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A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0001-6508-8355
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
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2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 3, 989-1003 p.Article in journal (Refereed) Published
Abstract [en]

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

Place, publisher, year, edition, pages
2014. Vol. 10, no 3, 989-1003 p.
Keyword [en]
Molecular-Dynamics Simulations, Particle Mesh Ewald, Qm/Mm Approach, Force-Fields, Gas-Phase, Energies, Systems, Model, Polarizabilities, Proteins
National Category
Chemical Sciences
URN: urn:nbn:se:kth:diva-144555DOI: 10.1021/ct400897sISI: 000332913500013ScopusID: 2-s2.0-84896288202OAI: diva2:714143
Swedish e‐Science Research Center

QC 20140425

Available from: 2014-04-25 Created: 2014-04-24 Last updated: 2014-08-26Bibliographically approved
In thesis
1. New efficient integral algorithms for quantum chemistry
Open this publication in new window or tab >>New efficient integral algorithms for quantum chemistry
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The contents of this thesis are centered in the developement of new efficient algorithms for molecular integral evaluation in quantum chemistry, as well as new design and implementation strategies for such algorithms aimed at maximizing their performance and the utilization of modern hardware.

This thesis introduces the K4+MIRROR algorithm for 2-electron repulsion integrals, a new ERI integral scheme effective for both segmented and general contraction, which surpasses the performance of all previous ERI analytic algorithms published in the literature. The performance of the K4 kernel contraction schemeis further boosted by the use of some new recurrence relations, CDR/AERR family of recurrences, and the algorithms is further refined for spherical GTOs with the also new SKS method.

New prescreening methods for two-electron integrals are also derived, allowing a more consistent methodology for discarding negligible ERI batches. This thesis introduces new techniques useful to pack integrals efficiently and better exploit the underlying modern SIMD or stream processing hardware. These algorithms and methods are implemented in a new library, the Echidna Fock Solver, a hybrid parallelized module for computing Coulomb and Exchange matrices which has been interfaced to the Dalton suite of quantum chemistry programs. Self-Consistent Field and Response Theory calculations in Dalton using the new EFS library are substantially accelerated, also enabling for the first time the use of general contraction basis sets as default basis for extended calculations.

The thesis further describes the derivation and implementation of an integral algorithm for evaluating the matrix elements needed for the recently introduced QM/CMM method, for which many of the techniques previously derived are also used, along with a suitable prescreening method for the matrix elements. The implementation is also interfaced to the Dalton quantum chemistry program, and used in production calculations.

The last chapter of the thesis is devoted to the derivation of a general analytic solution for type-II Effective Core Potential integrals, arguably one of the most troublesome molecular integrals in quantum chemistry. A new recurrence is introduced for the integrals, and a screening method is presented. Based on these results, a new efficient algorithm for computing type-II ECPs is also described.


Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. xi, 103 p.
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:13
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
urn:nbn:se:kth:diva-149572 (URN)978-91-7595-237-6 (ISBN)
Public defence
2014-09-15, FB53, AlbaNova, Roslagstullsbacken, Stockholm, 14:00 (English)

QC 20140826

Available from: 2014-08-26 Created: 2014-08-24 Last updated: 2014-08-26Bibliographically approved

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Rinkevicius, ZilvinasLi, XinRosal Sandberg, Jaime AxelÅgren, Hans
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