly suppresses the catalytic reduction of NO by 13C2H5OH. Co-adsorbed O2 evidently exerts a suppressive effect. When oxygen is lean (relative to S18O2), the S18O2O2 reactions mainly give rise to surface sulphoxy species at temperatures between 400 and 500 K and thus, the NO-13C2H5OH reactions can still proceed. The NO reduction reaction is completely suppressed when oxygen is rich, a result of the Pt surface being passivated. This finding provides a valuable guide for optimizing the reaction atmosphere to improve the efficiency of the selective catalytic reduction of NO by hydrocarbons (or oxygen-containing fragments from oxidation of hydrocarbons in this case).

E[sbnd]H (E = N, O) bond activation by a nucleophilic palladium carbene

EH bond cleavage by [{PC(sp2)P}Pd(PMe3)] (1, PC(sp2)P = iPr2PC6H4CC6H4PiPr2) of alcohols led to a series of new square-planar tridentate palladium alkoxides, [{PC(sp3)HP}Pd(OiPr)] (3), [{PC(sp3)HP}Pd(OtBu)] (4), and [{PC(sp3)HP}Pd(OPh)] (5, PC(sp3)HP = bis[2-(di-iso-propylphosphino)phenyl]methyl). The analogous reaction with amines led to the formation of [{PC(sp3)HP}Pd(NPh2)] (6) and [{PC(sp3)HP}Pd(NHMes)] (7). The molecular structure of 7 was further probed by a CO2 insertion reaction into the PdN bond, yielding the corresponding carbamate 8. The molecular structures of 3–8 were determined by single-crystal X-ray diffraction and conform to the corresponding solution structures as determined by NMR spectroscopy. The reactivity of carbene 1 towards alcohols and amines is dictated by the nucleophilic/basic character at the carbene backbone carbon atom, the pKa and bond dissociation energy of the EH bond (E = N, O), and the steric properties of the organic substrates used.

Chain Folding Produces a Multilayered Morphology in a Precise Polymer: Simulations and Experiments.

Precise control over polymer architecture unlocks the potential for engineered self-assembled crystal structures with useful features on the nanometer length scale. Here we elucidate the structure of the ordered phase of a semicrystalline, functional polyethylene having a precise linear architecture, namely, pendant carboxylic acid groups precisely every 21st backbone carbon atom. By comparing the results of atomistic molecular dynamics simulations with experimental X-ray scattering and Raman spectroscopy data, we find that the polymer chains are folded in a hairpin manner near each carboxylic acid group, giving rise to multiple embedded layers of functional groups that have an interlayer distance of 2.5 nm. This is in contrast to other precise polyethylenes, where the chains are mostly trans within the crystals. Such layers could act as two-dimensional pathways for ionic or molecular transport given an appropriate choice of functional group.

Produce Molecular Brushes with Ultrahigh Grafting Density Using Accelerated CuAAC Grafting-Onto Strategy

A method was developed to synthesize molecular brushes with polymethacrylate backbone and ultrahigh density of grafted side chains (SCs), i.e., 1.34 SCs per backbone carbon atom, using accelerated copper-catalyzed azide–alkyne cycloaddition (CuAAC) grafting-onto strategy. This acceleration effect that benefits from the complexation of triazole with Cu was first confirmed in two model CuAAC reactions of (a) 1:1 molar ratio of a diazide compound and an alkynyl-terminated poly(ethylene oxide) (ay-PEO18 with average degree of polymerization DP = 18) and (b) 1:1 molar ratio of a dialkyne compound and an azido-terminated N3-PEO18. It was found that both model reactions produced ditriazoles as major products, although the former reaction exhibited a higher yield of PEO–PEO dimers, demonstrating better CuAAC acceleration effect. Following this principle, polymethacrylate backbones with multiazido dangling groups were subsequently used for grafting-onto reaction with ay-SCs to prepare an array of molecular brushes...

Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains.

The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M(β), is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from -1.8 to -2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature Tg where dynamic heterogeneity does not complicate the description of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔHa and entropy ΔSa of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a "critical" chain length, n ≈ 17. A close examination of this phenomenon indicates that a "buckling transition" from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔSa ∝ ΔHa, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔHa and ΔSa with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.

Thermotropic Behavior of Syndiotactic Polymethylenes with ω-[4-(trans-4-Pentylcyclohexyl)phenoxy]alkyloxycarbonyl Side Chains

A series of syndiotatic P5CPn polymethylenes was prepared with 4-(trans-4-pentylcyclohexyl)phenoxy moieties linked to each backbone carbon atom via an alkyloxycarbonyl spacer and with even numbers of alkyl carbons n ranging from 2 to 14, and their thermotropic behaviors were investigated. The P5CPn, except P5CP2, formed smectic phases in which the rod-like polymethylene backbones were arranged in rectangular lattices, and the side-chain mesogens were aggregated into layers parallel to the shorter sides of the rectangular lattices. The packing of the mesogens changed with decreasing temperature from smectic C-like to smectic I-like (SmI-like) for n = 4–8 and from smectic A-like to SmI-like for n = 10–14. In the SmI-like phases, each mesogen along the main-chain axis was connected to every sixth backbone carbon atom, revealing a correlation between the packing of the mesogens and the main-chain conformation of a 3/2 helix. Conversely, P5CP2 formed a smectic phase with the main chains arranged in rows and with the mesogens barely aggregated into layers due to the short spacers.

Influence of alkane chain length on adsorption on an α-alumina surface by MD simulations

Plasma surface techniques provide both an efficient and ecological tool for the functionalization of surfaces. Hence, a proper understanding of the plasma–surface interactions of precursors and radicals during the deposition process is of great importance. Especially during the initial deposition process, the deposition of molecules and fragments is difficult to investigate by experimental techniques and import insights can be obtained by molecular dynamics simulations. In this work, the reactive force field developed by the group of Kieffer at the University of Michigan was used to study the adsorption of single linear alkane chains on an α-alumina surface. The chain length was changed from 6 backbone carbon atoms to 16 carbon atoms, the deposition energy from 0.01 to 10eV and the incidence angle from 0° to 60° with respect to the surface normal. Results show that the adsorption depends a lot on the ratio of deposition energy to alkane chain length and the incidence angle. More grazing incidence reduces the adsorption probability and a low ratio of energy to chain length increases it.

A Statistical Overview of Experimentally Defined Anisotropic Displacement Parameters (ADP) Currently Deposited in the RCSB PDB

The potential of X-ray crystallography to provide information for protein dynamics has not yet been extensively investigated. In addition to atom XYZ coordinates, typical PDB files provide the temperature factor, also referred to as isotropic B-factor, which describes the magnitude of atomic fluctuations. Currently, approximately 5% (∼5500 unique pdb files) of the structures deposited in the RCSB PDB are high resolution (< 1.4 A). These high resolution structures generally provide an additional line for each atom entry, with the second containing a symmetric tensor with six integers that describes an ellipsoidal, instead of spherical, distribution of electron densities. Importantly, this asymmetric distribution of electron density reflects the anisotropic movement of the atomic nuclei. A diagonalization of this 3x3 tensor yields three eigenvalues (W1, W2, and W3), which define the distribution of electron density along those three prominent axes. The degree of anisotropy is defined as the ratio of W1 to W3 and varies between 0 (extremely anisotropic, like a rod or a pancake) and 1 (a sphere). Our preliminary analysis over the ADPs derived from ∼1500 high resolution structures revealed that interestingly, the backbone carbon atoms are more anisotropic than the C-α and C-β atoms. The C-α atoms show the lowest degree of anisotropy, and proceeding out along the side chain from C-α to C-e, the degree of anisotropy gradually increases. We also analyzed the trend of isotropic B-factors. Indeed, the value of isotropic B-factors increases outward from the backbone C to the C-e atom. In summary, we performed a statistical analysis over the ADPs of structures in the RCSB PDB, with the aim to obtain useful information in order to gain a better understanding of the physical basis of ADP.

Radiation effects on crystalline l-asparagine, revisited: Radical formation by EMR and periodic DFT after X-irradiation at 275 K

Radical formation by X-irradiation of single crystals of l-asparagine monohydrate at 275K has been investigated at 240K and 295K using Electron Paramagnetic Resonance (EPR), Electron Nuclear DOuble Resonance (ENDOR) and ENDOR-Induced EPR spectroscopic techniques. Free radical structures suggested by detailed analysis of the experimental data were assessed by Density Functional Theory calculations in a periodic approach. The combined experimental and computational evidence revealed three stable radical species at room temperature. Two of these could reliably be established as net H-abstracted species, one from the methylene group in the amino acid side chain and the second from the amino acid back-bone carbon atom. For the third room temperature radical species, a variety of deamination- and decarboxylation products were investigated and dismissed. Even if an unambiguous structure could not be established, this radical is tentatively suggested to descend from a side-chain O3-protonated amide anion by hydrogen atom transfer from the C3 to the C4 position.

Elucidation of pseurotin biosynthetic pathway points to trans-acting C-methyltransferase: generation of chemical diversity.

Pseurotins comprise a family of structurally related Aspergillal natural products having interesting bioactivity. However, little is known about the biosynthetic steps involved in the formation of their complex chemical features. Systematic deletion of the pseurotin biosynthetic genes in A. fumigatus and in vivo and in vitro characterization of the tailoring enzymes to determine the biosynthetic intermediates, and the gene products responsible for the formation of each intermediate, are described. Thus, the main biosynthetic steps leading to the formation of pseurotin A from the predominant precursor, azaspirene, were elucidated. The study revealed the combinatorial nature of the biosynthesis of the pseurotin family of compounds and the intermediates. Most interestingly, we report the first identification of an epoxidase C-methyltransferase bifunctional fusion protein PsoF which appears to methylate the nascent polyketide backbone carbon atom in trans.

Elucidation of Pseurotin Biosynthetic Pathway Points to Trans‐Acting C‐Methyltransferase: Generation of Chemical Diversity

AbstractPseurotins comprise a family of structurally related Aspergillal natural products having interesting bioactivity. However, little is known about the biosynthetic steps involved in the formation of their complex chemical features. Systematic deletion of the pseurotin biosynthetic genes in A. fumigatus and in vivo and in vitro characterization of the tailoring enzymes to determine the biosynthetic intermediates, and the gene products responsible for the formation of each intermediate, are described. Thus, the main biosynthetic steps leading to the formation of pseurotin A from the predominant precursor, azaspirene, were elucidated. The study revealed the combinatorial nature of the biosynthesis of the pseurotin family of compounds and the intermediates. Most interestingly, we report the first identification of an epoxidase C‐methyltransferase bifunctional fusion protein PsoF which appears to methylate the nascent polyketide backbone carbon atom in trans.

Design of Thermally Stable Amine–Imine Nickel Catalyst Precursors for Living Polymerization of Ethylene: Effect of Ligand Substituents on Catalytic Behavior and Polymer Properties

Nickel complexes bearing amine-imine ligands with various backbone substituents were synthesized and employed as ethylene polymerization catalysts on activation with Et2 AlCl. The substituent on the backbone carbon atom of the amine moiety is decisive for the living nature of ethylene polymerization. A bulky amine-imine nickel precursor with a tert-butyl group on the carbon atom of the amine group can polymerize ethylene in a living fashion at an elevated temperature of 65 °C, which is the highest temperature of living polymerization of ethylene with late transition-metal catalysts. The wide applicable temperature range for living polymerization and sensitivity of the branch structure of the polyethylene to temperature enable precise synthesis of di- and triblock polyethylenes featuring different branched segments by sequential tuning of the polymerization temperature.

Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s(-1), yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

Local Segmental Dynamics and Stresses in Polystyrene–C60 Mixtures

The polymer dynamics of homogeneous C$_{60}$-polystyrene mixtures in the molten state are studied via molecular simulations using two interconnected levels of representation for polystyrene nanocomposites: (a) A coarse-grained representation, in which each polystyrene repeat unit is mapped into a single "superatom" and each fullerene is viewed as a spherical shell. Equilibration of coarse-grained polymer-nanoparticle systems at all length scales is achieved via connectivity-altering Monte Carlo simulations. (b) An atomistic representation, where both nanoparticles and polymer chains are represented in terms of united-atom forcefields. Initial configurations for atomistic Molecular Dynamics (MD) simulations are obtained by reverse mapping well-equilibrated coarse-grained configurations. By analyzing MD trajectories under constant energy, the segmental dynamics of polystyrene (for neat and filled systems) is characterized in terms of bond orientation time autocorrelation functions. Nanocomposite systems are found to exhibit slightly slower segmental dynamics than the unfilled ones, in good agreement with available experimental data. Moreover, by employing Voronoi tessellation of the simulation box, the mean-squared displacement of backbone carbon atoms is quantified in the vicinity of each fullerene molecule. Fullerenes are found to suppress the average motion of polymeric chains, in agreement with neutron scattering data, while slightly increasing the dynamic and stress heterogeneity of the melt. Atomic-level and local (per Voronoi cell) stress distributions are reported for the pure and the filled systems.