Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field

Abstract

Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and non-equilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parameterized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is amongst the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, this data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches, and (2) enable more accurate treatments of energy transfer. 23.Hattig, C.; Tew, D. P.; Kohn, A., Communications: Accurate and efficient approximations to explicitly correlated coupled-cluster singles and doubles, CCSD-F12.

Atomic Partitioning of the MPn (n= 2, 3, 4) Dynamic Electron Correlation Energy by the Interacting Quantum Atoms Method: A Fast and Accurate Electrostatic Potential Integral Approach

“…Atomistic force fields continue to be developed given their growing use and impact in biological and materials science. Extensive comparisons between, traditional force fields can offer guidance in this development, as well as comparisons between machine‐learnt potentials.…”

Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA

“…The force field parameters developed and tested on amino acid sequences can also be applied to study larger systems like protein structures. Different force field methods, CHARMM, − AMBER, − OPLS-AA, − and many others, − depend on the respective topology and parameters for the considered system so as to accurately predict the structural properties of such systems. Again, larger systems like proteins can be very flexible, and thus, conformational flexibility may be impractical to deal with, provided data used for parameterization of these building blocks may be sufficient enough to match the results close to the experiment or the same as a QM method.…”

Temperature-Dependent Blue Shifting of O–H Stretching Frequencies in Crystalline Cellulose Explained

“…Consistent with the temperature-dependent infrared spectroscopy studies of cellulose, 11 covalent O−H stretching frequencies increase with temperature (Figure 4a), although the size of the predicted change (∼0.01 cm −1 K −1 ) is an order of magnitude smaller than that observed experimentally (∼0.1 cm −1 K −1 ). However, it is well known that bonded terms within molecular mechanic force fields tend to underestimate anharmonicity and overestimate the stiffness of covalent bonds, 30 hence reducing the sensitivity to thermally induced shifts. In addition, we are using an "infinite crystal" model with strict periodic boundary conditions that also limit the flexibility of the system.…”