Molecular electrostatic potentials and Mulliken charge populations of DNA mini-sequences

Theoretical study of Gibbs free energy and NMR chemical shifts, of the effect of methyl substituents on the isomers of (E)-1-(α,Ꞵ-Dimethylbenzyliden)-2,2-diphenylhydrazine

A theoretical analysis of free Gibbs Energy and NMR 1H 13C chemical shifts of the effect of introduce methyl groups on diphenyl rings, to produce different isomers of (E)-1-(α,Ꞵ-dimethylbenzylidene)-2,2-diphenylhydrazine, is presented. IR vibrational frequencies, Mulliken charges, molecular electrostatic potential (MEP), Gibbs free energy (G) and 1H- and 13C-NMR chemical shifts were obtained by theoretical calculations. In this analysis it was found that the position of the methyl group affects the values of the 1H- and 13C-NMR chemical shifts and the ∆G and ∆H thermodynamic properties of formation and reaction, these properties vary with the same trend, for the isomers studied. Gibbs free energy calculations show that the theoretical (E)-1-(3,4-Dimethylbenzylidene)-2,2-diphenylhydrazine isomer is the most stable, which explains the success of the experimental synthesis of this compound among the other isomers. For this molecule, the C of the HC=N group is the most nucleophilic and the H is the least acidic. The 1H-NMR chemical shifts of protons show a strong correlation with the C=N distance. It was also observed that methyl affects the ν(C=N) frequencies, the C=N distance increases when the inductive effect of the methyl groups is in the structure.

New Insights into the Structure and Reactivity of Uracil Derivatives in Different Solvents-A Computational Study

Ab initio calculations were carried out to understand the reactivity and stability of some uracil derivatives, cytosine, 1-methyl cytosine, and cytidine in solvents, water, dimethyl sulfoxide (DMSO), n-octanol, and chloroform. Geometries were fully optimized at MP2 and B3LYP using the 6-31+G(d,p) basis set by applying the Solvation Model on Density (SMD) in solvent systems. The syn conformer of cytidine (cytidine II) is the most stable conformer in the gas phase, while the anticonformer (cytidine IV) is most stable in all of the solvents. Solvation free energy and polarizability values in different solvents decrease in the order water > DMSO > n-octanol > chloroform, while dipole moment, first-order hyperpolarizability, and HOMO-LUMO energy gap values follow the order of polar protic solvent (water and n-octanol) > polar aprotic solvent (DMSO) > nonpolar solvent (chloroform). The solvation free energy, dipole moment, polarizability, and first-order hyperpolarizability values also follow the order of cytosine > 1-methyl cytosine > cytidine. To illustrate that the molecular properties correlate well with the reactivity of the molecules, ab initio calculations were carried out for the reaction of uracil derivatives with Br₂ in the gas phase, water, DMSO, n-octanol, and chloroform. All ground and transition state geometries were fully optimized at B3LYP/6-31+G(d,p), and energies were also calculated at G3MP2 for cytosine and 1-methyl cytosine. For cytosine and 1-methyl cytosine, Gibbs energies of activation decrease with the polarity of the solvent that is chloroform > n-octanol > DMSO > water, while the Gibbs energies of activation for the reaction with cytidine decrease in the order of water > DMSO > n-octanol > chloroform. These results suggest that solvent polarity is very important for the stability and reactivity of uracil derivatives. Hydrogen bonding may also play an important role mainly for cytidine. Free energies of activation decrease with the size of the molecule, i.e., cytosine > 1-methyl cytosine > cytidine.

Mechanochemical mechanism of rapid dechlorination of hexachlorobenzene

Recent researches indicate that mechanochemical treatment (MCT) is a promising method to degrade the environmental hazards, especially in the area of persistent organic pollutants (POPs) disposal. However, the mechanochemical dechlorination mechanism of POPs still needs to be further verified. In this mechanochemical process, hexachlorobenzene (HCB) was chosen as a model pollutant with aluminum and alumina (Al+Al₂O₃) powders as the co-milling regents. Both of the intermediate analysis and quantum chemical calculations were adopted to elucidate the free radical dechlorination mechanism of HCB. The solid residues were characterized by electron spin-resonance (ESR) spectroscopy, Fourier transform infrared (FTIR) spectra and X-ray photoelectron (XPS) spectra, which proposed that the radicals formed in the mechanochemical process were chlorinated phenoxyl radicals (CB-O). Four quantum chemical descriptors were selected in predicting the intermediates and reaction pathway: (i) atomic charge, (ii) electrostatic potential (ESP), (iii) frontier molecular orbitals (FMO) theory and (iv) dual descriptor. Then, a stepwise dechlorination mechanism based on CB-O was proposed. It was found that the intermediates and radical-related reactions in the mechanochemical dechlorination of HCB are quite different from that happen in a typical photocatalytic dechlorination process. Impacts of different radical reactions on the dechlorination of HCB were also compared at last.

An integrated experimental and theoretical investigation of the vibrational modes and molecular structure of a chelate, tetraaqua cysteine aluminum(III)

The complex formed by Al(3+) and cysteine in aqueous solution has been studied by potentiometry, Raman spectroscopy and DFT calculations (DFT:B3LYP/6-311++G(∗∗)). Atomic charges, frontier molecular orbitals, electrostatic potential contour surface, electrostatic potential map and donor-acceptor second order perturbative energies were examined. The [Al(Cys)(H2O)4](2+) complex adopts a distorted octahedral geometry. Cysteine should act as a bidentate ligand through the oxygen of the carboxylate and the nitrogen of the amino group. The molecule has high HOMO-LUMO energy gap, intense intramolecular charge transfer and positive electrostatic potential.

Crystal growth and properties of NLO optical crystal - Butylated Hydroxy Toluene (BHT)

Crystallographic, experimental and theoretical density functional theory (DFT) of Butylated Hydroxy Toluene (BHT) are investigated. The grown crystals were identified by single crystal X-ray analysis. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of BHT is calculated using B3LYP/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO/NLMO analysis. The molecular electrostatic potential (MESP) mapping is very useful in the investigation of the molecular structure with its physiochemical property relationship. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charge is also calculated. Because of vibrational analysis, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-Vis spectra and electronic absorption properties are explained and illustrated from the frontier molecular orbitals. The grown crystals were characterized by measuring their thermal properties by Differential Thermal Analysis (DTA) and Thermo Gravimetric Analysis (TGA) measurements.

Experimental and theoretical investigation of [Al(PCr)(H2O)] complex in aqueous solution

Phosphocreatine is a phosphorylated creatine molecule synthesized in the liver and transported to muscle cells where it is used for the temporary storage of energy. In Alzheimer's disease, the capture of glucose by cells is impaired, which negatively affects the Krebs cycle, leading to problems with the generation of phosphocreatine. Furthermore, the creatine-phosphocreatine system, regulated by creatine kinase, is affected in the brains of Alzheimer's disease patients. Aluminum ions are associated with Alzheimer's disease. Al(III) decreases cell viability and increases the fluidity of the plasma membrane, profoundly altering cell morphology. In this study, one of the complexes formed by Al(III) and phosphocreatine in aqueous solution was investigated by potentiometry, (31)P and (27)Al NMR, Raman spectroscopy and density functional theory (DFT) calculations. The log KAlPCr value was 11.37±0.03. Phosphocreatine should act as a tridentate ligand in this complex. The (27)Al NMR peak at 48.92ppm indicated a tetrahedral molecule. The fourth position in the arrangement was occupied by a coordinated water molecule. Raman spectroscopy, (31)P NMR and DFT calculations (DFT:B3LYP/6-311++G(**)) indicated that the donor atoms are oxygen in the phosphate group, the nitrogen of the guanidine group and the oxygen of the carboxylate group. Mulliken charges, NBO charges, frontier molecular orbitals, electrostatic potential contour surfaces and mapped electrostatic potential were also examined.

Experimental and theoretical study of p-nitroacetanilide

The spectroscopic properties of the p-nitroacetanilide (PNA) were examined by FT-IR, FT-Raman and UV-Vis techniques. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The UV-Vis absorption spectrum of the compound that dissolved in ethanol was recorded in the range of 200-400 nm. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional theory (DFT) employing B3LYP methods with the 6-31G(d,p) and 6-311+G(d,p) basis sets. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear optical (NLO) properties such as electric dipole moment and first hyperpolarizability have been computed using B3LYP quantum chemical calculation.

Molecular structure of tetraaqua adenosine 5'-triphosphate aluminium(III) complex: a study involving Raman spectroscopy, theoretical DFT and potentiometry

The Alzheimer's disease is one of the most common neurodegenerative diseases that affect elderly population, due to the formation of β-amyloid protein aggregate and several symptoms, especially progressive cognitive decline. The result is a decrease in capture of glucose by cells leading to obliteration, meddling in the Krebs cycle, the principal biochemical route to the energy production leading to a decline in the levels of adenosine 5'-triphosphate. Aluminium(III) is connected to Alzheimer's and its ion provides raise fluidity of the plasma membrane, decrease cell viability and aggregation of amyloid plaques. Studies reveal that AlATP complex promotes the formation of reactive fibrils of β-amyloid protein and independent amyloidogenic peptides, suggesting the action of the complex as a chaperone in the role pathogenic process. In this research, one of complexes formed by Al(III) and adenosine 5'-triphosphate in aqueous solution is analyzed by potentiometry, Raman spectroscopy and ab initio calculations. The value of the logK(AlATP) found was 9.21±0.01 and adenosine 5'-triphosphate should act as a bidentate ligand in the complex. Raman spectroscopy and potentiometry indicate that donor atoms are the oxygen of the phosphate β and the oxygen of the phosphate γ, the terminal phosphates. Computational calculations using Density Functional Theory, with hybrid functions B3LYP and 6-311++G(d,p) basis set regarding water solvent effects, have confirmed the results. Frontier molecular orbitals, electrostatic potential contour surface, electrostatic potential mapped and Mulliken charges of the title molecule were also investigated.

Direct studies on 5-coordinate intermediates formed during substitution at tetrahedral Fe sites: role of bound nucleophile in labilisation of leaving group

The substitution reactions of the tetrahedral Fe sites in [FeCl(4)](-), [Fe(2)S(2)Cl(4)](2-), [Fe(4)S(4)Cl(4)](2-) and [{MoFe(3)S(4)Cl(3)}(2)(micro-SEt)(3)](3-) with 4-RC(6)H(4)S(-) (R = MeO, Me, H, Cl or NO(2)) all involve rapid binding of the thiolate to a Fe site and formation of a kinetically and spectroscopically detectable intermediate. Kinetic studies allow calculation of the rate of Fe-Cl dissociation from the 5-coordinate site of the intermediate (k(2)(R)). The rate of Fe-Cl dissociation from the intermediate exhibits a marked dependence on the nature of the bound thiolate with log(10)(k(2)(R)) increasing in a linear manner with the calculated NBO charge on the sulfur atom of the coordinated thiolate. This behaviour indicates that Fe-Cl bond dissociation at the 5-coordinate intermediate involves a process in which Fe-thiolate bond shortening occurs prior to movement of the Fe-Cl bond.

Ab initio GB study of methylation reaction of adenine, cytosine, guanine, and thymine by methanediazonium ion

Methylation reaction at ten nucleophilic sites in four DNA base molecules by methanediazonium ion (N(2)Me+) was examined by ab initio MO/GB calculation which includes the solvent effect with the continuum model using the generalized Born formula. The stabilization energy of the ion-dipole complex as well as the energy of the transition state are roughly consistent with the experimental fraction of methylation by N -methyl- N -nitrosourea. For the guanine N7 site, which is the principal site of methylation, the stabilization energy is the largest and the energy of the transition state is low. The reactions at the guanine O6 and N7 sites were analysed by drawing the potential energy surface with respect to two parameters, the O6-C(Me) distance and the N7-C(Me) distance. The methylation reactions of the guanine O6 and N7 sites begin from the common geometry, the global minimum in the two-dimensional potential energy surface.