Measuring the transition between nonhyperbolic and hyperbolic regimes in open Hamiltonian systems

Nonlinear Dynamics - We show that the presence of KAM islands in nonhyperbolic chaotic scattering has deep implications on the unpredictability of open Hamiltonian systems. When the energy of the...     

Spatially restricted Double Z-Simplified Box Orbital basis sets: Optimization and comparison with some standard basis sets

As part of previous studies, we introduced a new type of basis function named Simplified Box Orbitals (SBOs) that belong to a class of spatially restricted functions which allow the zero differential overlap (ZDO) approximation to be applied with complete accuracy. The original SBOs and their Gaussian expansions SBO-3G form a minimal basis set, which was compared to the standard Slater-type orbital basis set (STO-3G). In the present paper, we have developed the SBO basis functions at double-zeta (DZ) level, and we have assessed the option of expanding the SBO-DZ as a combination of Gaussian functions. Finally, we have determined the quality of the new basis set by comparing the molecular properties calculated with SBO-nG with those achieved with some standard basis sets.     

Fractional damping enhances chaos in the nonlinear Helmholtz oscillator

Nonlinear Dynamics - The main purpose of this paper is to study both the underdamped and the overdamped dynamics of the nonlinear Helmholtz oscillator with a fractional-order damping. For that...     

Mechanism of [3+2] Cycloaddition of Alkynes to the [Mo3S4(acac)3(py)3][PF6] Cluster

A study, involving kinetic measurements on the stopped‐flow and conventional UV/Vis timescales, ESI‐MS, NMR spectroscopy and DFT calculations, has been carried out to understand the mechanism of the reaction of [Mo₃S₄(acac)₃(py)₃][PF₆] ([ 1 ]PF₆; acac=acetylacetonate, py=pyridine) with two RC?CR alkynes (R=CH₂OH (btd), COOH (adc)) in CH₃CN. Both reactions show polyphasic kinetics, but experimental and computational data indicate that alkyne activation occurs in a single kinetic step through a concerted mechanism similar to that of organic [3+2] cycloaddition reactions, in this case through the interaction with one Mo(μ‐S)₂ moiety of [ 1 ]⁺. The rate of this step is three orders of magnitude faster for adc than that for btd, and the products initially formed evolve in subsequent steps into compounds that result from substitution of py ligands or from reorganization to give species with different structures. Activation strain analysis of the [3+2] cycloaddition step reveals that the deformation of the two reactants has a small contribution to the difference in the computed activation barriers, which is mainly associated with the change in the extent of their interaction at the transition‐state structures. Subsequent frontier molecular orbital analysis shows that the carboxylic acid substituents on adc stabilize its HOMO and LUMO orbitals with respect to those on btd due to better electron‐withdrawing properties. As a result, the frontier molecular orbitals of the cluster and alkyne become closer in energy; this allows a stronger interaction.     

The Plasticity of the Carbohydrate Recognition Domain Dictates the Exquisite Mechanism of Binding of Human Macrophage Galactose-Type Lectin

The human macrophage galactose-type lectin (MGL), expressed on macrophages and dendritic cells (DCs), modulates distinct immune cell responses by recognizing N-acetylgalactosamine (GalNAc) containing structures present on pathogens, self-glycoproteins, and tumor cells. Herein, NMR spectroscopy and molecular dynamics (MD) simulations were used to investigate the structural preferences of MGL against different GalNAc-containing structures derived from the blood group A antigen, the Forssman antigen, and the GM2 glycolipid. NMR spectroscopic analysis of the MGL carbohydrate recognition domain (MGL-CRD, C181-H316) in the absence and presence of methyl α-GalNAc (α-MeGalNAc), a simple monosaccharide, shows that the MGL-CRD is highly dynamic and its structure is strongly altered upon ligand binding. This plasticity of the MGL-CRD structure explains the ability of MGL to accommodate different GalNAc-containing molecules. However, key differences are observed in the recognition process depending on whether the GalNAc is part of the blood group A antigen, the Forssman antigen, or GM2-derived structures. These results are in accordance with molecular dynamics simulations that suggest the existence of a distinct MGL binding mechanism depending on the context of GalNAc moiety presentation. These results afford new perspectives for the rational design of GalNAc modifications that fine tune MGL immune responses in distinct biological contexts, especially in malignancy.     

Chemistry of Lipid A: At the Heart of Innate Immunity

In many Gram‐negative bacteria, lipopolysaccharide (LPS) and its lipid A moiety are pivotal for bacterial survival. Depending on its structure, lipid A carries the toxic properties of the LPS and acts as a potent elicitor of the host innate immune system via the Toll‐like receptor 4/myeloid differentiation factor 2 (TLR4/MD‐2) receptor complex. It often causes a wide variety of biological effects ranging from a remarkable enhancement of the resistance to the infection to an uncontrolled and massive immune response resulting in sepsis and septic shock. Since the bioactivity of lipid A is strongly influenced by its primary structure, a broad range of chemical syntheses of lipid A derivatives have made an enormous contribution to the characterization of lipid A bioactivity, providing novel pharmacological targets for the development of new biomedical therapies. Here, we describe and discuss the chemical aspects regarding lipid A and its role in innate immunity, from the (bio)synthesis, isolation and characterization to the molecular recognition at the atomic level.     

Kinetics studies of 5-methyl-2-hexanol, 2,2-dimethyl-3-hexanol,and 2,4,4-trimethyl-1-pentanol with chlorine atoms: Photooxidation mechanism of 2,4,4-trimethyl-1-pentanol

The rate constants for the reaction between chlorine atoms and either 5-methyl-2-hexanol, 2,2-dimethyl-3-hexanol, or 2,4,4-trimethyl-1-pentanol at 298 K were determined using the relative method with 2-butanol and 1-pentanol as reference compounds. The values obtained for 5-methyl-2-hexanol, 2,2-dimethyl-3-hexanol, and 2,4,4-trimethyl-1-pentanol (k × 10¹⁰ cm³ molec⁻¹ s⁻¹) were, respectively, (2.64 ± 0.5), (2.72 ± 0.5), and (2.50 ± 0.4), in agreement with the values of the rate constants reported in bibliography for similar alcohols and the values estimated by structure activity relationship methods. The photooxidation products of 2,4,4-trimethyl-1-pentanol initiated by chlorine atoms were identified (formaldehyde, 2-propanone, 2,2-dimethyl propanal, 4,4,-dimethyl-2-pentanone, and 3,3-dimethylbutanal), and the reaction mechanism was determined.     

Cp*RuCl-Vinyl Carbenes: Two Faces and the Bifunctional Role in Catalytic Processes

Ruthenium vinyl carbenes derived from Cp/Cp*RuCl-based complexes (Cp=cyclopentadiene, Cp*=1,2,3,4,5-pentamethylcyclopentadiene) have been routinely invoked as key intermediates in tandem reactions involving a carbene/alkyne metathesis (CAM). A priori, these intermediates resemble the Grubbs-type family of catalysts, but they exhibit a completely different reactivity pattern that few, if any, other catalytic system can reproduce so far. The reactivity of these species with α-unsubstituted and α-substituted alkynals showcases the peculiarities of these intermediates. Although Z-vinyl dihydrooxazines are preferentially obtained with the former, Z-vinyl epoxypyrrolidines are obtained with the latter. A combination of spectroscopic and computational data now prove that a η³-coordination mode of the ruthenium vinyl carbene and the presence of a Lewis basic chloride ligand give rise to two markedly different stereoelectronic faces, which are responsible for the unconventional reactivity of these species.