Abstract:We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.

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The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields.

Ab initio theoretical methods are used to investigate the gas-phase ion pairs of the ionic liquid 1-butyl-3-methylimidazolium chloride. Multiple stable conformers with the chloride anion positioned (in-plane) around the imidazolium ring or above the C2-H bond are determined. The relative energy ordering of the conformers is examined at the B3LYP, MP2, and CCSD(T) levels. Zero-point energies, BSSE, and basis set effects are examined. For accurate results, correlation (dispersion) effects must be included. The most stable conformers are essentially degenerate and have the chloride H-bonding to, or lying above, the C2-H bond. Other conformers are found to lie approximately 30 and approximately 60 kJ mol(-1) higher in energy. Results are compared with those from recent simulations and experimental studies. The effect of the chloride anion on rotation of the butyl chain is investigated and found to lower some rotational barriers while enhancing others. The origin of the rotational barriers is determined. The number and type of hydrogen bonds formed between the imidazolium cation and chloride anion is found to vary significantly among conformers. No evidence of a possible intra C(alkyl)-H...pi interaction is obtained; however, hints of a Cl...pi interaction are found. The vibrational spectrum of each conformer is examined, and the origin of multiple (H-bonding) features in the vibrational spectrum of the ionic liquid explained.