Andrew D. Daniels

Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals

We propose and implement an alternative approach to the original Car–Parrinello method where the density matrix elements (instead of the molecular orbitals) are propagated together with the nuclear degrees of freedom. Our new approach has the advantage of leading to an O(N) computational scheme in the large system limit. Our implementation is based on atom-centered Gaussian orbitals, which are especially suited to deal effectively with general molecular systems. The methodology is illustrated by applications to the three-body dissociation of triazine and to the dynamics of a cluster of a chloride ion with 25 water molecules.

Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems containing thousands of atoms

Conventional semiempirical methods using diagonalization are not practical for calculations on molecular systems containing more than a few hundred atoms because of O(N3) time and O(N2) memory requirements, where N is the number of atoms. Currently, the time dominating step is diagonalization of the Fock matrix. This paper demonstrates how O(N3) diagonalization and O(N2) memory requirements are eliminated by using a conjugate gradient search for the density matrix with sparse matrix techniques. Our method makes high accuracy energy calculations on molecules containing thousands of atoms possible on the typical workstation. Benchmark examples are presented on polyglycine chains (20000 atoms), water clusters (up to 1800 atoms), and nucleic acids (up to 6304 atoms).

What is the best alternative to diagonalization of the Hamiltonian in large scale semiempirical calculations

Recently, several linear scaling approaches have been introduced which replace the time dominating diagonalization step in semiempirical methods, enabling practical calculations to be performed on very large molecules. This paper compares the accuracy and performance of pseudodiagonalization (PD), conjugate gradient density matrix search (CG-DMS), the Chebyshev polynomial expansion method (CEM), and purification of the density matrix (PDM) as linear scaling substitutions for diagonalization. The scaling, speed, and reliability of these methods are compared for AM1 single point energy calculations on polyglycine chains (up to 20 000 atoms), water clusters (up to 12 300 atoms), and nucleic acids (up to 6300 atoms).

Comparison of Conjugate Gradient Density Matrix Search and Chebyshev Expansion Methods for Avoiding Diagonalization in Large-Scale Electronic Structure Calculations

We report a comparison of two linear-scaling methods which avoid the diagonalization bottleneck of traditional electronic structure algorithms. The Chebyshev expansion method (CEM) is implemented for carbon tight-binding calculations of large systems and its memory and timing requirements compared to those of our previously implemented conjugate gradient density matrix search (CG-DMS). Benchmark calculations are carried out on icosahedral fullerenes from C60 to C8640 and the linear scaling memory and CPU requirements of the CEM demonstrated. We show that the CPU requisites of the CEM and CG-DMS are similar for calculations with comparable accuracy.

Geometry Optimization of Kringle 1 of Plasminogen Using the PM3 Semiempirical Method

The results of a geometry optimization on the 1226 atom Kringle 1 of plasminogen are presented. The energy and gradients were calculated using a linear- scaling PM3 semiempirical method with a conjugate gradient density matrix search replacing the diagonalization step. The geometry was optimized with the rational function optimization technique combined with a modified version of the direct inversion in the iterative subspace procedure. The optimization required 362 geometry update steps to reach a local minimum. An analysis is given of the optimization and timing results using a single processor on the SGI Origin2000. Q 2000 John Wiley & Sons, Inc. Int J

Converging difficult SCF cases with conjugate gradient density matrix search

The possibility of converging difficult self constent field (SCF) cases with the conjugate gradient density matrix search (CGDMS) method is investigated. Density functional theory calculations using various functionals and basis sets were performed on CrC, Cr2, UO2(OH)4 and UF4 which we deem representative of molecules which have SCF convergence problems. From calculations on these molecules we found that CGDMS has better SCF convergence properties than diagonalization alone, while it is comparable with diagonalization in combination with an adequately chosen level shift.

Synthesis and Characterization of 1,4-Dichlorospiropentadiene

Abstract 1,4-Dichlorospiropentadiene was prepared by vacuum gas-solid elimination of compound 3 over solid (n-Bu) 4 N + F − and characterized by 1 H and 13 C NMR spectroscopy at −103 °C.

Chalcogenide Exchange Reaction of [RGa(μ3-Te)]4 with Elemental Sulfur and Selenium: A Density Functional Theory Study

Thermodynamic and mechanistic features of the chalcogen exchange reaction between [RGa(μ3-Te)]4 and elemental sulfur or selenium have been studied employing density functional theory (DFT) calculations using the BL3YP basis set and Stuttgart pseudopotentials. For [MeGa(μ3-E)]4 (E=S, Se, Te) the correlation between the calculated parameters and diffraction data for their isolable analogs is greater than 98%. Each step of the conversion of [MeGa(μ3-Te)]4 to [MeGa(μ3-E)]4 via [Me4Ga4(μ3-Te)4−x(μ3-E)x] (E=S, Se) is predicted to occur as a series of isolated reactions. The entropy change for each chalcogen exchange is small in magnitude and corresponds to the degree of cage distortion within the cubane molecules. Calculations performed on [MeGa(μ3-Te)]4...S8 and [MeGa(μ3-Te)]4-S suggest that an increase in electrophilicity of the gallium next to a surface bound tellurium may result in nucleophilic cage opening for which intermediate structures are calculated.

Synthesis and characterization of 1-chloro-3-methylenecyclopropene

Abstract 1-Chloro-3-methylenecyclopropene was prepared by vacuum gas-solid elimination of 2,2-dichloro-1-methylene-3-(trimethylsilyl)cyclopropane over solid cesium fluoride and characterized by 1 H and 13 C NMR spectroscopy at −103 °C.

An investigation of the reaction of [RGa(μ3-Te)]4 with O2, SO2 and SeO2 using a combination of experiment and density functional theory

Reaction of [RGa(μ3-Te)]4 (R = tBu, CMeEt2) and O2, SO2 or SeO2 yields, in addition to tellurium metal, [RGa(μ3-O)]n (R = tBu, n = 9; R = CMeEt2, n = 6) and the mixed cubanes [R4Ga4(μ3-O)x(μ3-Te)4 − x] (x = 1, 2); neither [R4Ga4(μ3-O)3(μ3-Te)] or [RGa(μ3-O)]4 are observed; DFT calculations show no global minimum for [Me4Ga4(μ3-Te)2(μ3-O)2] or [Me4Ga4(μ3-Te)2(μ3-O)2], suggesting that these structures would rearrange to more favored structures on the pathway to a final geometry lower in energy.