What are the enthalpy of formation and the stabilization energy of acrolein?

Acrolein (propenal) is a ubiquitous compound in the global environment with diverse deleterious ramifications for human health. Despite its importance, its measured enthalpy of formation is still contentious. Using high level quantum chemical calculations, we recommend a consensus value of ?65 ± 3 kJ mol^?1 for the gas phase species. Comparison is made with the other “acrylo” species, acrylonitrile and acrylic acid, and to other conjugated species such as butadiene and crotonaldehyde.     

What are the limits to the size of effective dynamic combinatorial libraries?

Using simple computer simulations of model dynamic combinatorial libraries, we show that the best binders can be amplified to useful concentrations in libraries containing 10-10(6) compounds. [structure: see text]     

Competition of Ligands and the 18-mer Binding Domain of the RHAU Helicase for G-Quadruplexes: Orthosteric or Allosteric Binding Mechanism?

Stabilizing the DNA and RNA structures known as G-quadruplexes (G4s) using specific ligands is a strategy that has been proposed to fight cancer. However, although G-quadruplex:ligand (G4:L) interactions have often been investigated, whether or not ligands are able to disrupt G-quadruplex:protein (G4:P) interactions remains poorly studied. In this study, using native mass spectrometry, we have investigated ternary G4:L:P complexes formed by G4s, some of the highest affinity ligands, and the binding domain of the RHAU helicase. Our results suggest that RHAU binds not only preferentially to parallel G4s, but also to free external G-quartets. We also found that, depending on the G4, ligands could prevent the binding of the peptide, either by direct competition for the binding sites (orthosteric inhibition) or by inducing conformational changes (allosteric inhibition). Notably, the ligand Cu–ttpy (ttpy=4′-tolyl-2,2′:6′,2′′-terpyridine) induced a conformational change that increased the binding of the peptide. This study illustrates that it is important to not only characterize drug–target interactions, but also how the binding to other partners is affected.     

Does the DNA Binding Mode of a Molecule Affect its Ability to Interact With Singlet Oxygen?

Singlet oxygen is known to be a potent mutagenic agent and several biologically relevant molecules have been proposed to act as scavengers for this noxious species. However, numerous studies have been conducted in homogenous solution and the reactivity of singlet oxygen scavengers known to bind DNA has never been investigated in double-stranded DNA. In the following paper, we present the results obtained regarding the interaction between 4',6-diamidino-2-phenylindole (DAPI) and singlet oxygen. We show the molecule to be a potent scavenger of singlet oxygen in aqueous solution with an absolute rate constant (chemical and physical quenching of singlet oxygen) of (1.7 ± 0.3) × 10⁷  m ⁻¹ s⁻¹. In addition, we demonstrate that the binding mode of a singlet oxygen scavenger to DNA can strongly influence its reactivity toward singlet oxygen. In the case of DAPI, while the molecule exhibits a chemical reaction with singlet oxygen when the molecule is free in aqueous solution or intercalated in GC sequences of DNA, DAPI becomes chemically unreactive toward singlet oxygen when bound in the minor groove of DNA AT sequences.     

What tunes the structural anisotropy of magnetic fluids under a magnetic field?

In the present study, the structure of monophasic ionic magnetic fluids under a static magnetic field is explored. In these aqueous electrostatically stabilized ferrofluids, we vary both the isotropic interparticle interactions and the anisotropic dipolar magnetic interaction by tuning the ionic strength and the size of the nanoparticles. Small angle neutron scattering measurements carried out on nanoparticles dispersed in light water exhibit miscellaneous 2D nuclear patterns under a magnetic field with various q-dependent anisotropies. In this nondeuterated solvent where the magnetic scattering is negligible, this anisotropy originates from an anisotropy of the structure of the dispersions. Both the low q region and the peak of the structure factor can be anisotropic. On the scale of the interparticle distance, the structure is better defined in the direction perpendicular to the field. In the thermodynamic limit (q-->0), the model previously described in ref 10 matches the data without any fitting parameters: the interparticle interaction is more repulsive in the direction parallel to the magnetic field. At low q, the amplitude of the anisotropy of the pattern is governed by the ratio of two interaction parameters: the reduced parameter of the anisotropic magnetic dipolar interaction, gamma/Phi, over the isotropic interaction parameter, , in zero field, which is proportional to the second virial coefficient.     

What are the relative steric demands of carboxyl and methyl groups?

The relative steric demands of carboxyl and methyl groups are compared by contrasting the difference quantity H _f ^o (g, ArCOOH) — H _f ^o (g, ArCH₃) for a collection of alkylated benzoic acids and toluenes with the value for Ar=C₆H₅, the archetypical (i.e., unsubstituted) benzoic acid and toluene. We conclude that carboxyl and methyl groups are nearly the same size.     

‘Apples’ and ‘oranges’: comparing the structural aspects of biomineral- and ice-interaction proteins

The title of this review describes structural comparisons of protein classes whose task is to identify and interact with biological solids (minerals and ice). To date, the following trends have been noted: (1) biomineral-interaction proteins typically adopt unfolded, open conformations, and, where mineral binding motifs have been identified, these sequences exhibit structural trends towards extended, random coil, or other unstable secondary structures; (2) ice-interaction proteins typically adopt folded structures, featuring stable secondary structure preferences (α-helix, β-sheet, β-helix, etc.) and stable, planar ice binding motifs that exploit hydrophobicity and van der Waals’ interactions for ice binding.     

What are the practical limits for the specific surface area and capacitance of bulk sp~2 carbon materials?

The possible practical limits for the specific surface area and capacitance performance of bulk sp~2 carbon materials were investigated experimentally and theoretically using a variety of carbon materials. We find the limit for the specific surface area to be 3500–3700 m~2 g~(-1), and based on this, the corresponding best capacitance was predicted for various electrolyte systems. A model using an effective ionic diameter for the electrolyte ions was proposed and used to calculate the theoretical capacitance. A linear dependence of experimental capacitance versus effective specific surface area of various sp~2 carbon materials was obtained for all studied ionic liquid, organic and aqueous electrolyte systems. Furthermore, excellent agreement between the theoretical and experimental capacitance was observed for all the tested sp~2 carbon materials in these electrolyte systems, indicating that this model can be applied widely in the evaluation of various carbon materials for supercapacitors.     

Binding Mode Multiplicity and Multiscale Chirality in the Supramolecular Assembly of DNA and a π-Conjugated Polymer

Water-soluble π-conjugated polymers are increasingly considered for DNA biosensing. However, the conformational rearrangement, supramolecular organization and dynamics upon interaction with DNA have been overlooked, which prevents the rational design of such detection tools. To elucidate the binding of a cationic polythiophene (CPT) to DNA with atomistic resolution, we performed molecular simulations of their supramolecular assembly. Comparison of replicated simulations show a multiplicity of CPT binding geometries that contribute to the wrapping of CPT around DNA. The different binding geometries are stabilized by both electrostatic interactions between CPT lateral cations and DNA phosphodiesters and van der Waals interactions between the CPT backbone and the DNA grooves. Simulated circular dichroism (CD) spectra show that the induced CD signal stems from a conserved geometrical feature across the replicated simulations, i. e. the presence of segments of syn configurations between thiophene units along the CPT chain. At the macromolecular scale, we inspected the different shapes related to the CPT binding modes around the DNA through symmetry metrics. Altogether, molecular dynamics (MD) simulations, model Hamiltonian calculations of the CD spectra, and symmetry indices provide insights into the origin of induced chirality from the atomic to the macromolecular scale. Our multidisciplinary approach points out the hierarchical aspect of CPT chiral organization induced by DNA.     

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ significantly in regard to the nonbonded parameters for polar functional groups and their ability to reproduce the correct solvation and partitioning behavior of small molecular analogues of the amino acid side chains. Despite the differences in the force field parameters no major differences could be detected in a wide range of structural properties such as the root-mean-square deviation from the experimental structure, radii of gyration, solvent accessible surface, secondary structure, or hydrogen bond propensities on a 5 to 10 ns time scale. The small differences that were observed correlated primarily with the presence of charged residues as opposed to residues that differed most between the parameter sets. The work highlights the variation that can be observed in nanosecond simulations of protein systems and implications of this for force field validation, as well as for the analysis of protein simulations in general.     

What governs the charge transfer in DNA? The role of DNA conformation and environment

Charge transfer in DNA has received much attention in the last few years due to its role in oxidative damage and repair in DNA and also due to possible applications of DNA in nanoelectronics. Despite intense experimental and theoretical efforts, the mechanism underlying long-range hole transport is still unresolved. This is in particular due to the sensitive dependence of charge transfer on the complex structure and dynamics of DNA and the interaction with the solvent, which could not be addressed adequately in the modeling approaches up to now. In this work, we study the factors governing hole transfer in detail, using a DFT-based fragment-orbital method, which allows to compute the charge transfer parameters along multinanosecond molecular dynamics simulations. Environmental effects are captured using a hybrid quantum mechanics-molecular mechanics (QM/MM) coupling scheme. This methodology allows to analyze several factors responsible for charge transfer in DNA in detail. The fluctuation of counterions, strongly counterbalanced by the surrounding water, leads to large oscillations of onsite energies, which govern the energetics of hole propagation along the DNA strand. In contrast, the electronic couplings depend only on DNA conformation and are not affected by the solvent. In particular, the onsite energies are strongly correlated between neighboring nucleobases, indicating that a conformational-gating type of mechanism may be induced by the collective environmental degrees of freedom.     

Chemo-enzymatic Synthesis and RAFT Polymerization of 6-O-Methacryloyl Mannose: A Suitable Glycopolymer for Binding to the Tetrameric Lectin Concanavalin A?

Summary: The chemo-enzymatic synthesis of 6-O-methacryloyl mannose (MaM) glycomonomer was successfully performed for the first time. Subsequent aqueous RAFT polymerization of the monomer yielded well-defined, linear poly(6-O-methacryloyl mannose) (PMaM) glycopolymers without the need for protecting and deprotecting group chemistry. As well as investigating the RAFT polymerization kinetics of this monomer using various initial monomer to chain transfer agent concentration ratios, the protein binding ability of the generated glycopolymer was tested using concanavalin A, a known mannose-residue binding lectin.     

The reductionist paradox: are the laws of chemistry and physics sufficient for the discovery of new drugs?

Reductionism is alive and well in drug-discovery research. In that tradition, we continually improve experimental and computational methods for studying smaller and smaller aspects of biological systems. Although significant improvements continue to be made, are our efforts too narrowly focused? Suppose all error could be removed from these methods, would we then understand biological systems sufficiently well to design effective drugs? Currently, almost all drug research focuses on single targets. Should the process be expanded to include multiple targets? Recent efforts in this direction have lead to the emerging field of polypharmacology. This appears to be a move in the right direction, but how much polypharmacology is enough? As the complexity of the processes underlying polypharmacology increase will we be able to understand them and their inter-relationships? Is “new” mathematics unfamiliar in much of physics and chemistry research needed to accomplish this task? A number of these questions will be addressed in this paper, which focuses on issues and questions not answers to the drug-discovery conundrum.     

Synergic Binding of Carbon Monoxide and Cyanide to the FeMo Cofactor of Nitrogenase: Relic Chemistry of an Ancient Enzyme?

The first electrochemical and infra-red data on the binding of cyanide to the isolated iron-molybdenum cofactor of nitrogenase, FeMoco, is described. It is shown that cyanide stabilises a hitherto unrecognised, low-spin, EPR-active (S= 1/2), superoxidised form of FeMoco, and we provide the first evidence that carbon monoxide and cyanide bind synergically to the oxidised and semireduced states of the isolated cofactor, states which are unreactive to carbon monoxide alone.