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Using the Quantum Chemical Topology theory for modeling force fields for peptides using electron densities

Grant number: 15/22247-3
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): August 01, 2016
Effective date (End): July 31, 2017
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
Principal Investigator:Roy Edward Bruns
Grantee:Arnaldo Fernandes da Silva Filho
Supervisor: Paul Popelier
Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Research place: University of Manchester, England  
Associated to the scholarship:14/21241-9 - The inclusion of polarization effects in the description of amino acids and peptides through the use of atomic multipoles obtained from electron densities, BP.PD


The state in which force fields are used in molecular dynamics has changed very little over the past 30 years. The most energy-transferable way to describe an atom within a system is through Quantum Chemical Topology (QCT). QCT atoms are parameter-free 3D fragments of finite volume, naturally appearing in the electron density. They have sharp boundaries, do not overlap, and leave no gaps. Moreover, QCT atoms have a well-defined energy according that can be quantum mechanically justified. Therefore a force field based on QCT emerges as an attractive alternative to provide atomistic energies for molecular dynamics simulations. The QCT theory is based on four pillars to solve the problems of force fields: transferability, the QTAIM theory, use of atomic multipole expansion and the use of machine learning to model polarization. At the core of a future-proof force-field is a maximally energy-transferable atom. Combining the QCT partitioning with the universal quantum expression of energy, leads to 3 types of primary energy contributions: (i) intra-atomic energy, (ii) inter-atomic exchange-correlation energy and (iii) inter-atomic Coulomb energy. These contributions are physically well-defined. Moreover, the Coulomb interaction is categorically represented by atomic multipole moments. Through the QCT theory, we aim to improve the state-of-art of force fields to better describe interactions of peptides under solvation. We will test the importance of polarizability and charge transfer under such conditions. The peptides will be studied in the presence of water and ions, as the Coulomb terms obtained through our QCT multipoles are to be compared with the parameters used in current force fields.

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Scientific publications (7)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
MCDONAGH, JAMES L.; SILVA, ARNALDO F.; VINCENT, MARK A.; POPELIER, PAUL L. A.. Quantifying Electron Correlation of the Chemical Bond. Journal of Physical Chemistry Letters, v. 8, n. 9, p. 1937-1942, . (14/21241-9, 15/22247-3)
SAUZA-DE LA VEGA, ARTURO; DUARTE, LEONARDO J.; SILVA, ARNALDO F.; SKELTON, JONATHAN M.; ROCHA-RINZA, TOMAS; POPELIER, PAUL L. A.. Towards an atomistic understanding of polymorphism in molecular solids. Physical Chemistry Chemical Physics, v. 24, n. 18, p. 17-pg., . (18/24844-7, 17/22741-3, 15/22247-3, 14/21241-9)
SILVA, ARNALDO F.; POPELIER, PAUL L. A.. MP2-IQA: upscaling the analysis of topologically partitioned electron correlation. Journal of Molecular Modeling, v. 24, n. 8, . (14/21241-9, 15/22247-3)
VINCENT, MARK A.; SILVA, ARNALDO F.; MCDONAGH, JAMES L.; POPELIER, PAUL L. A.. The effects of higher orders of perturbation theory on the correlation energy of atoms and bonds in molecules. International Journal of Quantum Chemistry, v. 118, n. 8, . (14/21241-9, 15/22247-3)
MCDONAGH, JAMES L.; SILVA, ARNALDO F.; VINCENT, MARK A.; POPELIER, PAUL L. A.. Machine Learning of Dynamic Electron Correlation Energies from Topological Atoms. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 14, n. 1, p. 216-224, . (14/21241-9, 15/22247-3)
SILVA, ARNALDO F.; VINCENT, MARK A.; MCDONAGH, JAMES L.; POPELIER, PAUL L. A.. The Transferability of Topologically Partitioned Electron Correlation Energies in Water Clusters. ChemPhysChem, v. 18, n. 23, p. 3360-3368, . (14/21241-9, 15/22247-3)

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