The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding force...

In a previous study on matrix-assisted laser desorption ionization (MALDI) of peptides using α-cyano-4-hydroxycinnamic acid (CHCA) as a matrix, we found that the patterns of single-shot spectra obtained under different experimental conditions became similar upon temperature selection. In this paper, we report that absolute ion abundances are also similar in temperature-selected MALDI spectra, e...

Until recently, due to the absence of other suitable approaches, equilibrium concentrations in acid-base systems have been studied exclusively by measuring pH a solution. However, this method can not be used for organic (non-aqueous) solvent solutions. It is known that ionic strength solution, which fundamental component assessing activity coefficient and thermodynamic dissociation constant an ...

Ethylammonium nitrate (EAN) is composed of C(2)H(5)NH(3)(+) and NO(3)(-) ions, which behave as an acid and a base, respectively. The ionic liquid thus involves small amounts of C(2)H(5)NH(2) and HNO(3) molecules owing to proton transfer from C(2)H(5)NH(3)(+) to NO(3)(-). The equilibrium constant K(s) (= [C(2)H(5)NH(2)][HNO(3)]), which corresponds to the autoprotolysis constant of water, was obt...

As discussed in the main text, a hydrogen bond involves three atoms: the hydrogen H, the oxygen atom O it is covalently bound to and the acceptor oxygen O′. The proton transfer coordinate ν = d(O–H) − d(O′–H) provides a convenient structural parameter to characterise the hydrogen bond. When nuclear quantum effects are accounted for, the hydrogen H is strongly delocalised, with a small but not-n...

Water is the major component of all living cells, actually it composes 70% of our bodies. Its properties, very unusual when compared to other solvents, have made possible the life that we know. Water molecules spontaneously dissociate into a hydronium (H3O þ) and a hydroxide ion (OH). This autoprotolysis is a very rare event with the average lifetime of a single H2O molecule being ;14 h (Eigen,...