Theoretical characterization of the "very rapid" Mo(V) species generated in the oxidation of xanthine oxidase

Density functional theory calculations of the "very rapid" Mo(V) intermediate of xanthine oxidase (XO) result in a square pyramidal geometry with end-on coordination of the model substrate. The Mo-C8 distance is 3.18 A, longer than previously reported from ENDOR experiments (<2.4 A Howes; et al. Biochemistry 1996, 35, 1432; 2.7-2.9 A Mandikandan; et al. J. Am. Chem. Soc. 2001, 123, 2658). Theoretical gas-phase isotropic hyperfine coupling constants A(iso)(C8) (B3LYP/BSII, 7.68 MHz; B3P86/BSII, 8.64 MHz) compare well with experimental values for the "very rapid" Mo(V) intermediate of XO with xanthine (8.8 MHz, Howes et al.) and 2-hydroxy-6-methylpurine (7.9 MHz, Mandikandan et al.). Absolute values of A(iso) of the metal-bound substrate oxygen are similar in magnitude to that of experiment.     

Comment on "aromatic-backbone interactions in model alpha-helical peptides" [Palermo et al., J Comput Chem 2007, 28, 1208

Palermo et al. have recently published a method to correct for intramolecular basis set superposition errors (J Comput Chem 2007, 28, 1208) in intramolecular interactions occurring in peptides. By considering the intermolecular equivalent of this method, it is shown that the method presented by Palermo et al. underestimates the magnitude of the intramolecular BSSE.     

Comments on the article "On evaluating molecular-docking methods for pose prediction and enrichment factors"

The recent article "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors" (Chen H. et al. J. Chem. Inf. Model. 2006, 46, 401-415) contains a series of comments on a similar study we published in Proteins in 2004 (Perola et al. Proteins 2004, 56, 235-249). We believe that some of these comments are misleading, and we feel that an adequate response is in order.     

The Relationship of William Henry Perkin,Jr. and Sir Robert Robinson: Teacher and Student,then Student and Teacher

William Henry Perkin, Jr. FRS, the son of the inventor of mauve and other commercial dyes and credited for initiating the industrialization of chemistry, was himself a notable chemist. He was the Professor of Organic Chemistry at Manchester from 1892–1912 and then was the Waynflete Professor of Chemistry at Oxford and the first Head of the Dyson Perrins Laboratory from 1912–1929. One of Perkin's graduate students and research assistants at Manchester was Robert Robinson, subsequently Sir Robert Robinson, FRS and recipient of the 1947 Nobel Prize in Chemistry. Perkin and Robinson had perhaps the most productive and broad collaboration between a professor and one's student. Together, during and after Robinson's student days, they had 71 joint publications, 25 of which involved just the two of them, 17 of which involved the structure determination of strychnine, and eight of which were published after Perkin's death in 1929. Upon Perkin's early death, Robinson succeeded him as the fourth Waynflete Professor of Chemistry at the Dyson Perrins Laboratory, Oxford University. This Essay will examine the professional relationship of Perkin, Jr. and Robinson as revealed in their joint publications on the structure of strychnine.     

"Going KiNativ": probing the Native Kinome

In this issue, Patricelli et?al. (2011) describe an in?situ chemoproteomics approach (KiNativ?) for profiling the?kinome and kinome response to specific kinase inhibitors that enables characterization of inhibitor interactions with endogenously expressed kinases in native conditions.     

Density functional study of double ionization energies

In this paper, double ionization energies (DIEs) of gas-phase atoms and molecules are calculated by energy difference method with density functional theory. To determine the best functional for double ionization energies, we first study 24 main group atoms in the second, third, and fourth periods. An approximation is used in which the electron density is first obtained from a density functional computation with the exchange-correlation potential V xc known as statistical average of orbital potentials, after which the energy is computed from that density with 59 different exchange-correlation energy functionals E xc. For the 24 atoms, the two best E xc functional providing DIEs with average absolute deviation (AAD) of only 0.25 eV are the Perdew-Burke-Ernzerhof functional modified by Hammer et al. [Phys. Rev. B 59, 6413 (1999)] and one known as the Krieger-Chen-Iafrate-Savin functional modified by Krieger et al. (unpublished). Surprisingly, none of the 20 available hybrid functionals is among the top 15 functionals for the DIEs of the 24 atoms. A similar procedure is then applied to molecules, with opposite results: Only hybrid functionals are among the top 15 functionals for a selection of 29 molecules. The best E xc functional for the 29 molecules is found to be the Becke 1997 functional modified by Wilson et al. [J. Chem. Phys. 115, 9233 (2001)]. With that functional, the AAD from experiment for DIEs of 29 molecules is just under 0.5 eV. If the two suspected values for C2H2 and Fe(CO)5 are excluded, the AAD improves to 0.3(2) eV. Many other hybrid functionals perform almost as well.     

"Breaking the Rules": A Planar Phosphonium Cation

Long-standing tenets of a discipline must be questioned in an effort to fully understand the fundamentals of science. This is exemplified by the synthesis of planar-tetracoordinate compounds, such as the square-planar phosphonium ion 1 by Driess et al., which provide exceptions to van't Hoff - Le Bel rules.     

Comments on the article "Evaluation of pK(a) estimation methods on 211 druglike compounds"

The recent article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds" ( Manchester, J.; et al. J. Chem Inf. Model. 2010, 50, 565-571 ) reports poor results for the program Epik. Here, we highlight likely sources for the poor performance and describe work done to improve the performance. Running Epik in the mode intended to calculate pK(a) values for sequentially adding/removing protons, as needed to reproduce the experimental conditions, improves the root mean squared error (RMSE) from 3.0 to 2.18 for the 85 public compounds available from the paper. Despite this improvement, there are still other programs in the Manchester paper that outperform Epik. The primary reason is that the public portion of the data set is not diverse and Epik is missing a few key functional groups in this data set that are heavily represented. We show that incorporation of these missing functional groups into the Epik training set improves the RMSE for the public compounds to 1.04. Furthermore, these enhancements help improve the overall performance of Epik on a large druglike test set.     

Comment on "The nucleation behavior of supercooled water vapor in helium" [J. Chem. Phys. 117, 5647 (2002)

In a recent paper Peeters et al. published new experimental data on nucleation rates of water in the temperature range of 200-235 K. They reported about a drastic change in the nucleation rate at 207 K. An error in their experimental procedure has been found. The data of Peeters et al. have been reinterpreted. The jump in nucleation rate disappears and the corrected nucleation rate data are in good agreement with data found by Wolk and Strey with a different experimental facility.     

Epigenetics gets sweeter: O-GlcNAc joins the "histone code"

O-GlcNAcylation has now been added to the growing list of histone modifications making up the multifaceted "histone-code" (Sakabe et?al., 2010). The sites of O-GlcNAc-histone modification hint at a role in chromatin remodeling, thus adding to mounting evidence that O-GlcNAc cycling sits atop a robust regulatory network maintaining higher-order chromatin structure and epigenetic memory.     

Improving density functional theory for crystal polymorph energetics

We show that the quality of density functional theory (DFT) predictions for the relative stabilities of polymorphs of crystalline para-diiodobenzene (PDIB) is dramatically improved through a simple two-body correction using wavefunction-based electronic structure theory. PDIB has two stable polymorphs under ambient conditions, and like Hongo et al. [J. Phys. Chem. Lett., 1, 1789 (2010)] we find that DFT makes wildly variable predictions of the relative stabilities, depending on the approximate functional used. The two-body corrected scheme, using Grimme's spin-scaled variant of second-order M?ller-Plesset perturbation theory and any of the tested density functionals, predicts the α-polymorph to be more stable, consistent with experiment, and produces a relative stability that agrees with the benchmark quantum Monte-Carlo results of Hongo et al. within statistical uncertainty.     

Connection between the observable and centroid structural properties of a quantum fluid: application to liquid para-hydrogen

It is shown that the discrepancy between path integral Monte Carlo [M. Zoppi et al., Phys. Rev. B 65, 092204 (2002)] and path integral centroid molecular dynamics [F. J. Bermejo et al., Phys. Rev. Lett. 84, 5359 (2000)] calculations of the static structure factor of liquid para-hydrogen can be explained based on a deconvolution equation connecting centroid and physical radial distribution functions. An explicit expression for the kernel of the deconvolution equation has been obtained using functional derivative techniques. In the superposition approximation, this kernel is given by the functional derivative of the effective potential with respect to the pairwise classical potential. Results of path integral Monte Carlo calculations for the radial distribution function and the static structure factor of liquid para-hydrogen are presented.     

The role of exchange-correlation functionals in the potential energy surface and dynamics of N(2) dissociation on W surfaces

We study the dissociative adsorption of N(2) on W(100) and W(110) by means of density functional theory and classical dynamics. Working with a full six-dimensional adiabatic potential energy surface (PES), we find that the theoretical results of the dynamical problem strongly depend on the choice of approximate exchange-correlation functional for the determination of the PES. We consider the Perdew-Wang-91 [Perdew et al., Phys. Rev. B 46, 6671 (1992)] and Perdew-Burke-Ernzerhof (RPBE) [Hammer et al., Phys. Rev. B 59, 7413 (1999)] functionals and carry out a systematic comparison between the dynamics determined by the respective PESs. Even though it has been shown in earlier works that the RPBE may provide better values for the chemisorption energies, our study brings evidence that it gives rise to a PES with excessive repulsion far from the surface.     

Relative energy of the high-(5T2g) and low-(1A1g) spin states of the ferrous complexes [Fe(L)(NHS4)]: CASPT2 versus density functional theory

High-level ab initio calculations using multiconfigurational perturbation theory [complete active space with second-order perturbation theory (CASPT2)] were performed on the transition energy between the lowest high-spin (corresponding to (5T2g) in Oh) and low-spin (corresponding to 1A1g in Oh) states in the series of six-coordinated Fe(II) molecules [Fe(L)(NHS4)], where NHS4 is 2,2'-bis(2-mercaptophenylthio)diethylamine dianion and L=NH3, N2H4, PMe3, CO, and NO+. The results are compared to (previous and presently obtained) results from density functional theory (DFT) calculations with four functionals, which were already shown previously by Casida and co-workers [Fouqueau et al., J. Chem. Phys. 120, 9473 (2004); Ganzenmuller et al., ibid. 122, 234321 (2005); Fouqueau et al., ibid. 122, 044110 (2005); Lawson Daku et al., ChemPhysChem 6, 1393 (2005)] to perform well for the spin-pairing problem in these and other Fe(II) complexes, i.e., OLYP, PBE0, B3LYP, and B3LYP*. Very extended basis sets were used both for the DFT and CASPT2 calculations and were shown to be necessary to obtain quantitative results with both types of method. This work presents a sequel to a previous DFT/CASPT2 study of the same property in the complexes [Fe(H2O)6]2+, [Fe(NH3)6]2+, and [Fe(bpy)3]2+ [Pierloot et al., J. Chem. Phys. 125, 124303 (2006)]. The latter work was extended with new results obtained with larger basis sets and including the OLYP functional. For all considered complexes, the CASPT2 method predicts the correct ground state spin multiplicity. Since experimental data for the actual quintet-singlet (free) energy differences are not available, the performance of the different DFT functionals was judged based on the comparison between the DFT and CASPT2 results. From this, it was concluded that the generalized gradient OLYP functional performs remarkably well for the present series of ferrous compounds, whereas the success of the three hybrid functionals varies from case to case.     

Ambiguous origin: two sides of an ephrin receptor tyrosine kinase

The assembly of a functional receptor tyrosine kinase via expressed protein ligation using receptor segments produced in two different organisms by Singla et al. (2011) provides a tool for monitoring the order of tyrosine phosphorylation events upon ligand activation.     

Current through single conjugated molecules: calculations versus measurements

We use density functional theory based nonequilibrium Green's function to calculate the current through the different rodlike molecules at the finite temperatures self-consistently, which was compared to the experimental measurements presented by Reichert et al. [Phys. Rev. Lett. 88, 176804 (2002)] and by Mayor et al. [Angew. Chem. Int. Ed. 42, 5834 (2003)], respectively. Our results agree with the measurements very well, especially for the bias around +/-1.0 V. The investigation of the topological effect for the symmetrical molecule reveals the fact that the para position compound provides a considerably larger conductance than the meta one.     

Modeling a central ligand in the nitrogenase FeMo cofactor

In very recent work by Einsle et al. (Science 2002, 297, 1696), a new X-ray crystallographic structure of the FeMo cofactor of nitrogenase with a central ligand was presented. The central ligand is a light atom (N, O, or C), and Einsle et al. suggest that it is nitrogen. We present density functional calculations on the FeMo cofactor, and we investigate N, O, and C as central ligands. We show that both N and O lead to energetically stable FeMo cofactor structures, whereas C is energetically unfavorable. By comparison of bond geometries with the crystallographically determined values, we show that the central ligand is most likely nitrogen.     

On assignment of fundamental vibrational modes of hypophosphite anion and its deuterated analogue

Results of ab initio and density functional theory calculations on the structure and vibrational frequencies of hypophosphite anion indicate earlier experimental assignments of the fundamental vibrational modes are correct while the recent reassignments of several modes proposed by Bickley et al. are inconsistent with the calculated results.