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PubMedDate not supplied

'Inductive' charges on atoms in proteins: comparative docking with the extended steroid benchmark set and discovery of a novel SHBG ligand.

We have developed a novel iterative approach for calculation of partial charges in proteins within the framework of the 'molecular capacitance' model. The method operates by an effective 'inductive' electronegativity scale derived from a number of the conventional charge systems including CHARMM, AMBER, MMFF, OPLS, and PEOE among others. Our novel 'inductive' electronegativity equalization procedure allows rapid and conformation sensitive computation of adequate partial charges in proteins. Accuracy of the 'inductive' values was confirmed by their correlation with DFT-computed partial charges in common amino acids. A comparative docking study with an extended steroid data set not only illustrated the adequacy of 'inductive' protein charges but also demonstrated their superior performance compared to several conventional protein charging systems. Subsequent docking with 'inductive' charges resulted in identification of five potential leads as human Sex Hormone Binding Globulin (SHBG) ligands from a commercial library of natural compounds. When the selected substances were evaluated for their ability to bind SHBG in vitro, three of them displaced testosterone from the SHBG steroid-binding site, and with one compound this was achieved at micromolar concentrations.

Algorithms↗
PubMed2004

Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark.

One of the most useful ways of describing and analyzing enzyme catalysis is the description of the enzyme as an effective solvent for the reacting substrate. Here, we illustrate this concept by considering the S(N)2 reaction of haloalkan dehalogenase (DhlA), analyze the energetics and dynamics of the solvent coordinate, and evaluate their relative catalytic effect. It is demonstrated that almost the entire catalytic effect is associated with the preorganization of the protein-solvent coordinate. It is clarified that this effect is associated with the fact that the transition state is "solvated" by the protein more than in the reference solution reaction. This effect is fundamentally different than the frequently proposed desolvation mechanism. The possible catalytic role of dynamical effects is analyzed by considering several reasonable ways of defining "dynamical contributions to catalysis". It is found that these contributions are small regardless of the definition used. It is also shown that the effect of the difference in the relaxation time of the solvent coordinate in the enzyme and solution reaction is rather trivial relative to the effect of the corresponding changes in reorganization free energy.

Catalysis↗
PubMed2006

New benchmark for water photooxidation by nanostructured alpha-Fe2O3 films.

Thin films of silicon-doped Fe2O3 were deposited by APCVD (atmospheric pressure chemical vapor deposition) from Fe(CO)5 and TEOS (tetraethoxysilane) on SnO2-coated glass at 415 degrees C. HRSEM reveals a highly developed dendritic nanostructure of 500 nm thickness having a feature size of only 10-20 nm at the surface. Real surface area determination by dye adsorption yields a roughness factor of 21. XRD shows the films to be pure hematite with strong preferential orientation of the [110] axis vertical to the substrate, induced by silicon doping. Under illumination in 1 M NaOH, water is oxidized at the Fe2O3 electrode with higher efficiency (IPCE = 42% at 370 nm and 2.2 mA/cm2 in AM 1.5 G sunlight of 1000 W/m2 at 1.23 VRHE) than at the best reported single crystalline Fe2O3 electrodes. This unprecedented efficiency is in part attributed to the dendritic nanostructure which minimizes the distance photogenerated holes have to diffuse to reach the Fe2O3/electrolyte interface while still allowing efficient light absorption. Part of the gain in efficiency is obtained by depositing a thin insulating SiO2 interfacial layer between the SnO2 substrate and the Fe2O3 film and a catalytic cobalt monolayer on the Fe2O3 surface. A mechanistic model for water photooxidation is presented, involving stepwise accumulation of four holes by two vicinal iron or cobalt surface sites.

Adsorption↗
PubMed1999

Inversion Barrier of Corannulene. A Benchmark for Bowl-to-Bowl Inversions in Fullerene Fragments.

In a systematic ab initio study, the Hartree-Fock, B3LYP density functional, and MP2 methods are employed to calculate the bowl-to-bowl inversion barrier of corannulene (1). Basis sets ranging from a minimal basis (STO-3G) to a double polarized valence triple-zeta basis (6-311G(2d,2p)) were used. In comparison with experimental data, it was found that inclusion of dynamic electron correlation (e.g., B3LYP) and a 6-311G basis set (or other basis sets with similar complexity) are essential for quantitatively correct results. At B3LYP/6-311G, DeltaG()(298) = 44.9 kJ/mol. Thermal corrections to Gibbs energy of activation were of minor importance in the relevant range of temperatures. Inversion barriers (DeltaE()(Tot)) of the bowl-shaped fullerene fragments C(26)H(12) 4 and C(30)H(12) 5 and the chiral C(30)H(12) 6 are predicted to be 28.0, 199.4, and 277.3 kJ/mol, respectively, at B3LYP/6-311G. Predicted enthalpies of formations and strain energies are also discussed.

Journal Article↗
PubMed2006

An ab initio benchmark study of hydrogen bonded formamide dimers.

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity Møller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.

Algorithms↗
PubMed2001

Italian drug information centres: benchmark report.

OBJECTIVE: Pharmacist-operated Drug Information Centres (DICs) in Italy were surveyed to gather current information concerning the status, availability and scope of their services. METHODS: 40 DICs were identified and a questionnaire was mailed to them. Topics covered in the questionnaire included staffing, resources, activities and services. The results were compared with previous survey results to identify trends. RESULTS: Information from 36 DICs was analysed (response rate = 90%). Almost all regions of the country are represented. Pharmacists, part-time or full-time, are the most frequent employees working in the DICs. 91% of DICs participate in the P/T committee, 74% takes part in the technical scientific committee for clinical experimentation and/or to the Medical Ethics committee and 60% participate in the hospital infection committee. 90% of DICs produce newsletters and/or bulletins and are involved in research projects. Regarding the question-answer service, requests are mainly concerned with clinical comparative efficacy, therapeutic use, adverse effects. The most frequent users are physicians (67%) followed by pharmacists (16%) while other professionals use DICs to lesser extent. The most frequently used information sources, include "Goodman and Gilman's the pharmacological basis of therapeutics", Martindale: the Extra Pharmacopeia and Physician's Desk Reference; journals such as the Medical Letter, Adverse Drug Reactions Bulletin and Drug and Therapeutic Bulletin, Micromedex, Medline and IOWA databases. Data collected through the questionnaire and details about organisation and activity of Italian DICs are available in "Eupharma", the web-site of the Italian Society of Hospital Pharmacy (SIFO) at the URL http://www.sifo.it. CONCLUSION: The results parallel the European and American trends. In future communication and collaboration at European level could help to identify best practice models that would result in the standardisation of the activities and in the harmonisation of programs in common areas of interest.

Data Collection↗
PubMed1997

Benchmarks of social treatment for children with autism.

Data on the social behavior of typical children may inform practitioners and researchers regarding the appropriate goals of intervention for children with autism. This study assessed the ongoing levels of naturally occurring social behavior in 64 preschool-aged children. A 2 x 2 factorial design was used to analyze population (children with autism and typical children) and age (3 years 3 months vs. 4 years 4 months) differences at the time of preschool entry. Predictable population differences were found for key social behaviors of proximity to children, social bids from children, and focus of engagement on children, as well as for behavioral context variables of verbalizations, adult focus, and atypical behaviors. No differences were found in the amount of time spent focused on toys or objects. There were also no differences in the presenting behaviors of younger and older children with autism. Results are discussed in terms of implications for establishing early social intervention goals.

Adult↗
PubMed2005

Ni(N2)4 revisited: an analysis of the Ni-N2 bonding properties of this benchmark system on the basis of UV/Vis, IR and Raman spectroscopy.

Matrix isolation of Ni atoms in an N2 matrix leads to the formation of Ni(N2)4. This compound, being isoelectronic with the well known Ni(CO)4, represents an important bench-mark system. It has been characterised experimentally by UV/Vis, IR and Raman spectra. The vibrational spectra give evidence for both a1 modes, three of the four t2 modes, and one of the two e modes of the Td symmetric molecule. The experimental data obtained for Ni(14N2)4 and Ni(15N2)4 were used to determine the valence force constants f(Ni-N) and f(N-N), which are compared with those derived for Ni(N2) and for the corresponding carbonyl complexes Ni(CO) and Ni(CO)4. In addition, several overtones and combination modes of Ni(N2)4 were observed for the first time, providing further valuable information about the bond properties. The data allow for the first time a direct estimate of the Ni-N2 bond energy in Ni(N2)4 (120 kJ mol(-1)), that compares with a value of 148 kJ mol(-1) determined by the same method for Ni(CO)4.

Journal Article↗
PubMed2000

Achievable standards, benchmarks for reporting, and criteria for evaluating cervical cytopathology. Second edition including revised performance indicators.

Endocervical cells are not essential for an adequate smear, except where the previous abnormality was seen in endocervical cells. When three consecutive smears are reported as inadequate, the recommendation for colposcopy should be made at the discretion of the pathologist in the light of a review of the relevant slides and the clinical history of the woman concerned. The cellularity of previous sequential smears should not be combined in order to judge the present smear test as negative. There should be no more than three abnormal smears (including borderline) over any 10-year period without a recommendation for colposcopy. At least three negative smears, at least 6 months apart, should be reported before a woman is returned to routine recall following a smear showing mild dyskaryosis or borderline nuclear change. There is no evidence that demonstrates that selective double screening is any more effective in preventing false-negatives than rapid review and this practice cannot therefore be justified. Sensitivity should be based on all abnormalities detected on primary screening rather than on moderate dyskaryosis or worse. Ranges for reporting rates are based on the 10-90th percentiles of the range for laboratories reporting over 10000 screening smears per year in KC61 returns, but apply to all laboratories reporting screening smears.

Algorithms↗
PubMed1997

On the chaotic nature of turbulence observed in benchmark analysis of nonlinear plasma simulation.

Simulational results of two dissipative interchange turbulence (Rayleigh-Taylor-type instability with dissipation) models with the same physics are compared. The convective nonlinearity is the nonlinear mechanism in the models. They are shown to have different time evolutions in the nonlinear phase due to the different initial value which is attributed to the initial noise. In the first model (A), a single pressure representing the sum of the ion and electron components is used (one-fluid model). In the second model (B) the ion and electron components of the pressure fields are independently solved (two-fluid model). Both models become physically identical if we set ion and electron pressure fields to be equal in the model (B). The initial conditions only differ by the infinitesimally small initial noise due to the roundoff errors which comes from the finite difference but not the differentiation. This noise grows in accordance with the nonlinear development of the turbulence mode. Interaction with an intrinsic nonlinearity of the system makes the noise grow, whose contribution becomes almost the same magnitude of the fluctuation itself in the results. The instantaneous deviation shows the chaotic characteristics of the turbulence. (c) 1997 American Institute of Physics.

Journal Article↗