Atomic charges for molecular dynamics calculations

Photoisomerization of Spiropyran in Solution: A Surface Hopping Investigation

We performed a computational investigation of the photoisomerization of an unsubstituted spiropyran in solution using surface hopping molecular dynamics simulations in a semiempirical framework. To bring out the solvent effects on the excited state dynamics, we have run simulations in three different environments: chloroform, methanol, and ethylene glycol. We show that the interaction with a moderately polar solvent such as chloroform has little effect on the dynamics when compared to vacuum results previously obtained by our group. At variance, the interaction with the protic solvents considered considerably affects the reaction mechanism, the quantum yield, and the excited state lifetimes.

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

New model potentials for sulfur–copper(I) and sulfur–mercury(II) interactions in proteins: Fromab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).

Are azobenzenophanes rotation-restricted?

We simulated the photoisomerization dynamics of an azobenzenophane with a semiclassical surface hopping approach and a semiempirical reparametrized quantum mechanics/molecular mechanics Hamiltonian. Only one of the two azobenzene chromophores in the molecule is taken into account quantum mechanically: the other one is treated by molecular mechanics. Both n-->pi* and pi-->pi* excitations are considered. Our results show that the photoisomerization reaction mainly involves the rotation around the N=N double bond. The excited state relaxation features are in qualitative agreement with experimental time-resolved fluorescence results.