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Atomic decomposition of molecular properties
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0001-8571-1458
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. , p. 55
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2016:14
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
URN: urn:nbn:se:kth:diva-187168ISBN: 978-91-7729-014-8 OAI: oai:DiVA.org:kth-187168DiVA, id: diva2:929105
Public defence
2016-06-09, Svedbergshallen, Alba Nova, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20160517

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2017-03-02Bibliographically approved
List of papers
1. Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field
Open this publication in new window or tab >>Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field
2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, p. 3492-3502Article in journal (Refereed) Published
Abstract [en]

The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment electronic embedding and polarizable electronic embedding accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-150932 (URN)10.1021/ct5001318 (DOI)000340351200059 ()2-s2.0-84906236526 (Scopus ID)
Note

QC 20140912

Available from: 2014-09-12 Created: 2014-09-11 Last updated: 2017-12-05Bibliographically approved
2. Frequency-dependent force fields for QMMM calculations
Open this publication in new window or tab >>Frequency-dependent force fields for QMMM calculations
2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 12, p. 7800-7812Article 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.

National Category
Atom and Molecular Physics and Optics Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-165243 (URN)10.1039/c4cp05411c (DOI)000351437500025 ()25714984 (PubMedID)2-s2.0-84924871325 (Scopus ID)
Note

QC 20150504

Available from: 2015-05-04 Created: 2015-04-24 Last updated: 2017-12-04Bibliographically approved
3. Hyperpolarizabilities of extended molecular mechanical systems
Open this publication in new window or tab >>Hyperpolarizabilities of extended molecular mechanical systems
2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 12, p. 8710-8722Article in journal (Refereed) Published
Abstract [en]

We propose and evaluate algorithms for the calculation of molecular polarizabilities and hyperpolarizabilities of extended chemical systems. These algorithms are generalizations of the Silberstein-Applequist procedure involving interacting induced classical dipoles through the localized polarizabilities and hyperpolarizabilities. The models are evaluated in terms of interacting molecular units as well as interacting atomic units that result from the atomic decomposition scheme known as the LoProp transformation. We introduce a generalized LoProp scheme which applies to hyperpolarizabilities as well as to polarizabilities. The accuracy of the second-order Applequist method is tested for the first hyperpolarizability for the TIP3P water model using both Hartree-Fock and density functional theory evaluated with different basis sets. Possible applications and ramifications of the scheme are discussed.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2016
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-187159 (URN)10.1039/c5cp06688c (DOI)2-s2.0-84961843157 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC), 023/07-18Swedish National Infrastructure for Computing (SNIC), 2015-1-230
Note

QC 20160518

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2017-11-30Bibliographically approved
4. Modeling Rayleigh Scattering of Aerosol Particles
Open this publication in new window or tab >>Modeling Rayleigh Scattering of Aerosol Particles
2016 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 18, p. 4296-4301Article in journal (Refereed) Published
Abstract [en]

Rayleigh scattering of naturally polarized lightwas studied for systems with atmospheric relevance represent-ing growing water clusters with adsorbed cis-pinonic acid. Thescattering intensity was computed from the static anddynamical polarizabilities of the clusters obtained by a recentlyderived methodology for classical polarizabilities, in whichApplequist equations for interacting polarizable dipoles areused together with point-dipoles and polarizabilities obtainedby quantum chemistry and decomposed into the atomicdomain by the so-called LoProp transformation generalized forfrequency dependence. The Applequist interaction was foundto yield scattering intensities 20% larger for a cluster consistingof 1000 water molecules, as compared to the method where allof the polarizabilities of molecules are added withoutinteractions. It was confirmed that scattering intensity depends quadratically on the number of water molecules in the cluster,and that it also increases quadratically with increase in the mass constituent of the foreign substance. The adsorption of the cis-pinonic acid increases the contribution to the scattering intensity stemming from the anisotropic polarizability, as compared tothe isotropic contribution. The ramifications of the method in predicting Rayleigh scattering and the earth’s albedo with respectto man-made and natural gas emission are briefly discussed.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-187164 (URN)10.1021/acs.jpcb.6b02278 (DOI)000375968900012 ()2-s2.0-84969924848 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC), 023/07-18Swedish National Infrastructure for Computing (SNIC), 2015-1-230
Note

QC 20160518

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2017-11-30Bibliographically approved
5. First hyperpolarizability of collagen using the point dipole approximation
Open this publication in new window or tab >>First hyperpolarizability of collagen using the point dipole approximation
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The application of localized hyperpolarizabilities to predict a total protein hyperpolariz-ability is presented for the first time, using rat-tail collagen as a demonstration example. Weemploy a model comprising the quadratic Applequist point-dipole approach, the so-calledLoProp transformation and a procedure with molecular fractionation using conjugate capsin order to determine the atomic and bond contributions to the net β tensor of the collagen[(PPG)3 ]10 triple-helix. By using Tholes exponential damping modification to the dyadic ten-sor in the Applequist equations, a correct qualitative agreement with experiment is found. Theintensity of the βHRS signal and the depolarization ratios are best reproduced by decomposingthe LoProp properties into the atomic positions, and using Tholes exponential damping withthe original damping parameter. Some ramifications of the model for general protein propertyoptimization are briefly discussed.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-187167 (URN)
Funder
Swedish National Infrastructure for Computing (SNIC), 2015–1– 230
Note

QC 20160518

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2016-05-18Bibliographically approved
6. Local decomposition of imaginary polarizabilities and dispersion coefficients
Open this publication in new window or tab >>Local decomposition of imaginary polarizabilities and dispersion coefficients
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-187162 (URN)
Funder
Swedish National Infrastructure for Computing (SNIC), 2015–1–230
Note

QC 20160518

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2016-05-18Bibliographically approved
7. Quantum-classical calculations of X-ray photoelectron spectra of polymers –polymethyl methacrylate revisited
Open this publication in new window or tab >>Quantum-classical calculations of X-ray photoelectron spectra of polymers –polymethyl methacrylate revisited
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-187163 (URN)
Funder
Swedish National Infrastructure for Computing (SNIC), 2014/11-31Swedish National Infrastructure for Computing (SNIC), 2015/16-10Knut and Alice Wallenberg Foundation, KAW-2013.0020
Note

QC 20160614

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2016-06-14Bibliographically approved

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