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Frequency-dependent force fields for QMMM calculations
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0001-8571-1458
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-9123-8174
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-1763-9383
2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 12, 7800-7812 p.Article in journal (Refereed) Published
Abstract [en]

We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean (alpha) over bar is determined with respect to the size of the QM and MM parts of the total system.

Place, publisher, year, edition, pages
2015. Vol. 17, no 12, 7800-7812 p.
National Category
Atom and Molecular Physics and Optics Chemical Sciences
URN: urn:nbn:se:kth:diva-165243DOI: 10.1039/c4cp05411cISI: 000351437500025PubMedID: 25714984ScopusID: 2-s2.0-84924871325OAI: diva2:809585

QC 20150504

Available from: 2015-05-04 Created: 2015-04-24 Last updated: 2016-05-17Bibliographically approved
In thesis
1. Atomic decomposition of molecular properties
Open this publication in new window or tab >>Atomic decomposition of molecular properties
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, new methodology of computing properties aimed for multipleapplications is developed. We use quantum mechanics to compute propertiesof molecules, and having these properties as a basis, we set up equations basedon a classical reasoning. These approximations are shown to be quite good inmany cases, and makes it possible to calculate linear and non-linear propertiesof large systems.The calculated molecular properties are decomposed into atomic propertiesusing the LoProp algorithm, which is a method only dependent on the overlapmatrix. This enables the expression of the molecular properties in the two-site atomic basis, giving atomic, and bond-centric force-fields in terms of themolecular multi-pole moments and polarizabilities. Since the original LoProptransformation was formulated for static fields, theory is developed which makesit possible to extract the frequency-dependent atomic properties as well. Fromthe second-order perturbation of the electron density with respect to an externalfield, LoProp is formulated to encompass the first order hyperpolarizability.The original Applequist formulation is extended into a quadratic formula-tion, which produces the second-order shift in the induced dipole moments of thepoint-dipoles from the hyperpolarizability. This enables the calculation of a to-tal hyperpolarizability in systems consisting of interacting atoms and molecules.The first polarizability α and the first hyperpolarizability β obtained via theLoProp transformation are used to calculate this response with respect to anexternal field using the quadratic Applequist equations.In the last part, the implemented analytical response LoProp procedureand the quadratic Applequist formalism is applied to various model systems.The polarizable force-field that is obtained from the decomposition of the staticmolecular polarizability α is tested by studying the one-photon absorption spec-trum of the green fluorescent protein. From the frequency dispersion of thepolarizability α(ω), the effect of field perturbations is evaluated in classicaland QM/MM applications. Using the dynamical polarizabilities, the Rayleigh-scattering of aerosol clusters consisting of water and cis–pinonic acid moleculesis studied. The LoProp hyperpolarizability in combination with the quadraticApplequist equations is used to test the validity of the model on sample wa-ter clusters of varying sizes. Using the modified point-dipole model developedby Thole, the hyper-Rayleigh scattering intensity of a model collagen triple-helix is calculated. The atomic dispersion coefficients are calculated from thedecomposition of the real molecular polarizability at imaginary frequencies. Fi-nally, using LoProp and a capping procedure we demonstrate how the QM/MMmethodology can be used to compute x-ray photoelectron spectra of a polymer.

Abstract [sv]

I denna avhandling utvecklas ny metodik för beräkningar av egenskaper medolika tillämpningar. Vi använder kvantmekanik för att beräkna egenskaper hosmolekyler, och använder sedan dessa egenskaper som bas i klassiska ekvationer.Dessa approximationer visas vara bra i flera sammanhang, vilket gör det direktmöjligt att beräkna linjära och icke-linjära egenskaper i större system.De beräknade molekylära egenskaperna delas upp i atomära bidrag genomLoProp transformationen, en metod endast beroende av den atomära överlapps-matrisen. Detta ger möjligheten att representera en molekyls egenskaper i entvåatomsbasis, vilket ger atomära, och bindningscentrerade kraftfält tagna frånde molekylära multipoler och polarisabiliteter.Eftersom att den originella LoProp transformationen var formulerad medstatiska fält, så utvecklas och implementeras i denna avhandling LoProp meto-den ytterligare för frekvensberoende egenskaper. Genom den andra ordnin-gens störning med avseende på externa fält, så formuleras LoProp så att di-rekt bestämning av första ordningens hyperpolariserbarhet för atomära po-sitioner blir möjlig. De ursprungliga Applequist ekvationerna skrivs om tillen kvadratisk representation för att göra det möjligt att beräkna den andraordningens induktion av dipolmomenten för punktdipoler med hjälp av denförsta hyperpolariserbarheten. Detta gör det möjligt att beräkna den totalahyperpolariserbarheten för större system. Här används den statiska polariser-barheten och hyperpolariserbarheten framtagna via LoProp transformationenför att beräkna ett systems egenskaper då det utsätts av ett externt elektrisktfält via Applequists ekvationer till andra ordningen.Tillämpningar presenteras av den implementerade LoProp metodiken medden utvecklade andra ordnings Applequist ekvationer för olika system. Detpolariserbara kraftfältet som fås av lokalisering av α testas genom studier avabsorptionsspektrat för det gröna fluorescerande proteinet. Via beräkningar avden lokala frekvensavhängande polariserbarheten α(ω), testas effekten av de ex-terna störningar på klassiska och blandade kvant-klassiska egenskaper. Genomden linjära frekvensberoende polariserbarheten så studeras även Rayleigh sprid-ning av atmosfärs partiklar. Via LoProp transformationen av hyperpolariser-barheten i kombination med de kvadratiska Applequist ekvationerna så un-dersöks modellens rimlighet för vattenkluster av varierande storlek. Genom attanvända Tholes exponentiella dämpningsschema så beräknas hyper-Rayleighspridningen för kollagen. Den atomära dispersionskoefficienten beräknas via delokala bidragen till den imaginära delen av den linjära polariserbarheten. Slutli-gen visar vi hur LoProp tekniken tillsammans med en s.k. inkapslingsmetod kananvändas i QM/MM beräkningar av Röntgenfotoelektron spektra av polymerer.

Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2016. 55 p.
TRITA-BIO-Report, ISSN 1654-2312 ; 2016:14
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
urn:nbn:se:kth:diva-187168 (URN)978–91–7729–014–8 (ISBN)
Public defence
2016-06-09, Svedbergshallen, Alba Nova, Roslagstullsbacken 21, Stockholm, 10:00 (English)

QC 20160517

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2016-05-18Bibliographically approved

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