Journal of Theoretical and Computational Chemistry

The association behaviors between Uracil and Zn²⁺ in vacuum and in the presence of extra water molecules have been investigated systematically using the density functional theory (DFT). In these systems, the interaction of Zn²⁺ with the carbonyl oxygen O₄ is systematically favored relative to O₂. For Uracil-Zn²⁺ complexes, the more stable coordination mode among the possible complexes corresponds to the bidentate one, where the monodentate coordination mode is about 37 kcal/mol higher in energy relative to the bidentate case. Correspondingly, the stabilities of these structures are enhanced due to the formations of the four-membered chelate ring in the bidentate coordination processes. In the monodentate coordination complexes, the hydration effects are larger than those in the bidentate coordination complexes. The most basic center in the Uracil remains the same regardless of whether introducing the water molecules to Zn²⁺ or not. The calculated Zn²⁺ bonding energies in Uracil-Zn²⁺(H₂O) complexes are reduced in comparison to those of the unhydrated Uracil-Zn²⁺ complexes. Moreover, investigations of stepwise hydration of Zn²⁺ in the most stable Uracil-Zn²⁺ complex suggest that the successive hydration effect on the Zn²⁺ site can enhance the strength of C=O bond in the Uracil-Zn²⁺ complexes and reduce the association interaction of Uracil with Zn²⁺. Additionally, the most acidic site of Uracil has been changed from N₁- to N₃–H group before and after introducing the Zn²⁺ and there is a significant increase in the overall acidity of the system.

A molecular dynamics simulation of the folding of a short helical toxin peptide was carried out. The simulation gave a folding time of ~10 ns, which is longer than typical time of ~1 ns for the formation of 1–2 helical turns. The simulation demonstrates that a helical peptide with disulfide bonds, which may encounter extra steric hindrance compared with the peptide without disulfide bonds, can fold in nanosecond timescale. An analysis shows that this folding time should correspond to the folding time in weak denaturation condition in experiment. Interactions and factors affecting folding pathways are analyzed and discussed.

Quantitative structure-activity relationship (QSAR) studies of a series of benzo[b]acronycine derivatives as a novel class of antitumor agents have been carried out using the density functional theory (DFT), molecular mechanics (MM+) and statistical methods. Some calculated parameters of geometric structures, electronic structures and molecular properties of the compounds were adopted as generalized descriptors (variables). Via a stepwise regression analysis, some main independent factors affecting the activities of the compounds were selected out, and then the quantitative structure-activity relationship (QSAR) equation was established. The results suggest that the energy difference (Δ ε_L-H) between the lowest unoccupied molecular orbital and the highest occupied molecular orbital, the net charges of the nitrogen atom N₁₁ and the first atom of the substituent R₂, and the hydrophobic parameter (log P₁) of the substituent R₁ are the main independent factors contributing to the antitumor activities of the compounds. The fitting correlation coefficient (r²) and the cross-validation coefficient (q²) for the model established by this study are 0.865 and 0.721, respectively, showing this model with a good predictability. The QSAR equation can be used to estimate unknown antitumor activity of this kind of compound, and thus design new compounds with high antitumor activities. Here, based on this QASR study, 4 new compounds with predicted high antitumor activities have been theoretically designed and they are expecting experimental verification.

2-pyrones undergo intramolecular thermal rearrangement resulting in the migration of groups at 3-position to 5-position and vice-versa. Rearrangement of 6-halopyrone is a tandem process involving electrocyclic ring opening and closure (ERO & ERC), rotation, sigmatropic shift. It has been modeled at MP2/6-31g (d) level to understand the migratory aptitude of the halogens. Computations show that electrocyclic transition state and the corresponding intermediate which could not be located in 2-pyrone rearrangement have been located for 6-fluoropyrone and 6-chloropyrone. Halogens effectively modulate the barriers of all the steps involved and NBO (Natural Bond Orbital) analyses clearly reveal the involvement of lone pairs in activating rotation and sigmatropic shift, and deactivating ERO and ERC.

A theoretical study has been carried out for internal rotation of nitrosoureas at the B3LYP/6-311G* level of theory. For each nitrosourea compound, two ground state structures have been found and the E isomer is predicted to be more stable than the Z isomer. Two transition state conformations for the isomerization have also been obtained and the calculated results show that the isomerization through TS1 is easier than that through TS2. The relationship between energy barrier and toxicity has also been investigated. It is concluded that the carcinogenic potency increases along with the decrease of rotational energy barrier.

The electrode potentials of (E)-3-(4,5-dihydroxy-2-(phenylsulphonyl) phenyl) acrylic acid (DPA), as a new caffeic acid derivative, in aqueous solution have been calculated. DPA has two geometric structures, cis and trans. Since the cis structure of caffeic is unstable, it cannot be found in nature, but in this research, its electrode potential have been calculated theoretically. The calculations have been performed using ab initio molecular orbital calculations (HF), and density functional theory (DFT) with the inclusion of entropic and thermochemical corrections to yield free energies of redox reactions. The electrode potential was also obtained experimentally by means of an electrochemical technique (cyclic voltammetry) and it was 335 mV for trans structure. The theoretical and experimental values for the electrode potential of the studied molecule are in excellent agreement. Geometric parameters and vibrational frequencies values of DPA and (2E)-3-(3,4-dioxo-6-(phenylsulfonyl) cyclohexa-1,5-dienyl)acrylic acid (DPDA is the oxidized form of DPA), were computed using same methods. The calculated IR spectrum of DPA used for the assignment of IR frequencies was observed in the experimental FT-IR spectrum. Correlations between theoretical and experimental vibrational frequencies of DPA molecule were 0.996. The agreement mutually verifies the accuracy of the experimental method and the validity of the applied mathematical model.

This work presents a statistical analysis of errors in the ab initio determination of molecular energy. These sets of analyses have allowed us to separate the errors in systematic and random components and also to realize that differences between experimental data and theoretical calculations are larger than those initially suspected. Although there is a limit to how small this difference can be analyzed by our methods, procedures to improve ab initio molecular energies are proposed. This has been achieved by reducing the systematic error obtained by correlating the calculated results to the most accurate data (in this case CCSD (T)), as well as by reducing the random error by mixing the results of different standard procedures.

The torsion potential energy surface for cyclodecane has been examined using molecular mechanics and quantum chemical methods. The boat-chair-boat (BCB) conformer is predicted as the most stable structure at all levels of theory employed, in agreement with low temperature experiments. We found 13 low-energy conformers that cover a range of ~10 kcal mol^-1. The relative abundance of the main isomers (named BCB, TBC, TBCC and TCCC) as a function of the temperature is discussed. In addition, energy calculations at high correlated levels of theory (MP4(SDTQ) and CCSD(T)) were for the first time performed for these conformations. In general, the predicted Gibbs population is in fairly good agreement with the experimental data. The simulated IR, VCD and ¹³C NMR spectra were obtained showing good accordance with the observed data, providing important features for conformational analysis of cyclodecane.

The transient chronoamperometric current for a catalytic reaction mechanism (EC' reaction) at cylindrical ultramicroelectrodes is derived using Danckwerts' expression for short time and slow reaction rate. The transient current for an EC' reaction at cylindrical microelectrodes for all time and all reaction rate is also reported.

The discrete variable representation (DVR) matrix dynamics formulation of the path integral Monte Carlo (PIMC) method, implemented numerically in a way that enables Metropolis sampling to be employed, is proposed as a means of computing ground state quantum wavefunctions. A key advantage of the DVR-PIMC approach is that customized marginal potentials may be employed, leading to significantly larger PIMC time step sizes, and substantial reductions in computational (CPU) effort. An additional key advantage of the present implementation is that the DVR provides a natural set of interpolant functions that can be used for accurate interpolation and extrapolation of function and tensor quantities away from predefined grid points. The new method is applied here to compute the ground state wavefunction of a model one degree-of-freedom (1 DOF) Morse oscillator system. A one-to-two order-of-magnitude reduction in CPU effort is observed, in comparison with a conventional PIMC simulation. The generalization for many DOFs is straightforward, and expected to result in even greater performance enhancement.

The reaction mechanism of the activation of ethane by nickel atom has been investigated by density functional theory (DFT). The geometries and vibration frequencies of reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311 + +G(d, p) level. Two main pathways, C–C bond activation and C–H bond activation, are identified. In former channel, the rate-limiting step is found to be hydrogen-transferring step with a high barrier of 227 kJ · mol^-1. In the C–H bond activation pathway, the second hydrogen-transferring step is the rate-determining step of the whole reaction. The barrier of the step is 71 kJ · mol^-1. Our results show that the studied reaction would undergo along C–H bond activation pathway to form the products H₂ molecule and Ni⋯ethene complex. The present theoretical work indicates that Ni atom is more active than Ni⁺ cation in activating ethane.

The Oxidation potentials of pyrogallol and some of its derivatives in aqueous solutions have been calculated. The calculations have been performed using ab initio molecular orbital calculations (HF), and density functional theory (DFT) with the inclusion of entropic and thermochemical corrections to yield free energies of redox reactions. The polarizable continuum model is used to describe the solvent. It was also obtained experimentally with the aid of an electrochemical technique (cyclic voltammetry). The theoretical and experimental values for the oxidation potential of the studied pyrogallol and some derivatives are in excellent agreement with each other and there is only a discrepancy of 0.025 V and 0.020 V for B3LYP and HF methods, respectively, between experimental and theoretical results. The agreement mutually verifies the accuracy of the experimental method and the validity of the applied mathematical model.

This study investigated the RDX (1,3,5-Trinitro-1,3,5-triazine) molecule to elucidate its possible decomposition species and the corresponding energies by performing the density-functional theory (DFT) calculations. Reasonable decomposition mechanisms are proposed based on the bond energy calculated using the differential overlap (INDO) program, which yields the weakest bonding site for reference and determines the site of easy cleavage. Computational results indicate that the activation energy of direct cis-form HONO elimination is lower than that of direct trans-form HONO elimination and that of a two-stage elimination of two forms of HONO (N–N bond fission combined with C–H bond breaking) in the initial decomposition step, which are 213.9 kJ/mol and 93.8–101.8 kJ/mol, respectively. Two possible pathways are proposed; (1) N–N bond homolytic cleavage followed by elimination of cis-form HONO, and (2) N–N bond homolytic cleavage followed by elimination of trans-form HONO.

We investigate the photodetachment of H^- near an inelastic interface semiclassically. It is found that the inelasticity of an interface has significant influence on the photodetachment process. We have derived an analytical formula of the cross section of photodetachment. The spectrum of photodetachment consists of a smooth background and a sinusoidal oscillation whose frequency depends on the electronic energy, the reflection of the wall and the distance between the ion and the wall.

The equilibrium geometries, energies, harmonic vibrational frequencies, stability, and aromaticities for the , E₄Fe, and [Fe(η⁴ - E₄)₂]^2- (E = N, P, As, Sb, and Bi) species are studied using density functional theory (DFT). The ground states of the E₄Fe and [Fe(η⁴ - E₄)₂]^2- systems are predicted to be C_s and D_4d structures, respectively. Orbital analysis indicates that the orbital interactions between the π orbitals of the ligands and the atomic orbitals of the d⁶ iron center are the main bonding scheme for these [Fe(η⁴ - E₄)₂]^2- (D_4d) complexes. The stability of the [Fe(η⁴ - E₄)₂]^2- complexes exhibits the order P > As > Sb > Bi > N for E. On the basis of comparison with the known ferrocene, the NICS analysis confirms that the [Fe(η⁴ - E₄)₂]^2- (D_4d) as well as ferrocene are aromatic. The dissected NICS reveals that the aromaticities of the [Fe(η⁴ - E₄)₂]^2- (D_4d) are primarily attributed to the effects of their E–E π bonds and Fe lone pairs.

In this work, the interaction of hydroxyl and hydroperoxyl radicals with ethene in the presence of water molecules and the stability of C₂H₄ + HO_x + (H₂O)_y; x = 1–2, y = 0–5 clusters were investigated using computational methods. Also, hydrogen bond of these clusters was investigated using Density Functional Theory (DFT) and Atoms in Molecules (AIM) theory. Thermodynamical parameters for the interaction of hydroxyl and hydroperoxyl radicals with ethene in the presence of water molecules were also calculated. We report new results for the interaction of hydroxyl and hydroperoxyl radicals with ethene in the presence of water molecules.

The optimized geometries of the methoxy, ethoxy, iso-propoxy and tert-butoxy anions were calculated using the B3LYP/6-311++G(d, p) theoretical level. Thereby, these structures were used to explore their hydration clusters by means of the AGOA methodology. Analyzing the molecular electrostatic potential of the solute and using the TIP4P model to locate the water molecules over the alkoxide anions, it was observed that the energies of the hydration clusters decrease in order from methoxy to the tert-butoxy. These results corroborate the experimental acidity of the correspondent conjugate alcohols, indicating that the AGOA methodology can be used as an efficient computational methodology to appraise the structures of molecules in aqueous media.