Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson-Crick/Hoogsteen Base Pairs: A Computational Analysis.

The adsorption of 5-fluorouracil (5FU) on Watson-Crick (WC) base pairs and Hoogsteen (HT) base pairs has been studied using the dispersion-corrected density functional theory (DFT). The adsorption, binding energy, and thermochemistry for the drug 5FU on the WC and HT base pairs were determined. The most stable geometries were near planar geometry, and 5FU has a higher preference for WC than HT base pairs. The adsorption energies of 5FU on nucleobase pairs are consistently higher than pristine nucleobase pairs, indicating that nucleobase pair cleavage is less likely during the adsorption of the 5FU drug. The enthalpy change for the formation of 5FU-DNA base pairs is higher than that for the formation of 5FU-nucleobases and is enthalpy-driven. The E gap of AT base pairs is higher, suggesting that their chemical reactivity toward further reaction would be less than that of GC base pairs. The electron density difference (EDD) analysis shows a significant decrease in electron density in aromatic regions on the purine bases (adenine/guanine) compared to the pyrimidine bases. The MESP diagram of the stable 5FU-nucleobase pair complexes shows a directional interaction, with the positive regions in a molecule interacting with the negative region of other molecules. The atoms in molecule analysis show that the ρ(r) values of C=O···H-N are higher than those of N···H/N-H···O. The N···H intermolecular bonds between the base pair/drug and nucleobases are weak, closed shell interactions and are electrostatic in nature. The noncovalent interaction analysis shows that several new spikes are engendered along with an increase in their strength, which indicates that the H-bonding interactions are stronger and play a dominant role in stabilizing the complexes. Energy decomposition analysis shows that the drug-nucleobase pair complex has a marginal increase in the electrostatic contributions compared to nucleobase pair complexes.

Titanium-doped nickel clusters TiNi(n) (n = 1-12): geometry, electronic, magnetic, and hydrogen adsorption properties.

Using the first principles method, we study the growth behavior and electronic and magnetic properties of TiNi(n) (n = 1-12) clusters to clarify the effect of Ti modulation on the nickel nanostructures. Furthermore, chemisorption of H(2) was studied to understand the chemical reactivity of H(2) on the small Ni- and Ti-doped Ni clusters. The calculations are performed using the plane wave pseudopotential approach under the density functional theory and generalized gradient approximation for the exchange and correlation functional. The optimized geometries of TiNi(n-1) clusters indicate that the substitution of Ti brings a substantial structural reconstruction from 3D structure to a layer structure in which Ti atom is found to coordinate with Ni atoms to a maximum extent. This is accompanied by a significant enhancement in binding energies and reduction in chemical reactivity. Furthermore, the magnetic moments of the small Ti-doped Ni clusters are quenched because of the antiferromagnetic alignment of the Ti electrons. The lowest-energy structure of H(2) chemisorbed on Ni clusters shows that hydrogen prefers to adsorb on the edge site with two hydrogen atoms on these clusters in neighboring sites as the preferred arrangement. The incorporation of Ti atom improves the chemisorption energy of Ni clusters. Bader charge analysis indicates that with the formation of metal hydride, the H atoms withdraw charges from the metal centers, making them lose an electron, and carry a positive charge over them. Furthermore, Ti doping is found to enhance the chemical reactivity of Ni clusters.

Probing the structure, stability and hydrogen adsorption of lithium functionalized isoreticular MOF-5 (Fe, Cu, Co, Ni and Zn) by density functional theory.

Li adsorption on isoreticular MOFs with metal Fe, Cu, Co, Ni and Zn was studied using density function theory. Li functionalization shows a considerable structural change associated with a volume change in isoreticular MOF-5 except for the Zn metal center. Hydrogen binding energies on Li functionalized MOFs are seen to be in the range of 0.2 eV, which is the desired value for an ideal reversible storage system. This study has clearly shown that Li doping is possible only in Zn-based MOF-5, which would be better candidate to reversibly store hydrogen.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.

Oxidation of methionines by oxochromium(V) cations: a kinetic and spectral study.

The oxidation of methionine (Met) plays an important role during biological conditions of oxidative stress as well as for protein stability. By choosing [oxo(salen)chromium(V)] ions, [(salen)Cr(V)=O](+) (where salen = bis(salicylidene)ethylenediamine) as suitable biomimics for the peptide complexes that are formed during the reduction of Cr(VI) with biological reductants, the oxidation of methionine and substituted methionines with five [oxo(salen)chromium(V)] complexes in aqueous acetonitrile has been investigated by spectrophotometric, electron paramagnetic resonance (EPR) spectroscopy and electrospray ionization mass spectrometry (ESI-MS) methods. In aqueous solution [(salen)Cr(V)=O](+) ion is short lived, ligation of H(2)O to the Cr center takes place and [O=Cr(V)(salen)-H(2)O](+) adduct is the active oxidant. The reaction is found to be first order each in the oxidant and the substrate. The presence of water in the reaction system accelerates the reaction rate and an inactive, stable mu-oxo dimer is also formed during the course of the reaction. On the basis of spectral, kinetic and product analysis study a mechanism involving direct oxygen transfer from [O=Cr(V)(salen)-H(2)O](+) to methionine has been proposed as a suitable mechanism for the reaction.

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches.

The encapsulation of nucleobases inside CB7 has gained prominence due to its use as anticancer and antiviral drugs. With this respect, the nonconvalent interactions existing in the nucleobases encapsulated inside the CB7 cavity have been analyzed employing the dispersion corrected density functional theory. The CBn cavity has the ability to encapsulate two guest nucleobases molecules when they are aligned in parallel configuration. The computed association energy using the two- and three-body correction method computed at B3LYP-D3 level is close to the experimental estimate. The use of dispersion corrected DFs is essential to identify the correct binding energies. The solvation energy plays a vital role in the estimation of association energy. QTAIM analysis shows that the Laplacian of the charge density (∇2ρ) is negative and the presence of covalent interaction between the guest and host molecule. The NCI-RDG isosurface shows the presence of noncovalent intermolecular interactions such as van der Waals and hydrogen bonding. The existence of "splattering" of charges in guanine@CB7 molecule is responsible for its higher stability. From the AIM, NCI-RDG, and EDA results, we conclude that noncovalent and electrostatic interaction with partial covalent character exists in the intermolecular bonding between the host and the guest nucleobases. The ramification of such intermolecular bonds is reflected in the 1H NMR and 13NMR spectra.

Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis.

This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH⋯O/N-H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, SO⋯H-N type interaction have strongest hydrogen bond strength with high EHB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results.

Cooperativity of intermolecular hydrogen bonds in microsolvated DMSO and DMF clusters: a DFT, AIM, and NCI analysis.

Density functional theory (DFT) calculations are performed to study the hydrogen-bonding in the DMSO-water and DMF-water complexes. Quantitative molecular electrostatic potential (MESP) and atoms-in-molecules (AIM) analysis are applied to quantify the relative complexation of DMSO and DMF with water molecules. The interaction energy of DMSO with water molecules was higher than in DMF-water complexes. The existence of cooperativity effect helps in the strong complex formation. A linear dependence was observed between the hydrogen bond energies EHB, and the total electron densities in the BCP's of microsolvated complexes which supports the existence of cooperativity effect for the complexation process. Due to the stronger DMSO/DMF and water interaction, the water molecules in the formed complexes have a different structure than the isolated water clusters. NCI analysis shows that the steric area is more pronounced in DMF-water complex than the DMSO-water complex which accounts for the low stability of DMF-water complexes compared to the DMSO-water complex. Graphical abstract NCI analysis shows that the steric area is more pronounced in DMF-water complex than the DMSO-water complex which accounts for the low stability of DMF-water complexes compared to the DMSO-water complex.

Theoretical prediction of the complexation behaviors of antitumor platinum drugs with cucurbiturils.

The inclusion complex formation ability between CB[n] (n = 6-9) and Pt-drugs (oxaliplatin, nedaplatin, carboplatin, and cisplatin) in gas phase as well as water phases has been investigated using the using density functional theory. The results reveal the existence of several stable inclusion complexes in aqueous solution with high solvation energies compared to the guest and host molecule. It has been shown that the formation of complexes between CB[6] and Pt-drugs resulted in structural change in the CB[6], with the calculated deformation energies being higher for the inclusion complexes. The inclusion complexes are stabilized by the hydrogen bonding and the charge transfer between the Pt-drugs and the CB[n] host. Calculated enthalpy and Gibbs free energy of formation in aqueous solution revels that the formation of CB[7]-oxaliplatin is spontaneous, and hence its experimental synthesis is feasible. Among the CB's studied, CB[8]-Pt-drug inclusion complexes have exothermic enthalpy and low Gibbs free energy of formation. Computed (1)NMR spectra in CB[7]-oxaliplatin showed high chemical shielding for the cyclohexane ring, indicating the existence of charge transfer in the inclusion complex. The amine protons in the guest Pt-drugs are shielded due to the hydrogen bonding interaction with CB's oxygen portal.

Cucurbit[7]uril encapsulated cisplatin overcomes cisplatin resistance via a pharmacokinetic effect.

The cucurbit[n]uril (CB[n]) family of macrocycles has been shown to have potential in drug delivery where they are able to provide physical and chemical stability to drugs, improve drug solubility, control drug release and mask the taste of drugs. Cisplatin is a small molecule platinum-based anticancer drug that has severe dose-limiting side-effects. Cisplatin forms a host-guest complex with cucurbit[7]uril (cisplatin@CB[7]) with the platinum atom and both chlorido ligands located inside the macrocycle, with binding stabilised by four hydrogen bonds (2.15-2.44 Å). Whilst CB[7] has no effect on the in vitro cytotoxicity of cisplatin in the human ovarian carcinoma cell line A2780 and its cisplatin-resistant sub-lines A2780/cp70 and MCP1, there is a significant effect on in vivo cytotoxicity using human tumour xenografts. Cisplatin@CB[7] is just as effective on A2780 tumours compared with free cisplatin, and in the cisplatin-resistant A2780/cp70 tumours cisplatin@CB[7] markedly slows tumour growth. The ability of cisplatin@CB[7] to overcome resistance in vivo appears to be a pharmacokinetic effect. Whilst the peak plasma level and tissue distribution are the same for cisplatin@CB[7] and free cisplatin, the total concentration of circulating cisplatin@CB[7] over a period of 24 hours is significantly higher than for free cisplatin when administered at the equivalent dose. The results provide the first example of overcoming drug resistance via a purely pharmacokinetic effect rather than drug design or better tumour targeting, and demonstrate that in vitro assays are no longer as important in screening advanced systems of drug delivery.

Electronic and steric effects on the oxygenation of organic sulfides and sulfoxides with oxo(salen)chromium(V) complexes.

The kinetics of oxygenation of several para-substituted phenyl methyl sulfides and sulfoxides with a series of 5-substituted and sterically hindered oxo(salen)chromium(V) complexes have been studied by a spectrophotometric technique. Though the reaction of sulfides follows simple second-order kinetics, sulfoxides bind strongly with the metal center of the oxidant and the oxygen atom is transferred from the oxidant-sulfoxide adduct to the substrate. The reduction potentials, E(red), of eight Cr(V) complexes correlate well with the Hammett sigma constants, and the reactivity of the metal complexes is in accordance with the E(red) values. The metal complexes carrying bulky tert-butyl groups entail steric effects. Organic sulfides follow a simple electrophilic oxidation mechanism, and the nonligated sulfoxides undergo electrophilic oxidation to sulfones using the oxidant-sulfoxide adduct as the oxidant. Sulfoxides catalyze the Cr(V)-salen complexes' oxygenation of organic sulfides, and the catalytic activity of sulfoxides is comparable to pyridine N-oxide and triphenylphosphine oxide. The rate constants obtained for the oxidation of sulfides and sulfoxides clearly indicate the operation of a pronounced electronic and steric effect in the oxygenation reaction with oxo(salen)chromium(V) complexes.

Electron transfer reaction of oxo(salen)chromium(V) ion with anilines.

The kinetics of oxidation of 16 meta-, ortho-, and para-substituted anilines with nine oxo(salen)chromium(V) ions have been studied by spectrophotometric, ESIMS, and EPR techniques. During the course of the reaction, two new peaks with lambda(max) at 470 and 730 nm appear in the absorption spectrum, and these peaks are due to the formation of emeraldine forms of oligomers of aniline supported by the ESIMS peaks with m/z values 274 and 365 (for the trimer and tetramer of aniline). The rate of the reaction is highly sensitive to the change of substituents in the aryl moiety of aniline and in the salen ligand of chromium(V) complexes. Application of the Hammett equation to analyze kinetic data yields a rho value of -3.8 for the substituent variation in aniline and +2.2 for the substituent variation in the salen ligand of the metal complex. On the basis of the spectral, kinetic, and product analysis studies, a mechanism involving an electron transfer from the nitrogen of aniline to the metal complex in the rate controlling step has been proposed. The Marcus equation has been successfully applied to this system, and the calculated values are compliant with the measured values.