Search

The article proposes a method for the coefficients reconstruction of a discrete autocorrelation function of random signals with a unimodal power spectral density to construct their parametric models. The method is based on finding the optimal values of the relative width ΔFT and the weighting factor α in [0; 1] of the spectral mode, which characterizes the share of the Gaussian and resonant components in the spectrum envelope. The proposed method makes it possible to reduce by 1.5–4 times the discrepancy between the control and estimated spectra in comparison with the known approaches to parametric spectral analysis. An increase in the adequacy of spectral estimation makes it possible to reduce the length M of the analyzed time sample by a factor of 2.3–4 times, while maintaining the accuracy of the spectral analysis achieved by other known parametric methods. Winnings are achieved by using a priori information about the spectral properties of the analyzed process.

Identity proton-transfer reactions between 21 acids, Y-X-H, and their conjugate bases, (-)X-Y, were studied according to the reaction scheme, Y-X-H + (-)X-Y --(Y-X-H...(-)X-Y)(cx) --[Y-X...H...X-Y](ts) --(Y-X..H-X-Y)(cx) --Y-X(-) + H-X-Y, where cx indicates an ion-molecule complex and ts indicates the proton-transfer transition state. All species were optimized at the MP2/6-311+G level, and these geometries were used for single-point calculations by other methods: coupled-cluster, DFT (gas phase), and a polarizable continuum aqueous solvent model (COSMO). All methods gave enthalpies of deprotonation which correlate well with experimental measurements of deltaH(ACID) (gas) or pK(a) (aq). Calculated gas-phase enthalpies of deprotonation (deltaH(ACID)) and enthalpies of activation (deltaH(#)) are poorly correlated except for small, carefully selected sets. This result stands in contrast to the many aqueous phase Brönsted correlations of kinetic and equilibrium acid strength. On the other hand, gas-phase enthalpies of complexation and deltaH(#) are well correlated, indicating that factors which stabilize the transition state are at work in the bimolecular ion-molecule complex although to a smaller degree. We infer that intermoiety electrostatic and other interactions, similar within the complex and the transition state, but absent in the separated reactants (products), cause the lack of correlation between deltaH(ACID) and the other two quantities. Such differences are strongly attenuated in water because reactants and products do interact with polar/polarizable matter (the solvent) if not with each other. Charge distributions (NPA) were computed, allowing calculation of Bernasconi's "transition state imbalance parameter". Such measures provide intuitively satisfactory trends, but only if the reaction termini, X, are kept the same. As X is made more electronegative, the magnitude of the apparent imbalance increases, a result of greater negative charge on X in the transition state. This result gives additional support for the importance of the ion-triplet structure, [YX(-)...H(+)...(-)XY], to the stability of the transition state. Additional qualitative support for this conclusion is provided by the inverse relationship between the activation barrier and the charge on the in-flight hydrogen in the transition state, and by the dominance of polar over resonance substituent effects on the stability of the transition state. Calculations also show that the "nitroalkane anomaly", well established in solution, does not exist in the gas phase. The COSMO model partly reproduces this anomaly and performs adequately except when strong, specific intermolecular forces such as hydrogen bonding between solvent and anions are important.

Gradient corrected density functional theory is applied to evaluate the structure and energetics of hydrogenation patterns in the C36 molecule and its component fragments. Overall strain and resonance energies for these compounds are determined using homodesmotic reactions that connect C36 and its constituent chemical components to simpler non-aromatic, unstrained compounds. Our calculations indicate that the dramatic difference in energetic stability between two similar solid C36 structures is due to the number of disrupted aromatic rings rather than to differential strain.

RHF, MP2, and TCSCF ab initio theory and B3LYP, B3PW91, and SVWN density functional theory were used to study the series of cyclopropenyl-fused tricycles 9−12. In each of 9−12, the cyclopropenyl double bond is exceptionally pyramidalized (butterfly angle ψ ∼41−50°) with both endo and exo bent isomers. In the norbornyl systems (9 and 10), the endo bent isomers are more stable than the exo bent isomers, whereas in the bicyclo[2.2.2]octadiene 12 the reverse is true with the exo bent isomer being the low energy form. The activation barriers for the endo/exo interconversions are calculated to be relatively low (ΔH⧧ ∼6−13 kcal/mol).

The nitrogen mustard based DNA alkylating agents were the first effective anticancer agents and remain important drugs against many forms of cancer. More than fifty years of research on the nitrogen mustards has yielded a broad range of therapeutically useful compounds and a detailed knowledge of the biochemical mechanism of these drugs. Nevertheless, there is much ongoing research on the phos­ phosphoramidic and other nitrogen mustards to increase their potency and reduce their toxic and mutagenic side effects. To understand the existing nitrogen mustards, and to design the next generation of these drugs, more knowledge is needed about the effects of chemical modifications on their activation and selectivity. Because of the existing knowledge of these drugs, atomic-level chemical modeling can play an important role in the understanding of the phosphoramidic mustard compounds; however, it has not proved straight forward to directly relate the activity of these mustards with simple chemical properties such as bond lengths or atomic charges. Instead, quantum chemical simulations will be required to simulate the activation and alkylation reactions of these compounds, which will require the newest generation of quantum chemical and solvent modeling methods. Additionally, molecular dynamics simulations of the adducted DNA can provide data on the factors favoring crosslinking and its structural consequences. This review summarizes the extensive literature on the metabolism, activation, and action of the phosphoramidic mustards, with an emphasis on the roles that chemical modeling has and will play in the development of this important class of drugs.

The nitrogen mustard based DNA alkylating agents were the first effective anticancer agents and remain important drugs against many forms of cancer. More than fifty years of research on the nitrogen mustards has yielded a broad range of therapeutically useful compounds and a detailed knowledge of the biochemical mechanism of these drugs. Nevertheless, there is much ongoing research on the phosphosphoramidic and other nitrogen mustards to increase their potency and reduce their toxic and mutagenic side effects. To understand the existing nitrogen mustards, and to design the next generation of these drugs, more knowledge is needed about the effects of chemical modifications on their activation and selectivity. Because of the existing knowledge of these drugs, atomic-level chemical modeling can play an important role in the understanding of the phosphoramidic mustard compounds; however, it has not proved straight forward to directly relate the activity of these mustards with simple chemical properties such as bond lengths or atomic charges. Instead, quantum chemical simulations will be required to simulate the activation and alkylation reactions of these compounds, which will require the newest generation of quantum chemical and solvent modeling methods. Additionally, molecular dynamics simulations of the adducted DNA can provide data on the factors favoring crosslinking and its structural consequences. This review summarizes the extensive literature on the metabolism, activation, and action of the phosphoramidic mustards, with an emphasis on the roles that chemical modeling has and will play in the development of this important class of drugs.

Density functional theory (DFT) simulations were used to determine the binding strength of 12 electron-donating analytes to the zinc metal center of a zinc phthalocyanine molecule (ZnPc monomer). The analyte binding strengths were compared to the analytes' enthalpies of complex formation with boron trifluoride (BF(3)), which is a direct measure of their electron donating ability or Lewis basicity. With the exception of the most basic analyte investigated, the ZnPc binding energies were found to correlate linearly with analyte basicities. Based on natural population analysis calculations, analyte complexation to the Zn metal of the ZnPc monomer resulted in limited charge transfer from the analyte to the ZnPc molecule, which increased with analyte-ZnPc binding energy. The experimental analyte sensitivities from chemiresistor ZnPc sensor data were proportional to an exponential of the binding energies from DFT calculations consistent with sensitivity being proportional to analyte coverage and binding strength. The good correlation observed suggests DFT is a reliable method for the prediction of chemiresistor metallophthalocyanine binding strengths and response sensitivities.

The NO chemisorption dynamics on ordered multilayer iron phthalocyanine (FePc) and quasiamorphous multilayer tetra-t-butyl FePc (ttbu-FePc) films on a Au(111) substrate was investigated using the King and Wells reflection technique. The NO zero coverage or initial sticking probabilities (S(0)) were measured as a function of sample temperature (T(s)) and beam energy (E(i)). The experimental results for both films show a monotonic decrease in S(0) with increasing T(s) and E(i) consistent with NO adsorption occurring via a multiple pathway precursor-mediated mechanism in which the adsorbate initially physisorbs to the FePc organics, diffuses, and chemisorbs to the Fe metal center. The saturation coverage is 3% for the multilayer FePc surface and only 2% for the multilayer ttbu-FePc surface consistent with NO chemisorption occurring only on the Fe metal, where NO chemisorbs to 100% of the surface Fe metal centers. The reduced saturation coverage in the ttbu-FePc film is attributed to fewer Fe metal centers in the less dense ttbu-FePc films. A comparison of NO sticking on a multilayer FePc/Au(111) film with NO sticking on a monolayer FePc/Au(111) film shows that S(0) is greater on the multilayer FePc film for all T(s) and E(i), consistent with an increase in collision inelasticity for NO/multilayer FePc/Au(111).

To develop an atomistic understanding of the binding of NO with iron phthalocyanine (FePc), the interaction between NO (an electron withdrawing gas) and NH3 (an electron donating gas) with an isolated FePc molecule (monomer) was compared with density functional theory. The simulations show that NO strongly chemisorbs to the Fe metal and physisorbs to all the nonmetal sites. Additionally, when NO physisorbs to the inner ring nitrogens, NO subsequently undergoes a barrierless migration to the deep chemisorption well on the Fe metal. Conversely, NH3 only weakly chemisorbs to the Fe metal and does not bind to any other sites. Projected density of states simulations and analysis of the atomic charges show that the binding of NO to the FePc metal results in a charge transfer from the Fe metal to the NO chemisorbate; the opposite effect is observed for the binding of NH3 to the Fe metal. Simulations of NO binding to the Fe metal of a monolayer FePc film and FePc trimer were also performed to show that intermolecular FePc-FePc interactions have a negligible effect on the FePc electronic structure and NO binding.

The gas-surface reaction dynamics of NO impinging on an iron(II) phthalocyanine (FePc) monolayer were investigated using King and Wells sticking measurements. The initial sticking probability was measured as a function of both incident molecular beam energy (0.09–0.4eV) and surface temperature (100–300K). NO adsorption onto FePc saturates at 3% of a monolayer for all incident beam energies and surface temperatures, suggesting that the final chemisorption site is confined to the Fe metal centers. At low surface temperature and low incident beam energy, the initial sticking probability is 40% and decreases linearly with increasing beam energy and surface temperature. The results are consistent with the NO molecule sticking onto the FePc molecules via physisorption to the aromatics followed by diffusion to the Fe metal center, or precursor-mediated chemisorption. The adsorption mechanism of NO onto FePc was confirmed by control studies of NO sticking onto metal-free H2Pc, inert Au(111), and reactive Al(111).