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MM calculations of unit cell packings of aquabis(L-valinato)copper(II) in simulated crystal lattice

Marković, Marijana; Judaš, Nenad; Sabolović, Jasmina
MM calculations of unit cell packings of aquabis(L-valinato)copper(II) in simulated crystal lattice // EMBO Young Scientists Forum Book of Abstracts
Zagreb, Hrvatska, 2009. str. 37-37 (poster, međunarodna recenzija, sažetak, znanstveni)

MM calculations of unit cell packings of aquabis(L-valinato)copper(II) in simulated crystal lattice

Marković, Marijana ; Judaš, Nenad ; Sabolović, Jasmina

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

EMBO Young Scientists Forum Book of Abstracts / - , 2009, 37-37

EMBO Young Scientists Forum

Mjesto i datum
Zagreb, Hrvatska, 15-17.06.2009

Vrsta sudjelovanja

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Bakar; aminokiselina; kristalna struktura; MM simulacija u kristalu; polje sila
(Copper; amino acid; crystal structure; MM crystal simulation; force field)

Bis(amino acidato)copper(II) complexes are biologically important compounds. They take part in transporting copper to copper enzymes (such as superoxide dismutase, cytochrome c oxidase and nitrous-oxide reductase) and electron-transfer copper proteins (e.g., plastocyanin, azurin). The X-ray crystal structures are the most common source of experimental information on the structural properties of this class of compounds. Bis(L-valinato)copper(II), Cu(L-Val)_2, crystallised from aqueous solution as a cis-isomer with one water molecule in the asymmetric unit (space group C2), as determined by the X-ray diffraction measurements. The coordination geometry of the copper(II) is a distorted pyramid, with a water oxygen atom at the pyramid apex. The molecules are bonded together via intermolecular N– H· · · O_carbonyl, N– H· · · O_carboxyl and O_water– H· · · O_carbonyl hydrogen bonds. Molecular mechanics force field FFWa-SPCE [1], developed for studying the properties of bis(amino acidato)copper(II) complexes with either cis- or trans-N_2O_2 copper(II) coordination geometry in the solid state and in vacuo by MM calculations, and in aqueous solution by MD simulations, was used for conformational analysis of the title compound. Each chelate ring of Cu(L-Val)_2 can have 6 conformations, with C^beta in 3 axial and 3 equatorial positions, and therefore the molecule can have 21 trans and 21 cis conformations. Conformational analysis in vacuo, without the influence of the intermolecular interactions, showed that the trans conformers were more stable than the cis ones (by ≈ 102 kJ mol^-1). To account the crystal lattice effects, the experimental molecule orientation, unit cell lengths and angles, as well as the C2 space group symmetry operations were taken as the starting input data for the geometry optimisation of all possible conformers. During the energy minimisation of a crystal all degrees of freedom were allowed to vary, except the alpha and gamma unit cell angles were kept fixed to 90^o. The calculations of the unit cell packings and intermolecular interactions for the series of conformers suggest the reasons why experimentally obtained conformer occurs in the real crystal structure. [1] J. Sabolović, V. Gomzi, J. Chem. Theory Comput. 2009 (accepted for publication)

Izvorni jezik

Znanstvena područja
Fizika, Kemija


Projekt / tema
022-0222148-2822 - Modeliranje i međudjelovanje kompleksa prijelaznih metala i bioliganada (Jasmina Sabolović, )
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )
119-1193079-1084 - Strukturno istraživanje bioloških makromolekula metodom rentgenske difrakcije (Dubravka Matković-Čalogović, )

Institut za medicinska istraživanja i medicinu rada, Zagreb,
Prirodoslovno-matematički fakultet, Zagreb