An improved generalized AMBER force field (GAFF) for urea

Abstract

We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.

Molecular-dynamics simulations of urea nucleation from aqueous solution

“…The experimentally known urea crystal structure (form I) (35) as well as the metastable polymorph (form II) are the result of the replication in a 3D lattice of two characteristic dimer structures, observed also in other studies of urea clusters in vacuum (36). Namely, form I is the result of the replication of head-to-tail dimers, whereas form II is characterized by interactions resembling those of cyclic dimers (9,36). Despite this difference, looking at the structural features of the coordination shell of a single urea molecule, one can observe that both the experimental structure of urea (form I) and the metastable polymorph (form II) are characterized by a similar local orientation of the C-O axis.…”

“…In our previous work, we have addressed the presence of a metastable polymorph studying the nucleation of urea from its melt (9). The experimentally known urea crystal structure (form I) (35) as well as the metastable polymorph (form II) are the result of the replication in a 3D lattice of two characteristic dimer structures, observed also in other studies of urea clusters in vacuum (36). Namely, form I is the result of the replication of head-to-tail dimers, whereas form II is characterized by interactions resembling those of cyclic dimers (9,36).…”

Switches of hydrogen bonds during ligand–protein association processes determine binding kinetics

“…48–50 The protein and substrates were modeled with the Amber 99SB and general Amber force field, respectively. 51,52 The atom charges of the intermediates were given by the vCharge model. 53 We carefully minimized the systems through hydrogen atoms, side chains, and the entire protein complex for 500, 5000, and 50,000 steps, respectively.…”

Urea homogeneous nucleation mechanism is solvent dependent

“…65 The former gives rise to the experimental crystal structure (form I), while the latter produces a distorted structure (form II), in which the relative orientation between carbonyl bonds of neighbouring molecules is preserved, while the relative orientation of the axis joining the two nitrogen atoms is changed. 65 The former gives rise to the experimental crystal structure (form I), while the latter produces a distorted structure (form II), in which the relative orientation between carbonyl bonds of neighbouring molecules is preserved, while the relative orientation of the axis joining the two nitrogen atoms is changed.…”