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Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models applicable to periodic solutes while crystallographic structures are commonly solved assuming a flat solvent model. Here we present a newly-developed periodic version of the 3D-RISM integral equation method that is able to solve for efficiently and describe accurately water and ions distributions in periodic systems; the code can compute accurate gradients that can be used in minimizations or molecular dynamics simulations. The new method includes an extension of the OZ equation needed to yield charge neutrality for charged solutes which requires an additional contribution to the excess chemical potential that has not been previously identified; this is an important consideration for nucleic acids or any other charged system where most or all of the counter- and co-ions are part of the disordered solvent. We present of several calculations of protein, RNA and small molecule crystals to show that X-ray scattering intensities and solvent structure predicted by the periodic 3D-RISM solvent model are in closer agreement with experiment than are intensities computed using the default flat solvent model in the refmac5 or phenix refinement programs, with the greatest improvement in the 2 to 4 {AA} range. Prospects for incorporating integral equation models into crystallographic refinement are discussed.
We present a protocol for the fully automated construction of quantum mechanical-(QM)-classical hybrid models by extending our previously reported approach on self-parametrizing system-focused atomistic models (SFAM) J. Chem. Theory Comput. 2020, 16,
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of efficiently
Recent studies of the hydration of micro- and nanoscale solutes have demonstrated a strong {it coupling} between hydrophobic, dispersion and electrostatic contributions, a fact not accounted for in current implicit solvent models. We present a theore
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory (KSDFT) bas
Two numerical methods are used to evaluate the relativistic spectrum of the two-centre Coulomb problem (for the $H_{2}^{+}$ and $Th_{2}^{179+}$ diatomic molecules) in the fixed nuclei approximation by solving the single particle time-independent Dira