A theoretical study of five nitrates: Electronic structure and bond dissociation energies

Three density-functional methods (B3P86, B3PW91, and B3LYP) are employed to investigate the O–NO₂ bond lengths, frontier orbital energies, and O–NO₂ bond dissociation energies (BDEs) of n-propyl nitrate (NPN), isopropyl nitrate (IPN), 2-ethylhexyl nitrate (EHN), triethylene glycol dinitrate (Tri-EGDN), and tetraethylene glycol dinitrate (Tetra-EGDN). It is found that the O–NO₂ bond lengthens (destabilizes) in the order of IPN, NPN, EHN, Tetra-EGDN, and Tri-EGDN. From the data of frontier orbital energies (E_HOMO, E_LUMO), and energy gaps (ΔE), we estimate the relative thermal stability ordering of five nitrates and their corresponding radicals. The predicted BDEs of O–NO₂ bond in NPN, IPN, EHN, Tri-EGDN, and Tetra-EGDN, are 176.6, 174.5, 168.1, 156.1, and 159.3 kJ mol⁻¹, respectively. Based on the finding that the present results of BDEs are well coincident with the experimental results of apparent activation energies from the literature, we can draw a conclusion that the experimental thermolysis of five nitrates is only unimolecular homolytical cleavage of the O–NO₂ bonds.     

Similarities and differences in the electron ionization-induced fragmentation of structurally related N-alkoxymethyl lactams and sultams

Unimolecular fragmentation patterns of the molecular ions of selected lactams and sultams bearing alkoxymethyl group at the nitrogen atom were studied. The main common fragmentation reaction observed for all compounds studied in this work is the elimination of an aldehyde molecule. This reaction is considered to proceed via two different mechanisms. For lactams, hydrogen rearrangement within an alkoxymethyl group is observed, which leads to the appropriate N-methyl derivatives. For sultams, transfer of the methyl group to the nitrogen and oxygen atoms, proceeding through an ion-neutral complex, dominates. Another important fragmentation channel characteristic exclusively for lactams is the loss of an alkyl radical. This process takes place within the N-alkoxymethyl moiety, yielding the appropriate protonated ion of N-formyllactams. This process is accompanied by relatively high kinetic energy release.     

Diffusion of Cesium Ions in Agar Gel Containing Alkali Metal Bromides

The present paper gives an account of different aspects of the tracer diffusion of Cs⁺ ions in alkali metal bromides. We have measured the diffusion coefficients, D, of cesium ions in 1% agar gel medium at 25 ^∘C using a zone-diffusion technique over a concentration range of 5 × 10⁻⁵ to 0.1 mol,dm⁻³. The values of the diffusion coefficients were found to deviate from theory, which are explained on the basis of different types of interactions occurring in the ion-gel-water system. The study is also focused on the effect of alkali metal bromides on the obstruction effect and activation energy for the tracer-diffusion of cesium ions in agar gel medium. It is observed that both parameters, extent of obstruction, ∝, and activation energy, E, decrease with increasing charge density of the cation of the supporting electrolyte. The influence of these trends is explained on the basis of competitive hydration between the ions and agar molecules, and the relative distortion in the water structure that is brought about by these different ions and agar molecules.     

Heavy metal phosphate nanophases in silica: influence of radiolysis probed via f-electron state properties

We have assessed the feasibility of carrying out time- and wavelength-resolved laser-induced fluorescence measurements of radiation damage in glassy silica. The consequences of alpha decay of Es-253 in LaPO₄ nanophases embedded in silica were probed based on excitation of 5f states of Cm³⁺, Bk³⁺, and Es³⁺ ions. The recorded emission spectra and luminescence decays showed that alpha decay of Es-253 ejected Bk-249 decay daughter ions into the surrounding silica and created radiation damage within the LaPO₄ nanophases. This conclusion is consistent with predictions of an ion transport code commonly used to model ion implantation. Luminescence from the ⁶D_7/2 state of Cm³⁺was used as an internal standard. Ion-ion energy transfer dominated the dynamics of the observed emitting 5f states and strongly influenced the intensity of observed spectra. In appropriate sample materials, laser-induced fluorescence provides a powerful method for fundamental investigation of alpha-induced radiation damage in silica.     

Ab initio Computational Modeling of Glyphosate Analogs: Conformational Perspective

A historical perspective on the application of conformational analysis to structure-based ligand design approach is presented. The application of isodensity molecular electrostatic potential surfaces with the conformational energy surfaces (CES) have allowed us to reach pertinent conclusions for aiding synthetic and biochemical studies. Here we illustrate such an application on the modeling of the potent analogs of an important, environmentally stringent herbicidal compound glyphosate by constructing conformational energy surfaces. The systems were modeled by substituting F, Cl, and NH— OH moiety to the position of pharmacophoric nitrogen center in glyphosate structure. All the calculations were thoroughly performed with ab initio MO theory at Hartree–Fock method using 3-21G(d) basis functions. On the basis of the results, we identified the bioactive conformations for N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate as (−38^∘, 77^∘), (−61^∘, 111^∘), and (−167^∘, −169^∘), respectively. Geometry optimization of certain selected conformations of these compounds using hybrid DFT method with 6–31+G(d) basis functions provides nearly equal values of φ and ψ. Moreover, the results indicate that the global minimum structures of N-fluoro and N-chloro analogs of glyphosate show cyclic conformation whereas the N-hydroxyamino-glyphosate global minimum structure shows spyrocyclic and zig-zag conformation. Also, the predicted bioactive conformation of N-hydroxyamino analog optimally overlaps with glyphosate backbone in EPSPS complex with 0.1 Å RMSD value. However, the other two compounds slightly deviate from the backbone of glyphosate with RMSD of 0.92 Å for N-fluoro-glyphosate and 0.83 Å for N-chloro-glyphosate. The linear N-hydroxyamino-glyphosate exhibits relatively more number of intermolecular hydrogen bond interactions as compared to the other two analogs. Further, comparison of CES of previously studied glyphosate analogs such as N-hydroxy-glyphosate (2.2 μM) and N-amino-glyphosate (0.61 μM) with the present systems reveals the order of activity as: N-hydroxyamino-glyphosate > N-fluoro-glyphosate > N-chloro-glyphosate based on CES flexibility. Also, the calculated heats of formation of N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate are −288, −209, and −288 kcal/mol, respectively, which clearly indicate that the N-hydroxyamino and N-fluoro analogs of glyphosate are thermodynamically more stable than N-amino-glyphosate (−278 kcal/mol).     

Apparent molal volumes of aqueous solutions of bis-tetraalkylammonium salts at 25°C: Methylene-group contribution to the limiting molal volume

Densities of aqueous solutions of a series of polymethonium chloride and bromide salts (CH₃)₃–N–(CH₂)_n–N–(CH₃)₃X₂ have been measured at 25°C. Apparent molal volumes have been calculated, and methylene-group contributions to the limiting apparent molal volumes °_v have been estimated. Constant values of the methylene-group contribution of 16.5 and 17.0 cm³-mole^–1 were obtained for the bromide and chloride salts, respectively. These values are consistent with methylene-group contributions reported for other series of organic electrolytes.     

Theoretical Study of Weakly Bound Dimers between Hydrogen Fluoride and Some Polar Molecules

Weakly bound linear and bent dimers, FH—X (where X = CO, OC, CNH, NCH, N₂O and ON₂), are investigated using the DFT B3LYP and ab initio MP2 methods with the same basis sets (6–311++G(3df,2pd)). The strengths of the H—C or H—N H‐bonds in dimers FH—CO, FH—CNH, and FH—N₂O are compared with those of the H—O or H—N H‐bonds in dimers FH—OC, FH—NCH, and FH—ON₂. The results obtained for the H‐bond distances, the elongation effect of the HF bond, the red shift of the HF stretching frequency, and the energy difference between the dimer and the charge transfer reveal that the H‐bonds of the first group of dimers are stronger than those of the second. The Gibbs energies calculated for the six dimer formations indicate that the weakly bound dimers are unstable at room temperature (T = 298 K) (FH—X's → FH + X's, ΔG < 0).     

Orbital correlation effects: The independent pair-potential approximation with application to the ground state and first ionized state of boron hydride

A new method is proposed for calculating correlation effects in atomic and molecular systems. The basis of the method is the formulation of a set of partial configuration expansions which yield directly variational orbital correlation corrections which are appropriately summed in order to obtain an estimate of the total correlation energy. This method is applied to the ground state of boron hydride and its cation at the equilibrium distance of BH. The results of the method are compared in detail with independent electron pair results and second order CI results. It is further shown that multiple substitutions are approximately accounted for in this method and the extent to which they are included is compared with other approximations. Finally, three methods of increasing accuracy, aimed at reducing the necessary computational effort, are given for determining the vertical ionization potential. The most economical method yields an IP of 9.70 eV or 0.03 eV less than the experimental IP. Completion of the basis is estimated to improve this value to 9.77 eV.     

Co-adsorption NO and organic molecules on Cu sites in zeolites: Quantum chemical DFT calculations

The co-adsorption of organic molecules: acetone, formaldehyde, ethene and acetylene together with NO on the same Cu⁺ site in zeolite CuZSM-5 was investigated by DFT calculations. The aim of this study was to follow the effect of NO on activation of multiple bonds in organic molecules and the effect of organic molecules on the activation of NO bond. The extent of activation of CO, CC, CC as well as of NO bonds was characterized by the result of calculation as the elongation of the multiple bonds, decrease of bond order as the decrease of stretching frequency, while population analysis gave information on the mechanism of activation. It has been found that the presence of NO co-adsorbed on the same Cu⁺ site as organic molecule resulted in more effective activation of CO bond in acetone and formaldehyde, but resulted in a less effective activation of CC and CC bond in ethane and acetylene. On the other hand, the presence of organic molecule resulted in more effective activation of NO bond (more important bond weakening) in NO molecule. The most significant NO bond weakening took place if NO was co-adsorbed with acetone or formaldehyde. Both acetone and formaldehyde transmit the most negative charge to the Cu⁺-zeolite system if adsorbed “solo” in Cu-zeolite. This negative charge may be next transmitted to antibonding NO orbitals resulting in so important NO bond weakening.     

Conformation of Tax-response elements in the human T-cell leukemia virus type I promoter

Background: HTLV I Tax is believed to activate viral gene expression by binding bZIP proteins (such as CRIB) and increasing their affinities for proviral THE target sites. Each 21 by THE target site contains an imperfect copy of the intrinsically bent CRE target site (the TRE core) surrounded by highly conserved flanking sequences. These flanking sequences are essential for maximal increases in DNA affinity and transactivation, but they are not, apparently, contacted by protein. Here we employ non-denaturing gel electrophoresis to evaluate TRE conformation in the presence and absence of bZIP proteins, and to explore the role of DNA conformation in viral transactivation.Results: Our results show that the TRE-1 flanking sequences modulate the structure and modestly increase the affinity of a CREB bZIP peptide for the TRE-1 core recognition sequence. These flanking sequences are also essential for a maximal increase in stability of the CREB-DNA complex in the presence of Tax.Conclusions: The CRE-like TRE core and the TRE flanking sequences are both essential for formation of stable CRIB-TRE-1 and Tax-CREB-TRE-1 complexes. These two DNA segments may have co-evolved into a unique structure capable of recognizing Tax and a bZIP protein.