Specific zinc binding to heliorhodopsin

Abstract

ATR-FTIR spectroscopy of heliorhodopsin mutants revealed E150 to be responsible for Zn2+-binding. Molecular dynamics simulations built a coordination structure of Zn2+, where E150 and protein bound water molecules participate direct coordination.

Organocatalytic‐racemization reaction elucidation of aspartic acid by density functional theory

“…[21][22][23][24] Additionally, this DFT approach provides accurate atomic charge distribution and structures of protein-active sites. [25][26][27] We used Chemcraft software 28 to visualize the molecular structures. The Cartesian coordinates of all obtained structures in this study are listed in Tables S1-S17.…”

“…We have assessed the reliability of the DFT method by reproducing the relative energies with an accuracy close to that of CCSD(T)/cc‐pVTZ and absorption spectra 21–24 . Additionally, this DFT approach provides accurate atomic charge distribution and structures of protein‐active sites 25–27 . We used Chemcraft software 28 to visualize the molecular structures.…”

Enantioselective amino acid interactions in solution

“…23 Moreover, such a DFT approach provided reliable structures for larger-size molecules containing intermolecular interactions in active sites of the proteins. [26][27][28] In the present study, DNPNO-CCSD(T)/cc-pVTZ calculations implemented in the ORCA 5.0 package 29 were further carried out to validate the DFT results. The solvation effect of water was incorporated by the polarizable continuum model (PCM).…”

Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids

“…The DFT approach can reproduce the stable molecular structures with relative energies of accuracy comparable to those obtained by the higher accuracy CCSD­(T) method for small size molecules . Moreover, the DFT method has been shown to be applicable for a sufficient number of conformational samplings and larger size molecules. − In the most stable conformations, photoabsorption (ε) and CD spectra have been computed. The CD value is defined as the difference of molar absorptivities between left-circular polarized light (CPL) and right-CPL, Δε = ε­(L) – ε­(R).…”