Journal of Theoretical and Computational Chemistry

The spatial knowledge is the first one of all information about an object. Molecular shape and size, molecular van der Waals surface and/or solvent-accessible surface etc. have been widely studied and applied. This paper is to show that a molecular face (MF) for a molecule may be defined uniquely and intrinsically via the molecular intrinsic characteristic contours (MICC) with coding the molecular electron density (ED) as the fourth dimension. The significant feature of an MF provides both molecular spatial appearance and its frontier electron density, being an intuitive picture as a molecular fingerprint or face. With simple examples, the physical significance of an MF is then demonstrated.

Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.

Out of several plausible isomeric structures of the toluene–ICl charge transfer (CT) complex, the most feasible one was determined by a detailed ab initio and DFT study at the HF, B3LYP, and mPW1PW91 levels using 6-31++G(d, p) basis set. Potential energy surface scans were performed with six possible structures (I and Cl facing the o-, m-, and p-carbon atoms of toluene separately); the structures at the local minima of the surfaces were subjected to frequency calculation and the ones having no negative frequency were accepted as the real structure in the ground state. These structures were then subjected to full optimization. It was observed that the I–Cl bond, with its I atom oriented toward the aromatic ring, stands vertically above a C-atom at the ortho or para positions, being inclined at about 9° to the line perpendicular to the aromatic ring. Complexation increases the I–Cl bond length. After correction for basis set superposition error through a counterpoise calculation, we conclude from the binding energy that the preferred structure is the one with ICl above the orthoC atom. The calculated binding energy closely matches the experimental free energy of complexation. The electronic CT transition energy (hν_CT) with this structure in the ground state was calculated in vacuo by the restricted configuration interaction singlets method and in carbontetrachloride medium by the time dependent density functional theory method under the polarizable continuum model. The value of hν_CT obtained from the ground-to-excited state transition electric dipole moments of the complex, is close to (somewhat underestimated) the reported experimental value.

The cytotoxic effects of terpenoid lactones are attributed to the alkylation of biological nucleophiles, especially sulfhydryl groups in proteins, by the α,β-unsaturated carbonyl moiety of lactones through Michael reaction. Therefore, the cytotoxicity could be reflected by the reactivity of the pharmacophores. In this work, the Michael reaction between 12 α,β-unsaturated-carbonyl-containing small species, i.e. 10 analogues of the alpha methylene gamma butyrolactone moiety of andrographolide, one cyclopentenone, and one methylene–pentanolide, and L-cysteine-methylester^-1 were investigated by ab initio methods to mimic the alkylation of proteins by terpenoid lactones. The trend in the calculated reaction free energies of the small species is qualitatively in accordance with the reported cytotoxicity of corresponding terpenoid lactones.

The reaction mechanism of the decomposition of the methanol catalyzed by hydroxyl ZnO has been investigated by density function theory (DFT). The geometries of reactants, intermediates, transition states, and products on both doublet and quartet potential energy surfaces (PESs) have been fully optimized at the B3LYP/6-31G* level. The calculated results show that the reaction is slightly endothermic by 5.3 kJ/mol, which is in good accordance with the previous experiment. The energies and structures of the crossing points (CPs) between two PESs have been determined. The CP appears after the formation of transition states. The two theoretical models chosen to study the reaction mechanism were compared and discussed.

Linkages between vinylidene (=C:) and nitrenes (-N:), through methyne and its derivatives (CX), give allylic carbenonitrenes, C=(X)C–N, as a new brand of reactive intermediates, with conceivable singlet, triplet, or quintet ground states (X=H, 1, X=CH₃, 2, X=COOH, 3, X=F, 4, X=OH, 5, XX=OMe, 6, XX=CF₃, 7, XX=CN, 8, and XX=NH₂, 9). High-spin quintet (⁵A″) ground states are found for 1 and 2 at eight ab initio and DFT levels of theory. At the same levels, triplet (³A″) ground states prevail for 3–8. Low-spin singlet (¹A') input structures of 1, 2, and 4–9 cyclize spontaneously through optimization to their corresponding aromatic X-azacyclopropenylidenes, with multiplicities irrelevant to allylic carbenonitrenes. Researchers may aim for generating 3–8 with triplet states, or even 1 and/or 2 with quintet states, but we do not recommend going for generation of 9 with any multiplicity, and/or formation of 1–8 with singlet states.

Hydrolysis of trans-dichloro(ammine)(quinoline)platinum, a novel potential anticancer drug, is believed to be the key activation step before the drug reaches its intracellular target DNA. To obtain an accurate hydrolysis mechanism for this nonclassical class of square-planar Pt(II) complex, five different models were used at the experimental temperature with the solvent effect B3LYP/PCM using hybrid density functional theory. The stationary points on the potential energy surfaces for the first and second hydrolysis steps, proceeding via a five-coordinate trigonal-bipyramidal (TBP)-like structure of transition state, were fully optimized and characterized. The most remarkable structural variations in the hydrolysis process were found to occur in the equatorial plane of the TBP-like structures of the intermediates and transition states. It was found that the explicit solvent effect originating from the inclusion of extra water molecules into the system is significantly stronger than those arising from the bulk aqueous medium, especially for the first aquation step, which emphasizes the use of appropriate models for these types of problems. The results give detailed energy profiles for the mechanism of hydrolysis of trans-dichloro(ammine)(quinoline)platinum, which may assist in understanding the reaction mechanism of the drug with DNA target and in the design of novel platinum-based anticancer drugs with trans geometries.

We show that the equations of continuum electrostatics can be obtained entirely and simply from a variational free energy comprising the Coulomb interactions among all charged species and a spring-like term for the polarization of the dielectric medium. In this formulation, the Poisson equation, the constitutive relationship between polarization and the electric field, as well as the boundary conditions across discontinuous dielectric boundaries, are all natural consequences of the extremization of the free energy functional. This formulation thus treats the electrostatic equations and the energetics within a single unified framework, avoiding some of the pitfalls in the study of electrostatic problems. Application of this formalism to the nonequilbrium solvation free energy in electron transfer is illustrated. Our calculation reaffirms the well-known result of Marcus. We address the recent criticisms by Li and coworkers who claim that the Marcus result is incorrect, and expose some key mistakes in their approach.

An active site model for generic hydroxylation of xenobiotes by the fungus Rhizopus oryzae ATCC 11145 has been developed. The model was constructed using data from known metabolites of R. oryzae, as reported in the chemical literature, including diterpenes and steroids. The model takes the form of an irregular polyhedron of 340 ų volume, with two hydrophilic patches and an active site region. It was validated using data for other known substrates, including terpenes, steroids, octalin, and hydrindenone derivatives, drawn from the literature. The interpretive and predictive abilities of the model are discussed.

The coupling interactions and self-exchange reaction mechanisms between NO and ONH (NOH) have been systematically investigated at the B3LYP/6-311++G** level of theory. All the equilibrium complexes are characterized by the intermolecular H-bonds and co-planar geometries. The cisoid NOH/ON species is the most stable one among all the complexes considered due to the formation of an N–N bond. Moreover, all the cisoid complexes are found to be more stable than the corresponding transoid ones. The origin of the blueshifts occurring in the selected complexes has been explored, employing the natural bond orbital (NBO) calculations. Additionally, the proton transfer mechanisms for the self-exchange reactions have been proposed, i.e. they can proceed via the three-center proton-coupled electron transfer or five-center cyclic proton-coupled electron transfer mechanism.

Density functional theory (DFT) study is performed to investigate the influence of carbon substituting in a representative model of armchair boron nitride nanotubes (BNNTs). To this aim, the electric field gradient (EFG) tensors at the sites of ¹¹B and ¹¹N nuclei are calculated in two models of (4,4) single-walled BNNT. Model one (raw) consists of 36 B and 36 N atoms with 12 saturating H atoms of two mouths while 7 B and 7 N atoms are substituted by 14 C atoms like a wire in model two (C-substituted). The converted EFG tensors to measurable nuclear quadrupole resonance (NQR) parameters, quadrupole coupling constant (C_Q) and asymmetry parameter (η_Q), reveal that the C_Q values in the length of raw BNNT are divided into some layers with equal magnitude and among them the mouth layers have the largest C_Q magnitudes. In the C-substituted model, in addition to the mouth layers, the C_Q of those B and N nuclei directly bonded to C atoms are increased to the magnitudes as large as those mouth nuclei meaning that the active sites are increased in the C-substituted BNNT model. It is worth noting that the NQR parameters of other nuclei rather than those directly bonded to C and also those in the first neighborhood of C atoms are almost in equal values in the two models. Comparing the results with a recent study on zigzag BNNT (Mirzaei M et al., Z. Naturforsch A62:56, 2007) reveals that armchair and zigzag BNNTs show almost similar electronic properties. However, there is a significant difference in the electronic properties of those B and N atoms located at the mouth of the two BNNTs whose mouths are similar in armchair, whereas there are two different mouths (B-mouth and N-mouth) in zigzag BNNT.