Chemistry and Biochemistry

The 2-photon resonant, 3-photon ionization spectrum of gaseous atomic copper is presented. The 2 D 5/2 3d 10 nd ← 2 S 1/2 3d 10 4s (n = 9-21) Rydberg series is observed in 2-photon excitation. The term energies of this series converge to the lowest ionization threshold with an apparent quantum defect of 0.92. The state which couples the ground 2 S 1/2 3d 10 4s state of copper to the 2 D 5/2 3d 10 nd Rydberg series is a non-stationary state composed primarily of the spin-orbit components of the lowest 2 P o atomic states.

The 2-photon resonant, 3-photon ionization spectrum of gaseous atomic copper is presented. The 2 D 5/2 3d 10 nd ← 2 S 1/2 3d 10 4s (n = 9-21) Rydberg series is observed in 2-photon excitation. The term energies of this series converge to the lowest ionization threshold with an apparent quantum defect of 0.92. The state which couples the ground 2 S 1/2 3d 10 4s state of copper to the 2 D 5/2 3d 10 nd Rydberg series is a non-stationary state composed primarily of the spin-orbit components of the lowest 2 P o atomic states.

Semiempirical AM1 calculations were performed for a representative series of 4-substituted bicyclooctane carboxylic acids and quinuclidines. It was found that the Hammett constant, σI, and the Swain and Lupton field constant, F, correlate linearly with the differences in the heat of formation of isodesmic reactions. These constants also correlate with the charges on the acid moiety of the bicyclooctane acids and their anions, and with the hydrogen net charge on the protonated quinuclidines. For all cases, the NO2 was the poorest correlated substituent. Copyright © 2003 John Wiley & Sons, Ltd.

We investigate the energetic, structural, electronic and thermodynamics properties of hydrogen fluoride cluster, (HF)n, in the range n=2-8, by ab initio methods and density functional theory (DFT). The ab initio methods chosen were Hartree-Fock (RHF) and second-order Møller-Plesset perturbation theory (MP2). The DFT calculations were based on Becke's hybrid functional and the Lee-Yang-Parr correlation functional (B3LYP). We found that symmetric cyclic clusters are the most stable structure, and that large cooperative effects, particularly from trimer to tetramer are present, in binding energy, and hydrogen bond distance. An analysis of the topology of the electron density reveals a linear correlation between the binding energy per hydrogen bond and the density at the hydrogen bond critical point and the Cioslowski covalent bond order. Based on these correlations, hydrogen bond cooperativity is associated with the electronic delocalization between monomers units. Analysis of the thermodynamics properties shows that the enthalpy changes are determined by the electronic cooperative effects, while the entropic statistical factors are fundamental in the relative stability of these clusters. Finally, for the trimer and tetramer, nonstable linear zigzag chains where found in a detailed analysis of the potential energy surfaces.

We investigate the energetic, structural, electronic and thermodynamics properties of hydrogen fluoride cluster, (HF) n , in the range nϭ2 -8, by ab initio methods and density functional theory ͑DFT͒. The ab initio methods chosen were Hartree-Fock ͑RHF͒ and second-order Mo "ller-Plesset perturbation theory ͑MP2͒. The DFT calculations were based on Becke's hybrid functional and the Lee-Yang-Parr correlation functional ͑B3LYP͒. We found that symmetric cyclic clusters are the most stable structure, and that large cooperative effects, particularly from trimer to tetramer are present, in binding energy, and hydrogen bond distance. An analysis of the topology of the electron density reveals a linear correlation between the binding energy per hydrogen bond and the density at the hydrogen bond critical point and the Cioslowski covalent bond order. Based on these correlations, hydrogen bond cooperativity is associated with the electronic delocalization between monomers units. Analysis of the thermodynamics properties shows that the enthalpy changes are determined by the electronic cooperative effects, while the entropic statistical factors are fundamental in the relative stability of these clusters. Finally, for the trimer and tetramer, nonstable linear zigzag chains where found in a detailed analysis of the potential energy surfaces.

In this work we present an alternative method, based on the Hellmann–Feynman theorem, to generate energy corrections within the standard Rayleigh–Schrödinger perturbation theory. As a result, compact expressions for the corrections to the energy at different orders are obtained. We also review a method that allows us to calculate the corrections to the wave function needed in the energy calculations. Finally, our results are compared with those obtained by other authors by a different technique.

The amino acid substitution or post‐translational modification of a cytosolic protein can cause unpredictable changes to its electrophoretic mobility during SDS‐PAGE. This type of “gel shifting” has perplexed biochemists and biologists for decades. We identify a mechanism for “gel shifting” that predominates among a set of ALS (amyotrophic lateral sclerosis) mutant hSOD1 (superoxide dismutase) proteins, post‐translationally modified hSOD1 proteins, and homologous SOD1 proteins from different organisms. By first comparing how 39 amino acid substitutions throughout hSOD1 affected SDS‐PAGE migration, we found that substitutions that caused gel shifting occurred within a single polyacidic domain (residues ∼80–101), and were nonisoelectric. Substitutions that decreased the net negative charge of domain 80–101 increased migration; only one substitution increased net negative charge and slowed migration. Capillary electrophoresis, circular dichroism, and size exclusion chromatography demon...

The amino acid substitution or post-translational modification of a cytosolic protein can cause unpredictable changes to its electrophoretic mobility during SDS-PAGE. This type of ''gel shifting'' has perplexed biochemists and biologists for decades. We identify a mechanism for ''gel shifting'' that predominates among a set of ALS (amyotrophic lateral sclerosis) mutant hSOD1 (superoxide dismutase) proteins, post-translationally modified hSOD1 proteins, and homologous SOD1 proteins from different organisms. By first comparing how 39 amino acid substitutions throughout hSOD1 affected SDS-PAGE migration, we found that substitutions that caused gel shifting occurred within a single polyacidic domain (residues~80-101), and were nonisoelectric. Substitutions that decreased the net negative charge of domain 80-101 increased migration; only one substitution increased net negative charge and slowed migration. Capillary electrophoresis, circular dichroism, and size exclusion chromatography demonstrated that amino acid substitutions increase migration during SDS-PAGE by promoting the binding of three to four additional SDS molecules, without significantly altering the secondary structure or Stokes radius of hSOD1-SDS complexes. The high negative charge of domain 80-101 is required for SOD1 gel shifting: neutralizing the polyacidic domain (via chimeric mouse-human SOD1 fusion proteins) inhibited amino acid substitutions from causing gel shifting. These results demonstrate that the pattern of gel shifting for mutant cytosolic proteins can be used to: (i) identify domains in the primary structure that control interactions between denatured cytosolic proteins and SDS and (ii) identify a predominant chemical mechanism for the interaction (e.g., hydrophobic vs. electrostatic).

The essential oil components of geranium oil cultivated in center of Iran were identified and determined using gas chromatography-mass spectrometry data combined with the chemometric resolution techniques. A total of 61 components accounting for 91.51% were identified using similarity searches between the mass spectra and MS database. This number was extended to 85 components using chemometric techniques. Various chemometric methods such as morphological scores, simplified Borgen method (SBM) and fixed size moving window evolving factor analysis (FSMWEFA) were used for determining the number of components, pure variables, zero concentration and selective regions. Then the overlapping peak clusters were resolved into pure chromatograms and pure mass spectra using heuristic evolving latent projections (HELP) method. A characteristic feature of the Iranian geranium oil is the absence of 10-epi-␥-eudesmol in its constituents compared with the oil from northern and southern parts of India. The results of this work show that combination of hyphenated chromatographic methods and resolution techniques provide a complementary method for accurate analysis of essential oils.

A Quantitative Structure-Property Relationship (QSPR) relating atom-based calculated descriptors to 13C NMR chemical shifts was developed to accurately simulate 13C NMR spectra of polyhydroxy and methoxy substituted dibenzo pyrons (xanthones). A dataset consisting of 35 xanthones was employed for the present analysis. A set of 132 topological, geometrical, and electronic descriptors representing various structural characteristics was calculated for each of 497 unique carbon atoms in the dataset. Principal Component Analysis (PCA)-ranking and Artificial Neural Networks (ANNs) were used as descriptor selection and model building methods, respectively. Analyses of the results revealed a correlation coefficient and Root Mean Square Error (RMSE) of 0.998 and 1.42 ppm, respectively, for the prediction set.

A Quantitative Structure-Property Relationship (QSPR) relating atom-based calculated descriptors to 13 C NMR chemical shifts was developed to accurately simulate 13 C NMR spectra of polyhydroxy and methoxy substituted dibenzo pyrons (xanthones). A dataset consisting of 35 xanthones was employed for the present analysis. A set of 132 topological, geometrical, and electronic descriptors representing various structural characteristics was calculated for each of 497 unique carbon atoms in the dataset. Principal Component Analysis (PCA)-ranking and Artificial Neural Networks (ANNs) were used as descriptor selection and model building methods, respectively. Analyses of the results revealed a correlation coefficient and Root Mean Square Error (RMSE) of 0.998 and 1.42 ppm, respectively, for the prediction set.

Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H/D exchange reactions was utilized to explore the existence of different b 5+ and b 4+ fragment ion conformers/isomers of hexapeptide WHWLQL in the gas phase. Distinct H/D exchange trends for protonated WHWLQL ([M + H]+) and its b 5+ and b 4+ fragment ions (with ND3) were observed. Isolated 12Call isotopomers of both b 5+ and b 4+ fragment ions yielded bimodal distributions of H/D exchanged product ions. The H/D exchange reaction kinetics also confirmed that b 5+ and b 4+ fragment ions exist as combination of slow-exchanging (“s”) and fast-exchanging (“f”) species. The calculated rate constant for the first labile hydrogen exchange of [M + H]+ (k[M + H]+ = 3.80 ± 0.7 × 10−10 cm3 mol−1 s−1) was ∼30 and ∼5 times greater than those for the “s” and “f” species of b 5+, respectively. Data from H/D exchange of isolated “s” species at longer ND3 reaction times confirmed the existence of different conformers or isomers for b 5+ fragment ions. The sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) of WHWLQL combined with the H/D exchange reactions indicate that “s” and “f” species of b 5+ and b 4+ fragment ions can be produced in the ICR cell as well as the ESI source. The significance of these observations for detailed understanding of protein sequencing and ion fragmentation pathways is discussed.