A model for the hydrogen-bond-length probability distributions in the crystal structures of small-molecule components of the nucleic acids (original) (raw)
Related papers
The Journal of Physical Chemistry A, 1999
In the present paper, we have analyzed the conformational energy and geometrical parameters of the isolated 2′-deoxyribonucleosides and ribonucleosides. Geometry optimization of these nucleic acid constituents has been undertaken by means of density functional theory with the Becke-Lee-Yang-Parr exchange and correlation functional and split valence basis sets, 6-31G (/) , including nonstandard polarization functions on carbon, nitrogen, and oxygen atoms. For each nucleoside, three major conformers, i.e., C2′-endo/anti, C3′endo/anti, and C3′-endo/syn, have been taken into consideration, where C3′-endo and C2′-endo refer to the north (N)-type and south (S)-type sugar puckering, respectively, and anti and syn designate the orientation of the base with respect to the sugar. In both families (2′-deoxyribonucleosides and ribonucleosides) the anti orientation of the base stabilized by an intramolecular C-H‚‚‚O hydrogen bond formed between the base and the O5′ atom of the sugar moiety corresponds to the lowest energy states. In the 2′-deoxyribonucleosides including uracil, guanine, and adenine bases the lowest energy conformer is C2′-endo/anti, whereas in 2′deoxycytidine the most stable conformer is C3′-endo/anti. In ribonucleosides, the C3′-endo/anti and C2′endo/anti conformers nearly have the same energy, except in cytidine, where the most stable conformer is C3′-endo/anti. Therefore, a general discussion has been devoted to the exceptional cases of 2′-deoxycytidine and cytidine compared to the other nucleosides. The present calculated results have also been compared with those recently reported at the MP2 level by other authors on the 2′-deoxyribonucleosides or smaller model compounds on one hand, and with the experimental results based on a statistical survey of nucleoside crystal structures on the other hand.
J Phys Chem B, 2000
In the present paper, we have analyzed the conformational energy and geometrical parameters of the isolated 2′-deoxyribonucleosides and ribonucleosides. Geometry optimization of these nucleic acid constituents has been undertaken by means of density functional theory with the Becke-Lee-Yang-Parr exchange and correlation functional and split valence basis sets, 6-31G (/) , including nonstandard polarization functions on carbon, nitrogen, and oxygen atoms. For each nucleoside, three major conformers, i.e., C2′-endo/anti, C3′endo/anti, and C3′-endo/syn, have been taken into consideration, where C3′-endo and C2′-endo refer to the north (N)-type and south (S)-type sugar puckering, respectively, and anti and syn designate the orientation of the base with respect to the sugar. In both families (2′-deoxyribonucleosides and ribonucleosides) the anti orientation of the base stabilized by an intramolecular C-H‚‚‚O hydrogen bond formed between the base and the O5′ atom of the sugar moiety corresponds to the lowest energy states. In the 2′-deoxyribonucleosides including uracil, guanine, and adenine bases the lowest energy conformer is C2′-endo/anti, whereas in 2′deoxycytidine the most stable conformer is C3′-endo/anti. In ribonucleosides, the C3′-endo/anti and C2′endo/anti conformers nearly have the same energy, except in cytidine, where the most stable conformer is C3′-endo/anti. Therefore, a general discussion has been devoted to the exceptional cases of 2′-deoxycytidine and cytidine compared to the other nucleosides. The present calculated results have also been compared with those recently reported at the MP2 level by other authors on the 2′-deoxyribonucleosides or smaller model compounds on one hand, and with the experimental results based on a statistical survey of nucleoside crystal structures on the other hand.
Geometric parameters in nucleic acids: nitrogenous bases
1996
We present estimates of the bond-length and bond-angle parameters for the nitrogenous base side groups of nucleic acids. These values are the result of a statistical survey of small molecules in the Cambridge Structural Database for which high-resolution X-ray and neutron crystal structures are available. The statistics include arithmetic means and standard deviations for the different samples, as well as comparisons of the population distributions for sugar-and non-sugar-derivatized bases. These accumulated data provide appropriate target values for refinements of oligonucleotide structures, as well as sets of standard atomic coordinates for the five common bases.
Geometrical and Electronic Structure Variability of the Sugar− phosphate Backbone in Nucleic Acids
The Journal of …, 2008
The anionic sugar-phosphate backbone of nucleic acids substantially contributes to their structural flexibility. To model nucleic acid structure and dynamics correctly, the potentially sampled substates of the sugar-phosphate backbone must be properly described. However, because of the complexity of the electronic distribution in the nucleic acid backbone, its representation by classical force fields is very challenging. In this work, the three-dimensional potential energy surfaces with two independent variables corresponding to rotations around the R and γ backbone torsions are studied by means of high-level ab initio methods (B3LYP/ 6-31+G*, MP2/6-31+G*, and MP2 complete basis set limit levels). The ability of the AMBER ff99 [Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074] and parmbsc0 [Perez, A.; Marchan, I.; Svozil, D.; Š poner, J.; Cheatham, T. E.; Laughten, C. A.; Orozco, M. Biophys. J. 2007, 92, [3817][3818][3819][3820][3821][3822][3823][3824][3825][3826][3827][3828][3829] force fields to describe the various R/γ conformations of the DNA backbone accurately is assessed by comparing the results with those of ab initio quantum chemical calculations. Two model systems differing in structural complexity were used to describe the R/γ energetics. The simpler one, SPM, consisting of a sugar and methyl group linked through a phosphodiester bond was used to determine higher-order correlation effects covered by the CCSD(T) method. The second, more complex model system, SPSOM, includes two deoxyribose residues (without the bases) connected via a phosphodiester bond. It has been shown by means of a natural bond orbital analysis that the SPSOM model provides a more realistic representation of the hyperconjugation network along the C5′-O5′-P-O3′-C3′ linkage. However, we have also shown that quantum mechanical investigations of this model system are nontrivial because of the complexity of the SPSOM conformational space. A comparison of the ab initio data with the ff99 potential energy surface clearly reveals an incorrect ff99 force-field description in the regions where the γ torsion is in the trans conformation. An explanation is proposed for why the R/γ flips are eliminated so successfully when the parmbsc0 force-field modification is used.
The Journal of Physical Chemistry B, 1997
Hydrogen bonding between base pairs in nucleic acids is a key determinant of their structures. We have examined the distance dependence of the hydrogen bonding of AT-WC (Watson-Crick), GC-WC, and AT-H (Hoogsteen) base pairs using ab initio quantum mechanics, LMP2/cc-pVTZ(-f) energies at HF/cc-pVTZ(-f) optimized geometries. From these curves, we have extracted Morse potentials between the H atoms and the acceptor atoms that accurately reproduce the quantum mechanical energies for a range of geometries. Using these parameters, we have calculated the complexation energies of the remaining 26 possible pairwise combinations, and the agreement with previously reported ab initio calculations is excellent. We have also extracted off-diagonal Lennard-Jones 12-6 parameters to be used with the popular AMBER95 and CHARMM95 force fields that significantly improve their descriptions of the base-pairing energy and optimum geometry.
Hydrogen bonding in DNA base pairs: Reconciliation of theory and experiment
Journal of The American Chemical Society, 2000
Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson-Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine-thymine (AT) and guanine-cytosine (GC) base pairs at various levels (i.e., BP86, PW91, and BLYP) of nonlocal density functional theory (DFT) in combination with different Slater-type orbital (STO) basis sets. Best agreement with available gas-phase experimental A-T and G-C bond enthalpies (-12.1 and -21.0 kcal/mol) is obtained at the BP86/TZ2P level, which (for 298 K) yields -11.8 and -23.8 kcal/mol. However, the computed hydrogen bond lengths show again the notorious discrepancy with experimental values. The origin of this discrepancy is not the use of the plain nucleic bases as models for nucleotides: the disagreement with experiment remains no matter if we use hydrogen, methyl, deoxyribose, or 5′-deoxyribose monophosphate as the substituents at N9 and N1 of the purine and pyrimidine bases, respectively. Even the BP86/DZP geometry of the Watson-Crick-type dimer of deoxyadenylyl-3′,5′deoxyuridine including one Na + ion (with 123 atoms our largest model for sodium adenylyl-3′,5′-uridine hexahydrate, the crystal of which had been studied experimentally with the use of X-ray diffraction) still shows this disagreement with experiment. The source of the divergence turns out to be the molecular environment (water, sugar hydroxyl groups, counterions) of the base pairs in the crystals studied experimentally. This has been missing, so far, in all theoretical models. After we had incorporated the major elements of this environment in our model systems, excellent agreement between our BP86/TZ2P geometries and the X-ray crystal structures was achieved.