Hydrogen bonds in polymer folding.

J Borg; M H Jensen; K Sneppen; G Tiana

doi:10.1103/physrevlett.86.1031

Home/Archive/PubMed

PubMed · 11178002

Hydrogen bonds in polymer folding.

J Borg·M H Jensen·K Sneppen·G Tiana

View original source ↗Export metadata ↓

Abstract

We studied the thermodynamics of a homopolymeric chain with both van der Waals and directed hydrogen bond interaction. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give rise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated states. The consequences of this transition for protein folding and, in particular, for the problem of prions are discussed.

Explore related subjects

Hydrogen Bonding Models, Molecular Molecular Conformation Polymers Proteins Journal Article

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

J Borg, M H Jensen, K Sneppen, G Tiana. 2001-02-05. Hydrogen bonds in polymer folding.. https://doi.org/10.1103/physrevlett.86.1031

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations.

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.

Hydrogen Bonding↗

PubMed2007

A double-stranded helix by complexation of two polymer chains with a helical supramolecular assembly.

Explore the source record for details and available documents.

Hydrogen Bonding↗

PubMed2007

Unicorns in the world of chemical bonding models.

The appearance and the significance of heuristically developed bonding models are compared with the phenomenon of unicorns in mythical saga. It is argued that classical bonding models played an essential role for the development of the chemical science providing the language which is spoken in the territory of chemistry. The advent and the further development of quantum chemistry demands some restrictions and boundary conditions for classical chemical bonding models, which will continue to be integral parts of chemistry.

Hydrogen Bonding↗