Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides

Gruza, Jan; Koča, Jaroslav; Pérez, Serge

doi:10.1016/s0166-1280(97)00149-8

Cited by 15 publications

(11 citation statements)

References 17 publications

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“…The use of molecular mechanics algorithms to generate and minimize a large number of conformers, a portion of which are then studied at higher levels of theory has been previously reported for pyranose ring systems, including di- and trisaccharides . However, these methods have not been widely used with furanose-containing molecules …”

Section: Resultsmentioning

confidence: 99%

Computational Studies of the Arabinofuranose Ring: Conformational Preferences of Fully Relaxed Methyl α-d-arabinofuranoside

et al. 2001

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Two approaches for identifying the minimum energy conformers of methyl R-D-arabinofuranoside 1, in the gas phase have been explored and compared. In the first approach (the constrained envelope method), 30 previously reported envelope geometries of 1 were allowed to fully optimize at the B3LYP/6-31G* level. B3LYP/6-31+G** single-point energies of these optimized structures were also determined, which led to the identification of the 3 T 4 and 2 T 1 ring conformers as the Northern (N) and Southern (S) minima, respectively, with the latter being the global minimum. The importance of intramolecular hydrogen bonding was probed by optimizing another set of 30 envelope geometries with initial geometries biased against the formation of these stabilizing interactions. These calculations led to the same two families of low-energy ring conformers ( 3 T 4 and 2 T 1 ); however, the N, and not the S, conformer was the global minimum without hydrogen bonding. The second approach involved the identification of conformers for 1 through the use of a Monte Carlo search coupled with molecular mechanics and then further optimization of these structures at higher levels of theory (HF/6-31G* and B3LYP/6-31G*). Subsequent B3LYP/6-31+G** single-point energy calculations afforded results that are similar to the constrained envelope method, but the stochastic approach led to more lowenergy conformers, and to a new global minimum. A comparison of these computational results with the experimentally determined solution conformation of 1 is also presented.

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Section: Resultsmentioning

confidence: 99%

Computational Studies of the Arabinofuranose Ring: Conformational Preferences of Fully Relaxed Methyl α-d-arabinofuranoside

et al. 2001

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“…Ribose and Nucleosides. Preliminary calculations have been performed at the HF, ,, DFT, and MP2 −,, levels on the molecular models containing a furanose ring. The molecular model called ribose in this work (Figure ) is in fact a subunit of the nucleoside containing three hydroxyl groups at the 2‘, 3‘, and 5‘ positions.…”

Section: Theoretical Detailsmentioning

confidence: 99%

“…As far as the previous theoretical investigations on the nucleic acid constituents are concerned, one can recall the pioneering calculations of Saran and Pullman based on the perturbative configuration interaction over localized orbitals (PCILO) method for constructing the conformational energy map of nucleosides and nucleotides by single-point calculations. Other calculations based on particular conformations of nucleosides, modified nucleosides, or their constituents performed at the Hartree−Fock (HF), − density fuctional theory (DFT) and semiempirical − levels are also worth mentioning. Some other recent results at the HF 25 and MP2 levels, based on the model compounds whose chemical structures are close to the nucleosides and nucleotides involved in nucleic acid chains, should also be mentioned.…”

Section: Introductionmentioning

confidence: 99%

Ground State Properties of the Nucleic Acid Constituents Studied by Density Functional Calculations. I. Conformational Features of Ribose, Dimethyl Phosphate, Uridine, Cytidine, 5‘-Methyl Phosphate−Uridine, and 3‘-Methyl Phosphate−Uridine

et al. 1999

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Ground state energies and geometries have been determined at the DFT/B3LYP level for different model compounds such as ribose, dimethyl phosphate, uridine, cytidine, 3‘-methyl phosphate−uridine, and 5‘-methyl phosphate−uridine as a function of the most prominent conformations adopted by each of them. The counterion used for neutralizing the phosphate negative charge was an ammonium ion (NH4 +). This systematic study allowed us to analyze the stability of a ribonucleotide (base+ribose+phosphate) which is the chemical repeating unit of RNA. In the dimethyl phosphate model, the lowest energy corresponds to the gauche--gauche- conformation, as also predicted by previous calculations on this motif at different theoretical levels. In the ribose model, the C2‘-endo (S-type) conformer has a lower energy than the C3‘-endo (N-type) one. When a pyrimidine base (uracil or cytosine) is added to the ribose to form a ribonucleoside, the electronic energies of the three optimized conformers with the C3‘-endo and C2‘-endo sugar puckers as well as the anti and syn orientations of the base with respect to the sugar are located in the following order: C3‘-endo/anti < C2‘-endo/anti < C3‘-endo/syn. However, the energy difference between these conformers depends on the type of the pyrimidine base connected to the ribose. The optimization of the ribonucleotides confirms the stability of the conformers containing A- and Z-form conformational angles. The role of the intramolecular O−H···O and C−H···O hydrogen bonds in the overall stability of ribose, nucleosides, and ribonucleotides has been discussed.

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“…That approach facilitated precise fitting to QM rotational data, but was specific to six‐membered ring forms (pyranosides) and to the anomeric configuration. This limited the ability to readily introduce new chemical functionality into GLYCAM, to study ring conformational interconversions, and to apply it to other ring sizes (furanosides, in particular) 42…”

Section: Introductionmentioning

confidence: 99%

GLYCAM06: A generalizable biomolecular force field. Carbohydrates

et al. 2007

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A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both α-and β-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.

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Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides

Cited by 15 publications

References 17 publications

Computational Studies of the Arabinofuranose Ring: Conformational Preferences of Fully Relaxed Methyl α-d-arabinofuranoside

Computational Studies of the Arabinofuranose Ring: Conformational Preferences of Fully Relaxed Methyl α-d-arabinofuranoside

Ground State Properties of the Nucleic Acid Constituents Studied by Density Functional Calculations. I. Conformational Features of Ribose, Dimethyl Phosphate, Uridine, Cytidine, 5‘-Methyl Phosphate−Uridine, and 3‘-Methyl Phosphate−Uridine

GLYCAM06: A generalizable biomolecular force field. Carbohydrates

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