Highly accurate atomistic quantum chemical to coarse grained study of DNA and RNA
EMSL Project ID
33695
Abstract
The project is focused on study of physical and chemical properties of DNA and RNA at scales ranging from atomistic quantum chemistry to mesoscopic coarse-grained description by means of advanced large-scale massively parallel computer simulation methods.
Project Details
Project type
Exploratory Research
Start Date
2009-03-16
End Date
2010-03-21
Status
Closed
Released Data Link
Team
Principal Investigator
Related Publications
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set
Grafova L, J Rezac, M Pitonak, and P Hobza. 2010. "Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set." Journal of Chemical Theory and Computation 6(8):2365-2376. doi:10.1021/ct1002253
Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories
Riley KE, M Pitonak, P Jurecka, and P Hobza. 2010. "Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories." Chemical Reviews 110(9):5023-5063. doi:10.1021/cr1000173
Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study
Pitonak M, P Neogrady, and P Hobza. 2009. "Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study." Physical Chemistry Chemical Physics. PCCP 12:1369 - 1378. doi:10.1039/b919354e
On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X−H···π): WFT and DFT Calculations
Riley KE, M Pitonak, J Cerny, and P Hobza. 2009. "On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H· · ·?): WFT and DFT Calculations." Journal of Chemical Theory and Computation 6(1):66-80. doi:10.1021/ct900376r
Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data
Pitonak M, P Neogrady, J Cerny, S Grimme, and P Hobza. 2008. "Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data." Chemphyschem 10(1):282-289. doi:10.1002/cphc.200800718
Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description
Morgado CA, P Jurecka, D Svozil, P Hobza, and J Sponer. 2009. "Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description." Journal of Chemical Theory and Computation 5:1524-1544. doi:10.1021/ct9000125
Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic−Aromatic Side Chain Interactions in Proteins
Valdes H, K Pluhackova, and P Hobza. 2009. "Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins." Journal of Chemical Theory and Computation 5(9):2248-2256. doi:10.1021/ct900174f