A polarizable electrostatic model of the N‐methylacetamide dimer

Abstract

ABSTRACT:Our previously developed polarizable electrostatic model is applied to isolated N-methylacetamide (NMA) and to three hydrogen-bonded configurations of the NMA dimer. Two versions of the model are studied. In the first one (POL1), polarizability along the valence bonds is described by induced bond charge increments, and polarizability perpendicular to the bonds is described by cylindrically isotropic induced atomic dipoles. In the other version (POL2), the induced bond charge increments are replaced by induced atomic dipoles along the bonds. The parameterization is done by fitting to ab initio MP2/6-31++G(d,p) electric potentials. The polarizability parameters are determined by subjecting the NMA molecule to various external electric fields. POL1 turns out to be easier to optimize than POL2. Both models reproduce well the ab initio electric potentials, molecular dipole moments, and molecular polarizability tensors of the monomer and the dimers. Nonpolarizable models are also investigated. The results show that polarization is very important for reproducing the electric potentials of the studied dimers, indicating that this is also the case in hydrogen bonding between peptide groups in proteins.

Potential energy functions: From consistent force fields to spectroscopically determined polarizable force fields

“…This is undoubtedly correct as long as the CN t coordinate is also planar, with the peptide group resonance at its maximum. However, our results 40 indicate that, for nonplanar values of the CN t coordinate, the reference value of the NH ob angle should not be zero but should vary with the torsion angle. The ab initio [MP2/6-31ϩϩG(d,p)] NH ob potential energy in NMA for two different values of CN t is shown in Figure 3.…”

“…This dependence will not only be important in obtaining accurate frequencies but can be expected to influence molecular dynamics simulations, which in turn, through the dynamics of the NH bond vector, could be important in the interpretation of NMR spectra. 41 In connection with these studies, we noticed that there are large charge fluxes associated with the NH ob deformation in NMA, 40 the largest charge variation occurring on the N atom. This effect, which is ϳ 25% when the out-of-plane angle varies between 0°a nd 45°, is shown in Figure 4.…”

“…In order to obtain the vdW parameters for the peptide group, this procedure has been implemented for N-methylacetamide (NMA) dimers, producing parameters that are consistent with our optimized electrostatic parameters. 29 As discussed above, now that V nb is available, the valence force constants and intrinsic geometry parameters are readily determined from Eqs. (13) and (14), respectively.…”

“…40 In current force fields it is assumed that the NH ob coordinate is intrinsically planar, so its reference value is set to zero. This is undoubtedly correct as long as the CN t coordinate is also planar, with the peptide group resonance at its maximum.…”

Preferred Configurations of Peptide–Peptide Interactions

“…Due to the delicacy involved in comparisons of different sorts of geometries, with differing origins of stability, it would be injudicious to base any decisions of relative stability on any but high-level correlated calculations, of which there have been several performed in recent years. Concerning studies of peptide analogues such as formamide and N-methylacetamide, the majority were limited primarily to standard H-bonded geometries [25][26][27][28][29] , especially those wherein the two molecules occupied the same plane [30][31][32][33][34] . There have been a handful of works that went beyond this simple paradigm and noted dimer geometries that had significant elements of nonplanarity [35][36][37][38][39] , but did not pursue this issue in any detail.…”