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PubMed1996

Vibrational coupling between the nitro groups in 1,4-dinitrobenzene and 1,3-dinitrobenzene molecules: ab initio and normal coordinate analyses treatments.

Ab initio quantum chemical computations have been performed for 1,4-dinitrobenzene and 1,3-dinitrobenzene and their (15)N isotope-labeled derivatives at the 3-21G, 6-31G and 6-31G(*) basis set levels. The results have been compared with the experiment: the best coincidence has been obtained by the 6-31G method for 1,4-dinitrobenzene and by the 6-31G(*) method for 1,3-dinitrobenzene. The isotopic frequency shifts of the nitro group bands, induced by (14)N-(15)N labeling and the vibrational coupling between the nitro groups, calculated with GAMESS software, have been in accordance with the measured ones. A normal coordinate analysis has been carried out for the 1,4-dinitro- benzene molecule using a slightly modified force field of 1,3-dinitrobenzene, reasonable fit between the observed and calculated frequencies has been obtained. The results support the conclusion that the electronic contribution to the vibrational coupling between the two nitro groups in the studied dinitrobenzenes is negligible: thus, it may be suggested that the dynamical coupling will predominate.

Journal Article↗
PubMed1996

Analysis of IR spectra of carbon clusters trapped in noble gas matrices using algorithms based on digital filtering techniques.

IR spectra of carbon clusters C(n) (n>/=3) trapped in noble gas matrices (Ar and Kr) at temperatures of 13, 30 and 35 K are analyzed using algorithms based on digital filtering techniques and non-linear least-squares fitting. The spectral features at different temperatures and in different matrices are discussed. The majority of the resolved lines are assigned to C(n) cluster species based on data obtained via quantum chemical computations and from tunable laser IR spectrometry of C(n) species in the gas phase. A complete analysis of the IR spectra is available upon request.

Journal Article↗
PubMed2002

The effect of steric constraints on the adsorption of phenyltin onto the dipalmitoylphosphatidylcholine bilayer.

In this paper, we present studies concerning phenyltin adsorption onto the dipalmitoylphosphatidylcholine bilayer. Phenyltin compounds are known to be biologically active, and their molecular geometry makes it possible to study the effect of steric constraints on their ability to penetrate the model lipid membrane. Using a fluorescence probe as a reporter of the amount of adsorbed compound, we evaluated their affinity to the membrane as a function of the membrane state. The amount of the adsorbed compound was found to depend on the adsorbing molecule's geometry and lipid bilayer organization. The fluorescence measurements were supported by the density functional theory (DFT) method of quantum mechanical computations. The penetrant location was correlated with the possible relative positions of its polar and hydrophobic moieties to determine if it could adopt structural requirements of the local membrane environment. Molecules were deformed by a model force, mimicking interactions within the membrane interfacial region. Computations show that the diphenyltin molecule can be deformed to such an extent that it can adopt an amphiphilic conformation. Triphenyltin is different, as its bending requires more energy. Born repulsion energies from hydrophobic fluid into water for phenyltins were also computed in an isodensity-polarized continua model of DFT computation. Our results indicate that the phenyltin compounds incorporate into the interface of the lipid membrane, although diphenyltin integrates more deeply than triphenyltin, which locates on the double layer's surface, and this is due to the fact that the main role is played by steric and not electrostatic interactions.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2005

Proximal effects in the modulation of nitric oxide synthase reactivity: a QM-MM study.

Nitric oxide synthases (NOS) are heme proteins that have a cysteine residue as axial ligand, which generates nitric oxide (NO). The proximal environment, specifically H-bonding between tryptophan (Trp) 178 and thiolate, has been proposed to play a fundamental role in the modulation of NOS activity. We analyzed the molecular basis of this modulation by performing electronic structure calculations on isolated model systems and hybrid quantum-classical computations of the active sites in the protein environment for wild-type and mutant (Trp 178 x Gly) proteins. Our results show that in the ferrous proteins NO exhibits a considerable trans effect. We also showed that in the ferrous (Fe(+2)) mutant NOS the absence of Trp, experimentally associated to a protonated cysteine, weakens the Fe-S bond and yields five coordinate complexes. In the ferric (Fe(+3)) state, the NO dissociation energy is shown to be slightly smaller in the mutant NOS, implying that the Fe(+3)-NO complex has a shorter half-life. We found computational evidence suggesting that ferrous NOS is favored in wild-type NOS when compared to the Trp mutant, consistently with the fact that Trp mutants have been shown to accumulate less Fe(+2)-NO dead end species. We also found that the heme macrocycle showed a significant distortion in the wild-type protein, due to the presence of the nearby Trp 178. This may also play a role in the subtle tuning of the electronic structure of the heme moiety.

Binding Sites↗
PubMed2004

Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution.

Molecular dynamics (MD) simulations on heparin-water-sodium systems were carried out in order to establish a simulation protocol able to represent heparin solution conformation under physiological conditions. Atomic charges suitable for heparin oligosaccharides were obtained from ab initio quantum-mechanical computations, at the 6-31G(**) level. The GROMACS forcefield, the SPC, and SPC/E water models were employed. Also heparin was simulated with IdoA residues in 1C(4) or 2S(0) conformational states. The results of the performed MD simulations are in agreement with the available experimental data, suggesting that this approach can be applied for the study of heparin interactions with its target proteins and thus play a role in the development of new antithrombotic agents.

Carbohydrate Conformation↗
PubMed2005

Vibrational spectroscopic encoding of polystyrene-based resin beads: converting the encoding peaks into barcodes.

A detailed approach is described for the vibrational spectroscopic encoding of polystyrene-based resin beads by converting the infrared absorption peaks suitable for encoding (encoding peaks) into barcodes. Based on combining the FT-IR measurements and the quantum-chemical computations, the vibrational characteristics of p-tert-butylstyrene monomer, polystyrene and poly(p-tert-butylstyrene) resin beads are analyzed, which are helpful for the selection of encoding peaks. The vibrational spectroscopic encoding of polystyrene-based resin beads could be obtained by converting the wavenumber, intensity and full width at half maximum (FWHM) of the encoding peaks into barcodes automatically through a computer program designed in our laboratory.

Electronic Data Processing↗
PubMed1999

Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21.

Quantum chemical computations using the ab initio molecular orbital (MO) method have been performed to investigate the molecular switching mechanism of Ras protein p21, which has an important role in intracellular signal cascades. Lys(16) was demonstrated to be crucial to the function of Ras p21, and the hydrolysis of GTP to GDP was found to be an one-step reaction. The potential energy barrier of this hydrolysis reaction from GTP to (GDP + P) was calculated to be approximately 42 kcal/mol. The role of GAP (GTPase-activating protein) was also discussed in terms of the delivery of the water molecules required for the hydrolysis.

Animals↗
PubMedDate not supplied

The electronic structures and properties of open-ended and capped carbon nanoneedles.

The existence of a family of very thin carbon needlelike nanostructures is predicted: the geometry and stability of several carbon nanoneedles (CNNs) formed by C4 and C6 units have been studied by quantum chemistry computational modeling methods. The structures of carbon nanoneedles are tighter than even the smallest single wall nanotubes (SWNTs) based on (4, 0) naphthacene. The electronic properties, energetic stability of geometrical structures with various terminal units are investigated. The relatively large band gaps, the strong bonding, and additional orbital interactions within the C4 rings and between the C4 layers make the H4(C4)(n)H4 type molecules nonmetallic. We have found indications that if the CNN (3, 0) structures are very long (in the limit of infinite-length), then they are likely to have semiconducting properties and could possibly be used as actual semiconductors. The studied families of CNNs can be considered as carbon nanostructures with unique structural and chemical properties and with possible potential for unusual electronic properties, with likely practical applications as nanomaterials and nanostructure devices.

Journal Article↗
PubMedDate not supplied

Stability and electronic properties of nitrogen nanoneedles and nanotubes.

The electronic structures and stability of nitrogen nanostructures, nanotubes, and fiberlike nanoneedles of various diameters, formed by units N2m (m = 2-6), were studied by quantum chemistry computational modeling methods. The geometrical structures with various cross-sections and terminal units, their energetic stability, and their rather peculiar electron density distributions were investigated. The tightest nitrogen nanoneedle (NNN) studied theoretically in this work is the structure (N4n with D2h symmetry, whereas the nitrogen nanotube (NNT) with the largest diameter discussed here is the structure (N12)n with D2 symmetry. These families of NNNs and NNTs can be considered as nanostructures not only for potential applications as devices in nanotechnology or as possible scaffold structures but also as ligands in synthetic chemistry and high-energy density materials (HEDMs). As a consequence of the lone-pair electrons present around the walls of these NNNs and NNTs, these nitrogen nanostructures and the nitrogen nano-bundles (NNB) formed by aligning and combining them using intermediate carbon atoms, can have highly variable electronic properties controlled by the changing charge environment. In particular, for extended systems based on the units studied here, the band gaps of each of these systems can be affected greatly by the local charge of the environment.

Journal Article↗
PubMed2001

Modeling platinum group metal complexes in aqueous solution.

We construct force fields suited for the study of three platinum group metals (PGM) as chloranions in aqueous solution from quantum chemical computations and report experimental data. Density functional theory (DFT) using the local density approximation (LDA), as well as extended basis sets that incorporate relativistic corrections for the transition metal atoms, has been used to obtain equilibrium geometries, harmonic vibrational frequencies, and atomic charges for the complexes. We found that DFT calculations of [PtCl(6)](2-).3H(2)O, [PdCl(4)](2-).2H(2)O, and [RhCl(6)](3-).3H(2)O water clusters compared well with molecular mechanics (MM) calculations using the specific force field developed here. The force field performed equally well in condensed phase simulations. A 500 ps molecular dynamics (MD) simulation of [PtCl(6)](2-) in water was used to study the structure of the solvation shell around the anion. The resulting data were compared to an experimental radial distribution function derived from X-ray diffraction experiments. We found the calculated pair correlation functions (PCF) for hexachloroplatinate to be in good agreement with experiment and were able to use the simulation results to identify and resolve two water-anion peaks in the experimental spectrum.

Journal Article↗
PubMed2001

Computed ligand electronic parameters from quantum chemistry and their relation to Tolman parameters, Lever parameters, and Hammett constants.

The calculated (DFT, B3PW91) A(1) nu(CO) frequency in LNi(CO)(3) defines an electronic parameter that reliably predicts the relative donor powers of a wide variety of cationic, neutral, and negatively charged ligands. These calculated parameters correlate very well with the available Tolman and Lever parameters, and also with Hammett's sigma(m), where available. The method avoids any experimental limitations and, in particular, can be used for proposed ligands not yet experimentally available.

Journal Article↗
PubMed2005

Derivatives of 1,5-diamino-1H-tetrazole: a new family of energetic heterocyclic-based salts.

1,5-Diamino-1H-tetrazole (2, DAT) can easily be protonated by reaction with strong mineral acids, yielding the poorly investigated 1,5-diaminotetrazolium nitrate (2a) and perchlorate (2b). A new synthesis for 2 is introduced that avoids lead azide as a hazardous byproduct. The reaction of 1,5-diamino-1H-tetrazole with iodomethane (7a) followed by the metathesis of the iodide (7a) with silver nitrate (7b), silver dinitramide (7c), or silver azide (7d) leads to a new family of heterocyclic-based salts. In all cases, stable salts were obtained and fully characterized by vibrational (IR, Raman) spectroscopy, multinuclear NMR spectroscopy, mass spectrometry, elemental analysis, X-ray structure determination, and initial safety testing (impact and friction sensitivity). Most of the salts exhibit good thermal stabilities, and both the perchlorate (2b) and the dinitramide (7c) have melting points well below 100 degrees C, yet high decomposition onsets, defining them as new (7c), highly energetic ionic liquids. Preliminary sensitivity testing of the crystalline compounds indicates rather low impact sensitivities for all compounds, the highest being that of the perchlorate (2b) and the dinitramide (7c) with a value of 7 J. In contrast, the friction sensitivities of the perchlorate (2b, 60 N) and the dinitramide (7c, 24 N) are relatively high. The enthalpies of combustion (Delta(c)H degrees ) of 7b-d were determined experimentally using oxygen bomb calorimetry: Delta(c)H degrees (7b) = -2456 cal g(-)(1), Delta(c)H degrees (7c) = -2135 cal g(-)(1), and Delta(c)H degrees (7d) = -3594 cal g(-)(1). The standard enthalpies of formation (Delta(f)H degrees ) of 7b-d were obtained on the basis of quantum chemical computations using the G2 (G3) method: Delta(f)H degrees (7b) = 41.7 (41.2) kcal mol(-)(1), Delta(f)H degrees (7c) = 92.1 (91.1) kcal mol(-)(1), and Delta(f)H degrees (7d) = 161.6 (161.5) kcal mol(-)(1). The detonation velocities (D) and detonation pressures (P) of 2b and 7b-d were calculated using the empirical equations of Kamlet and Jacobs: D(2b) = 8383 m s(-)(1), P(2b) = 32.2 GPa; D(7b) = 7682 m s(-)(1), P(7b) = 23.4 GPa; D(7c) = 8827 m s(-)(1), P(7c) = 33.6 GPa; and D(7d) = 7405 m s(-)(1), P(7d) = 20.8 GPa. For all compounds, a structure determination by single-crystal X-ray diffraction was performed. 2a and 2b crystallize in the monoclinic space groups C2/c and P2(1)/n, respectively. The salts of 7 crystallize in the orthorhombic space groups Pna2(1) (7a, 7d) and Fdd2 (7b). The hydrogen-bonded ring motifs are discussed in the formalism of graph-set analysis of hydrogen-bond patterns and compared in the case of 2a, 2b, and 7b.

Journal Article↗
PubMed1996

Theoretical Study of Electronic Structures and Spectra of Chalcogenido Complexes of Molybdenum, trans-Mo(Q)(2)(PH(3))(4) (Q = O, S, Se, Te).

Electronic structures of the title complexes have been studied using quantum chemical computations by different methods. It is shown that the results of Xalpha calculations agree well with expectations from classical ligand-field theory, but both are far from being in agreement with the results given by ab initio calculations. The HOMO in the ab initio Hartree-Fock molecular orbital diagrams of all these complexes is a chalcogen p(pi) lone pair orbital rather than the metal nonbonding d(xy)() orbital previously proposed. Electronic transition energies were calculated by CASSCF and CI methods. The results suggest that in the cases when Q = S, Se, and Te the lowest energy transitions should be those from the p(pi) lone pair orbitals to the metal-chalcogen pi orbitals. The calculated and observed electronic spectra of the oxo complex are in good agreement and very different from the spectra of the other complexes, and the lowest absorptions were accordingly assigned to transitions of different origins.

Journal Article↗
PubMed2001

Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets.

Ab initio quantum mechanical computations of force fields (FF) and atomic polar and axial tensors (APT and AAT) were carried out for triamide strands Ac-A-A-NH-CH(3) clustered into single-, double-, and triple-strand beta-sheet-like conformations. Models with phi, psi, and omega angles constrained to values appropriate for planar antiparallel and parallel as well as coiled antiparallel (two-stranded) and twisted antiparallel and parallel sheets were computed. The FF, APT, and AAT values were transferred to corresponding larger oligopeptide beta-sheet structures of up to five strands of eight residues each, and their respective IR and vibrational circular dichroism (VCD) spectra were simulated. The antiparallel planar models in a multiple-stranded assembly give a unique IR amide I spectrum with a high-intensity, low-frequency component, but they have very weak negative amide I VCD, both reflecting experimental patterns seen in aggregated structures. Parallel and twisted beta-sheet structures do not develop a highly split amide I, their IR spectra all being similar. A twist in the antiparallel beta-sheet structure leads to a significant increase in VCD intensity, while the parallel structure was not as dramatically affected by the twist. The overall predicted VCD intensity is quite weak but predominantly negative (amide I) for all conformations. This intrinsically weak VCD can explain the high variation seen experimentally in beta-forming peptides and proteins. An even larger variation was predicted in the amide II VCD, which had added complications due to non-hydrogen-bonded residues on the edges of the model sheets.

Circular Dichroism↗
PubMed2002

Dissociative electron transfer to haloacetonitriles. An example of the dependency of in-cage ion-radical interactions upon the leaving group.

The reductive cleavage of the haloacetonitriles (Cl, Br, I) in DMF provides additional examples of the formation of a fragment cluster upon dissociative electron transfer, which is able to survive in this polar solvent thanks to the electron-withdrawing character of the cyano group. The remarkable sensitivity of the activation energy to small changes of the interaction energies allows, with help of the "sticky" dissociative electron-transfer model, the precise determination of interaction energies down to a few millielectronvolts from the cyclic voltammetric data. The interaction energy rapidly decreases from Cl to Br and to I, correlated with the increase of the halide radius. These observations add to the previously gathered evidence to confirm the existence of such interactions and to highlight their electrostatic character. This is further corroborated by the quantum chemical computation of the potential energy profiles, which exhibit a long-distance energy minimum. This revisiting of the notion of sigma-ion radicals and of their status in a polar medium makes them appear as an electrostatic radical-ion pair rather than covalently bound molecules. Their stability is a function of the Lewis acid-base properties of both the radical and the leaving ion and is strongly influenced by the nature of the solvent.

Journal Article↗
PubMed2005

Separation of CO2 and N2 by adsorption in C168 schwarzite: a combination of quantum mechanics and molecular simulation study.

Using a hierarchical multiscale approach combining quantum mechanics and molecular simulation, we have investigated the adsorption of pure CO(2) and N(2) and their mixture at room temperature in C(168) schwarzite, as a model for nanoporous carbons. First, the adsorbate-adsorbent interaction potential is determined using ab initio quantum mechanics computations, and then the adsorption is predicted using full atomistic Monte Carlo simulations. The extents of adsorption, adsorption energies, and isosteric heats of pure CO(2) and N(2) simulated with the ab initio potential are found to be higher than those with the empirical Steele potential that had been developed from gas adsorption on planar graphite. The inclusion of the electric quadrupole moment of adsorbate in simulation has no discernible effect on N(2) adsorption but results in a larger extent of CO(2) adsorption at high coverages. The selectivity of CO(2) over N(2) in the C(168) schwarzite from a model flue gas is predicted to be significantly larger with the ab initio potential than with the Steele potential. This illustrates the importance of an accurate adsorbate-adsorbent interaction potential in determining gas adsorption and suggests that nanoporous carbons might be useful for the separation of flue gases. As a comparison, the adsorption and selectivity of CO(2) and N(2) in ZSM-5 zeolites are also simulated with the experimentally validated potential parameters. The selectivity in the C(168) schwarzite predicted with the ab initio or Steele potential is found to be larger than the selectivity in all-silica ZSM-5, but less than that in Na-exchanged ZSM-5 zeolites.

Journal Article↗
PubMed2004

Density functional calculations of the 13C NMR chemical shifts in (9,0) single-walled carbon nanotubes.

The electronic structure and (13)C NMR chemical shift of (9,0) single-walled carbon nanotubes (SWNTs) are investigated theoretically. Shielding tensor components are also reported. Density functional calculations were carried out for C(30)-capped and H-capped fragments which serve as model systems for the infinite (9,0) SWNT. Based on the vanishing HOMO-LUMO gap, H-capped nanotube fragments are predicted to exhibit "metallic" behavior. The (13)C chemical shift approaches a value of approximately 133 ppm for the longest fragment studied here. The C(30)-capped SWNT fragments of D(3d)/D(3h) symmetry, on the other hand, are predicted to be small-gap semiconductors just like the infinite (9,0) SWNT. The differences in successive HOMO-LUMO gaps and HOMO and LUMO energies, as well as the (13)C NMR chemical shifts, converge slightly faster with the fragment's length than for the H-capped tubes. The difference between the H-capped and C(30)-capped fragments is analyzed in some detail. The results indicate that (at least at lengths currently accessible to quantum chemical computations) the H-capped systems represent less suitable models for the (9,0) SWNT because of pronounced artifacts due to their finite length. From our calculations for the C(30)-capped fragments, the chemical shift of a carbon atom in the (9,0) SWNT is predicted to be about 130 ppm. This value is in reasonably good agreement with experimental estimates for the (13)C chemical shift in SWNTs.

Magnetic Resonance Spectroscopy↗