Prediction of conformationally dependent atomic multipole moments in carbohydrates
نویسندگان
چکیده
The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings.
منابع مشابه
Evaluation of net atomic charges and atomic and molecular electrostatic moments through topological analysis of the experimental charge density
The atoms in molecules (AIM) theory may be used to derive atomic charges, atomic volumes and molecular dipole moments from the charge density. The theory is applied to theoretical periodic Hartree-Fock (PHF), density-functional (DFT) and experimental X-ray densities of p-nitroaniline using the program TOPOND and a newly developed program, TOPXD, for topological analysis of densities described b...
متن کاملA charge analysis derived from an atomic multipole expansion
A new charge analysis is presented that gives an accurate description of the electrostatic potential from the charge distribution in molecules. This is achieved in three steps: first, the total density is written as a sum of atomic densities; next, from these atomic densities a set of atomic multipoles is defined; finally, these atomic multipoles are reconstructed exactly by distributing charge...
متن کاملHPAM: Hirshfeld partitioned atomic multipoles
An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l(max) on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole mo...
متن کاملA point-charge model for electrostatic potentials based on a local projection of multipole moments
We introduce a method for obtaining atomic point-charges that yield accurate representations of the electrostatic potentials (ESP) of large systems. The method relies on a decomposition of the density and subsequent projection of the multipole moments of the density components onto neighbouring atomic sites. The resulting local multipole-derived charges (LMDCs) are well-defined, do not require ...
متن کاملAtomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence
Currently, all standard force fields for biomolecular simulations use point charges to model intermolecular electrostatic interactions. This is a fast and simple approach but has deficiencies when the electrostatic potential (ESP) is compared to that from ab initio methods. Here, we show how atomic multipoles can be rigorously implemented into common biomolecular force fields. For this, a compr...
متن کامل