Geometry optimization of the cytosine molecules in a cytosine stack using the B3LYP crystal orbital method

The B3LYP DFT crystal orbital method was applied (with helical periodicity) to calculate the total energy per unit cell of a cytosine (C) molecule in a C stack. Applying afterwards the multidimensional metric method in its BFGS form, the geometry of a C molecule was optimized in the stack of DNA B (3.36 Å stacking distance, 36° rotation). For comparison, we optimized also the geometry of a C trimer and pentamer (in DNA B form) using the Gaussian 03 program for the B3LYP molecular calculation and the default method for the geometry optimization. The results of the two completely different calculations agree quite well, which supports our confidence in the results of our C stack calculation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005