Methylated uracil dimers: potential energy and free energy surfaces

The nature of intermolecular interactions between aromatic amino acid residues

“…The main difference between the MM and the ab initio minimum energy structure is found for the H(TRP)‐ring(PHE/TYR) distance which, in the ab initio minimized dimer, is shorter than in the corresponding starting MM structure. These findings confirm a widely observed result:14, 17, 20, 28–31 MM methods with an AMBER‐like force field, with RESP atomic charges determined on the monomeric units, is a quite reliable and computationally convenient recipe to explore the PES of aromatic‐aromatic interactions. Furthermore, the low cost of the methodology step enables an exhaustive search of the minima, thus avoiding the ambiguities and uncertainties of a partial scanning of the conformational space 17…”

“…Following a well‐established procedure,14, 17, 20, 28–31 all possible minima in the intermolecular PES of the TRP‐PHE, TRP‐TYR, PHE‐TYR, and TYR‐TYR complexes were determined by quenching 4000 structures regularly sampled from a MD simulation (4 ns for each pair) at 300 K of the two molecules in a cubic box of 25 Å side length with minimum image convention and interacting through the AMBER force field 34. The conjugate gradient method35 was used for minimization.…”

“…These studies started with the case of TRP‐HIS pair in gas phase14 and in various solvents,15 continued with the toluene (PHE) homo‐dimer,17 and has been extended in the present study to all the other relevant aromatic amino acid residues pairs: TRP‐PHE, TRP‐TYR, PHE‐TYR, and TYR‐TYR (where TYR stands for tyrosine), excluding only the very uncommon TRP‐TRP pair† and the pairs involving HIS, which is generally considered as a special aromatic residue 22. The PES for each pair is determined with a well‐established14, 17, 20, 28–31 mixed classical/ab initio method, in which the PES is scanned by using classical MD simulation and minimum geometries are searched by quenching many randomly selected and uncorrelated phase space points taken from the MD trajectory. The binding energies at the quenched minimum structures are determined by using MP2 calculations corrected by the basis set superposition error (BSSE) 32.…”

Noncovalent Interactions in the Gas Phase: The Anisole–Phenol Complex

“…As a first step, an extensive sampling of the intermolecular PES of the anisole dimer has been performed with a molecular dynamics simulation in the NVT (constant number of particles, volume, and temperature) thermodynamical ensemble, and all possible minima have been located by quenching about 5000 regularly sampled structures. − The temperature was set to 300 K, and the simulation box had a 25 Å side cube. Such a temperature is sufficient to guarantee the breaking and re-forming of the complex several times during the simulation, and the box is large enough to allow for the complete separation of the two units.…”

Potential energy and free energy surfaces of the formic acid dimer: Correlated ab initio calculations and molecular dynamics simulationsElectronic supplementary information (ESI) available: Optimised geometries of the structures in Tables 1 and 2. See http://www.rsc.org/suppdata/cp/b1/b110872g/

“…The potential energy surface (PES) of polyatomic molecular clusters is very complex and the location of virtually all energy minima requires the use of an efficient search procedure. In this study (as well as in previous ones [3][4][5] ), we adopted the molecular dynamics/quenching method combined with the force field of Cornell et al 6 Proper sampling of the whole PES was ensured by varying the kinetic energy and the length of the run. After location of all energy minima, the calculated stabilization energies (determined with the Cornell et al 6 force field) were verified by comparing them with the stabilization energies obtained from correlated ab initio calculations.…”