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PubMed2004

Quantum and classical studies of the O(3P) + H2(v = 0-3,j = 0) --> OH + H reaction using benchmark potential surfaces.

We present results of time-dependent quantum mechanics (TDQM) and quasiclassical trajectory (QCT) studies of the excitation function for O(3P) + H2(v = 0-3,j = 0) --> OH + H from threshold to 30 kcal/mol collision energy using benchmark potential energy surfaces [Rogers et al., J. Phys. Chem. A 104, 2308 (2000)]. For H2(v = 0) there is excellent agreement between quantum and classical results. The TDQM results show that the reactive threshold drops from 10 kcal/mol for v = 0 to 6 for v = 1, 5 for v = 2 and 4 for v = 3, suggesting a much slower increase in rate constant with vibrational excitation above v = 1 than below. For H2(v > 0), the classical results are larger than the quantum results by a factor approximately 2 near threshold, but the agreement monotonically improves until they are within approximately 10% near 30 kcal/mol collision energy. We believe these differences arise from stronger vibrational adiabaticity in the quantum dynamics, an effect examined before for this system at lower energies. We have also computed QCT OH(v',j') state-resolved cross sections and angular distributions. The QCT state-resolved OH(v') cross sections peak at the same vibrational quantum number as the H2 reagent. The OH rotational distributions are also quite hot and tend to cluster around high rotational quantum numbers. However, the dynamics seem to dictate a cutoff in the energy going into OH rotation indicating an angular momentum constraint. The state-resolved OH distributions were fit to probability functions based on conventional information theory extended to include an energy gap law for product vibrations.

Journal Article↗
PubMed2004

Path integral Monte Carlo approach for weakly bound van der Waals complexes with rotations: algorithm and benchmark calculations.

A path integral Monte Carlo technique suitable for the treatment of doped helium clusters with inclusion of the rotational degrees of freedom of the dopant is introduced. The extrapolation of the results to the limit of infinite Trotter number is discussed in detail. Benchmark calculations for small weakly bound (4)He(N)--OCS clusters are presented. The Monte Carlo results are compared with those of basis set calculations for the He--OCS dimer. A technique to analyze the orientational imaginary time correlation function is suggested. It allows one to obtain information regarding the effective rotational constant for a doped helium cluster based on a model for the rotational Hamiltonian. The renormalization of the effective rotational constant for (4)He(N)--OCS clusters derived from the orientational imaginary time correlation function is in good agreement with experimental results.

Journal Article↗
PubMed2004

Cumulative isomerization probability studied by various transition state wave packet methods including the MCTDH algorithm. Benchmark: HCN-->CNH isomerization.

The 3D cumulative isomerization probability N(E) for the transfer of a light particle between two atoms is computed by one time-independent and two time-dependent versions of the transition state wave packet (TSWP) method. The time-independent method is based on the direct expansion of the microcanonical projection operator on Chebyshev polynomials. In the time-dependent TSWP methods, the propagations are carried out by the split operator scheme and the multiconfiguration time-dependent Hartree (MCTDH) algorithm. This is the very first implementation of the TSWP method in the Heidelberg MCTDH package [G. W. Worth, M. H. Beck, A. Jackle, and H.-D. Meyer, The MCDTH package, Version 8.2 (2000); H.-D Meyer, Version 8.3 (2002). See http://www.pci.uni-heidelberg.de/tc/usr/mctdh/]. The benchmark is the HCN-->CNH isomerization for zero total angular momentum. Particular insights are given into the tunneling region. In larger systems, the time-dependent version of TSWP making use of the MCTDH algorithm will permit to treat more and more modes quantum mechanically, for very accurate results. Therefore, it was important to calibrate the implementation. Besides, we also assess the efficiency of a reduced dimensionality approach by comparing the new exact 3D calculations of N(E) for the HCN-->CNH isomerization with results obtained via 1D or 2D active subspaces. This suggests that, it should be possible to take directly benefit of the present 3D approaches, adapted for triatomic Jacobi coordinates to compute N(E) for H-transfer in larger systems, via three active coordinates. The prerequisite is then the simplification of the reduced 3D kinetic energy operator with rigid constraint to take the form corresponding to a pseudo triatomic system in Jacobi coordinates with effective masses. This last step is checked in the methoxy radical and malonaldehyde. Finally, different ways to obtain reliable eigenvectors of the flux operator associated with a dividing surface are revisited.

Journal Article↗
PubMed2004

Ab initio benchmark study for the oxidative addition of CH4 to Pd: importance of basis-set flexibility and polarization.

To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order Møller-Plesset perturbation theory, fourth-order Møller-Plesset perturbation theory with single, double and quadruple excitations, coupled cluster theory with single and double excitations (CCSD), and with triple excitations treated perturbatively [CCSD(T)]) and hybrid density functional theory using the B3LYP functional, in combination with a hierarchical series of ten Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Counterpoise corrected relative energies of stationary points are converged to within 0.1-0.2 kcal/mol as a function of the basis-set size. Our best estimate of kinetic and thermodynamic parameters is -8.1 (-8.3) kcal/mol for the formation of the reactant complex, 5.8 (3.1) kcal/mol for the activation energy relative to the separate reactants, and 0.8 (-1.2) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). This agrees well with available experimental data. Our work highlights the importance of sufficient higher angular momentum polarization functions, f and g, for correctly describing metal-d-electron correlation and, thus, for obtaining reliable relative energies. We show that standard basis sets, such as LANL2DZ+1f for palladium, are not sufficiently polarized for this purpose and lead to erroneous CCSD(T) results. B3LYP is associated with smaller basis set superposition errors and shows faster convergence with basis-set size but yields relative energies (in particular, a reaction barrier) that are ca. 3.5 kcal/mol higher than the corresponding CCSD(T) values.

Journal Article↗
PubMed2004

The Cotton-Mouton effect of neon and argon: a benchmark study using highly correlated coupled cluster wave functions.

The Cotton-Mouton effect (magnetic field induced linear birefringence) has been studied for neon and argon using state-of-the-art coupled cluster techniques. The coupled cluster singles, doubles and triples (CCSDT) approach has been used to obtain static benchmark results and the CC3 model with an approximate treatment of triple excitations to obtain frequency-dependent results. In the case of neon the effect of excitations beyond triples has also been estimated via coupled cluster calculations including quadruple excitations (CCSDTQ), pentuple excitations (CCSDTQP), etc. up to the full configuration-interaction level. The results obtained for the anisotropy of the hypermagnetizability Deltaeta(omega), the molecular property that determines the magnetic field induced birefringence of spherically symmetric systems, are Deltaeta=2.89 a.u. for neon and Deltaeta=24.7 a.u. for argon, with a negligible effect of frequency dispersion. For neon we could estimate an absolute error on Deltaeta of 0.1 a.u. The accuracy of these results surpasses that of recently reported experimental data.

Journal Article↗
PubMed2004

Towards benchmark second-order correlation energies for large atoms: Zn2+ revisited.

To provide very accurate reference results for the second-order Møller-Plesset (MP2) energy and its various components for Zn(2+), which plays for 3d-electron systems a similar role as Ne for smaller atoms and molecules, we have performed extensive calculation by two completely different implementations of the MP2 method: the finite element method (FEM) and the variation-perturbation (VP) method. The FEM and VP calculations yield partial wave contributions up to l(max)=45 and 12, respectively. Detailed comparison of all FEM and VP energy components for l(max)=12 has disclosed an extraordinary similarity, which justifies using the present results as benchmarks. The present correlation energies are compared with other works. The dependability of an earlier version of FEM, already applied to very large closed-shell atoms, is confirmed. It has been found that for larger atoms the accuracy of the analytical Hartree-Fock results has an impact on the accuracy of the MP2 energies greater than for smaller atoms. Fields of applications of the present results in studies of various electron correlation effects in 3d-electron atoms and molecules are indicated.

Journal Article↗
PubMed2005

Benchmark calculations of the complete configuration-interaction limit of Born-Oppenheimer diagonal corrections to the saddle points of isotopomers of the H + H2 reaction.

We present a detailed ab initio study of the effect that the Born-Oppenheimer diagonal correction (BODC) has on the saddle-point properties of the H3 system and its isotopomers. Benchmark values are presented that are estimated to be within 0.1 cm(-1) of the complete configuration-interaction limit. We consider the basis set and correlation treatment requirements for accurate BODC calculations, and both are observed to be more favorable than for the Born-Oppenheimer energies. The BODC raises the H + H2 barrier height by 0.1532 kcal/mol and slightly narrows the barrier--with the imaginary frequency increasing by approximately 2%.

Journal Article↗
PubMed2006

The electronic spectrum of AgCl2: ab initio benchmark versus density-functional theory calculations on the lowest ligand-field states including spin-orbit effects.

The X 2pi(g), 2sigma(g)+, and 2delta(g) states of AgCl2 have been studied through benchmark ab initio complete active space self-consistent field plus second-order complete active space multireference Moller-Plesset algorithm (CASSCF+CASPT2) and complete active space self-consistent field plus averaged coupled pair functional (CASSCF+ACPF) and density-functional theory (DFT) calculations using especially developed basis sets to study the transition energies, geometries, vibrational frequencies, Mulliken charges, and spin densities. The spin-orbit (SO) effects were included through the effective Hamiltonian formalism using the LambdaSSigma ACPF energies as diagonal elements. At the ACPF level, the ground state is 2pi(g) in contradiction with ligand-field theory, SCF, and large CASSCF; the adiabatic excitation energies for the 2sigma(g)+ and 2delta(g) states are 1640 and 18,230 cm(-1), respectively. The inclusion of the SO effects leads to a pure omega = 32(2pi(g)) ground state, a omega = 12 (66%2pi(g) and 34%2sigma(g)+) A state, a omega = 12 (34%2pi(g) and 66%2sigma(g)+) B state, a omega = 52(2delta(g))C state, and a omega = 32(99%2delta(g))D state. The X-A, X-B, X-C, and X-D transition energies are 485, 3715, 17 246, and 20 110 cm(-1), respectively. The B97-2, B3LYP, and PBE0 functionals overestimate by approximately 100% the X 2pi(g)-2sigma(g)+T(e) but provide a qualitative energetic ordering in good agreement with ACPF results. B3LYP with variable exchange leads to a 42% optimal Hartree-Fock exchange for transition energies but all equilibrium geometries get worsened. Asymptotic corrections to B3LYP do not provide improved values. The nature of the bonding in the X 2pi(g) state is very different from that of CuCl2 since the Mulliken charge on the metal is 1.1 while the spin density is only 0.35. DFT strongly delocalizes the spin density providing even smaller values of around 0.18 on Ag not only for the ground state, but also for the 2sigma(g)+ state.

Journal Article↗
PubMed2006

Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters.

Ultrafast vibrational spectroscopy experiments, together with molecular-level theoretical interpretation, can provide important information about the structure and dynamics of complex condensed phase systems, including liquids. The theoretical challenge is to calculate the instantaneous vibrational frequencies of a molecule in contact with a molecular environment, accurately and quickly, and to this end a number of different methods have been developed. In this paper we critically analyze these different methods by comparing their results to accurate benchmark calculations on azide/water clusters. We also propose an optimized quantum mechanics/molecular mechanics method, which for this problem is superior to the other methods.

Azides↗
PubMed2006

Study of the molecular structure, ionization spectrum, and electronic wave function of 1,3-butadiene using electron momentum spectroscopy and benchmark Dyson orbital theories.

The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within approximately 0.2 eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense pi(-2) pi(*+1) satellite at approximately 13.1 eV in the ionization spectrum of the s-trans conformer.

Journal Article↗
PubMed2006

Benchmarking the performance of density functional theory based Green's function formalism utilizing different self-energy models in calculating electronic transmission through molecular systems.

Electronic transmission through a metal-molecule-metal system is calculated by employing a Green's function formalism in the scattering based scheme. Self-energy models representing the bulk and the potential bias are used to describe electron transport through the molecular system. Different self-energies can be defined by varying the partition between device and bulk regions of the metal-molecule-metal model system. In addition, the self-energies are calculated with different representations of the bulk through its Green's function. In this work, the dependence of the calculated transmission on varying the self-energy subspaces is benchmarked. The calculated transmission is monitored with respect to the different choices defining the self-energy model. In this report, we focus on one-dimensional model systems with electronic structures calculated at the density functional level of theory.

Journal Article↗
PubMed1996

An ab initio benchmark study of the H + CO --> HCO reaction.

The H + CO --> HCO reaction has been characterized with correlation consistent basis sets at five levels of theory in order to benchmark the sensitivities of the barrier height and reaction ergicity to the one-electron and n-electron expansions of the electronic wave function. Single and multireference methods are compared and contrasted. The coupled cluster method RCCSD(T) was found to be in very good agreement with Davidson-corrected internally-contracted multireference configuration interaction (MRCI+Q). Second-order Moller-Plesset perturbation theory (MP2) was also employed. The estimated complete basis set (CBS) limits for the barrier height (in kcal/mol) for the five methods, including harmonic zero-point energy corrections, are MP2, 4.66; RCCSD, 4.78; RCCSD(T), 4.15; MRCI, 5.10; and MRCI+Q, 4.07. Similarly, the estimated CBS limits for the ergicity of the reaction are: MP2, -17.99; RCCSD, -13.34; RCCSD(T), -13.79; MRCI, -11.46; and MRCI+Q, -13.70. Additional basis set explorations for the RCCSD(T) method demonstrate that aug-cc-pVTZ sets, even with some functions removed, are sufficient to reproduce the CBS limits to within 0.1-0.3 kcal/mol.

Astronomy↗
PubMed1997

Investigation of the potential impact of benchmark dose and pharmacokinetic modeling in noncancer risk assessment.

There has been relatively little attention given to incorporating knowledge of mode of action or of dosimetry of active toxic chemical to target tissue sites in the calculation of noncancer exposure guidelines. One exception is the focus in the revised reference concentration (RfC) process on delivered dose adjustments for inhaled materials. The studies reported here attempt to continue in the spirit of the new RfC guidelines by incorporating both mechanistic and delivered dose information using a physiologically based pharmacokinetic (PBPK) model, along with quantitative dose-response information using the benchmark dose (BMD) method, into the noncancer risk assessment paradigm. Two examples of the use of PBPK and BMD techniques in noncancer risk assessment are described: methylene chloride, and trichloroethylene. Minimal risk levels (MRLs) based on PBPK analysis of these chemicals were generally similar to those based on the traditional process, but individual MRLs ranged from roughly 10-fold higher to more than 10-fold lower than existing MRLs that were not based on PBPK modeling. Only two MRLs were based on critical studies that presented adequate data for BMD modeling, and in these two cases the BMD models were unable to provide an acceptable fit to the overall dose-response of the data, even using pharmacokinetic dose metrics. A review of 10 additional chemicals indicated that data reporting in the toxicological literature is often inadequate to support BMD modeling. Three general observations regarding the use of PBPK and BMD modeling in noncancer risk assessment were noted. First, a full PBPK model may not be necessary to support a more accurate risk assessment; often only a simple pharmacokinetic description, or an understanding of basic pharmacokinetic principles, is needed. Second, pharmacokinetic and mode of action considerations are a crucial factor in conducting noncancer risk assessments that involve animal-to-human extrapolation. Third, to support the application of BMD modeling in noncancer risk assessment, reporting of toxicity results in the toxicological literature should include both means and standard deviations for each dose group in the case of quantitative endpoints, such as relative organ weights or testing scores, and should report the number of animals affected in the case of qualitative endpoints.

Animals↗
PubMed2001

Behavioural surveillance of sexually-related risk behaviours of the Chinese male general population in Hong Kong: a benchmark study.

The objective of the study was to establish a behavioural surveillance system (BSS) for sexually-related risk behaviours of the Hong Kong adult male general population. Benchmark data were obtained by interviewing 1,020 male respondents, age 18 to 60. The results showed that: (1) 14% of the respondents had engaged in commercial sex in the past six months, (2) 27% of the male commercial sex clients did not always use condoms when having sexual intercourse with commercial sex workers (CSWs), (3) 1.5% of the respondents had contracted sexually transmitted diseases (STDs) in the past six months, (4) 6.1% of respondents had only ever had sex with a man, (5) 0.8% of the respondents had practised unprotected anal intercourse with a man in a six-month period, (6) 4.4% of respondents practised sexually-related high risk behaviours, defined as unprotected sex with a CSW or unprotected anal intercourse with a man, and (7) 36.4% of those who engaged in commercial sex had not used condoms with their regular sex partners. Commercial sex was often practised outside Hong Kong, very commonly in Mainland China or Macau, and was often practised at multiple locations by the same client. Effective programmes have to be able to reduce the size of the at-risk population. This study together with future ones, will form the first BSS in Hong Kong for the general male population and will provide a relevant yardstick for programme evaluation.

Adult↗
PubMed2006

Estimation of benchmark doses for urinary cadmium based on beta2-microglobulin excretion in cadmium-polluted regions of the Kakehashi River basin, Japan.

A benchmark dose low (BMDL) is used as a replacement for the no observed adverse effect level. The threshold levels of urinary cadmium (Cd) as BMDL were estimated using data from the Kakehashi River basin. The target population (>or=50 years) comprised 3178 and 294 participants inhabiting Cd-polluted and non-polluted areas, respectively. Cut-off values for beta2-MG-uria were defined as the 84 and 95% upper limit values calculated from control subjects, and 1000 microg/l or microg/g cr of beta2-MG. Using these cut-off values, the BMDL at which the excess risk is 0.05 was determined to be 2.9 - 4.0 microg/g cr (males) and 1.5 - 3.6 microg/g cr (females). The present study demonstrated that a BMD approach is useful to estimate the threshold level of urinary Cd in Cd-exposed subjects and people living in general environment without any known Cd-pollution since a BMD approach does not need abnormality rates of urinary findings in the controls.

Aged↗
PubMed2005

Quality benchmark for trans-tibial prostheses in low-income countries.

Based on four series of patients (N=141) participating in clinical field testing of prosthetic feet and all provided with trans-tibial prostheses in accordance with the polypropylene component and assembly system developed by the International Committee of the Red Cross (ICRC) a series of quality benchmarks was developed and tested against historical data. The patient compliance demands were set for walking >1 km at 90 +/- 10%, non-users at 5 +/- 5%, discomfort at 10 +/- 10%, pain at 10 +/- 10%, and patient satisfaction at 90 +/- 10%. The technical performance demands were set for good socket fit at 60 +/- 10%, misalignment at 15 +/- 10%, insufficient craftsmanship at 10 +/- 10%, and requirements for socket change at 10 +/- 10%.

Adolescent↗
PubMed2002

Critical issues in benchmark calculations from continuous data.

The benchmark dose (BMD) is a dose that causes a specified low level of additional risk and is estimated using a statistical dose-response analysis. Regulatory agencies are using a statistical lower bound on the BMD in the place of the NOAEL for establishing exposure limits. However, there are still several issues regarding the BMD for which no clear consensus has emerged, particularly with respect to calculation of BMD from continuous response data. These include: (1) how to define the BMD from continuous data so that they are comparable to BMD derived from binary data, (2) what dose-response models and levels of additional risk should be used to calculate the BMD. The "hybrid" approach (Gaylor and Slikker, 1990; Crump, 1995) expresses the BMD from continuous data in terms that are directly comparable to those obtained using binary data. Several features of the hybrid approach are examined, with the emphasis on application to epidemiological data. The effect on the BMD of converting continuous data to binary form is quantified. Model uncertainty is explored, and the need for controlling this uncertainty by restricting the class of allowable models is demonstrated. Control data, which are often not available in epidemiological studies, are shown to have a limited effect upon the BMD so long as the model for the mean response is linear or convex. Such models are also biologically plausible, at least at low doses. Based on these and other considerations, suggestions are made for selecting a model for applying the hybrid approach and for selecting the level of additional risk on which to base the BMD.

Algorithms↗
PubMed2000

Use of Monte Carlo computation in benchmarking radiotherapy treatment planning system algorithms.

Radiotherapy treatments are becoming more complex, often requiring the dose to be calculated in three dimensions and sometimes involving the application of non-coplanar beams. The ability of treatment planning systems to accurately calculate dose under a range of these and other irradiation conditions requires evaluation. Practical assessment of such arrangements can be problematical, especially when a heterogeneous medium is used. This work describes the use of Monte Carlo computation as a benchmarking tool to assess the dose distribution of external photon beam plans obtained in a simple heterogeneous phantom by several commercially available 3D and 2D treatment planning system algorithms. For comparison, practical measurements were undertaken using film dosimetry. The dose distributions were calculated for a variety of irradiation conditions designed to show the effects of surface obliquity, inhomogeneities and missing tissue above tangential beams. The results show maximum dose differences of 47% between some planning algorithms and film at a point 1 mm below a tangentially irradiated surface. Overall, the dose distribution obtained from film was most faithfully reproduced by the Monte Carlo N-Particle results illustrating the potential of Monte Carlo computation in evaluating treatment planning system algorithms.

Algorithms↗