Lysozyme adsorption on polyethylene surfaces: why are long simulations needed?

The adsorption of lysozyme onto a polyethylene (PE) surface in an aqueous environment was investigated via molecular dynamics (MD) simulation. The adsorption can be divided into three processes: diffusion to the surface, dehydration induced by hydrophobic surface-protein interactions, and denaturation. The dehydration process is very long, around 70 ns. Structural deformations start soon after the protein reaches the surface and continue during the whole trajectory. The hydrophobic residues are slowly driven toward the surface, inducing changes in the protein's secondary structure. The protein's secondary structural components near the surface are more disturbed than those farther away from the surface. The lysozyme is adsorbed with its long axis parallel to the surface and displays an anisotropic mobility on the surface that is probably due to the intrinsic structure of the PE surface. Our study demonstrates the need for long-time atomistic simulation in order to gain a complete understanding of the adsorption process.     

Does the TauD Enzyme Always Hydroxylate Alkanes, While an Analogous Synthetic Non-Heme Reagent Always Desaturates Them?

This theoretical work addresses the mechanistic switch between hydroxylase (alcohol formation) and desaturase (olefin formation) activities during alkane oxidation by two non-heme high-valent oxoiron reagents, the enzyme taurine:α-ketoglutarase dioxygenase (TauD) and the synthetic shape-selective catalyst (TpOBzFe), toward cyclohexadiene, cyclohexane, cyclopentane, and ethane. As we show, the desaturase/hydroxylase steps obey unique orbital selection rules, and the mechanistic switch is determined by intrinsic reactivity factors that depend on the ligand-sphere flexibility of the oxoiron species, the substrate, and the spin states of the reaction pathways. Testable predictions are outlined.     

The Nature of the Fourth Bond in the Ground State of C2: The Quadruple Bond Conundrum

Does, or doesn’t C₂ break the glass ceiling of triple bonding? This work provides an overview on the bonding conundrum in C₂ and on the recent discussions regarding our proposal that it possesses a quadruple bond. As such, we focus herein on the main point of contention, the 4th bond of C₂, and discuss the main views. We present new data and an overview of the nature of the 4th bond—its proposed antiferromagnetically coupled nature, its strength, and a derivation of its bond energy from experimentally based thermochemical data. We address the bond‐order conundrum of C₂ arising from generalized VB (GVB) calculations by comparing it to HC?CH, and showing that the two molecules behave very similarly, and C₂ is in no way an exception. We analyse the root cause of the deviation of C₂ from the Badger Rule, and demonstrate that the reason for the smaller force constant (FC) of C₂ relative to HC?CH has nothing to do with the bond energies, or with the number of bonds in the two molecules. The FC is determined primarily by the bond length, which is set by the balance between the bond length preferences of the σ‐ versus π‐bonds in the two molecules. This interplay in the case of C₂ clearly shows the fingerprints of the 4th bond. Our discussion resolves the points of contention and shows that the arguments used to dismiss the quadruple bond nature of C₂ are not well founded.     

Topology of Electron Charge Density for Chemical Bonds from Valence Bond Theory: A Probe of Bonding Types

Covalent, ionic, or something new? A new interpretation of the topology of the electron density at the bond critical point is proposed to characterize covalent, ionic, and charge‐shift bonding from the density point of view (see figure). The topological properties of the density representation confirm the reality of charge‐shift bonds, in which the covalent contribution is weak or repulsive, and most of the bonding is due to the covalent–ionic resonance energy.

     

Enhanced Reactivities of Iron(IV)‐Oxo Porphyrin π‐Cation Radicals in Oxygenation Reactions by Electron‐Donating Axial Ligands

The proximal axial ligand in heme iron enzymes plays an important role in tuning the reactivities of iron(IV)‐oxo porphyrin π‐cation radicals in oxidation reactions. The present study reports the effects of axial ligands in olefin epoxidation, aromatic hydroxylation, alcohol oxidation, and alkane hydroxylation, by [(tmp)^+. Fe^IV(O)(p‐Y‐PyO)]⁺ ( 1 ‐Y) (tmp=meso‐tetramesitylporphyrin, p‐Y‐PyO=para‐substituted pyridine N‐oxides, and Y=OCH₃, CH₃, H, Cl). In all of the oxidation reactions, the reactivities of 1 ‐Y are found to follow the order 1 ‐OCH₃ > 1 ‐CH₃ > 1 ‐H > 1 ‐Cl; negative Hammett ρ values of ?1.4 to ?2.7 were obtained by plotting the reaction rates against the σ_p values of the substituents of p‐Y‐PyO. These results, as well as previous ones on the effect of anionic nucleophiles, show that iron(IV)‐oxo porphyrin π‐cation radicals bearing electron‐donating axial ligands are more reactive in oxo‐transfer and hydrogen‐atom abstraction reactions. These results are counterintuitive since iron(IV)‐oxo porphyrin π‐cation radicals are electrophilic species. Theoretical calculations of anionic and neutral ligands reproduced the counterintuitive experimental findings and elucidated the root cause of the axial ligand effects. Thus, in the case of anionic ligands, as the ligand becomes a better electron donor, it strengthens the FeO? H bond and thereby enhances its H‐abstraction activity. In addition, it weakens the Fe?O bond and encourages oxo‐transfer reactivity. Both are Bell–Evans–Polanyi effects, however, in a series of neutral ligands like p‐Y‐PyO, there is a relatively weak trend that appears to originate in two‐state reactivity (TSR). This combination of experiment and theory enabled us to elucidate the factors that control the reactivity patterns of iron(IV)‐oxo porphyrin π‐cation radicals in oxidation reactions and to resolve an enigmatic and fundamental problem.     

A High Token Indicativity Account of Knowledge

In this paper, I provide a probabilistic account of factual knowledge, based on the notion of chance, which is a function of an event (or a fact — I will use ‘fact’ to cover both) given a prior history. This account has some affinity with my chance account of token causation, but it neither relies on it nor presupposes it. Here, I concentrate on the core cases of perceptual knowledge and of knowledge by memory (based on perception). (The account can be extended to the other modes of knowledge, but not in this paper.) The analysis of knowledge presented below is externalist. The underlying intuition guiding the treatment of knowledge in this paper is that knowledge boils down to high token discriminative indicativeness. Type indicativeness or type discriminability are neither necessary nor sufficient for knowledge: the token aspect comes out in the strong dependence on the specific circumstances and chances of the case. The main condition of the first section, the indicativity condition (KI), properly refined, yields pertinent (token) indicativity as a main constituent. Very roughly, it involves the chance of the content clause p being higher given the subject's believing that p than otherwise. The discriminability condition in question (section 3) captures the sense of discriminability appropriate for knowledge and yield the indicativity condition: it is an extension of the indicativity condition KI. Roughly, the subject’s ability to discriminate the object in front of her being red from its being green is captured by holding fixed, in the indicativity condition, the condition “the object in front of her is red or green.” A major element in the analysis is the so-called Contrast Class, which governs the scope of discriminability. This is the class of features that have to be taken into account in the discriminability condition, and it is characterized by two constraints. Very roughly, according to the first constraint, for a feature to be in the contrast class, it must not represent a sub-type of (the feature specified by) the predicate in the content clause. According to the second constraint, which is a central condition with many implications, the chance that the object specified in the content clause has a feature represented in the contrast class must not under the circumstances be too low. This constraint, within the framework of the discriminability condition, brings out a major constitutive aspect of knowledge: knowledge amounts to a limited vulnerability to mistakes of the belief in question under the circumstances at hand. The contrast class plays a major role in my treatment of skepticism. The second constraint on the Contrast Class together with the VHP condition below bring out precisely the way in which perceptual knowledge is fallible.     

The Periodic‐Table—A Universal Icon: Its Birth 150 Years Ago,and Its Popularization Through Literature Art and Music

This Essay projects the spark of genius of Mendeleev, whose efforts led to the effective formulation of the periodic table, which has placed the entire world of chemical matter on a palm. The periodic table gave rise to a central paradigm, which did for chemistry what Newton had done for physics and Darwin for biology. Subsequently the Essay recounts the popularization of the Periodic Table through literature by Primo Levi, Oliver Sacks and others, and through music and art by composers and artists, such as Jerry Feldman, the King Crimson band, Tom Lehrer, and George Brecht, Blair Bradshaw, Eugènia Balcells, etc.     

A Case Study of a Non-Compensatory Approach to Ranking Transportation Projects

This paper examines the use of a concordance-type model for prioritizing transportation projects. In the particular case examined, multiple criteria are involved, and projects can be rated only on a qualitative basis. The model augments the well-known ELECTRA methodology with a tournament ranking procedure. The resulting procedure, known as SELECTRA, is presently being used to rank order over 200 investment projects within the Ontario Ministry of Transportation and Communications.