BOOK REVIEW

Book reviewed in this article:
Advances in Photochemistry, Vol. 10. Edited by J. N. Pitts, Jr., G. S. Hammond and K. Gollnick.     

BOOK REVIEWS

Book reviewed in this article:
Advances in Photochemistry, Volume 2, Edited by W. A lbert N oyes Jr., G eorge S. H ammond and J. N. P itts Jr. Interscience,
Primary Processes in Photosynthesis. M artin D. K amen .     

Effect of molecular rotation on the atomic alignment dependence in the oriented Ar (3P2) + CF3H reaction

Atomic alignment effect for the CF3* formation in the oriented Ar (3P2, MJ = 2) + CF3H reaction has been investigated at different two CF3H beam conditions: effusive and supersonic beams. The chemiluminescence intensity of CF3* was measured as a function of the magnetic orientation field direction in the collision frame. A significant contribution of rank 4 moment was recognized. The cross-section for each magnetic M'(J) substate in the collision frame, sigma|M'(J)|, was determined to be sigma(|M'(J)|=0):sigma(|M'(J)|=1):sigma(|M'(J)|=2) = 1.00:0.84 +/- 0.02:0.88 +/- 0.02 for the effusive CF3H beam condition. The atomic alignment effect was found to significantly depend on the CF3H beam condition. For the supersonic beam condition, sigma(|M'(J)|=0&1) was changed to be smaller than sigma(|M'(J)|=2).     

Comment on “Analytical evaluation for two-center nuclear attraction integrals over Slater type orbitals by using Fourier transform method” by S. ?zcan and E. ?ztekin (J. Math. Chem. DOI 10.1007/s10910-008-9398-z)

S. ?zcan and E. ?ztekin, (J. Math. Chem. doi:) published formulas for evaluating the two-center nuclear attraction integrals over Slater type orbitals. It is shown that the analytical relations for these integrals through the expansion coefficients of the electron charge density for the one-center case and the overlap integrals presented in Sect. 3 of this work can easily be derived by means of a simple algebra from the formulas published in our papers (I.I. Guseinov, J Mol Struct (Theochem) 417:117, 1997; J Math Chem 42:415, 2007 and B.A. Mamedov, Chin J Chem 22:545, 2004). It should be noted that the formulas of overlap integrals presented by E. ?ztekin et al., in previous paper (E. ?ztekin, M. Yavuz, Ş. Atalay, J Mol Struct (Theochem) 544:69, 2001) for the calculation of two-center nuclear attraction integrals also are obtained from our papers (see Comment: I.I. Guseinov, J Mol Struct (Theochem) 638:235, 2003).     

Slice imaging of the quantum state-to-state cross section for photodissociation of state-selected rovibrational bending states of OCS (v2=0,1,2/JlM)+hnu-->CO(J)+S(1D2)

Using hexapole quantum state-selection of OCS (v(2)=0,1,2/JlM) and high-resolution slice imaging of quantum state-selected CO(J), the state-to-state cross section OCS (v(2)=0,1,2/JlM)+hnu-->CO(J)+S((1)D(2)) was measured for bending states up to v(2)=2. The population density of the state-selected OCS (v(2)=0,1,2 /JlM) in the molecular beam was obtained by resonantly enhanced multiphoton ionization of OCS and comparison with room temperature bulk gas. A strong increase of the cross section with increasing bending state is observed for CO(J) in the high J region, J=60-67. Integrating over all J states the authors find sigma(v(2)=0):sigma(v(2)=1):sigma(v(2)=2)=1.0:7.0:15.0. A quantitative comparison is made with the dependence of the transition dipole moment function on the bending angle.     

An ab initio study of cooperative effects in ternary complexes X:CNH:Z with X, Z = CNH, FH, ClH, FCl, and HLi: structures, binding energies, and spin-spin coupling constants across intermolecular bonds

A systematic ab initio investigation has been carried out to determine the structures, binding energies, and spin-spin coupling constants of ternary complexes X:CNH:Z and corresponding binary complexes X:CNH and CNH:Z, for X, Z = CNH, FH, ClH, FCl, and HLi. The enhanced binding energies of ternary complexes X:CNH:Z for fixed X as a function of Z decrease in the same order as the binding energies of the binary complexes CNH:Z. In contrast, the enhanced binding energies of the ternary complexes for fixed Z as a function of X do not decrease in the same order as the binding energies of the binary complexes X:CNH, a consequence of the increased stabilities of ternary complexes FCl:CNH:Z due to very strong chlorine-shared halogen bonds. For complexes in which the X···CNH interaction is a D-H···C hydrogen bond for D-H the proton-donor group (N-H, F-H, or Cl-H), spin-spin coupling constants (1)J(D-H) and (2h)J(D-C) in ternary complexes X:CNH:Z decrease in absolute value as the binding energies of binary complexes CNH:Z and the enhanced binding energies of the ternary complexes for fixed X as a function of Z also decrease. However, (2X)J(F-C) increases as the enhanced binding energies of the ternary complexes FCl:CNH:Z decrease, a consequence of the nature of the chlorine-shared halogen bond. The one-bond coupling constants (1)J(N-H) for the CNH···Z interaction in ternary complexes vary significantly, depending on the nature of the X···CNH interaction. The largest values of (1)J(N-H) are found for ternary complexes with FCl as X. Two-bond coupling constants (2h)J(N-A) for A the proton-acceptor atom of Z, and (2d)J(N-H) decrease in absolute value in the order of decreasing enhancement energies of ternary complexes X:CNH:Z for fixed Z as a function of X.     

Ab initio study of ternary complexes X:(HCNH)(+):Z with X, Z = NCH, CNH, FH, ClH, and FCl: diminutive cooperative effects on structures, binding energies, and spin-spin coupling constants across hydrogen bonds

Ab initio calculations have been performed on a series of complexes in which (HCNH)(+) is the proton donor and CNH, NCH, FH, ClH, and FCl (molecules X and Z) are the proton acceptors in binary complexes X:HCNH(+) and HCNH(+):Z, and ternary complexes X:HCNH(+):Z. These complexes are stabilized by C-H(+)···A and N-H(+)···A hydrogen bonds, where A is the electron-pair donor atom of molecules X and Z. Binding energies of the ternary complexes are less than the sum of the binding energies of the corresponding binary complexes. In general, as the binding energy of the binary complex increases, the diminutive cooperative effect increases. The structures of these complexes, data from the AIM analyses, and coupling constants (1)J(N-H), (1h)J(H-A), and (2h)J(N-A) for the N-H(+)···A hydrogen bonds, and (1)J(C-H), (1h)J(H-A), and (2h)J(C-A) for the C-H(+)···A hydrogen bonds provide convincing evidence of diminutive cooperative effects in these ternary complexes. In particular, the symmetric N···H(+)···N hydrogen bond in HCNH(+):NCH looses proton-shared character in the ternary complexes X:HCNH(+):NCH, while the proton-shared character of the C···H(+)···C hydrogen bond in HNC:HCNH(+) decreases in the ternary complexes HNC:HCNH(+):Z and eventually becomes a traditional hydrogen bond as the strength of the HCNH(+)···Z interaction increases.     

Erratum to: Determination of metal ion content of beverages and estimation of target hazard quotients: a comparative study

This is a correction to the following paper: Hague T, Petroczi A, Andrews PR, Barker J, Naughton DP: Determination of metal ion content of beverages and estimation of target hazard quotients: a comparative study. Chem Central J 2008, 2:13.     

Book Reviews

Book reviewed in this article:
Inorganic Carbon Uptake by Aquatic Photosynthetic Organisms-Proceedings of an international workshop on bicarbonate use in photosynthesis. Edited by W. J. Lucas and J. A. Berry.
Photochemistry in Organic Synthesis. Edited by J. D. Coyle.     

BOOK REVIEWS

Book reviewed in this article:
Primitive Sensory and Communication Systems. Edited by M. J. C arlile ,
Chemical Kinetics, Edited by D. R. Herschbach.
An Introduction to Radiation Chemistry (2nd Edition). J. W. T. Spinks and R. J. Woods     

Total synthesis of hapalindoles J and U

The total synthesis of D,L-hapalindoles J and U has been accomplished. Hapalindole J was prepared in 11% overall yield over 11 synthetic steps and hapalindole U was prepared in 25% overall yield over 13 synthetic steps from commercially available materials. The route employs a novel silyl ether-based strategy for accessing the 6:5:6:6 ring system of the hapalindoles rapidly and in good yields.     

BOOK REVIEW

Book Review in This Article:
The Science of Photomedicine. Edited by J.D. R egan and J.A. P arrish .     

Hyperfine splittings in spin-frustrated trinuclear Cu(3) clusters

The hyperfine structures of the EPR spectra of the spin-frustrated and distorted Cu(II) trimers were calculated in the spin-coupling model. The correlations between the hyperfine structures of the EPR spectra and geometry of the Cu(3) clusters (equilateral, isosceles, and scalene triangles) were found. For the EPR spectrum of the spin-frustrated ground state 2(S = 1/2) of an equilateral triangle Cu(3) cluster (J(12) = J(13) = J(23) = J), the calculated hyperfine structure represents the complicated spectrum of the 24 hyperfine lines, of total length 5a, where a is the hyperfine constant of the mononuclear Cu center. For an isosceles Cu(3) cluster (J(12) not equal J(13) = J(23)), the hyperfine splittings of the EPR spectra of the two split S = 1/2 levels with intermediate spins S(12) = 0 and S(12) = 1 are essentially different. The EPR signal of the |(S(12) = 0)S = 1/2> level is characterized by the four equally spaced hyperfine lines (interval A = a) with the same relative spectral amplitudes 16:16:16:16 and total length 3a. For the |(S(12) = 1)S = 1/2> level, the calculated hyperfine structure represents the spectrum of the 16 hyperfine lines with equal spacing (interval A' = a/3), the spectral intensity distribution 1:1:3:3:5:5:7:7:7:7:5:5:3:3:1:1 and total length 5a. These hyperfine spectra differ from the hyperfine structure (10 lines with interval a/3) of the EPR signals of the excited S = 3/2 level of the Cu(3) cluster. The quartet hyperfine structure, characteristic of a single Cu(2+) nucleus, which was observed experimentally for the doublet ground state of the spin-frustrated Cu(3)(II) clusters, corresponds to the hyperfine structure of the EPR signal of the |(S(12) = 0)S = 1/2> level. This hyperfine structure is evidence of the lowering of the Cu(3) cluster symmetry from trigonal to orthorhombic and the small splitting of the spin-frustrated 2(S = 1/2) ground state.     

Teaching Chemistry with Electron Density Models. 2. Can Atomic Charges Adequately Explain Electrostatic Potential Maps?

Electrostatic potential maps generated from quantum mechanical calculations are widely used to teach students about molecular polarity and assign atomic charges (Shusterman, G. P.; Shusterman, A. J. J. Chem. Educ. 1997, 74, 771–776; Hehre, W. J.; Shusterman, A. J.; Nelson, J. E. The Molecular Modeling Workbook for Organic Chemistry: Wavefunction: Irvine, CA, 1998). The assumption that potential equals charge is only valid, however, when comparing atoms of similar size. The proper use of potential maps requires consideration of atomic charge, atomic radius, and the electron configuration (orbital occupancy) of the atom in question. These points are illustrated through the analysis of the potential maps of various halogen-containing molecules.The first article in this series is Shusterman, G. P.; Shusterman, A. J. J. Chem. Educ. 1997, 74, 771.776.     

2JC,H index: a nondestructive NMR method for differentiation of aldohexopyranosyl residues

A new 2J(C,H) index method is described for identification of aldohexopyranose. This method is based on a fact that 2J(C,H) values reflect the stereochemistry for glycol connectivity. Based on the observed 2J(C,H) values for galactose, glucose, and mannose, 2J(C,H) profiles for other aldohexopyranoses are proposed. A combination of 2J(C,H) values was found to be useful for identification of aldohexopyranosyl residues in glycans. [structure: see text]     

Biostimulation of Na,K-ATPase by low-energy laser irradiation (685 nm, 35 mW): comparative effects in membrane, solubilized and DPPC:DPPE-liposome reconstituted enzyme

OBJECTIVE: The aim of the present work was to investigate the effect of low-energy laser irradiation (685 nm, 35 mW) on the ATPase activity of the different forms of the Na,K-ATPase. METHODS: Membrane-bound and solubilized (alphabeta)(2) form of Na,K-ATPase was obtained from the dark red outer medulla of the kidney and proteoliposomes of DPPC:DPPE and Na,K-ATPase was prepared by the co-solubilization method. Irradiations were carried out at 685 nm using an InGaAIP diode laser. RESULTS: The ATPase activity of the membrane fraction was not altered with exposition to irradiation doses between 4 and 24 J/cm(2). However, with irradiation doses ranging from 32 to 40 J/cm(2), a 28% increase on the ATPase activity was observed while when using up to 50 J/cm(2) no additional enhancement was observed. When biostimulation was done using the solubilized and purified enzyme or the DPPC:DPPE-liposome reconstituted enzyme, an increase of about 36-40% on the ATPase activity was observed using only 4-8 J/cm(2). With irradiation above these values (24 J/cm(2)) no additional increase in the activity was observed. These studies revealed that the biostimulation of ATPase activity from different forms of the Na,K-ATPase is dose dependent in different ranges of irradiation exposure. The stimulation promoted by visible laser doses was modulated and the process was reverted after 2 h for the enzyme present in the membrane and after about 5 h for the solubilized or the reconstituted in DPPC:DPPE-liposomes.     

异双核X-M之间的磁耦合交换作用: Keggin型杂多酸衍生物[M(H2O)XW11O39]7-(X=FeⅢ, CoⅢ; M=CoⅡ)的密度泛函研究

采用DFT-BS方法研究异双核的Keggin型杂多酸衍生物[M(H2O)XW11O39]7-(Ⅰ: X=FeⅢ, M=CoⅡ; Ⅱ: X=CoⅢ, M=CoⅡ)的磁耦合作用, 计算得到耦合常数(J)为负值, 表明所研究体系具有反铁磁性; J值大小顺序为|J(Ⅰ)|<|J(Ⅱ)|, 说明磁耦合作用增强; 体系Ⅰ与Ⅱ相比, X由FeⅢ变成CoⅢ, M不变, 桥氧原子Ob和Ob2(O′b2)上的自旋密度增大, 进一步从相关BS态的磁轨道比较得出, 体系Ⅱ中轨道重叠程度大于体系Ⅰ, 结果使X-M之间的反铁磁耦合作用加强.     

QSID Tool: a new three-dimensional QSAR environmental tool

QSID Tool (Quantitative structure–activity relationship tool for Innovative Discovery) was developed to provide an easy-to-use, robust and high quality environmental tool for 3D QSAR. Predictive models developed with QSID Tool can accelerate the discovery of lead compounds by enabling researchers to formulate and test hypotheses for optimizing efficacy and increasing drug safety and bioavailability early in the process of drug discovery. QSID Tool was evaluated by comparison with SYBYL^® using two different datasets derived from the inhibitors of Trypsin (Böhm et al., J Med Chem 42:458, 1999) and p38-MAPK (Liverton et al., J Med Chem 42:2180, 1999; Romeiro et al., J Comput Aided Mol Des 19:385, 2005; Romeiro et al., J Mol Model 12:855, 2006). The results suggest that QSID Tool is a useful model for the prediction of new analogue activities.     

Photomodulation of Oxidative Metabolism and Electron Chain Enzymes in Rat Liver Mitochondria

Abstract— Low-level laser irradiation has been applied in a variety of laboratory studies and clinical trials for photobiostimulation over the last three decades. Considerable skepticism exists regarding the concept of photostimulation within the medical community. One of the major difficulties with photoirradiation research is that it lacks experimentally supportable mechanisms for the alleged photobiostimulatory effects. This study was undertaken to determine whether oxidative metabolism and electron chain enzymes in rat liver mitochondria can be modulated by photoirradiation. Oxygen consumption, phosphate potential, and energy charge of rat liver mitochondria were determined following photoirradiation. Activities of mitochondrial enzymes were analyzed to assess the specific enzymes that are directly involved with the photostimulatory process. An argon-dye laser at a wavelength of 660 nm and at a power density of 10 mW/cm² was used as a photon source. Photoirradiation significantly increased oxygen consumption (0.6 J/cm² and 1.2 J/cm², P < 0.05), phosphate potential, and the energy charge (1.8 J/cm² and 2.4 J/cm², P < 0.05) of rat liver mitochondria and enhanced the activities of NADH: ubiquinone oxidoreductase, ubiquinol: ferricytochrome C oxidoreductase and ferrocytochrome C: oxygen oxidoreductase (0.6 J/cm², 1.2 J/cm², 2.4 J/cm² and 4.8 J/cm², P < 0.05). The activities of succinate ubiquinone oxidoreductase, ATPase, and lactate dehydrogenase were not affected by photoirradiation.     

Alchemical prediction of hydration free energies for SAMPL

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4-2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242-2254, 2007, J Chem Theory Comput 5(2):350-358, 2009, J Phys Chem B 115:1329-1332, 2011; Nicholls et al. in J Med Chem 51:769-779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307-316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329-1332, 2011). Switching to OPLS Lennard-Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not.