Natural Orbital Population Analysis Research Articles

Spin-Crossover Temperature Predictable from DFT Calculation for Iron(II) Complexes with 4-Substituted Pybox and Related Heteroaromatic Ligands.

Spin-crossover (SCO) is a reversible transition between low and high spin states by external stimuli such as heat. The SCO behavior and transition temperature (T1/2) of a series of [FeII(X-pybox)2](ClO4)2 were studied to establish a methodology for ligand-field engineering, where X-pybox stands for 2,6-bis(oxazolin-2-yl)pyridine substituted with X at the 4-position of the pyridine ring. We utilized X = MeO, Me, 3-thienyl, Ph, H, MeS, 2-thienyl, N3, Cl, Br, 3-pyridyl, and 4-pyridyl. The solution susceptometry on five new derivatives with X = Me, 2-thienyl, N3, Br, and 3-pyridyl was performed in acetone, giving the SCO temperatures of 220, 260, 215, 280, and 270 K, respectively. The density-functional-theory molecular orbital (MO) calculation was performed on the ligands with geometry optimization. The atomic charge on the pyridine nitrogen atom [ρ(Npy)] was extracted from the natural orbital population analysis. Positive correlation appeared in the T1/2 versus ρ(Npy) plot with R2 = 0.734, being consistent with the analysis using the Hammett substituent constants (σp and σp+). This finding well agrees with the mechanism proposed: the rich electron density lifts the t2g energy level through the dπ–pπ interaction, resulting in a narrow t2g–eg energy gap and favoring the high-spin state and low T1/2. The MO method was successfully applied to the known SCO-active iron(II) compounds involving 4-substituted 2,6-bis(pyrazol-1-yl)pyridines. A distinct positive correlation appeared in the T1/2 versus ρ(Npy) plot. The comparison of correlation coefficients indicates that ρ(Npy) is a more reliable parameter than σp or σp+ to predict a shift of T1/2. Furthermore, this method can be more generalized by application to another known SCO family having 3-azinyl-4-p-tolyl-5-phenyl-1,2,4-triazole ligand series, where azinyl stands for a 2-azaaromatic ring. A good linear correlation was found in the T1/2 versus ρ(NA) plot (NA is the ligating nitrogen atom in the azaaromatic ring). Finally, we will state a reason why the present treatment is competent to predict the SCO equilibrium position only by consideration on the electronic perturbation.

Reaction mechanism of oxidative desulfurization of heterocyclic organic sulfides: a computational study

The potential energy surfaces of the oxidation of two model heterocyclic organic sulfides thiophene and benzothiophene were examined using H2O2 and HCO3H as oxidants adopting CCSD(T), ωB97X-D, M06-2X and B3LYP at the 6-311+G (d,p) level of theory. Stationary points on the potential energy surfaces for the first and second oxidation reaction were fully optimized and characterized. The natural orbital population analysis was also performed to understand the charge distribution. The results suggest that the oxidation of benzothiophene is faster than that of thiophene using both oxidants, and HCO3H is more efficient than H2O2 in oxidation of both sulfides, which are in accordance with the experimental observation. Such results may assist in understanding the reaction mechanism of the oxidative desulfurization of sulfides.

Oxidation mechanism of dibenzothiophene compounds: A computational study

The potential energy surfaces of the oxidation of three model heterocyclic organic sulfides dibenzothiophene (DBT), 4-methylbenzothiophene (MDBT) and 4,6-dimethyldibenzothiophene (2MDBT) were examined using HCO3H as oxidants adopting MP2, ωB97X-D, M06-2X and B3LYP methods at 6-311+G (d,p) level. The stationary points on the potential energy surfaces for the first and second oxidation reaction were fully optimized and characterized. The natural orbital population analysis (NPA) was also performed to understand the charge distribution. The calculated results may contribute to understanding the reaction mechanism of the ODS of refractory DBT sulfides.

A theoretical study on transition state of the antitumor drug: Gold(III) dithiocarbamate derivative interaction with cysteine and DNA purine bases

Interactions of hydrated Au III(DMDT)Cl 2 (DMDT = N, N-dimethyldithiocarbamate) complexes with sulfur-containing cysteine and DNA purine bases are performed using the density functional theory (DFT) with the B3LYP/(LanL2DZ + 6-31G(d,p)/6-311++G (2d,2p)) functional. The calculated energy profiles show that the corresponding activation barriers for the substitution reactions of the chloroaqua complex are far lower than those of the diaqua complex except adenine. Remarkably, there exist intrinsic kinetic competitions among three active sites (S, N and O) of cysteine. The N and S sites of cysteine are equally favorable and superior to N7 of guanine in the reactions of the chloroaqua complex, whereas N7 of guanine is the strongest and the soft metal center Au prefers N site of cysteine over S in those of the diaqua complex, and the O site is the weakest in all reactions. Moreover, to estimate the environmental effect, the investigation of the activation free energies for the substitution reactions in dependence of the dielectric constant ε (4, 24 and 78.39) is systematically performed, and it is demonstrated that the environmental effect has only an impact on the reactions of the diaqua complex binding to cysteine to some extent. Lastly, the natural orbital population analysis (NPA) performed in this work proves that the change in electron density between the metal center and ligands has occurred in the reactions.

Theoretical study of anticancer drug trans-[Pd(dmnp)2Cl2] binding to DNA purine bases, phosphate group and amino acid residues

The reaction mechanism of the binding of the completely hydrolyzed trans-[Pd(dmnp)2Cl2] (dmnp = 2,6-dimethyl-4-nitropyridine) complexes to DNA and peptides was investigated computationally using model molecules and density functional theory calculations at the B3LYP level. To test the solvent effect, single-point energy calculations for the structures optimized in all reactions were conducted by employing the polarizable continuum model (IEF-PCM). The pentammineruthenium fragment had been intensively studied and also constituted a good model for antitumor trans-[Pd(dmnp)2Cl2], while the considered bases/ligands had been chosen as models for the main binding sites of DNA, nucleobases, and phosphate backbone and proteins, nitrogen-containing histidyl, and sulfur-containing residue such as methionine or cysteine. The activation free energies had been calculated for all the considered metal binding sites both in the gas phase and in solution and allowed building a binding affinity order for the considered nucleic acid or protein binding sites. Additionally, to better understand the interactions between the compounds and binding sites, the natural orbital population analysis (NPA) was adopted for every stationary point to employ the mutative trend of the net charge on the three important atoms which directly related to the reactions.

Theoretical study of anticancer drug cis-dichloro(pyridin-2-ylcarboxaldimine)-palladium(II) compounds containing bulky fluorinated aryl groups binding to purine bases: The activity of three isomers

The reaction mechanism for the monofunctional and bifunctional binding of the three isomers of cis-dichloro(pyridin-2-ylcarboxaldimine)-palladium(II) compounds containing bulky fluorinated aryl groups to guanine (G) and adenine (A) were investigated using density functional theory calculations at the B3LYP level. To test the solvent effect, we performed single-point energy calculations for several selected structures by employing the polarizable continuum model (IEF-PCM). The calculations indicate that the hydrogen bonds play an important role in stabilizing the complexes included in the first and second substitution. Particularly, H⋯F TFM hydrogen bond was observed in the reactions. The activation free energies for the monofunctional and bifunctional binding of the three isomers, referred to as d, e and f, to DNA base increases in the order d < f < e (see Scheme 1), respectively, which is in agreement with the experimental result reported by Scales et al. The electronic factors are more dominant than steric factors in the substitution reaction of purine base with water. Additionally, to better understand the interactions between the compounds and binding sites, the natural orbital population analysis (NPA) was adopt for every stationary point to employ the mutative trend of the net charge on the three important atoms which directly related to the reactions.

Binding to DNA purine bases and amino acid residues of a ruthenium(II) antitumor complex: A density functional study

The hydrolyzed α-[Ru(azpy) 2Cl 2] (azpy is 2-(phenylazo)pyridine; α indicates that the isomer in which the coordinating pairs Cl, N(py), and N(azo) are cis, trans, and cis, respectively) binding to guanine (G), adenine (A), methionine (Met), and histidine (His) residues were investigated by using density functional theory. Reactant complexes (RC), product complexes (PC), and transition states (TS) involved were fully characterized. The calculated energy profiles showed that the activation free energies for the substitutions of hydrolyzed α-[Ru(azpy) 2Cl 2] with Met was apparently lower than those of guanine and adenine. This indicate that the hydrolyzed α-[Ru(azpy) 2Cl 2] compounds may preferentially bind to the sulfur-containing amino acids residues in vivo. Moreover, the natural orbital population analysis (NPA) showed that the Ru atom gained the greatest negative charges in the reactions of hydrolyzed α-[Ru(azpy) 2Cl 2] with Met, which may contribute to their remarkably low activation free energies partially.

Binding of ansa- and non-ansa-titanocene anticancer drugs to DNA: a DFT study

The complexes [Ti(η5-C2H4{CMe2CH2CH2CH=CH2})2Cl2] (1) and [Ti{Me2Si(η5-C5Me4)(η5-C5H3{CMe2CH2CH2CH=CH2})}Cl2] (2) exhibited significant antitumor activity, but the detailed mechanism of antitumor effect remains unknown. In current research, we studied the hydrated 1 and 2 bindings to potential biological targets, purine bases, and phosphate group, using density functional theory and IEF-PCM solvation models. Our calculations reveal that the monoaquated complex binding to guanine shows the lowest activation free-energy with 15.3 and 21.5 kcal/mol for the complexes 1 and 2, respectively. In the diaquaed 1, the lowest activation-free energy is 16.7 kcal/mol for the guanine and closely followed by the phosphate group is 18.3 kcal/mol, while the lowest activation-free energy is 16.9 kcal/mol for the complex 2 binding to the phosphate group. In addition, natural orbital population analysis (NPA) method was performed for the investigation of major electronic characteristics.

Theoretical study of 3d‐metal mononitrides using DFT method

Abstract3d‐Metal mononitrides are studied using the density functional theory method. The lowest spin state for these dimers is obtained using the B3LYP hybrid functional with the 6‐311+G* basis set. The equilibrium geometries, vibrational frequencies, binding energies, Mulliken, and natural orbital population analysis charges, natural orbital electronic configuration, electron affinity, and ionization potential are obtained. Mulliken as well as natural orbital population analysis charges indicate that for all dimers, in cations most of the positive charge localized on the transition metal atom where in anions most of the negative charge localized on nitrogen atom. The binding energies for 3d‐metal mononitrides are higher than those for monocarbides and monoxides. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

A theoretical investigation on the [formula omitted] clusters by density functional theory methods

The first systematic study of the Ti ( H 2 O ) n 0 , 1 + ( n = 1 – 5 ) series of clusters is herein presented at the level of the DFT B3LYP method in conjunction with electron core potential basis sets. The investigated structures are relevant for laser-induced and laser-ablation syntheses of titanium compounds, and also for fundamental spectroscopy studies of metal-bearing species in the gas phase. Calculated properties include optimal geometries, total energies, bond lengths, bond angles, natural orbital population analysis charges, and hydration dissociation energies inter alia. Present results reveal a strict correlation between the clusters total energy and their spin state. Without exception, the most stable neutral (cation) clusters Ti ( H 2 O ) 1 – 5 0 + [ Ti ( H 2 O ) 1 – 5 1 + ] are those with spin state S = 1 ( S = 3/2). Comparisons with a few available theoretical results show good agreement.

A computational study on CunN0,±1 (n=1–4) clusters by density functional methods

Abstract Clusters of the type CunN0,±1 (n=1–4) are investigated computationally using density functional theory methods. Equilibrium geometries are optimized under the constraint of well-defined point-group symmetries at the B3LYP level employing a pseudo-potential method in conjunction with double-zeta basis sets. In this article, different molecular properties such as total energies, electron affinities, ionization potentials, fragmentation energies and equilibrium geometries of the CunN0,±1 (n=1–4) clusters are systematically calculated and discussed. In particular, the photoelectron spectra of the anionic CunN−1 (n=2–4) clusters are calculated showing a good agreement with the available experimental results. In addition, Mulliken and natural orbital population analyses, and natural orbital configurations are calculated in order to elucidate the charge distributions in the clusters.