'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks.

N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit -Man3GlcNAc2- lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal -GlcNAc-GlcNAc- unit acts as a rigid rod, while the central, and unusual, -Man-ß-1,4-GlcNAc- linkage is more flexible and is modulated by the distal Man-α-1,3- and Man-α-1,6- branching units. Solvation stiffens the 'rod' but leaves the distal residues flexible, through a ß-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies.

Reduced dimensionality spin-orbit dynamics of CH3 + HCl ⇌ CH4 + Cl on ab initio surfaces.

A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH(3) + HCl ⇌ CH(4) + Cl((2)P(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions.

An improved treatment of spectator mode vibrations in reduced dimensional quantum dynamics: application to the hydrogen abstraction reactions mu + CH4, H + CH4, D + CH4, and CH3 + CH4.

A method for projecting chemical reaction surface coordinates from a Hessian in curvilinear internal coordinates has recently been developed. Here we introduce a modification to this approach which allows for analytical evaluation of the necessary coordinate derivatives, thus reducing the number of ab initio calculations required. We apply this method to the determination of spectator mode frequencies and zero-point energies for the series of hydrogen abstraction reactions X + CH(4) --> XH + CH(3), X = muonium (mu), H, D, CH(3). Comparison of these frequencies with those obtained using rectilinear coordinates allows us to examine how the mass of X affects the coordinate sensitivity of the spectator modes. We carry out two-dimensional quantum reactive scattering calculations for these reactions to highlight instances where the choice of coordinates may have a significant impact on the evaluated thermal rate constants.

Reduced dimensionality quantum dynamics of CH3 + CH4 --> CH4 + CH3: symmetric hydrogen exchange on an Ab initio potential.

The symmetric title reaction CH(3) + CH(4) --> CH(4) + CH(3) is studied using quantum scattering theory. Quantum dynamics calculations are performed in hyperspherical coordinates with a two-dimensional effective potential energy surface consisting of an analytical 18-parameter double Morse function fit to ab initio data at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. Spectator modes are treated adiabatically by inclusion of projected zero-point energy corrections in the effective potential. The close-coupled equations are solved via R-matrix propagation. Energy and J-shifted thermal rate constants are compared to experimental data and highlight the importance of quantum tunneling. Oscillating reactivity and metastable bound state resonances are observed in the cumulative and state-to-state reaction probabilities. State-to-state differential and initial state-selected integral cross sections are presented and discussed. Primary and secondary kinetic isotope effects for two symmetric deuterated variants of the title reaction are also presented.