Performance Test of Multicomponent Quantum Mechanical Calculation with Polarizable Continuum Model for Proton Chemical Shift

Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid ¹H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5′-monophospho-<i>N</i>-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S_N1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP

Strong Hydrogen Bonds at the Interface between Proton-Donating and -Accepting Self-Assembled Monolayers on Au(111)

Hydrogen-bonding heterogeneous bilayers on substrates have been studied as a base for new functions of molecular adlayers by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and density functional theory (DFT) calculations. Here, we report the formation of the catechol-fused bis­(methyl­thio)­tetra­thia­ful­valene (H₂Cat-BMT-TTF) adlayer hydrogen bonding with an imidazole-terminated alkanethiolate self-assembled monolayer (Im-SAM) on Au(111). The heterogeneous bilayer is realized by sequential two-step immersions in solutions for the individual Im-SAM and H₂Cat-BMT-TTF adlayer formations. In the measurements by AFM, a grained H₂Cat-BMT-TTF adlayer on Im-SAM is revealed. The coverage and the chemical states of H₂Cat-BMT-TTF on Im-SAM are specified by XPS. On the vibrational spectrum measured by IRAS, the strong hydrogen bonds between H₂Cat-BMT-TTF and Im-SAM are characterized by the remarkably red-shifted OH stretching mode at 3140 cm^–1, which is much lower than that for hydrogen-bonding water (typically ∼3300 cm^–1). The OH stretching mode frequency and the adsorption strength for the H₂Cat-BMT-TTF molecule hydrogen bonding with imidazole groups are quantitatively examined on the basis of DFT calculations