The role of the basis set and the level of quantum mechanical theory in the prediction of the structure and reactivity of cisplatin

How can the cisplatin analogs with different amine act on DNA during cancer treatment theoretically?

Cisplatin is a widely used anti-cancer drug which inhibits the replication and polymerization of DNA molecule while showing some side effects and drug resistance. For this reason, to enhance its therapeutic index, researchers have synthesized several thousand analogs and tested their properties. In this project, several cisplatin analogs were designed to theoretically study the biological activity and lipophilicity effects on amine changes. The amines of the cisplatin molecule were substituted with aliphatic amines in different analogs. Computational methods such as molecular dynamics simulation, molecular docking, and molecular mechanics Poisson-Boltzmann surface area analysis were performed to investigate the binding of six cisplatin derivatives with DNA. The binding affinity and potential interactions of these drugs with double-strand DNA were analyzed. The stability effect of these drugs was investigated via root-mean-square deviation and root-mean-square fluctuation analysis, which showed that some analogs can break base-pair interaction at the end of DNA and reduced the stability of DNA. Also, the results revealed that the hydrogen bond is one of the most important factors in the binding of cisplatin's adduct to DNA. Molecular mechanics Poisson-Boltzmann surface area analysis indicated that electrostatic and van der Waals interactions are the most important deriving forces to the binding of cisplatin's drug to DNA. Finally, data revealed that cisplatin and the cis-dichloro-dimethylamine-platin tendency for binding to DNA are greater than that of other analogs.

Vibrational frequencies and intramolecular force constants for cisplatin: assessing the role of the platinum basis set and relativistic effects

The role of platinum basis set (PTBS) and relativistic effects for predicting the vibrational frequencies and intramolecular force constants for cisplatin are discussed. Nonrelativistic and relativistic computational protocols were built at B3LYP/PTBS/jorge-DZP/C-PCM and B3LYP-DKH2/PTBS/jorge-DZP-DKH/C-PCM levels, respectively, where 19 distinct PTBS were tested. As expected, the structural parameters were not very sensitive to the PTBS, however, the inclusion of relativistic effects improves the description of the cisplatin structure. When it comes to the vibrational frequencies, the results show that the PTBS, and mainly the relativistic effects, are both important. Moreover, the PBE0 functional led to better results than B3LYP in the protocols PBE0/LANL2TZ(f)/jorge-DZP/C-PCM (P20) and PBE0-DKH2/Sapporo-DKH3-DZP-2012/jorge-DZP-DKH/C-PCM (P22), which provided a mean absolute deviation (MAD) of only 10.8 cm^-1 and 9.5 cm^-1, respectively, for vibrational frequencies, which are excellent choices to study Pt complexes. Finally, a discussion of the intramolecular force constants for cisplatin is carried out, with the calculated bond and angles force constants with P20 and P22 protocols being recommended for the parameterization of the force field of cisplatin.

The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin

The composition of the plasma membrane of malignant cells is thought to influence the cellular uptake of cisplatin and to take part in developing resistance to this widespread anti-cancer drug. In this work we study the permeation of cisplatin through the model membranes of normal and cancer cells using molecular dynamics simulations. A special attention is paid to lipid asymmetry and cholesterol content of the membranes. The loss of lipid asymmetry, which is common for cancer cells, leads to a decrease in their permeability to cisplatin by one order of magnitude in comparison to the membranes of normal cells. The change in the cholesterol molar ratio from 0% to 33% also decreases the permeability of the membrane by approximately one order of magnitude. The permeability of pure DOPC membrane is 5-6 orders of magnitude higher than one of the membranes with realistic lipid composition, which makes it as an inadequate model for the studies of drug permeability.

Fate of cisplatin and its main hydrolysed forms in the presence of thiolates: a comprehensive computational and experimental study

Thiolations and bidentations drive the chemical fate of cisplatin compounds in intracellular medium.

Prediction of 195 Pt NMR of photoactivable diazido- and azine-Pt(IV) anticancer agents by DFT computational protocols

¹⁹⁵ Pt NMR chemical shifts for a series of large-sized photoactivable anticancer diazido-Pt(IV), homopiperizine-Pt(IV) and multifunctional azine-Pt(IV) complexes hardly to be probed experimentally and by sophisticated four-component and two-component relativistic calculations are predicted with high accuracy by density functional theory computational protocols. The calculated ¹⁹⁵ Pt NMR chemical shifts constitute a crucial descriptor for making highly predictive one-parameter quantitative structure activity relationships models that help in designing photoactivable Pt(IV)-based antitumor agents with high cytotoxicity and selectivity. Copyright © 2016 John Wiley & Sons, Ltd.

Developing multisite empirical force field models for Pt(II) and cisplatin

We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water. Comparison has been made with experimental and quantum mechanical results. We have demonstrated that both versions are generally capable of reproducing key properties of the system, but the second-order polarizable POSSIM formalism permits more accurate quantitative results to be obtained. For example, the energy of formation of cisplatin as calculated with the modified OPLS-AA exhibited an error of 9.9%, while the POSSIM error for the same quantity was 6.2%. The produced parameter sets are transferable and suitable to be used in protein-metal binding simulations in which position or even coordination of the ion does not have to be constrained using preexisting knowledge. © 2016 Wiley Periodicals, Inc.

Activation of C-H Bonds in Pt(+) + x CH4 Reactions, where x = 1-4: Identification of the Platinum Dimethyl Cation

Activation of C-H bonds in the sequential reactions of Pt(+) + x(CH4/CD4), where x = 1-4, have been investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and theoretical calculations. Pt(+) cations are formed by laser ablation and exposed to controlled amounts of CH4/CD4 leading to [Pt,xC,(4x-2)H/D](+) dehydrogenation products. Irradiation of these products in the 400-2100 cm(-1) range leads to CH4/CD4 loss from the x = 3 and 4 products, whereas PtCH2(+)/PtCD2(+) products do not decompose at all, and x = 2 products dissociate only when formed from a higher order product. The structures of these complexes were explored theoretically at several levels of theory with three different basis sets. Comparison of the experimental and theoretical results indicate that the species formed have a Pt(CH3)2(+)(CH4)x-2/Pt(CD3)2(+)(CD4)x-2 binding motif for x = 2-4. Thus, reaction of Pt(+) with methane occurs by C-H bond activation to form PtCH2(+), which reacts with an additional methane molecule by C-H bond activation to form the platinum dimethyl cation. This proposed reaction mechanism is consistent with theoretical explorations of the potential energy surface for reactions of Pt(+) with one and two methane molecules.

Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

(195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6 - n ](2-) complexes. The simple computational protocol is easily implemented even by synthetic chemists in platinum coordination chemistry that dispose limited software availability, or locally existing routines and knowhow. Copyright © 2016 John Wiley & Sons, Ltd.

Empirical force field for cisplatin based on quantum dynamics data: case study of new parameterization scheme for coordination compounds

Parameterization of molecular complexes containing a metallic compound, such as cisplatin, is challenging due to the unconventional coordination nature of the bonds which involve platinum atoms. In this work, we develop a new methodology of parameterization for such compounds based on quantum dynamics (QD) calculations. We show that the coordination bonds and angles are more flexible than in normal covalent compounds. The influence of explicit solvent is also shown to be crucial to determine the flexibility of cisplatin in quantum dynamics simulations. Two empirical topologies of cisplatin were produced by fitting its atomic fluctuations against QD in vacuum and QD with explicit first solvation shell of water molecules respectively. A third topology built in a standard way from the static optimized structure was used for comparison. The later one leads to an excessively rigid molecule and exhibits much smaller fluctuations of the bonds and angles than QD reveals. It is shown that accounting for the high flexibility of cisplatin molecule is needed for adequate description of its first hydration shell. MD simulations with flexible QD-based topology also reveal a significant decrease of the barrier of passive diffusion of cisplatin accross the model lipid bilayer. These results confirm that flexibility of organometallic compounds is an important feature to be considered in classical molecular dynamics topologies. Proposed methodology based on QD simulations provides a systematic way of building such topologies.

The conformation effect of the diamine bridge on the stability of dinuclear platinum(II) complexes and their hydrolysis

In this paper, the hydrolysis process of a bisplatinum complex containing the flexible chain 1,6-hexanediamine between the two metal centers was investigated through the use of density functional theory (DFT) with the analysis of the role of the spacing group arrangement on the values of free energy activation barrier. All structures were fully optimized in aqueous solution using implicit model for solvent at DFT level. The energy profiles for the hydrolysis reaction were determined by using the supermolecule approach. Five transition states were proposed differing by the conformation of the bridge group, and the activation free energy calculated as a weighted average within the selected forms. The Gibbs population for reactant was used as a statistical weight leading to the predicted value of 23.1kcalmol(-1), in good accordance with experiment, 23.8kcalmol(-1). Our results suggests that for 1,6-hexanediamine bridge ligand, the extend forms with average torsional angle over the carbon chain larger than 130° have the greatest contribution to the hydrolysis kinetics. The results presented here point out that the hydrolysis mechanism might follow different paths for each conformation and each of these contributes to the observed energy barrier.

Conformational insights and vibrational study of a promising anticancer agent: the role of the ligand in Pd(ii)–amine complexes

This study reports the first complete vibrational analysis of a dinuclear polyamine-based compound displaying antitumour properties.

Asymmetric environmental effects on the structure and vibrations of cis-[Pt(NH3)2Cl2] in condensed phases

We report the structural and vibrational properties of anticancer drug cisplatin (cis-[Pt(NH3)2Cl2]) in gas phase, in solid phase, and in aqueous solution using density functional theory (DFT) calculations, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics, and effective normal modes analysis. In contrast with the gas-phase case, asymmetric hydrogen bonding environments are found in both solid phase and aqueous solution. It is shown that the discrepancy of the molecular geometry between previous gas phase calculations and the X-ray crystal structure can be resolved by considering intermolecular hydrogen bonds in the calculations of solid phase. In addition, our simulations in solid phase and aqueous solution reveal that asymmetric environmental effects lead to several spectral features observed in experiments, such as the blue-shift in the N-H stretching region and the frequency splitting of NH3 symmetric deformation modes. Furthermore, a similar decoupling and localization of several vibrational modes of cisplatin is found in solid phase and aqueous solution, in comparison to those of O-H stretching modes of water molecules in liquid water [ J. Phys. Chem. Lett. 2013 , 4 ( 19 ), 3245 - 3250 ].

Accurate prediction of 195Pt NMR chemical shifts for a series of Pt(ii) and Pt(iv) antitumor agents by a non-relativistic DFT computational protocol

Exhaustive benchmark DFT calculations reveal that the non-relativistic GIAO-PBE0/SARC-ZORA(Pt)∪6-31+G(d)(E) computational protocol predicts accurate ¹⁹⁵Pt NMR chemical shifts for a wide range of square planar Pt(ii) and octahedral Pt(iv) anticancer agents.

Polymorphism in cisplatin anticancer drug

This study reports a combined experimental and theoretical study of the solid-state polymorphism of the anticancer agent cisplatin. A complete assignment was performed for the inelastic neutron scattering (INS) and Raman spectra collected simultaneously for cisplatin, at different temperatures, with a view to obtain reliable and definitive evidence of the relative thermal stability of its α and β polymorphic species. A marked temperature-dependent hysteresis was observed, as previously reported in the literature. Theoretical calculations were carried out at the density functional theory level, using a plane-wave basis set approach and pseudopotentials. A detailed comparison with the experimental Raman and INS data showed that the α polymorph is present at the lowest temperatures, whereas the β form occurs near room temperature. Furthermore, regions of coexistence of both forms are identified, which depend on the working mode (heating or cooling). These findings imply that Raman spectroscopy allows clear identification of the α and β polymorphs at a given temperature and can unambiguously discriminate between them. Elucidation of the polymorphic equilibrium of this widely used anticancer drug is paramount for its pharmaceutical preparation and storage conditions.