Vibrational Spectroscopy and Theory of the Protonated Benzene Dimer and Trimer

Direct observation on argon tagging nitrobenzene radical anion in gas phase: Infrared photodissociation spectroscopy and theoretical calculation

The infrared photodissociation spectroscopy was applied to characterize nitrobenzene radical anion (NB^-). NB^- tagged by argon [NB(Ar)^-] was prepared by a mixture of nitrobenzene/Ar through a supersonic ion source and then selected by a time-of-flight mass spectrometer. Eight strong peaks observed at 977.9, 999.6, 1059.8, 1275.7, 1309.7, 1339.7, 1367.6 and 1581.7 cm^-1 in the fingerprint region were assigned to NB(Ar)^-, corresponding to CC bending, CC stretching, CC bending + symmetric O-N stretching vibration, antisymmetric O-N and CC stretching vibration, antisymmetric O-N stretching and CH rocking vibration, CC stretching + antisymmetric O-N stretching vibration, C-N stretching vibration, and symmetric CC stretching vibration. Most interestingly, the distinguishable CH stretching vibrations were observed at 3006.5, 3048.6 and 3084.5 cm^-1 absorptions. Combined with density functional theoretical (DFT) calculation, five tagging argon NB^- isomers were optimized and analyzed with no imaginary frequency. The results indicated that most bond lengths in NB^- become longer than those of neutral NB, except for the C1-C2/C4-C5 bonds, which are only slightly shorter than those of neutral NB, and the C-N bond, which is 0.085 A shorter in the anion. The NB^- tagged by argon located on the nitro group had no change on bond parameters with Ar-tagging or not theoretically. Natural population analysis (NPA) show that the negative natural charges are mainly distributed on both oxygen atoms. And the one electron resonates between the nitro group and benzene ring. N-O bonds in NB^- become much more polar than those of the neutral NB. This paper proved the usefulness to characterize NB(Ar)^- and further explore the structures of NB_n^- (n > 1) clusters by infrared photodissociation spectroscopy combining with the time-of-flight mass spectrometer.

Molecular mechanism for the encapsulation of the doxorubicin in the cucurbit[n]urils cavity and the effects of diameter, protonation on loading and releasing of the anticancer drug:Mixed quantum mechanical/ molecular dynamics simulations

BACKGROUND AND OBJECTIVES

Doxorubicin is a common apoptotic chemotherapeutic which has shown an obvious inhibitory effect in cancer chemotherapy. Here, cucurbit[n]urils (n = 7,10) have been proposed as a doxorubicin carrier, and the effects of diameter, protonation on loading and releasing of the anticancer drug doxorubicin has been studied.

METHODS

The Density Functional Theory (DFT) calculation and Molecular Dynamics (MD) simulation are performed to study the adsorption process of the (guest) Doxorubicin molecule in the neutral and protonated states within the (host) cucurbit[n]urils (n = 7,10).

RESULTS

DFT results show that the adsorption process in water is thermodynamically favorable. It is found that the binding energies for protonated drug encapsulation in cucurbit[n]urils are weaker than those of the neutral drug, implying the protonation of doxorubicin can promote the drug release from the adsorption situation. The electron density values and their Laplacian are evaluated to identify the nature of the intermolecular interactions through the topological parameters using the Bader's theory of atoms in molecules. Furthermore, the natural bond orbital analysis shows that the electrons aretransferred from cucurbit[n]urils to drug in all complexes. MD simulation results indicate that value of drug diffusion coefficient is small, therefore, we expect DOX to be slowly released from the CB cavity.

CONCLUSIONS

Based on obtained results, cucurbit[n]urils may be a prominent nano-carrier to loading and release drug on to target cells.

UV spectroscopy of cold ions as a probe of the protonation site

Where does the proton go?

Appraisal of molecular tailoring approach for large clusters

High level ab initio investigations on molecular clusters are generally restricted to those of small size essentially due to the nonlinear scaling of corresponding computational cost. Molecular tailoring approach (MTA) is a fragmentation-based method, which offers an economical and efficient route for studying larger clusters. However, due to its approximate nature, the MTA-energies carry some errors vis-à-vis their full calculation counterparts. These errors in the MTA-energies are reduced by grafting the correction at a lower basis set (e.g., 6-31+G(d)) onto a higher basis set (e.g., aug-cc-pvdz or aug-cc-pvtz) calculation at MP2 level of theory. Further, better estimates of energies are obtained by making use of many-body interaction analysis. For this purpose, R-goodness (Rg) parameters for the three- and four-body interactions in a fragmentation scheme are proposed. The procedure employing grafting and many-body analysis has been tested out on molecular clusters of water, benzene, acetylene and carbon dioxide. It is found that for the fragmentation scheme having higher three- and four-body Rg-values, the errors in MTA-grafted energies are reduced typically to ~0.2 mH at MP2 level calculation. Coupled with the advantage in terms of computational resources and CPU time, the present method opens a possibility of accurate treatment of large molecular clusters.