Noncovalent interactions between cisplatin and graphene prototypes

Cisplatin (CP) has been widely used as an anticancer drug for more than 30 years despite severe side effects due to its low bioavailability and poor specificity. For this reason, it is paramount to study and design novel nanomaterials to be used as vectors capable to effectively deliver the drug to the biological target. The CP square‐planar geometry, together with its low water solubility, suggests that it could be possibly easily adsorbed on 2D graphene nanostructures through the interaction with the related highly conjugated π‐electron system. In this work, pyrene has been first selected as the minimum approximation to the graphene plane, which allows to properly study the noncovalent interactions determining the CP adsorption. In particular, electronic structure calculations at the MP2C and DFT‐SAPT levels of theory have allowed to obtain benchmark interaction energies for some limiting configurations of the CP–pyrene complex, as well as to assess the role of the different contributions to the total interaction: it has been found that the parallel configurations of the aggregate are mainly stabilized around the minimum region by dispersion, in a similar way as for complexes bonded through π‐π interactions. Then, the benchmark interaction energies have been used to test corresponding estimations obtained within the less expensive DFT to validate an optimal exchange‐correlation functional which includes corrections to take properly into account for the dispersion contribution. Reliable DFT interaction energies have been therefore obtained for CP adsorbed on graphene prototypes of increasing size, ranging from coronene, ovalene, and up to C₁₅₀H₃₀. Finally, DFT geometry optimizations and frequency calculations have also allowed a reliable estimation of the adsorption enthalpy of CP on graphene, which is found particularly favorable (about −20 kcal/mol at 298 K and 1 bar) being twice that estimated for the corresponding benzene adsorption. © 2017 Wiley Periodicals, Inc.     

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

In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis‐diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all‐electron basis sets (ABS). In addition, a modified all‐electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6‐31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol^?1, which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol^?1. For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol^?1, respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree‐Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6‐31+G(d) or B3PW91/mDZP/6‐31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP‐DNA complex), the lower levels B3LYP/LANL2DZ/6‐31+G(d) and B3LYP/SBKJC‐VDZ/6‐31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol^?1, respectively, which is only 13% higher than the actual value. © 2012 Wiley Periodicals, Inc.     

Ab initio reaction path for cisplatin interaction with L‐cysteine and L‐methionine

Ab initio calculations are used to track the reaction pathway of interaction between cisplatin and the sulfur‐containing amino acids cysteine (Cys) and methionine (Met). Structures of all reactive species as well as thermodynamic and kinetic properties were calculated and discussed based on the role played by the level of theory. Twenty‐three different levels of theory were examined including HF, DFT, and perturbation theory at MP2 and MP4(SDQ) orders. The rate constant for a second‐order associative ligand exchange mechanism (k₂) was calculated by means of transition state theory. This quantity is quite sensitive to small fluctuation of activation free energy, therefore is a good benchmark to assess the performance of different methods of calculations. The k₂ values predicted by DFT methods were in best agreement with experiment, found equal to (10²k₂ in M^?1 s^?1) 3.42 for Met (PBE1PBE) and 1.90 for Cys (B3P86). The experimental values are 3.6 and 2.2 for Met and Cys, respectively. The solvent effect plays a primary role to the kinetic properties, accounting for ～30% of the activation Gibbs free energy. The outcomes from the present study promptly show the adequacy of distinct theoretical approaches to describe the reactivity of cisplatin, thus might be useful for further studies involving other Pt(II) complexes. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Quantum chemistry of quantum size‐effects in semiconductors: Small clusters electronic structure calculations

Ab initio RHF SCF calculations are used for some small clusters M_xX_y, where M=Cd, Ag; X=S, I; and x, y≤7. Variation of electronic structure with size for some clusters with the bulklike tetrahedral coordination and with the lower symmetry allows one to predict their possible geometries which are compared with experimental data on the existence of the clusters. The chemical‐bonding factor (the chemical nature of bounded atoms, coordination number for metal and nonmetal atoms, hybridization, etc.) is of more importance for properties of the clusters than is the familiar quantum confinement effect of semiconductor clusters. The essential difference in regularities of small cluster formation is analyzed for CdS‐ and AgI‐based structures. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 337–341, 1999     

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

Banana-shaped molecules peculiarly oriented in a magnetic field: (2)H NMR spectroscopy and quantum mechanical calculations.

The orientational properties of the banana-shaped liquid crystal 4-chloro-1,3-phenylenebis{4-[4'-(10-undecenyloxy)]benzoyloxy} benzoate (ClPbis11BB) are reported in the nematic phase under the effect of an external magnetic field. A new hypothesis, which states that the central ring of the aromatic core is oriented perpendicularly to the external magnetic field, is proposed. In support of this hypothesis, a series of studies based on (2)H NMR spectroscopy, both in the bulk and in solution, are discussed. (2)H NMR measurements on three selectively deuterium-labelled isotopomers are presented, together with DFT results from B3LYP/cc-pvDz calculations performed on the aromatic core. The rather flat shape of the investigated intramolecular energy surface allows for several different conformations to be populated, the computed magnetic susceptibilities of which are consistent with the proposed hypothesis of peculiar orientation of banana-shaped molecules. Moreover, the orientation of the magnetic susceptibility tensor is shown to be strongly dependent on the internal conformation of the banana-shaped molecules.     

Loss of amine from platinum(II) complexes: implications for cisplatin inactivation, storage, and resistance

Potential consequences of the binding of the anticancer drug cisplatin to various biomolecules in the cell have been investigated by using a combined density functional theory and continuum dielectric model approach. Since the amine ligands remain coordinated at the metal upon formation of the most frequent DNA adducts, whereas they were found to be displaced from the metal upon formation of drug metabolites, we have analyzed the factors governing amine loss from platinum(II) complexes as a possible pathway of cisplatin inactivation. The calculations systematically show the effect of 1) the trans ligand, 2) the charge of complex, 3) the nucleophile, and 4) the environment on the thermodynamic instability and kinetic lability of the platinum-amine bonds. After initial binding of cisplatin hydrolysis products to thioethers or thiols, loss of the amine trans to this sulfur ligand rather than replacement of the sulfur ligand itself by other nucleophiles like guanine-N7 is predicted to be the predominant reaction. The results of this study contribute to an understanding of the modes of cisplatin inactivation prior to DNA binding, for example, by elevated glutathione levels in cisplatin-resistant cancer cells.     

The nature of intermolecular CuI...CuI interactions: a combined theoretical and structural database analysis

The nature of intermolecular interactions between dicoordinate Cu(I) ions is analyzed by means of combined theoretical and structural database studies. Energetically stable Cu(I).Cu(I) interactions are only found when the two monomers involved in the interaction are neutral or carry opposite charges, thus allowing us to speak of bonding between the components of the bimolecular aggregate. A perturbative evaluation of the components of the intermolecular interaction energies, by means the IMPT scheme of Stone, indicates that both the Coulombic and dispersion forces are important in determining the Cu(I).Cu(I) bonding interactions, because only a small part of that energy is attributable to Cu.Cu interactions, while a large component results from Cu.ligand interactions. The electrostatic component is the dominant one by far in the interaction between charged monomers, while in the interaction between neutral complexes, the electrostatic component is found to be of the same order of magnitude as the dispersion term. Bimolecular aggregates that have like charges are repulsive by themselves, and their presence in the solid state results from anion.cation interactions with ions external to this aggregate. In these cases, the short-contact Cu.Cu interactions here should be more properly called counterion-mediated Cu.Cu bonds.     

Anion-pi interactions in cyanuric acids: a combined crystallographic and computational study

Several structures of pi complexes of isocyanuric acid and of several thio derivatives with anions have been computed by using high level ab initio calculations. The nature of the complexes has been studied by means of the method of molecular interaction potential with polarization (MIPp) and Bader's theory of atoms-in-molecules. These molecules form favorable complexes with anions and can be used as binding units for building receptors for the molecular recognition of anions. In several cases, the anion-pi interaction has been demonstrated experimentally by means of X-ray crystallography.     

Enthalpy and Entropy Barriers Explain the Effects of Topology on the Kinetics of Zeolite‐Catalyzed Reactions

The methylation of ethene, propene, and trans‐2‐butene on zeolites H‐ZSM‐58 (DDR), H‐ZSM‐22 (TON), and H‐ZSM‐5 (MFI) is studied to elucidate the particular influence of topology on the kinetics of zeolite‐catalyzed reactions. H‐ZSM‐58 and H‐ZSM‐22 are found to display overall lower methylation rates compared to H‐ZSM‐5 and also different trends in methylation rates with increasing alkene size. These variations may be rationalized based on a decomposition of the free‐energy barriers into enthalpic and entropic contributions, which reveals that the lower methylation rates on H‐ZSM‐58 and H‐ZSM‐22 have virtually opposite reasons. On H‐ZSM‐58, the lower methylation rates are caused by higher enthalpy barriers, owing to inefficient stabilization of the reaction intermediates in the large cage‐like pores. On the other hand, on H‐ZSM‐22, the methylation rates mostly suffer from higher entropy barriers, because excessive entropy losses are incurred inside the narrow‐channel structure. These results show that the kinetics of crucial elementary steps hinge on the balance between proper stabilization of the reaction intermediates inside the zeolite pores and the resulting entropy losses. These fundamental insights into their inner workings are indispensable for ultimately selecting or designing better zeolite catalysts.     

O~3＋NH→HNO＋O~2反应机理的量子化学研究

用密度泛函(DFT)的B3LYP方法(6－31++G^*^*)研究了臭氧与NH自由基反应的微观机理,优化得到反应途径上的反应物,过渡态,中间体和产物的构型,通过振动分析对过渡态和中间体进行了确认。对单点用QCISD(T)/6－31++G^*^*方法计算能量,同时进行零点能校正。研究结果表明：NH与O~3反应有两条不同的反应通道,且均表现为亲电反应特征,两条不同的反应均为强放热反应。     

DFT description of the electronic structure and spectromagnetic properties of strongly correlated electronic systems: NiII, CuII and ZnII o-dioxolene complexes

The spectroscopic and magnetic properties of dioxolene complexes of zinc, copper and nickel were studied by DFT calculations on model complexes of formulas [(NH(3))(4)M(II)(SQ)](+) (M=Zn, Ni; SQ=semiquinonato) and [(NH(3))(2)Cu(II)(SQ)](+). Standard approaches such as time-dependent DFT (TDDFT), the Slater transition state (STS), and broken symmetry (BS) were found to be unable to completely account for the physical properties of the systems, and complete active space-configuration interaction (CAS-CI) calculations based on the Kohn-Sham (KS) orbitals was applied. The CAS-CI energies, properly corrected with multireference perturbation theory (MR-PT), were found to be in good agreement with experimental data. We present here a calculation protocol that has a low CPU cost/accuracy ratio and seems to be very promising for interpreting the properties of strongly correlated electronic systems in complexes of real chemical size.     

Substitutional carbon defects in silicon: A quantum mechanical characterization through the infrared and Raman spectra

The infrared (IR) and Raman spectra of eight substitutional carbon defects in silicon are computed at the quantum mechanical level by using a periodic supercell approach based on hybrid functionals, an all electron Gaussian type basis set and the CRYSTAL code. The single substitutional C _s case and its combination with a vacancy (C _sV and C _sSiV) are considered first. The progressive saturation of the four bonds of a Si atom with C is then examined. The last set of defects consists of a chain of adjacent carbon atoms C, with i = 1–3. The simple substitutional case, C _s, is the common first member of the three sets. All these defects show important, very characteristic features in their IR spectrum. One or two C related peaks dominate the spectra: at 596 cm⁻¹ for C _s (and C _sSiV, the second neighbor vacancy is not shifting the C _s peak), at 705 and 716 cm⁻¹ for C _sV, at 537 cm⁻¹ for C and C (with additional peaks at 522, 655 and 689 for the latter only), at 607 and 624 cm⁻¹, 601 and 643 cm⁻¹, and 629 cm⁻¹ for SiC, SiC, and SiC, respectively. Comparison with experiment allows to attribute many observed peaks to one of the C substitutional defects. Observed peaks above 720 cm⁻¹ must be attributed to interstitial C or more complicated defects.     

Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue.

A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity M?ller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.