Journal of Theoretical and Computational Chemistry

The luteolin has been extracted from Euphorbia schimperiana then ¹H NMR, ¹³C NMR and 2D NMR spectra were measured. The ground-state geometries have been computed by using density functional theory (DFT) at B3LYP/6-31G* and M06/6-31++G** level of theories. The time dependent density functional theory (TD-DFT) has been applied to compute the absorption spectra with and without solvent. The absorption spectra have been computed in methanol to check the effect of solvent using the polarized continuum model (PCM). On the basis of bond dissociation enthalpy (BDE) and the adiabatic ionization potential (IP), we have explained the antioxidant activity of luteolin and its rotamer/positional isomer. Two mechanisms have been explained for the radical scavenging processes, i.e. hydrogen atom transfer and one-electron transfer.

This paper presents a first principles calculation of the structure and electronic properties of four crystal GeO₂ structures and two rare-earth element oxides CeO₂ and La₂O₃. A GGA was used to optimize structures and calculate band structure and density of states (DOS). It is found that La₂O₃ has the largest band gap (4.19 eV) among all the six structures, which also means it is the best insulator among them. When it comes to four crystal GeO₂ structures, which were calculated to make a comparison with two insulators CeO₂ and La₂O₃, we found the q-GeO₂ and b-GeO₂ are more likely to work as the dielectrics used in MOS devices than the other two crystalline forms. Three of the four GeO₂ forms have larger band gap than that of CeO₂ (2.09 eV), which indicates CeO₂ is not a wise choice when deposited directly on the surface of Ge substrate.

In order to identify the structure of the most stable tautomers of 6-amino-5-formyluracil and its N-methylated derivatives in different pH conditions, relative stabilities of potential tautomers in aqueous phase have been calculated taking into account the entropy effects over the tautomeric equilibria. In each medium, the tautomer with lower energy must be the most representative form at the corresponding pH and the knowledge of the effect of the medium in the tautomerization energies allows evaluating the possible effect of the medium over the molecular stability. The results show that, in aqueous phase, the order of basicity of protonation sites in the 6-amino-5-formyluracil derivatives is N9 > (N3 > N1) > (O8 > O4 > O2). The 6-amino-5-formyluracil derivatives act as an amino-formyl-keto tautomer with a strong imino character, although, upon successive deprotonations, a growing contribution of enolyzed forms which explain the increasing labilization of carbonyl bonds must be pointed out.

The nature of alumazine⋯M (M = Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, AND Ca²⁺) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical shift (NICS) method was applied for evaluating the variation in aromaticity of alumazine ring upon complexation.

An accurate prediction of the molecular acidity by employing ab initio or density functional approaches for typical molecular systems is still challenging. Recently, we proposed to utilize two quantum descriptors, molecular electrostatic potential (MEP) and the sum of valence natural atomic orbital (NAO) energies on the nucleus of both the acidic atom and leaving proton, to quantitatively evaluate the pK_a values. This new approach has been validated by a number of organic and inorganic systems and justified within the framework of density functional reactivity theory (DFRT). In this work, we apply the approach to building blocks of biological systems, namely, 20 natural α-amino acids and 5 DNA/RNA bases, together with a few other biologically relevant species. Our results show that there exists a strong linear correlation between MEP on the nucleus of the N atom and the sum of N 2p NAO energies, with the correlation coefficient R² = 0.99. Also, we observe that both MEP on the nitrogen nucleus and the sum of N 2p NAO energies correlate well with experimental pK_a values, with the correlation coefficient equal to 0.91. Using this established model, we predicted the trend of pK_a changes of amino acids in proteins with different dielectric constants. We also applied the model to predict pK_a values for dipeptides. Implications of these linear relationships to understand functions and reactivity of biological systems are discussed as well.

Comparative study about the adsorption and dissociation behaviors of H₂O molecule on clean and vacancy defective Al (111) surface was conducted by extensive density functional theory (DFT) calculations, the interaction mechanisms between H₂O molecule and Al (111) surface were also figured out. Geometry optimization results indicated that H₂O molecule was apt to be adsorbed at top site on these two kinds of surfaces, whereas, the adsorption configurations, the adsorption type and inclination of H₂O molecule planes away from the normal were different. The calculated adsorption energies demonstrated that the adsorption of H₂O molecule occurred more readily on vacancy defective Al (111) surface. The electron density distribution indicated that the vacancy defect enhanced the interactions between H₂O molecule and surface Al atoms. Further analysis of the density of states (DOS) showed that the vacancy defect increased the number of bonding electrons between H₂O molecule and surface Al atoms. The detailed exploration of dissociation pathways demonstrated that the dissociation of H₂O molecule on these two kinds of surfaces was a two-step process: (1)H₂O→H+OH, (2)OH→H+O. However, for each step the dissociation pathway variations on vacancy defective Al (111) surface were different with those on clean Al (111) surface. Compared with the first step, the dissociation of hydroxyl group into O atom and H atom was kinetically difficult. The calculated lower activation energy barriers on vacancy defective Al (111) surface showed that the vacancy defect had catalytic effect for the dissociation of H₂O molecule to some extent, especially for the first step.

Density functional theory (DFT) calculation has been carried out to investigate the isomers of N-(1-phenyl-3-methyl-4-propenylidene-5-pyrazolone)-salicylidene. Chemical potential, chemical hardness and global electrophilicity, which are considered as global indices, have been calculated to assess the stability and reactivity of the tautomers. The condensed Fukui function is calculated for predicting the most probable sites for electrophilic attack. Molecular electrostatic potential is calculated to predict the regions for electrophilic attack.

Oseltamivir (OTV) is widely used in the treatment of both influenza virus A and B infections. Additionally, OTV is an effective antiviral drug in treating the 2009 A (H1N1) influenza virus. Clinical studies concluded that OTV is readily extensively converted to the active carboxylate metabolite after oral administration. In order to investigate the metabolism mechanism of OTV, we carried out density functional theory (DFT) quantum mechanical calculations. The molecule orbital (MO) theory and natural population analysis (NPA) were also employed to help understanding the reaction mechanism. All possible reaction pathways for OTV metabolism are considered, involving hydrolysis of ester and amide. Two mechanisms were considered in this work, viz. concerted mechanism and stepwise mechanism. Our results indicate the stepwise mechanism is more favorable in both hydrolysis reactions and the rate-determining stage is the formation of the tetrahedral intermediate. In addition, the hydrolysis reactions can be assisted by substrate NH2 group and solvent water molecules. The substrate-assisted mechanism for the formation of the carboxylate metabolite is the most favorable one.

Artemisinin is widely employed to treat malaria. A variety of experiments have been done to research the dissolution property of artemisinin in different solvents. To have an in-depth understanding of the property, it is essential to explore the dissolution property from molecular level with molecular dynamics (MD) simulation, which needs a satisfactory force field of artemisinin. Therefore in the research a quantum chemistry based force field was developed. The quantum chemical calculation at different levels was done and Hartree–Fock (HF) level calculation gives satisfactory results. The charge distribution was then determined successfully. The van der Waals (VDW) parameters of the C unit with sp³-C were tuned according to the difference between the dissolution enthalpy of artemisinin in ethanol and ethyl acetate. With the developed force field, MD method was employed to successfully simulate the dissolution property of artemisinin in different solvents. The simulation results show that artemisinin molecules tends to aggregate in water, while in the aqueous solution of ethanol, the same number of artemisinin molecules tends to disperse. Furthermore, simulation results show that 8 M ethyl acetate aqueous solution has better dissolution ability than 8 M ethanol aqueous. The simulation gave agreements with the experimental results.

The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values of thiazolylazopyrimidine chromophores have been investigated by using density functional theories (DFT/B3LYP, PBE1PBE and BHand-HLYP) and Hartree–Fock (HF) methods with 6–31++G(d,p) basis set. The computed IR and NMR spectra are used to determine the types of the experimental bands observed. Also, the vibrational frequencies are supported on the basis of the potential energy distribution (PED) analysis calculated by using PBE1PBE method. The UV-vis spectrum has been obtained by TD-DFT and TD-HF methods. Total static dipole moment (μ), the mean polarizability (〈α〉), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (〈β〉), highest occupied molecular orbital (HOMO), and lowest occupied molecular orbital (LUMO) energies of thiazolylazopyrimidine chromophores also have been investigated with quantum chemical calculations. Obtained nonlinear optical (NLO) parameters are compared with experimental ones. Additionally, the molecular hardness (η) and electronegativity (χ) parameters have been obtained by using the frontier molecular orbital energies. Obtained data from thiazolylazopyrimidine chromophores are important for associating the experimental and theoretical spectra with molecular structure and their properties.

In this work, a detailed theoretical investigation of the substituent groups effect on the geometric and electronic properties of the newly proposed molecular wire has been performed with the DFT-B3LYP/6-31G* level of theory by considering the influence from the external electric field (EF). The results show that the performance of molecular wire is very sensitive to the electron donating (–NH₂ and –OH), electron withdrawing (–NO₂ and –F) groups and external EF intensities. The energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), E_LUMO–E_HOMO (HLG) in all cases decreased, furthermore, the electron withdrawing –NO₂ group had a much lower HLG than the other substituted groups. Results of this study indicate that the substitutions and external electric field can be used to tune the properties of a molecular scale device effectively.

Using traditional theoretical imaging method, we predict invisible oscillations in the photodetachment cross section of near a thin soft surface. A laser which is polarized parallel to the surface is used to knock off electron from . Analytical expressions are derived for detached electron flux and photodetachment cross section. The results depend on the inter ion surface distance and separation of the atomic centers of the molecular anion. It is found that the surface strongly affects the detached electron flux and the photodetachment cross section. Unlike the detached electron flux the cross section displays non-oscillating structure. The non-oscillating structure is attributed to the parallel orientation of the laser polarization direction with the thin elastic surface.

Time-Dependent Discrete Variable Representation (TDDVR) method was implemented by involving "classical" trajectories on each degrees of freedom (DOF) for the dynamics of multi-surface multi-mode Hamiltonian. The major focus of this article is to explore the efficiency of the serial and parallelized TDDVR algorithm for relatively large dimensional quantum dynamics in presence of non-adiabaticity among the electronic states. As a model system, the complex photoelectron spectra and non-radiative decay dynamics of trifluoroacetonitrile radical cation (CF₃CN⁺) are theoretically simulated with the aid of such parallelized algorithm, where the five lowest electronic states (X²E, A²A₁, B²A₂, C²A₁, and D²E) of the Hamiltonian are interconnected through several conical intersections in the vicinity of Frank–Condon region with twelve (12) active vibrational modes. The Jahn–Teller splitting of the X²E and D²E states makes the coupled five-surface system to a more challenging quantum dynamical seven-surface twelve-mode model. The results obtained from the TDDVR approach show very good agreement with the profiles of both Multi Configuration Time-Dependent Hartree (MCTDH) methodology and experimental technique, where its' sequencial and parallelized algorithm depict closely linear scalability with the increasing number of basis set vis-a-vis DOFs.

The change of bond dissociation energy (ΔBDE) in the C–NO₂ bond upon the formation of the intermolecular hydrogen-bonding or molecule-cation interaction between the nitro group of seven kinds of nitro-1,2,4-triazoles and HF or Na⁺ was investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df, 2p) and aug-cc-pVTZ basis sets. The C–NO₂ bond strength was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitro-1,2,4-triazole molecule. The increment of the C–NO₂ BDEs correlated well with the H-bonding interaction energy or molecule-cation interaction energy. The analysis of AIM, NBO and electron density shifts showed that the electron density shifted toward the C–NO₂ bond upon complex formation, leading to the strengthened C–NO₂ bond and the possibly reduced explosive sensitivity. The ΔBDE of the C–NO₂ bond in the Na⁺ complex is far larger greater than that in the corresponding HF system. Thus, introducing cation into the structure of the nitrotriazole might be more efficacious to reduce explosive sensitivity than the formation of the intermolecular hydrogen-bonded complex.

Theoretical calculations 6-311++G(d,p) have been performed in order to obtain binding energies and molecular properties of complexes involving nitrous oxide (N₂O) and two HX (X = F, Cl, Br and CN) molecules. Our calculations have revealed the existence of eleven stable structures. The vibrational changes which take place in the HX acid after complexation follow the usual behavior: the HX stretching frequency is shifted downward whereas its IR intensity is much enhanced. The new vibrational modes arising upon H-bond formation, were verified, especially, those associated with the out-of-plane and in-plane HX bending modes, which are pure rotations in the HX isolated molecule.

We present detailed theoretical studies of the proton transfer (PT) in the 3-Mercapto-propenethial (MP) and in some of its derivatives. The effect of substitution on the transition state structures corresponding to the PT in R2 or R1(3) positions is studied by using B3LYP/6-311++G** level of theory in gas phase and water solution. The following substituents have been taken into consideration: Cl, F, OH, SH, OCH₃, SCH₃, CHO, NO₂, CCH and OCF₃. For the different derivatives of 3-MP, we have computed geometries and potential energy curves for the intramolecular PT in their ground. Also, the excited-state properties of intramolecular hydrogen bonding in substituted systems have been investigated theoretically using the time-dependent density functional theory method. The π-electron delocalization parameter (Q) and HOMA index as a geometrical indicator of a local aromaticity are investigated. Natural bond orbital (NBO) analysis was also performed for better understanding the nature of intramolecular interactions. The results of analysis by Quantum theory of "Atoms in Molecules" and NBO method fairly support the DFT results. Correlations between the PT reaction barrier versus topological parameters, ν(S–H) and γ(S–H) are also probed. The obtained results showed a strong influence of the R substituent on the PT reaction barrier changes. Numerous correlations between topological, geometrical, thermodynamic properties and energetic parameters were also found.