Adenine⋯2,4-difluorotoluene (modified base) pair: potential and free-energy surfaces

Orbital Interactions in Strong and Weak Hydrogen Bonds are Essential for DNA Replication We thank the National Research School Combination—Catalysis (NRSCC) for a postdoctoral fellowship for C.F.G. and the National Computer Facilities (NCF) foundation of the Netherlands Organization for Scientific Research (NWO) for financial support.

“…The base‐pairing energy Δ E (at 0 K) for AF (−3.0 kcal mol −1 ) is about four‐times smaller than for AT (−13.0 kcal mol −1 ) and that the hydrogen bonds in AF are 0.4–0.6 Å longer than in AT (Scheme ), in good agreement with other theoretical studies 3e,3g. These results raise a number of questions: 1) is F really an isoster of T if it leads to such enormous changes in the geometry relative to the Watson–Crick pair?…”

The World of Non-Covalent Interactions: 2006

“…First, individual base pairs were studied (uracil dimer 143 , the adenine...2,4-difluorotoluene pair 144 , methyluracil dimers 145 , the adenine...thymine pair 146 and the methyladenine...methylthymine pair 147 ), and, later, all the DNA base pairs and methylated DNA base pairs were also considered 148 .…”

The nature of intermolecular interactions between aromatic amino acid residues

“…Following a well‐established procedure,14, 17, 20, 28–31 all possible minima in the intermolecular PES of the TRP‐PHE, TRP‐TYR, PHE‐TYR, and TYR‐TYR complexes were determined by quenching 4000 structures regularly sampled from a MD simulation (4 ns for each pair) at 300 K of the two molecules in a cubic box of 25 Å side length with minimum image convention and interacting through the AMBER force field 34. The conjugate gradient method35 was used for minimization.…”

“…These studies started with the case of TRP‐HIS pair in gas phase14 and in various solvents,15 continued with the toluene (PHE) homo‐dimer,17 and has been extended in the present study to all the other relevant aromatic amino acid residues pairs: TRP‐PHE, TRP‐TYR, PHE‐TYR, and TYR‐TYR (where TYR stands for tyrosine), excluding only the very uncommon TRP‐TRP pair† and the pairs involving HIS, which is generally considered as a special aromatic residue 22. The PES for each pair is determined with a well‐established14, 17, 20, 28–31 mixed classical/ab initio method, in which the PES is scanned by using classical MD simulation and minimum geometries are searched by quenching many randomly selected and uncorrelated phase space points taken from the MD trajectory. The binding energies at the quenched minimum structures are determined by using MP2 calculations corrected by the basis set superposition error (BSSE) 32.…”