caa a22 4500 605488266 CHVBK 20210128100454.0 cr unu---uuuuu 210128e20150501xx s 000 0 eng 10.1007/s00214-015-1671-1 doi (NATIONALLICENCE)springer-10.1007/s00214-015-1671-1 Manukyan Anna Department of Natural Sciences, CUNY Hostos Community College, 475 Grand Concourse, 10451, Bronx, NY, USA aut Development of force field parameters for cyclopentane-modified peptide nucleic acids [Elektronische Daten] [Anna Manukyan] CHARMM force field parameters were developed for cyclopentane-modified peptide nucleic acid (cpPNA) analogs. As in the original force field parameterization, a self-consistent step-wise optimization approach was taken that involved the iterative adjustments of internal and external parameters until convergence was obtained. The geometry parameters such as standard bond lengths and bond angles were obtained by reproducing ab initio gas-phase geometries of model compounds. The internal force constants used for stretch and bend deformations were optimized to fit the calculated vibrational spectra. Torsional parameters were modified to fit the rotational barriers about single bonds in model compounds. The partial atomic charges were optimized based on interaction energies of complexes between water and the model compound. Our parameterization accurately reproduced high-level quantum mechanical calculations. The parameters were validated by series of molecular dynamics simulations of cpPNA in explicit water. Together with the existing force field for nucleic acids, these parameters will enable simulations of cpPNA complexes with RNA and DNA. Springer-Verlag Berlin Heidelberg, 2015 CHARMM force field nationallicence Force field parameterization nationallicence Quantum mechanical calculations nationallicence Molecular dynamics simulation nationallicence Nucleic acid analogs nationallicence Theoretical Chemistry Accounts Springer Berlin Heidelberg 134/5(2015-05-01), 1-21 1432-881X 134:5<1 2015 134 214 https://doi.org/10.1007/s00214-015-1671-1 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00214-015-1671-1 text/html Onlinezugriff via DOI NATIONALLICENCE 100 1- Manukyan Anna Department of Natural Sciences, CUNY Hostos Community College, 475 Grand Concourse, 10451, Bronx, NY, USA aut NATIONALLICENCE 773 0- Theoretical Chemistry Accounts Springer Berlin Heidelberg 134/5(2015-05-01), 1-21 1432-881X 134:5<1 2015 134 214