Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution

Abstract

The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...

Origin of Enantioselectivity in Engineered Cytochrome c-Catalyzed Carbon-Radical FePP Hydrolysis Revealed Using QM/MM (ABEEM Polarizable Force Field) and MD Simulations

“…Here, we briefly describe the ABEEM PFF. The potential energy of the ABEEM PFF can be written as the sum of bonded ( E bonded ) and nonbonded ( E nonbonded ) terms: − E normalA normalB normalE normalE normalM normalP normalF normalF = E normalb normalo normaln normald normale normald + E normaln normalo normaln normalb normalo normaln normald normale normald …”

“…Consequently, this method is well suited for simulating biomolecular systems. ABEEM PFF has been applied in gas-phase water clusters and bulk water, aqueous ionic solutions, and biomolecules, − e.g., peptides, proteins, and DNAs. Thus, the influence of proteins on the structure of the active center and the interaction between reactants can be effectively characterized using the ABEEM PFF.…”

Unifying Charge-Flow Polarization Models

“…The FQ model is therefore also known in the literature as electronegativity equalization, − and since the chemical potential is the negative of the electronegativity, chemical potential equalization, charge equilibration, ,, and charge equalization are further names for the same underlying model, , but they may differ in terms of the parameterization strategy and/or choice of Coulombic screening function. The atom-bond electronegativity equalization method corresponds to FQ with additional non-nuclear charge sites at bond and lone-pair positions …”

“…The latter can in a finite difference version be calculated as the average of the ionization potential and electron affinity, which clearly is dependent on the molecular structure, although only slightly for geometries near equilibrium, and the hardness parameters must also be functions of the geometry . The infinite distance CT problem can be prevented by additional Lagrange multipliers, ,,,, one for each fragment, or explicitly expressing selecting atomic charges as a function of the remaining charges, − but this rapidly becomes cumbersome and also prevents genuine CT. The infinite distance CT can be modulated by solving the FQ equations within local constrained regions of space, but this requires a manual definition of the local regions .…”

“…The atom-bond electronegativity equalization method corresponds to FQ with additional non-nuclear charge sites at bond and lonepair positions. 85 The molecular polarizability α in eq 32 is obtained from the Lagrange form in eqs 20/21, where the last term arises from the charge conservation constraint, 72,86,87 and is required to make the polarizability translational invariant (Supporting Information). 72 It may alternatively be expressed by only the first term, but with a modified J ̃matrix where the charge constraint has been explicitly included, 73−75 or the last term has in some cases been omitted.…”