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1.
Efficient protocol for quantum Monte Carlo calculations of hydrogen abstraction barriers: Application to methanol 下载免费PDF全文
Ellen T. Swann Michelle L. Coote Amanda S. Barnard Manolo C. Per 《International journal of quantum chemistry》2017,117(9)
Accurate calculation of hydrogen abstraction reaction barriers is a challenging problem, often requiring high level quantum chemistry methods that scale poorly with system size. Quantum Monte Carlo (QMC) methods provide an alternative approach that exhibit much better scaling, but these methods are still computationally expensive. We describe approaches that can significantly reduce the cost of QMC calculations of barrier heights, using the hydrogen abstraction of methanol by a hydrogen atom as an illustrative example. By analysing the combined influence of trial wavefunctions and pseudopotential quadrature settings on the barrier heights, variance, and time‐step errors, we devise a simple protocol that minimizes the cost of the QMC calculations while retaining accuracy comparable to large‐basis coupled cluster theory. We demonstrate that this protocol is transferable to other hydrogen abstraction reactions. 相似文献
2.
Plasencia MD Isailovic D Merenbloom SI Mechref Y Novotny MV Clemmer DE 《Journal of the American Society for Mass Spectrometry》2008,19(11):1706-1715
Ion mobility-mass spectrometry (IMS-MS) and molecular modeling techniques have been used to characterize ovalbumin N-linked
glycans. Some glycans from this glycoprotein exist as multiple isomeric forms. The gas-phase separation makes it possible
to resolve some isomers before MS analysis. Comparisons of experimental cross sections for selected glycan isomers with values
that are calculated for iterative structures generated by molecular modeling techniques allow the assignment of sharp features
to specific isomers. We focus here on an example glycan set, each having a m/z value of 1046.52 with formula [H5N4+2Na]2+, where H corresponds to a hexose, and N to a N-acetylglucosamine. This glycan appears to exist as three different isomeric forms that are assignable based on comparisons
of measured and calculated cross sections. We estimate the relative ratios of the abundances of the three isomers to be in
the range of ∼1.0:1.35:0.85 to ∼1.0:1.5:0.80. In total, IMS-MS analysis of ovalbumin N-linked glycans provides evidence for
19 different glycan structures corresponding to high-mannose and hybrid type carbohydrates with a total of 42 distinct features
related to isomers and/or conformers. 相似文献
3.
Manolo C. Per Emily K. Fletcher Ellen T. Swann Deidre M. Cleland 《Journal of computational chemistry》2020,41(27):2378-2382
We assess the performance of variational (VMC) and diffusion (DMC) quantum Monte Carlo methods for calculating the radical stabilization energies of a set of 43 carbon-centered radical species. Even using simple single-determinant trial wavefunctions, both methods perform exceptionally well, with mean absolute deviations from reference values well under the chemical accuracy standard of 1 kcal/mol. In addition, the use of DMC results in a highly concentrated spread of errors, with all 43 results within chemical accuracy at the 95% confidence level. These results indicate that DMC is an extremely reliable method for calculating radical stabilization energies and could be used as a benchmark method for larger systems in future. 相似文献
4.
Michael J. Blandamer John Burgess Manolo Balon Pilar Guardado Alfredo Maestre 《Transition Metal Chemistry》1988,13(4):313-316
Summary Partial molal volumes of the perchlorate or chloride salts of several tris-diimine-iron(II) cations have been determined in aqueous and methanol-water solutions by vibrating-tube densimetry. Partial molal volumes of the cations at infinite dilution have been estimated for aqueous solution, and compared with values for related cations. Trends of limiting partial molal volumes for perchlorate salts in methanol-water media are compared with trends in transfer chemical potentials for the respective cations; both are discussed in terms of ligand-dependent preferential solvation behaviour. 相似文献
5.
Dyke JM Levita G Morris A Ogden JS Dias AA Algarra M Santos JP Costa ML Rodrigues P Andrade MM Barros MT 《Chemistry (Weinheim an der Bergstrasse, Germany)》2005,11(5):1665-1676
The thermal decompositions of methyl azidoformate (N3COOMe), ethyl azidoformate (N3COOEt) and 2-azido-N,N-dimethylacetamide (N3CH2CONMe2) have been studied by matrix isolation infrared spectroscopy and real-time ultraviolet photoelectron spectroscopy. N2 appears as an initial pyrolysis product in all systems, and the principal interest lies in the fate of the accompanying organic fragment. For methyl azidoformate, four accompanying products were observed: HNCO, H2CO, CH2NH and CO2, and these are believed to arise as a result of two competing decomposition routes of a four-membered cyclic intermediate. Ethyl azidoformate pyrolysis yields four corresponding products: HNCO, MeCHO, MeCHNH and CO2, together with the five-membered-ring compound 2-oxazolidone. In contrast, the initial pyrolysis of 2-azido-N,N-dimethyl acetamide, yields the novel imine intermediate Me2NCOCH=NH, which subsequently decomposes into dimethyl formamide (HCONMe2), CO, Me2NH and HCN. This intermediate was detected by matrix isolation IR spectroscopy, and its identity confirmed both by a molecular orbital calculation of its IR spectrum, and by the temperature dependence and distribution of products in the PES and IR studies. Mechanisms are proposed for the formation and decomposition of all the products observed in these three systems, based on the experimental evidence and the results of supporting molecular orbital calculations. 相似文献
6.
In the article [2] Ennio De Giorgi conjectured that any compact n-dimensional regular submanifold M of ℝ
n+m
,moving by the gradient of the functional
where ηM is the square of the distance function from the submanifold M and Hn is the n-dimensional Hausdorff measure in ℝ n+m, does not develop singularities in finite time provided k is large enough, depending on the dimension n.
We prove this conjecture by means of the analysis of the geometric properties of the high derivatives of the distance function
from a submanifold of the Euclidean space. In particular, we show some relations with the second fundamental form and its
covariant derivatives of independent interest. 相似文献
7.
8.
Luca Bergamaschi Jacek Gondzio Manolo Venturin Giovanni Zilli 《Computational Optimization and Applications》2007,36(2-3):137-147
Issues of indefinite preconditioning of reduced Newton systems arising in optimization with interior point methods are addressed
in this paper. Constraint preconditioners have shown much promise in this context. However, there are situations in which
an unfavorable sparsity pattern of Jacobian matrix may adversely affect the preconditioner and make its inverse representation
unacceptably dense hence too expensive to be used in practice. A remedy to such situations is proposed in this paper. An approximate
constraint preconditioner is considered in which sparse approximation of the Jacobian is used instead of the complete matrix.
Spectral analysis of the preconditioned matrix is performed and bounds on its non-unit eigenvalues are provided. Preliminary
computational results are encouraging. 相似文献
9.
A simple method is presented which ensures the electron-nucleus cusp condition is satisfied by the Slater-Jastrow wavefunctions commonly employed in quantum Monte Carlo simulations. The method is applied in variational energy calculations of the neon atom and a selection of molecules using both Gaussian and Slater basis sets. In addition, we discuss the relationship between the electron-nucleus cusps and the variance of forces, and investigate the sensitivity of forces to the quality of the cusps for various diatomic molecules. 相似文献
10.
Jos Camacho David Lauri Barry Lennox Manolo Escabias Mariano Valderrama 《Journal of Chemometrics》2015,29(6):338-348
Run to run (R2R) optimization based on unfolded Partial Least Squares (u‐PLS) is a promising approach for improving the performance of batch and fed‐batch processes as it is able to continuously adapt to changing processing conditions. Using this technique, the regression coefficients of PLS are used to modify the input profile of the process in order to optimize the yield. When this approach was initially proposed, it was observed that the optimization performed better when PLS was combined with a smoothing technique, in particular a sliding window filtering, which constrained the regression coefficients to be smooth. In the present paper, this result is further investigated and some modifications to the original approach are proposed. Also, the suitability of different smoothing techniques in combination with PLS is studied for both end‐of‐batch quality prediction and R2R optimization. The smoothing techniques considered in this paper include the original filtering approach, the introduction of smoothing constraints in the PLS calibration (Penalized PLS), and the use of functional analysis (Functional PLS). Two fed‐batch process simulators are used to illustrate the results. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献