Abstract
Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.
Highlights
Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules
We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces
For electrostatic and van der Waals-London dispersion (vdW) interactions, the microscopic part follows from ab initio QM calculations, www.nature.com/scientificreports that are in general of different types, focused on the electronic structure calculations, which ideally yield the partial charges of all the atoms composing the interacting molecules, or on the frequency-dependent dielectric function of the whole molecule, respectively[7]
Summary
Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Interactions between biological macromolecules can be deduced from standard principles of colloid and nanoscale stability theory[1] that identify different types of direct long range interactions as well as different types of short-range solvent-mediated interactions, together governing the molecular recognition and self-assembly of biological macromolecules[2] The former include electrostatic interactions[3], depending on the specific nature of molecular charges and the net charge on a body, polar interactions[4] arising from dipolar and higher order charge multipoles, and van der Waals-London dispersion (vdW) interactions[4], that in their turn depend on the details of the dielectric response properties of the molecular materials. One should note here, that these studies are available only in the setting of biochemistry, nanotechnology, and medicine, while no quantitat-
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