250
V. Poltev et al.
Fig. 8 Initial structure extracted from a DNA fragment with NDB id UDJ060 (upper row) and
DFT/PW91-ulg optimized structure (lower row) of dApdC:dGpdT. A:T pair with H-bonds marked
by black dotted line resides closer to observer; dGpdC (left chain) is in 117 conformation family;
and dApdC (right chain) is in BI family
angles and the resemblance in base ring superposition for cdDMP structures optimized by using these two functionals. Based on the conducted computational study
of various simple DNA fragments including various configurations of pairwise base
complexes this functional could be recommended for the study of regularities in 3D
structure formation of various DNA conformations. Unfortunately, we can use this
functional only with the ADF program since Gaussian software does not support it.
Final observation relates to the unexpected difference in GAUSSIAN and ADF
packages that has been revealed in DFT computation of cdDMPs. For some of the
latter systems (shown in Tables 2 and 3) we have been able to obtain optimized
structures by using the PW91 functional as implemented in the ADF program. The
conformational characteristics of these structures closely resemble those obtained
V. Poltev et al.
Fig. 8 Initial structure extracted from a DNA fragment with NDB id UDJ060 (upper row) and
DFT/PW91-ulg optimized structure (lower row) of dApdC:dGpdT. A:T pair with H-bonds marked
by black dotted line resides closer to observer; dGpdC (left chain) is in 117 conformation family;
and dApdC (right chain) is in BI family
angles and the resemblance in base ring superposition for cdDMP structures optimized by using these two functionals. Based on the conducted computational study
of various simple DNA fragments including various configurations of pairwise base
complexes this functional could be recommended for the study of regularities in 3D
structure formation of various DNA conformations. Unfortunately, we can use this
functional only with the ADF program since Gaussian software does not support it.
Final observation relates to the unexpected difference in GAUSSIAN and ADF
packages that has been revealed in DFT computation of cdDMPs. For some of the
latter systems (shown in Tables 2 and 3) we have been able to obtain optimized
structures by using the PW91 functional as implemented in the ADF program. The
conformational characteristics of these structures closely resemble those obtained