Combined theoretical and computational study of interstrand DNA guanine-guanine cross-linking by trans-[Pt(pyridine)2] derived from the photoactivated prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2].

Molecular modeling and extensive experimental studies are used to study DNA distortions induced by binding platinum(II)-containing fragments derived from cisplatin and a new class of photoactive platinum anticancer drugs. The major photoproduct of the novel platinum(IV) prodrug trans,trans,trans-[Pt(N(3))(2)(OH)(2)(py)(2)] (1) contains the trans-{Pt(py)(2)}(2+) moiety. Using a tailored DNA sequence, experimental studies establish the possibility of interstrand binding of trans-{Pt(py)(2)}(2+) (P) to guanine N7 positions on each DNA strand. Ligand field molecular mechanics (LFMM) parameters for Pt-guanine interactions are then derived and validated against a range of experimental structures from the Cambridge Structural Database, published quantum mechanics (QM)/molecular mechanics (MM) structures of model Pt-DNA systems and additional density-functional theory (DFT) studies. Ligand field molecular dynamics (LFMD) simulation protocols are developed and validated using experimentally characterized bifunctional DNA adducts involving both an intra- and an interstrand cross-link of cisplatin. We then turn to the interaction of P with the DNA duplex dodecamer, d(5'-C(1)C(2)T(3)C(4)T(5)C(6)G(7)T(8)C(9)T(10)C(11)C(12)-3')·d(5'-G(13)G(14)A(15)G(16)A(17)C(18)G(19)A(20)G(21)A(22)G(23)G(24)-3') which is known to form a monofunctional adduct with cis-{Pt(NH(3))(2)(py)}. P coordinated to G(7) and G(19) is simulated giving a predicted bend toward the minor groove. This is widened at one end of the platinated site and deepened at the opposite end, while the P-DNA complex exhibits a global bend of ∼67° and an unwinding of ∼20°. Such cross-links offer possibilities for specific protein-DNA interactions and suggest possible mechanisms to explain the high potency of this photoactivated complex.

Photodissociation of methyl iodide embedded in a host-guest complex: a full dimensional (189D) quantum dynamics study of CH3I@resorc[4]arene.

Accurate full dimensional quantum dynamics calculations studying the photodissociation of CH(3)I@resorc[4]arene on an ab initio based potential energy surface (PES) model are reported. The converged 189D quantum dynamics calculations are facilitated by the multilayer multi-configurational time-dependent Hartree (ML-MCTDH) approach combined with the correlation discrete variable representation (CDVR) for the evaluation of potential energy matrix elements. The potential employed combines an established ab initio PES describing the photodissociation of methyl iodide in the A band with a harmonic description of the resorc[4]arene host and a bilinear modeling of the host-guest interaction. All potential parameters required in the description of the vibrations of the host molecule and the host-guest interaction are derived from ab initio calculations on the host-guest complex. Absorption spectra at 0 K and 300 K are calculated and the electronic population dynamics during the bond breaking process occurring in the first 20-30 fs after the photoexcitation is investigated. Weak but significant effects resulting from the host-guest interaction on this time scale are found and interpreted. The present study demonstrates that accurate fully quantum mechanical dynamics calculations can be preformed for systems consisting of more than 50 atoms using the ML-MCTDH/CDVR approach. Utilizing an efficient statistical approach for the construction of the ensemble of initial wavepackets, these calculations are not restricted to zero temperature but can also study the dynamics at 300 K.

Anthracene-resorcin[4]arene-based capsules: synthesis and photoswitchable features.

Herein we present the synthesis and the photochemical behavior of several new hemicarcerands containing anthracene units as photoactive species. By means of NMR investigations of compounds 9 and 11 the dimerization mode was revealed as a 9,10-9',10'-dimerization, classically known from anthracene. Nevertheless only compound 11 could be converted to the opened form upon irradiation with 300 nm. Reopening of compounds 9 and 10 could not be achieved so far either by heating or by irradiation.

Extending ligand field molecular mechanics to modelling organometallic π-bonded systems: applications to ruthenium-arenes.

The ligand field molecular mechanics method has been extended to treat η(6)-arene ligands coordinated to a ruthenium(II) centre by employing a dummy atom located at the centroid of the arene ring and distributing the forces on the dummy to the arene carbon atoms. Angular overlap model parameters based on orbital energies derived from Kohn-Sham density functional theory (KS-DFT) calculations show that, relative to the Ru-dummy vector, the arene behaves as a very strong π donor and weak σ donor. Based on KS-DFT geometries, partial atomic charges and potential energy scans for a series of homoleptic and half sandwich complexes spanning arene, am(m)ine, imine, pyridyl, hydride and chloride ligands, a new LFMM force field has been developed which accurately reproduces the KS-DFT data. This FF was validated against 47 half-sandwich complexes obtained from the Cambridge Structural Database which, after minor corrections to account for the systematic errors between our chosen functional (BP86) and the experimental structures, yields a 'structurally tuned' FF where 93% of the Ru-L contacts are reproduced to 0.05 Å or better and all bar two bond lengths are within 0.1 Å of experiment. Over half the systems have non-hydrogen-atom rmsds of less than 0.5 Å. Larger differences are usually due to rotation of the arene moiety which is shown by ligand field molecular dynamics (LFMD) simulations to be an inherently low-energy process. Comparisons between LFMD and Car-Parrinello MD for [Ru(p-cymene)(ethylenediamine)Cl](+)show that LFMD is equally accurate but much faster enabling modelling of dynamic properties which occur on a timescale beyond the scope of CPMD.

Molecular dynamics simulations of dendrimer-encapsulated alpha-Keggin ions in trichloromethane solution.

We report on molecular dynamics simulations of dendrimer-encapsulated alpha-Keggin ions in trichloromethane solution. The simulations were done within the NVE ensemble at temperatures around T = 300 K. The eight examined systems are model compounds for dendrizymes, a hybrid material where a polyoxometalate ion (the core) is surrounded by amphiphilic cationic dendrimers (the shell) such that the complete system may exhibit enzyme-like regioselectivity and substrate selectivity, e.g., in olefin oxidation. The influence of dendrimer type, dendrimer generation, and number of dendritic cations bound by electrostatic interaction to the polyoxometalate core on the structure and dynamics of the shell has been studied. It is shown that the resulting distribution of trichloromethane molecules within the shell may serve as an indicator for the shell's permeability for small molecules. The dendritic shell causes a size exclusion effect that influences the access of small molecules to the central polyoxometalate ion, i.e., to that part where the enzyme-like reaction of a dendrizyme is supposed to take place.

A new fluorescent calix crown ether: synthesis and complex formation with alkali metal ions.

We synthesised a new N-benzylaza-21-crown-7 ether 5 with a dihydroxy coumarin as a fluorescence sensor and investigated the binding behaviour towards alkali metal cations in methanol by fluorescence titrations. The association constants are within one order of magnitude, with the exception of sodium. Potassium is the preferred binding partner (K(Na)=330 M(-1); K(K)=8600 M(-1); K(Rb)=8200 M(-1); K(Cs)=4400 M(-1)). The corresponding aza-21-crown-7 ether (6) was attached by a methylene unit to a resorcarene to give fluorescent calix crown ether 12. The binding abilities of the calix crown ether towards alkali metal ions in methanol have also been investigated, and an increasing complex stability, distinct for potassium and rubidium in comparison with 5, was found: K(Na)=440 M(-1); K(K)=110,000 M(-1); K(Rb)=63,000 M(-1); K(Cs)=20,000 M(-1). Like bis(crown ether)s, a cooperative complexation of the crown ether and the cavitand scaffold can be assumed. The proposed complex geometry is supported by Kohn-Sham DFT calculations for the potassium and caesium complexes.