Howard R. Mayne

Global optimization of atomic and molecular clusters using the space‐fixed modified genetic algorithm method

A modified genetic algorithm approach has been applied to atomic Ar clusters and molecular water clusters up to (H2O)13. Several genetic operators are discussed which are suitable for real‐valued space‐fixed atomic coordinates and Euler angles. The performance of these operators has been systematically investigated. For atomic systems, it is found that a mix of operators containing a coordinate‐averaging operator is optimal. For angular coordinates, the situation is less clear. It appears that inversion and two‐point crossover operators are the best choice.

Spectroscopy of the transition state (theory). II. Absorption by H‡3 in H+H2→H‡3→H2+H

Absorption spectra of transition state configurations in the reaction H+H2→H‡3 →H2+H have been computed. The density of H‡3 in configuration space was obtained from a classical trajectory study of collinear reaction on the Siegbahn, Liu, Truhlar, and Horowitz (SLTH) ab initio potential energy surface (PES). Vertical transitions were assumed to an upper PES H*3 modeled on limited ab initio data; four different model PES for H*3 were examined. The effects of varying reagent collision energy, varying reagent vibrational excitation, varying isotopic mass, and varying optical transition moment were explored. Transition state spectra were also computed for thermal distributions of H+H2, at 300 and 1000 K. The transition state spectra obtained constituted a wing extending as far as 40 000 cm−1 to the ‘‘red’’ of the Lyman‐α transition. As illustrated here, the wing exhibited features that reflected the dynamics of reaction on the SLTH PES.

A study of genetic algorithm approaches to global geometry optimization of aromatic hydrocarbon microclusters

We have carried out potential energy minimization calculations on benzene, naphthalene, and anthracene clusters using model potential energy functions. The primary purpose was to examine several techniques which use concepts from the field of genetic algorithms (GA). In particular, we compared the “traditional GA” in which the variables of the problem are coded into binary and genetic operations performed on these, and recent methods which use real-valued variables. Our primary technique, the “space-fixed modified GA” (SFMGA), also uses a conjugate gradient descent on the geometries generated by the GA. Our results show the convergence to the global minimum is greatly improved by the use of the descent minimization. In fact, it appears unlikely that the traditional GA’s are useful for any but the very simplest clusters. We have also compared the SFMGA with simulated annealing (SA) and Wales and Doye’s recent basin-hopping (BH) technique. We find our method to be superior to SA, and comparable to BH.

The effect of reagent rotation in the reaction OH( j)+H2( j’)→H2O+H

Classical trajectory calculations on the reaction OH( j)+H2( j’)→H2O+H have been carried out with j≤40 and j’≤15 on both the Schatz–Elgersma [Chem. Phys. Lett. 73, 21 (1980)] and the Rashed–Brown [J. Chem. Phys. 82, 5506 (1985)] potential energy surfaces. When there is no rotation in the OH, then a plot of reaction cross section, SR( j’) resembles that for an atom–diatom system: Just above threshold, rotation decreases reactivity for small j’, but increases it for high j’; at higher translational energies this trend is less obvious, but still present. When j’=0, then SR( j) is a complicated function, decreasing for low j, then climbing to a maximum, finally decreasing once more at very large values of j. We have also carried out calculations with isotopically substituted H in OH, and show that these effects scale as the mass of the hydrogen isotope. We show that this behavior is due to artifacts in both the potential surfaces. Using a simple model we are able to rationalize this behavior. Using this same ...

Classical trajectory calculations on gas-phase reactive collisions

Abstract The recent (since 1983) literature on classical trajectory calculations on gas phase reactions is reviewed. It is seen that this continues to be a vigorous area of research, yielding considerable insight into the microscopic details of reaction mechanisms, as well as being a relatively simple means of calculating cross-sections and rate constants. The necessary theoretical background is touched upon briefly, and several caveats are pointed out. A few model reactions continue to be the subject of intensive activity, most notably the reactions H + H2→H2 + H and F + H2→FH + H, the prototypical thermoneutral and exoergic systems respectively. These reactions are unusual in that their potential energy surfaces are relatively well known. For this reason, among others, comparisons of quantum and classical dynamics on these systems are common. Recent advances in quantum mechanical scattering theory have greatly increased the feasibility of exact calculations for the transfer of H atoms between heavier at...

An investigation of two approaches to basin hopping minimization for atomic and molecular clusters

Abstract We have carried out potential energy minimization searches for atomic and molecular clusters using two variants of the basin hopping strategy. We find that the significant structures basin hopping (SSBH) performs better than the raw structures basin hopping (RSBH) when both use optimized step sizes. The SSBH was able to locate previously-identified global minima for (LJ) n ( n =19, 30, 38) and (benzene) n ( n =6, 10) The (benzene) 14 cluster minimum presented here is a new result.

Minimization of small silicon clusters using the space-fixed modified genetic algorithm method

Abstract A space-fixed modified genetic algorithm (SFMGA) approach was used to obtain global minima for the silicon clusters (Si) n using a semiempirical potential. One modification to the usual GA is the use of gradient-driven minimization of each geometry. A novel feature of the method is the use of space-fixed atomic coordinates. The advantages of these coordinates are discussed. The method found all minima previously reported for n = 3−10, and improved on those for n = 5−8. That the commonly-used method of seeding a cluster can actually detract from minimization efficiency, is also shown.

Nighttime nitrate radical chemistry at Appledore Island, Maine during the 2004 International Consortium for Atmospheric Research on Transport and Transformation

Received 5 April 2007; revised 22 June 2007; accepted 7 August 2007; published 2 November 2007. [1] Trace gases including nitrogen dioxide (NO2), nitrate radical (NO3), ozone (O3), and a suite of volatile organic compounds (VOCs) were measured within the New England coastal marine boundary layer on Appledore Island (AI), Maine, USA as part of the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) field campaign. These measurements, together with local meteorological records and published kinetic data were used to investigate nighttime NO3 chemistry at AI during the period of 8–28 July 2004. Among the VOCs, isoprene, monoterpenes and dimethylsulfide (DMS) were the dominant NO3 reactants; on average, DMS accounted for 51 ± 34% of the total reactivity. For three case studies, NO3 mixing ratios were calculated from measured parameters with resultant uncertainties of � 30%. Discrepancies with measured NO3 appeared to result primarily from input parameter variability and exclusion of heterogeneous dinitrogen pentoxide (N2O5) chemistry. We indirectly determined that nighttime NO3 and NOx (=NO + NO2) removal via N2O5 chemistry (gas-phase + heterogeneous) was on average 51–54% and 63–66% of the total respectively. Our analysis suggested that the minimum average NO3 and NOx removal via heterogeneous N2O5 chemistry was � 10% of the total. Reducing gas-phase N2O5 reactivity in accord with Brown et al. (2006a) increased the importance of heterogeneous N2O5 chemistry substantially. It is plausible that the latter pathway was often comparable to gas-phase removal of NO3 and NOx. Overall, 24 h-averaged NOx removal was � 11 ppbv, with nighttime chemical pathways contributing � 50%.

Effect of reactant rotation on reactivity: a comparison of classical and quantum effects in a model system

Abstract The effect of reactant rotation on reactivity has been investigated using a model system. Classical and exact quantum results are in excellent agreement above threshold. Trends are found which mirror those seen in recent trajectory studies on H + H 2 .

The effect of reagent rotation on chemical reactivity: F+H2 revisited

Classical trajectory calculations on the gas phase reaction F+H2 ( j)→HF+H have been carried out. Different reactivity trends were seen depending on whether there was a chemically significant and anisotropic well in the entrance channel of the potential surface. For those in which there is no such well, rotation may decrease reactivity at low values of j, but increases it thereafter. The reaction cross section SR ( j) decreases slowly from j=0, reaching a minimum near j=6 then increases again. This behavior has been reported for several systems, including H+H2, and seems to be the ‘‘canonical’’ behavior for SR ( j) for most direct chemical reactions. For F+D2 the minimum does not occur until j=8. However, this does correspond to the same amount of rotational energy as the minimum for F+H2 . For potentials in which there is a deep anisotropic well, it is found that the j=0 results are dominated by the presence of the well, and that the SR ( j=0) is anomalously high. On such surfaces there is normally a sud...