title: Exploring a reaction mechanism for acetato ligand replacement in paddlewheel tetrakisacetatodirhodium (II,II) complex by ammonia: computational density functional theory study.
abstract: This study focuses on the first step of interaction between DNA and the paddle-wheel dirhodium complex. The ammonia molecule was used to model the oligonucleotide sequence. The reaction was considered in neutral and acidic conditions, in gas phase, and in solvent, using the COSMO model. Molecular structures of the complexes were optimized in both models at the B3PW91/6-31G(d) level. The B3LYP functional and aug-cc-pvdz basis set were employed for single-point energy determination and electron distribution analyses. It was shown that in neutral solution the replacement of axial aqua ligand is mildly exoergic. The reaction is characterized by a relatively low activation barrier (10-12 kcal/mol), and, according to Eyring transition state theory, it proceeds very quickly. The breaking of the Rh-O(ac) bond in neutral solution is mildly endoergic (less than 1 kcal/mol) with an activation barrier of about 21 kcal/mol. However, this process can occur much more spontaneously (ΔG of -14 kcal/mol) when the dirhodium complex is protonated at the acetyl oxygen in remote position.
authors.affiliation: Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
authors.forename: Zdenĕk
authors.initials: Z
authors.lastname: Futera
authors.forename: TomáS
authors.initials: T
authors.lastname: Koval
authors.forename: Jerzy
authors.initials: J
authors.lastname: Leszczynski
authors.forename: Jiande
authors.initials: J
authors.lastname: Gu
authors.forename: Mariusz
authors.initials: M
authors.lastname: Mitoraj
authors.forename: Monika
authors.initials: M
authors.lastname: Srebro
authors.forename: Jaroslav V
authors.initials: JV
authors.lastname: Burda
mesh_terms: D000641:Ammonia / Q000737:chemistry*; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D005740:Gases / Q000737:chemistry*; D008024:Ligands; D008956:Models, Chemical; D015394:Molecular Structure; D009942:Organometallic Compounds / Q000737:chemistry*; D012238:Rhodium / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D005740:Gases; D008024:Ligands; D009942:Organometallic Compounds; D012997:Solvents; D000641:Ammonia; D004247:DNA; D012238:Rhodium