Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an intermediate of the synthesis of pyruvate and a very important building block in nature, can be generated by converting free dihydroxyacetone (Dha) through the action of the dihydroxyacetone k...

The mechanisms for the base-catalyzed condensation reactions in phenol-formaldehyde resin synthesis were investigated by using the density functional theory method. The structures of the intermediates and transition states, as well as the potential energy barriers of the involved reactions, were obtained. The hypothesis of quinine methide (QM) formation was theoretically confirmed. Two mechanis...

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry s...

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between t...

We developed a double-quantum mechanical/molecular mechanical (d-QM/MM) method for investigation of full outer-sphere electron transfer (ET) processes between a donor and an acceptor (DA) in condensed matter. In the d-QM/MM method, which employs the novel concept of multiple QM regions, one can easily specify the number of electrons, spin states and appropriate exchange-correlation treatment in...

Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a ...

This paper is an introduction to the following articles in the scope of the Quantum Mechanic for Space Study initiated by ESA and lead by ONERA. The context of Quantum Mechanics for Space is summarised, and fields under development concerned are briefly introduced. On one hand, technological applications in space of quantum mechanics are explored and on the other hand some test of quantum mecha...

An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Che...

Blue mold caused by Penicillium expansum is the most important postharvest disease of apple worldwide and results in significant financial losses. There are no defined sources of resistance to blue mold in domesticated apple. However, resistance has been described in wild Malus sieversii accessions, including plant introduction (PI)613981. The objective of the present study was to identify the ...