A quantum chemical study on the mechanism of the consecutive addition of HCN to propionitrile

MINDO/3 MO method has been used to study the mechanism of the consecutive addition of HCN to propionitrile. The results obtained for the first five steps show that the reaction is exothermic, and step 1 is the rate determining step.     

A quantum chemical study on the reactivity of four licorice flavonoids scavenging ·OOCl3C

Structural Chemistry - Isoliquiritigenin, liquiritigen, uralenol, and neouralenol are four natural licorice flavonoid compounds extracted from licorice, which have the ability of scavenging free...     

A quantum chemical study of the infrared absorption intensities of the isoelectronic C2v systems H2F+, H2O and NH−2

The results of a comparative theoretical study of the dipole moment derivatives and infrared absorption intensities within the double harmonic approximation are presented for the isoelectronic, isostructural C_2v molecules: H₂F⁺, H₂O and NH⁻₂. The calculations, performed at the ab initio SCF and CI levels of theory, utilize basis sets of triple zeta+two polarization functions quality. For the ions H₂F⁺ and NH⁻₂, in the absence of adequate experimental data the equilibrium geometries and force constants were also calculated. The trends observed in the dipole moment derivatives for the three systems are indicative of the amount of electronic charge associated with the hydrogen atoms and are very similar to the trends noted for a set of C_3v hydrides.     

How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study

A comprehensive conformational analysis of isolated 2'-beta-deoxy-thymidine (T), canonical DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) level of theory. At 298.15 K, all 92 conformers of isolated dT are within a 7.49 kcal/mol Gibbs energy range. Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature: syn/anti = 61.6%:38.4% and S/N = 74.5%:25.5%. However, at 420 K, the majority of conformers contain anti base and the population of North (N) sugars increases: syn/anti = 38.0%:62.0% and S/N = 59.5%:40.5%. The whole conformational parameters (P, chi, gamma, delta, beta, epsilon, nu max) were analyzed as well as the energies of the OH...O intramolecular H-bonds on the basis of nu(OH) stretching vibrations. Convolution of calculated IR spectra of all of the T conformers appears consistent with its low-temperature matrix spectrum (Ivanov et al. Low Temp. Phys. 2003, 29, 809). The maximal discrepancy in frequencies between calculated and experimental spectra is less than 1%. A conclusion was made that for reliable reconstruction of the isolated nucleoside IR spectrum the quasi whole set of conformers should be taken into consideration. In essence, this result opens up a possibility to reconstruct IR spectra of isolated nucleosides at physiological temperatures with rather satisfactory probability.     

Structure of aluminum(III (μ-OXO)bis [phthalocyaninate]): A quantum chemical study

The quantum chemical (U)B3LYP/6-31G(d ₅,p) method is used to determine the structural parameters and ionization potentials of aluminum(III) (μ-oxo)bis[phthalocyaninate] and monophthalocyaninate PcAlCl. Two (PcAl)₂O structures with similar energies are obtained: an eclipsed high-symmetry (D _4h ) structure with a rectangular AlOAl group and a retarded low-symmetry (C _s ) structure with the AlOAl bond angle of 167.5°. The AlO bonds include a substantial π component. The energy needed for the detachment of two electrons from a free (PcAl)₂O molecule is 13.46 eV.     

A functional feature analysis on diverse protein–protein interactions: application for the prediction of binding affinity

Protein–protein interactions (PPIs) play crucial roles in diverse cellular processes. There are different types of PPIs based on the composition, affinity and whether the association is permanent or transient. Analyzing the diversity of PPIs at the atomic level is crucial for uncovering the key features governing the interactions involved in PPI. A systematic physico-chemical and conformational studies were implemented on interfaces involved in different PPIs, including crystal packing, weak transient heterodimers, weak transient homodimers, strong transient heterodimers and homodimers. The comparative analysis shows that the interfaces tend to be larger, less planar, and more tightly packed with the increase of the interaction strength. Meanwhile the strong interactions undergo greater conformational changes than the weak ones involving main chains as well as side chains. Finally, using 18 features derived from our analysis, we developed a support vector regression model to predict the binding affinity with a promising result, which further demonstrate the reliability of our studies. We believe this study will provide great help in more thorough understanding the mechanism of diverse PPIs.     

Primary photoprocesses of 3,3’-diethylthiacarbocyanine in the presence of cucurbit[7]uril: Laser flash photolysis and quantum chemical calculations

The effect of cucurbit[7]uril on the phototransformation of 3,3′-diethylthiacarbocyanine iodide dye in aqueous solution has been investigated by nanosecond laser flash photolysis. The presence of cucurbit[7]uril results in the formation of its complex with the dye molecule producing a dimer. The dimer formation is evident from the ground and triplet-triplet absorption spectra. The dimers in the triplet state are capable of electron transfer. The structure of the complexes is suggested on the basis of quantum chemical calculations.     

A rotating disk electrode study of the catalytic waves produced by dismutation of O2− in the presence of superoxide dismutase

An equation is derived for the catalytic currents controlled by different dismutation processes of superoxide ion and by diffusion at a rotating disk electrode. Experimental data confirming the theoretical conclusions are presented for Cu, Zn superoxide dismutase.     

Water-mediated interactions in the CRP–cAMP–DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0 ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP.     

A calorimetric adsorption study on the interaction of water with hydroxylated surface of γ-Al2O3

The curve for the differential heat of adsorption of water on γ aluminum oxide has parts related to the interaction of the adsorbed water molecules with surface molecules of coordinated water and with acid and basic hydroxyl groups. Estimates have been made of the effective charges and hydration numbers for three of these adsorption centers. Textural changes have been observed in the γ-Al₂O₃ particles related to interplate swelling in the secondary sorbent packets into which the primary particles are linked. A. V. Dumanskii Institute for Colloid and Water Chemistry, National Academy of Sciences of Ukraine, 42 Prospekt Akademika Vernadskogo, Kiev-142 03680, Ukraine. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 36, No. 2, pp. 121–125, March–April, 2000.     

Organic quantum chemistry—XVI : A theoretical study of the structures and electronic spectra of cyclobutadiene and dimethylenecyclobutene

The structure and UV spectrum of cyclobutadiene have been studied theoretically by a modification of the Pariser-Parr method, which explicitly includes the effect of the sigma system in determining molecular geometry. It was concluded that the ground state is probably a triplet with the geometry of a regular square. The UV spectrum for the actual triplet molecule is predicted to show a strong absorption band at about 363 mμ, and the compound should be colored, probably yellow. The lowest singlet state has a rectangular geometry, and it is predicted to show no allowed transitions above 200 mμ, but because of forbidden transitions at 439 and 487 mμ, should appear red in color.     

A quantum chemical study of the infrared absorption intensities of the isolectronic C3v systems NH3, H3O+ and CH−3

The dipole moment derivatives and the infrared absorption intensities for the isoelectronic, isostructural species NH₃, H₃O⁺ and CH⁻₃, calculated by ab initio quantum methods within the double harmonic approximation, are reported. The calculations were performed at the SCF, CI and CPA″ levels of theory using basis sets of triple zeta+two polarization functions quality. For the ions H₃O⁺ and CH⁻₃, in the absence of adequate experimental information, the calculations are fully ab initio, since the equilibrium geometries as well as the force constants had to be computed. The applicability of the harmonic treatment to systems with inversion potentials is discussed, especially with regard to H₃O⁺. The dipole moment derivatives of the three systems show interesting, regular trends in accordance with the amount of electronic charge associated with the hydrogen atoms.     

A study of the mechanism of rhodium/phosphine-catalyzed hydroformylation: use of 1,1′-bis(diarylphosphino)ferrocene ligands

Rhodium/phosphine-catalyzed hydroformylation was studied using 1,1′-bis(diphenylphosphino)ferrocene and several derivatives containing substituents on the phenyl groups (p-Cl, m-F, and p-CF₃). The results with these disphosphine ligands suggest that the operative mechanism differs in several ways from the accepted mechanism for hydroformylation catalyzed by Rh/Ph₃P. The most important difference is that the most selective catalyst has three phosphorus atoms bound to each rhodium atom and is postulated to be a dirhodium complex. Using these ligands, selectivities to products were correlated by a Hammett σ-ϱ plot, with electron-withdrawing groups (less basic ligands) affording higher rates and higher linear : branched aldehyde ratios. This confirms previous work which qualitatively indicated that the linear : branched ratio increases as ligand basicity decreases.     

A quantum chemical study of conformational and tautomeric preferences, intramolecular hydrogen bonding and π-electron delocalization on dinitrosomethane; in gas phase and water solution

HF, B3LYP, and MP2 methods with the standard basis set, 6-311++G(d,p), were employed to study various aspects of dinitrosomethane (DNM). These results are compared with the outcomes of G2, G2MP2, G3, and CBS-QB3 methods. In the present study, we first characterized the equilibrium conformations, especially global minima. In general, the nitroso-oxime (NO) tautomers of DNM are stabler than the dioxime and dinitroso ones. Furthermore, it was found that the stablest form of NO tautomer is global minima among the known local minima. Surprisingly, the chelated form of NO tautomer, with O–H···O intramolecular hydrogen bond (IMHB), is less stable than the global minimum. In spite of this instability, we comprehensively studied various aspects of IMHB to evaluate the effect of heteroatom’s (N). The results of open–close and related rotamer models predict that the heteroatoms weaken the hydrogen bond, whereas, the geometric, topologic, and natural bond orbital parameters emphasize on opposite conclusion. The HOMA of aromaticity aromaticity index clearly predicts that the π-electron delocalization of chelated form of NO tautomer is greater than the malonaldehyde. Finally, the solvent effects on the properties of DNM tautomers have been estimated by continuum (PCM, IPCM, and SCIPCM), discrete, and mixed models. Theoretical results clearly show that the potential energy surface of DNM, especially global minima, is strongly affected by the solvent.     

Evaluation of the effect of the chiral centers of Taxol on binding to β-tubulin: A docking and molecular dynamics simulation study

Taxol is one of the most important anti-cancer drugs. The interaction between different variants of Taxol, by altering one of its chiral centers at a time, with β-tubulin protein has been investigated. To achieve such goal, docking and molecular dynamics (MD) simulation studies have been performed. In docking studies, the preferred conformers have been selected to further study by MD method based on the binding energies reported by the AutoDock program. The best result of docking study which shows the highest affinity between ligand and protein has been used as the starting point of the MD simulations. All of the complexes have shown acceptable stability during the simulation process, based on the RMSDs of the backbone of the protein structure. Finally, MM-GBSA calculations have been carried out to select the best ligand, considering the binding energy criteria. The results predict that two of the structures have better affinity toward the mentioned protein, in comparison with Taxol. Three of the structures have affinity similar to that of the Taxol toward the β-tubulin.