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Azolylpentazoles as high-energy materials: a computational study.

The structures of highly energetic substituted pentazole compounds and their decomposition to give dinitrogen and the corresponding azide were investigated by ab initio quantum chemical methods. The substituents include azolyl groups (five-membered aromatic rings with different numbers of nitrogen atoms), CH(3), CN, and F. The decomposition pathway was followed for several substituted azolyl- and phenylpentazoles and compared to the known experimental and theoretical results. The NMR parameters of most of the as-yet unknown pentazole compounds were predicted. The activation energy for the decomposition increases, while the decomposition energy of the substituted pentazole decreases with greater electron-donating character of the substituent of the pentazole. Thus, anionic pentazoles are more stable than neutral pentazoles. Methylpentazole is predicted to be among the most stable pentazoles, even though it does not contain an aromatic system.

Journal Article↗

Lévy-Ciesielski random series as a useful platform for Monte Carlo path integral sampling.

We demonstrate that the Lévy-Ciesielski implementation of Lie-Trotter products enjoys several properties that make it extremely suitable for path-integral Monte Carlo simulations: fast computation of paths, fast Monte Carlo sampling, and the ability to use different numbers of time slices for the different degrees of freedom, commensurate with the quantum effects. It is demonstrated that a Monte Carlo simulation for which particles or small groups of variables are updated in a sequential fashion has a statistical efficiency that is always comparable to or better than that of an all-particle or all-variable update sampler. The sequential sampler results in significant computational savings if updating a variable costs only a fraction of the cost for updating all variables simultaneously or if the variables are independent. In the Lévy-Ciesielski representation, the path variables are grouped in a small number of layers, with the variables from the same layer being statistically independent. The superior performance of the fast sampling algorithm is shown to be a consequence of these observations. Both mathematical arguments and numerical simulations are employed in order to quantify the computational advantages of the sequential sampler, the Lévy-Ciesielski implementation of path integrals, and the fast sampling algorithm.

Journal Article↗

Rotational resonance NMR: separation of dipolar coupling and zero quantum relaxation.

The solid state NMR technique of rotational resonance (R2) has been used extensively to measure distances approaching 5-6 A between 13C nuclei in a variety of compounds including amyloidogenic peptides and membrane proteins. The accuracy of the distance information extracted from the time-dependent spin dynamics at R2 is often limited by the accuracy with which the relevant zero-quantum lineshape parameters are estimated. Here we demonstrate that measurement of spinning frequency dependent magnetization exchange dynamics provides data from which both distance and zero-quantum relaxation parameters can be extracted independently. In addition to providing more accurate distance information, this technique allows examination of the zero-quantum lineshape, which can indicate the presence of correlated relaxation or chemical shift distributions between dipolar-coupled sites. With this approach we have separated the contribution of dipolar couplings and zero quantum relaxation to R2 exchange curves. Thus, we have significantly improved the accuracy of the measurement of the intramolecular, internuclear distances between a pair of 13C's in two model compounds (N-acetyl-D,L-valine and glycylglycine.HCl) that lie in the distance range 4.6-4.7 A.

Carbon Isotopes↗

PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.

A program package for molecular simulations of biological molecules was developed. The package, "PEACH version 4 with ABINIT-MP version 20021029," was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [Chem.Phys. Lett. 313 (1999) 701], into PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities of the package were demonstrated. First, high parallel efficiency of FMO was demonstrated in a single point calculation of a protein. Second,FMO-MD simulations [Chem. Phys. Lett. 372 (2003) 342] of a peptide were performed with and without explicit solvent, and the simulations showed the influence of the solvent on the electronic state of the peptide.

Computational Biology↗

Double-quantum filtered rotational-echo double resonance.

The homonuclear scalar coupling of a directly bonded 13C-13C pair has been used to create a double-quantum filter (DQF) to remove the natural-abundance 13C background in 13C{15N} rotational-echo double-resonance (REDOR) experiments. The DQF scalar and REDOR dipolar evolution periods are coincident which is important for sensitivity in the event of weak 13C-15N dipolar coupling. Calculated and observed 13C{15N} DQF-REDOR dephasings were in agreement for a test sample of mixed recrystallized labeled alanines. Glycine metabolism in a single uniform-15N soybean leaf labeled for 6 min by 13CO2 was measured quantitatively by 13C{15N} DQF-REDOR with no background interferences.

Algorithms↗

A comparison of the physical imaging properties of Fuji ST-V, ST-VA, and ST-VN computed radiography image plates.

The physical imaging performance of ST-V, ST-VA, and ST-VN computed radiography image plates, read with a Philips AC3 acquisition system, was investigated at 70 kVp with 0.5 mm of copper beam filtration for four different entrance air kerma values: 0.5, 2.6, 26, and 260 micro Gy. Measurements included characteristic response, presampling-modulation transfer function, and Wiener spectrum analysis for (18 x 24) cm2 image plates, sampled at 10 pixels/mm. These results were used to calculate DQE spectral descriptions of system performance. ST-VN image plates exhibited a slightly superior DQE performance for the two lower entrance air kerma values investigated.

Quantum Theory↗

Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives.

The mutagenic activity of 23 triazenes and, in a different set, of 24 halogenated hydroxyfuranones (MX derivatives) is quantitatively related to new features of contemporary molecular wave functions. Nowadays affordable computers are powerful enough to rapidly generate geometry-optimised ab initio wave functions at HF/3-21G*, HF/6-31G* and B3LYP/6-311 + G(2d,p) level for all molecules. The bonds of a common molecular skeleton are described by their ab initio bond lengths and local properties provided by the theory of quantum chemical topology (QCT). The chemometric analysis involves two types: one to generate a statistically validated quantitative model, and one to isolate the active center. In the former a genetic algorithm (GA) selects bond descriptors in order to optimise the cross-validation error, q2, followed by a full partial least squares (PLS) analysis, which also yields randomisation statistics. In the latter type principal components (PCs) are constructed from the original bond descriptors and their variables important to the projection (VIPs) are plotted in a histogram. This analysis suggests a preferred mechanistic pathway for the initial hydroxylation of the triazenes, an issue that has remained ambiguous so far. In the case of the hydroxyfuranones the proposed method aids the elucidation of a mechanistic ambivalence.

Algorithms↗

FT-IR, FT-Raman spectra and scaled quantum mechanical study of 2,3-dihydroxy pyridine and 2,4-dihyroxy-3-nitropyridine.

The vibrational spectra of 2,3-dihydroxy pyridine (DHP) and 2,4-dihyroxy-3-nitropyridine (DHNP) have been computed using B3LYP methodology and 6-31G** basis set. The solid phase FTIR and FT Raman spectra were recorded in the region 4000-400 and 3500-100 cm(-1), respectively. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors.

Molecular Structure↗

Quantum chemical modeling of through-hydrogen bond spin-spin coupling in amides and ubiquitin.

Through-hydrogen bond spin-spin coupling has been investigated computationally in the formamide dimer and in fragments of the protein ubiquitin. The Fermi-contact term was calculated by finite perturbation theory with the B3LYP DFT method with several basis sets. The distance and angular dependence of the 3J(N,C') coupling constant (N-H--O=C) in the hydrogen-bonded formamide dimer was firstly examined for a wide range of mutual arrangements, also in relation to the stability of the dimer. The magnitude of 3J(N,C') is relatively insensitive to the dihedral angle between the two amide planes, whereas values between 1-2 Hz are calculated for a variety of arrangements, including non-linear hydrogen bonds, in agreement with the shape of some occupied, low-lying molecular orbitals which connect donor and acceptor. Then, fragments of the ubiquitin protein (for which such coupling constants are experimentally available) were generated by removing from the experimental structure all amino acids except those involved in hydrogen bonding, and coupling constants were calculated for such fragments. Although calculated 3J(N,C') values are sometimes overestimated, they generally correlate with the corresponding experimental values.

Amides↗

Trifluoroacetylsulfenyl trifluoroacetate, CF(3)C(O)-S-O-C(O)CF(3), a novel compound with a symmetrically substituted S-O bond: synthesis, spectroscopic characterization, and quantum chemical calculations.

The new compound trifluoroacetylsulfenyl trifluoroacetate, CF(3)C(O)SOC(O)CF(3), which possesses two identical carbonyl substituents attached to the S-O bond, has been synthesized. The IR and UV spectra of the gas phase as well as the (13)C NMR spectrum of the solution in CDCl(3) were recorded and assigned. Quantum chemical calculations were performed with the ab initio methods HF and MP2 and the density functional approach B3LYP. The 6-31G basis set was chosen in all calculations. The molecule possesses a skew structure, and according to all computational methods, the syn-syn structure (C=O bonds of both C(O)CF(3) groups synperiplanar to S-O bond) represents the most stable conformer. In agreement with the quantum chemical calculations, the presence of small amounts (< or =5%) of a second conformer (anti-syn) cannot be excluded on the basis of the IR spectrum. The calculated values for the torsional angle around the S-O bond (delta(C-S-O-C)) of the syn-syn form are smaller than 80 degrees (72-78 degrees). Comparison with theoretical results for the corresponding disulfide CF(3)C(O)SSC(O)CF(3) and peroxide CF(3)C(O)OOC(O)CF(3) indicates that the structural properties of sulfenyl compounds are more similar to those of disulfides than to those of peroxides.

Journal Article↗

Computational modeling of the catalytic reaction in triosephosphate isomerase.

We present a comprehensive analysis of the catalytic cycle of the enzyme triosephosphate isomerase (TIM), including both the reactive chemistry and the catalytic loop and side-chain motions. Combining accurate mixed quantum mechanics/molecular mechanics (QM/MM) and protein structure prediction methods, we have modeled both the structural and chemical aspects of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde 3-phosphate (GAP), for which there is a wealth of experimental data. The conjunction of this novel computational approach with the use of the recent near-atomic resolution TIM-DHAP Michaelis complex PDB structure, 1NEY.pdb, has enabled us to obtain robust qualitative and, where available, quantitative agreement with a wide range of experimental data. Among the principal conclusions that we are able to draw are the importance of the monoanionic (as opposed to dianioic) form of the substrate phosphate group in the catalytic cycle, detailed positioning and energetics of the key catalytic residues in the active-site, the flexible nature of Glu165, which favors its direct involvement in the formation of the enediol intermediate, energetics of the open and closed form of the catalytic loop region in the presence and absence of substrate, and quantitative reproduction of various experimentally measured reaction rates, typically to within approximately 1 kcal/mol. Our results are consistent with the available experimental data, and provide an initial picture as to why loop opening when GAP is the product has a higher barrier than when DHAP is the product.

Algorithms↗

Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation.

We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog-enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%.

Adenosine Triphosphate↗

Structural and quantum chemical factors affecting mutagenic potency of aminoimidazo-azaarenes.

A set of 16 mutagenic aminoimidazo-azaarenes, including four that have been isolated from cooked foods and identified as bacterial mutagens and rodent carcinogens, was selected from a larger series previously published [Hatch et al. (1991): Environ Mol Mutagen 17:4-19] for an in-depth structure-activity study using computational methods. Structural features believed to affect mutagenic potency were tabulated. Molecular orbital energies and other electronic properties of these compounds were calculated using Huckel, semiempirical AM1, and ab initio quantum mechanical methods. Factor interrelationships were studied by multiple linear regression and canonical correlation analyses. Our goal was an improved understanding of the chemical basis of mutagenicity for this class of heterocyclic amines. The major findings were as follows: 1) mutagenic potency is related to the size of the aromatic ring system; 2) potency is enhanced by the presence and location of an N-methyl group; 3) potency is enhanced by addition of ring nitrogen atoms in pyridine, quinoline, and quinoxaline configurations; 4) potency is inversely related to the energy of the LUMO (lowest unoccupied molecular orbital) of the parent amines; 5) potency is directly, though weakly, related to the LUMO energy of the derived nitrenium ions; and 6) the calculated thermodynamic stability of the nitrenium ions (relative to the parent amine) is directly correlated with nitrenium LUMO energy and with the negative charge on the exocyclic nitrogen atom. Although this study raises several intriguing issues relating mutagenicity to chemical properties, further study will be required to determine the plausibility of the nitrenium ion as the ultimate mutagen for binding to DNA.

Benzimidazoles↗

Self-assembly of concentric quantum double rings.

We demonstrate the self-assembled formation of concentric quantum double rings with high uniformity and excellent rotational symmetry using the droplet epitaxy technique. Varying the growth process conditions can control each ring's size. Photoluminescence spectra emitted from an individual quantum ring complex show peculiar quantized levels that are specified by the carriers' orbital trajectories.

Arsenicals↗

Musculoskeletal computed radiography in children: scatter reduction and improvement in bony trabecular sharpness using air gap placement of the imaging plate.

The effect of various air gaps on computed radiographic musculoskeletal images was investigated using a knee phantom. Scatter to primary radiation ratios were measured using the beam stop method at air gaps ranging from 0 to 30 in. (0-762-mm). Bony trabecular sharpness, line pair resolution, quantum mottle and visualization of low-contrast beads in the soft tissues were evaluated. A significant reduction of scatter to primary radiation ratio, from a value of almost 1 at table top to about 0.4 at 10-in. (254-mm) air gap and about 0.2 at 25-in. (635-mm) air gap placement of the computed radiography (CR) imaging plate, was obtained. A progressive improvement in bony trabecular sharpness and line pair resolution, compared with the table top and Bucky images was observed on 10-in. (254-mm) through 25-in. (635-mm) air gap images. Sharpness of the bony trabeculae and line pair resolution were best on the 25-in. (635-mm) air gap images. The skin entrance radiation dose does not have to be increased for air gap digital radiography. The radiographic noise or quantum mottle is highest on the Bucky image, higher on air gap images and minimal on the table top images, despite a high scatter to primary radiation ratio at the table top. The lower quantum mottle on the table top images allowed for maximal visualization of low contrast densities in the soft tissues. Air gap radiography further improves musculoskeletal computed imaging by reducing the scatter to primary radiation ratio without an increase in the skin entrance dose. For significant reduction of the scatter to primary radiation ratio and best evaluation of line pair spatial resolution and bony trabeculae, a 25-in. (635-mm) air gap with digital radiography would be optimal. For evaluation of low contrast densities in the soft tissues, table top placement would be the technique of choice.

Air↗

[Limiting resolution of X-ray computer tomography in examination of man].

It is shown as necessary to increase the intensity of radiation source by at least 20 times in order to ensure a 2-fold enhancement of resolution. It predetermines the permissible values of dose per object, which in their turn, condition the permissible values of quantum noise per image (tomogram) as well space and density resolutions. The dose, when intensified purposefully in order to enhance the tomography image resolution, is apparently a limitation for examination of man by X-ray computer tomography.

Humans↗

A computational study on the amine-oxidation mechanism of monoamine oxidase: insight into the polar nucleophilic mechanism.

The proposed polar nucleophilic mechanism of MAO was investigated using quantum chemical calculations employing the semi-empirical PM3 method. In order to mimic the reaction at the enzyme's active site, the reactions between the flavin and the p-substituted benzylamine substrate analogs were modeled. Activation energies and rate constants of all the reactions were calculated and compared with the published experimental data. The results showed that electron-withdrawing groups at the para position of benzylamine increase the reaction rate. A good correlation between the log of the calculated rate constants and the electronic parameter (sigma) of the substituent was obtained. These results agree with the previous kinetic experiments on the effect of p-substituents on the reduction of MAO-A by benzylamine analogs. In addition, the calculated rate constants showed a correlation with the rate of reduction of the flavin in MAO-A. In order to verify the results obtained from the PM3 method single-point B3LYP/6-31G*//PM3 calculations were performed. These results demonstrated a strong reduction in the activation energy for the reaction of benzylamine derivatives having electron-withdrawing substituents, which is in agreement with the PM3 calculations and the previous experimental QSAR study. PM3 and B3LYP/6-31G* energy surfaces were obtained for the overall reaction of benzylamine with flavin. Results suggest that PM3 is a reasonable method for studying this kind of reaction. These theoretical findings support the proposed polar nucleophilic mechanism for MAO-A.

Amines↗