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Computational Design of Molecular Motors and Excited-State Studies of Organic Chromophores
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis presents computational quantum chemical studies of molecular motors and excited electronic states of organic chromophores.

The first and major part of the thesis is concerned with the design of light-driven rotary molecular motors. These are molecules that absorb light energy and convert it into 360° unidirectional rotary motion around a double bond connecting two molecular halves. In order to facilitate potential applications of molecular motors in nanotechnology, such as in molecular transport or in development of materials with photo-controllable properties, it is critical to optimize the rates and efficiencies of the chemical reactions that produce the rotary motion. To this end, computational methods are in this thesis used to study two different classes of molecular motors.

The first class encompasses the sterically overcrowded alkenes developed by Ben Feringa, co-recipient of the 2016 Nobel Prize in Chemistry. The rotary cycles of these motors involve two photoisomerization and two thermal isomerization steps, where the latter are the ones that limit the attainable rotational frequencies. In the thesis, several new motors of this type are proposed by identifying steric, electronic and conformational approaches to accelerate the thermal isomerizations. The second class contains motors that incorporate a protonated Schiff base and are capable to achieve higher photoisomerization rates than overcrowded alkene-based motors. In the thesis, a new motor of this type is proposed that produces unidirectional rotary motion by means of two photochemical steps alone. Also, this motor lacks both a stereocenter and helical motifs, which are key features of almost all synthetic rotary motors developed to date.

The second part of the thesis focuses on the design and assessment of composite computational procedures for modeling excited electronic states of organic chromophores. In particular, emphasis is put on developing procedures that facilitate the calculations of accurate 0−0 excitation energies of such compounds in a cost-effective way by combining quantum chemical methods with different accuracies.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2016. , 64 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1794
National Category
Theoretical Chemistry Organic Chemistry Chemical Sciences
Identifiers
URN: urn:nbn:se:liu:diva-132611DOI: 10.3384/diss.diva-132611ISBN: 9789176856741 (Print)OAI: oai:DiVA.org:liu-132611DiVA: diva2:1047085
Public defence
2016-12-15, Schrödinger (E324), Fysikhuset, Campus Valla, Linköping, 13:15 (English)
Opponent
Supervisors
Available from: 2016-11-16 Created: 2016-11-16 Last updated: 2016-11-17Bibliographically approved
List of papers
1. Computational study of the working mechanism and rate acceleration of overcrowded alkene-based light-driven rotary molecular motors
Open this publication in new window or tab >>Computational study of the working mechanism and rate acceleration of overcrowded alkene-based light-driven rotary molecular motors
2014 (English)In: RSC Advances, ISSN 2046-2069, Vol. 4, no 20, 10240-10251 p.Article in journal (Refereed) Published
Abstract [en]

In recent years, much progress has been made in the design, synthesis and operation of light-driven rotary molecular motors based on chiral overcrowded alkenes. Through consecutive cistrans photoisomerization and thermal helix inversion steps, where the latter dictate the overall rate of rotation, these motors achieve a full 360° unidirectional rotation around the carbon–carbon double bond connecting the two (rotator and stator) alkene halves. In this work, we report quantum chemical calculations indicating that a particularly fast-rotating overcrowded alkene-based motor capable of reaching the MHz regime, can be made to rotate even faster by the substitution of a rotator methyl group with a methoxy group. Specifically, using density functional theory methods that reproduce the rate-limiting 35 kJ mol−1 thermal free-energy barriers shown by the methyl-bearing motor with errors of 5 kJ mol−1 only, it is predicted that this substitution reduces these barriers by a significant 15–20 kJ mol−1. This prediction is preceded by a series of benchmark calculations for assessing how well density functional theory methods account for available experimental data (crystallographic, UV-vis absorption, thermodynamic) on the rotary cycles of overcrowded alkenes, and a detailed examination of the thermal and photochemical reaction mechanisms of the original motor of this type.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2014
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-104688 (URN)10.1039/C3RA46880A (DOI)000332061300048 ()2-s2.0-84894247198 (ScopusID)
Available from: 2014-02-22 Created: 2014-02-22 Last updated: 2016-11-16Bibliographically approved
2. Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects
Open this publication in new window or tab >>Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects
2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 33, 21740-21751 p.Article in journal (Refereed) Published
Abstract [en]

We report a systematic computational investigation of the possibility to accelerate the rate-limiting thermal isomerizations of the rotary cycles of synthetic light-driven overcrowded alkene-based molecular motors through modulation of steric interactions. Choosing as a reference system a second-generation motor known to accomplish rotary motion in the MHz regime and using density functional theory methods, we propose a three-step mechanism for the thermal isomerizations of this motor and show that variation of the steric bulkiness of the substituent at the stereocenter can reduce the (already small) free-energy barrier of the rate-determining step by a further 15-17 kJ mol(-1). This finding holds promise for future motors of this kind to reach beyond the MHz regime. Furthermore, we demonstrate and explain why one particular step is kinetically favored by decreasing and another step is kinetically favored by increasing the steric bulkiness of this substituent, and identify a possible back reaction capable of impeding the rotary rate.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2015
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-121153 (URN)10.1039/c5cp02303c (DOI)000359596600080 ()26234787 (PubMedID)
Note

Funding Agencies|Linkoping University; Swedish Research Council; Olle Engkvist Foundation; Wenner-Gren Foundations; NSFC [11404141]; National Supercomputer Centre (NSC) in Linkoping

Available from: 2015-09-08 Created: 2015-09-08 Last updated: 2016-11-16
3. On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents
Open this publication in new window or tab >>On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents
2016 (English)In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 22, no 9, 219- p.Article in journal (Refereed) Published
Abstract [en]

We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors.

Place, publisher, year, edition, pages
SPRINGER, 2016
Keyword
Electronic effects; Molecular motors; Quantum chemistry; Rotary rates; Steric effects
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-131672 (URN)10.1007/s00894-016-3085-y (DOI)000382748100024 ()27553304 (PubMedID)
Note

Funding Agencies|Linkoping University; Swedish Research Council [621-2011-4353]; Olle Engkvist Foundation; Carl Trygger Foundation

Available from: 2016-10-03 Created: 2016-09-30 Last updated: 2016-11-16
4. Computational Insight to Improve the Thermal Isomerisation Performance of Overcrowded Alkene-Based Molecular Motors through Structural Redesign
Open this publication in new window or tab >>Computational Insight to Improve the Thermal Isomerisation Performance of Overcrowded Alkene-Based Molecular Motors through Structural Redesign
2016 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, no 21, 3399-3408 p.Article in journal (Refereed) Published
Abstract [en]

Synthetic overcrowded alkene-based molecular motors achieve 360° unidirectional rotary motion of one motor half (rotator) relative to the other (stator) through sequential photochemical and thermal isomerisation steps. In order to facilitate and expand the use of these motors for various applications, it is important to investigate ways to increase the rates and efficiencies of the reactions governing the rotary motion. Here, we use computational methods to explore whether the thermal isomerisation performance of some of the fastest available motors of this type can be further improved by reducing the sizes of the motor halves. Presenting three new redesigned motors that combine an indanylidene rotator with a cyclohexadiene, pyran or thiopyran stator, we first use multiconfigurational quantum chemical methods to verify that the photoisomerisations of these motors sustain unidirectional rotary motion. Then, by performing density functional calculations, we identify both stepwise and concerted mechanisms for the thermal isomerisations of the motors and show that the rate-determining free-energy barriers of these processes are up to 25 kJ mol−1 smaller than those of the original motors. Furthermore, the thermal isomerisations of the redesigned motors proceed in fewer steps. Altogether, the results suggest that the redesigned motors are useful templates for improving the thermal isomerisation performance of existing overcrowded alkene-based motors.

Place, publisher, year, edition, pages
Wiley-Blackwell Publishing Inc., 2016
Keyword
Density functional calculations, isomerisation, molecular motors, rotary rates, stepwise versus concerted mechanisms
National Category
Theoretical Chemistry Materials Chemistry Chemical Engineering
Identifiers
urn:nbn:se:liu:diva-132609 (URN)10.1002/cphc.201600766 (DOI)27550708 (PubMedID)
Available from: 2016-11-16 Created: 2016-11-16 Last updated: 2016-11-22Bibliographically approved
5. How method-dependent are calculated differences between vertical, adiabatic, and 0-0 excitation energies?
Open this publication in new window or tab >>How method-dependent are calculated differences between vertical, adiabatic, and 0-0 excitation energies?
2014 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 23, 4157-4171 p.Article in journal (Refereed) Published
Abstract [en]

Through a large number of benchmark studies, the performance of different quantum chemical methods in calculating vertical excitation energies is today quite well established. Furthermore, these efforts have in recent years been complemented by a few benchmarks focusing instead on adiabatic excitation energies. However, it is much less well established how calculated differences between vertical, adiabatic and 0-0 excitation energies vary between methods, which may be due to the cost of evaluating zero-point vibrational energy corrections for excited states. To fill this gap, we have calculated vertical, adiabatic, and 0-0 excitation energies for a benchmark set of molecules covering both organic and inorganic systems. Considering in total 96 excited states and using both TD-DFT with a variety of exchange-correlation functionals and the ab initio CIS and CC2 methods, it is found that while the vertical excitation energies obtained with the various methods show an average (over the 96 states) standard deviation of 0.39 eV, the corresponding standard deviations for the differences between vertical, adiabatic, and 0-0 excitation energies are much smaller: 0.10 (difference between adiabatic and vertical) and 0.02 eV (difference between 0-0 and adiabatic). These results provide a quantitative measure showing that the calculation of such quantities in photochemical modeling is well amenable to low-level methods. In addition, we also report on how these energy differences vary between chemical systems and assess the performance of TD-DFT, CIS, and CC2 in reproducing experimental 0-0 excitation energies.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2014
National Category
Physical Sciences
Identifiers
urn:nbn:se:liu:diva-109132 (URN)10.1021/jp501974p (DOI)000337497300017 ()24848558 (PubMedID)
Available from: 2014-08-13 Created: 2014-08-11 Last updated: 2016-11-16Bibliographically approved
6. Assessment of a composite CC2/DFT procedure for calculating 0-€“0 excitation energies of organic molecules
Open this publication in new window or tab >>Assessment of a composite CC2/DFT procedure for calculating 0-€“0 excitation energies of organic molecules
2016 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, 1-16 p.Article in journal (Refereed) Epub ahead of print
Abstract [en]

The task to assess the performance of quantum chemical methods in describing electronically excited states has in recent years started to shift from calculation of vertical (ΔEve) to calculation of 0-€“0 excitation energies (ΔE00). Here, based on a set of 66 excited states of organic molecules for which high-resolution experimental ΔE00 energies are available and for which the approximate coupled-cluster singles and doubles (CC2) method performs particularly well, we explore the possibility to simplify the calculation of CC2-quality ΔE00 energies using composite procedures that partly replace CC2 with more economical methods. Specifically, we consider procedures that employ CC2 only for the ΔEve part and density functional theory methods for the cumbersome excited-state geometry optimisations and frequency calculations required to obtain ΔE00 energies from ΔEve ones. The results demonstrate that it is indeed possible to both closely (to within 0.06-€“0.08 eV) and consistently approximate ‘true’ CC2 ΔE00 energies in this way, especially when CC2 is combined with hybrid density functionals. Overall, the study highlights the unexploited potential of composite procedures, which hitherto have found widespread use mostly in ground-state chemistry, to also play an important role in facilitating accurate studies of excited states.

Place, publisher, year, edition, pages
Taylor & Francis, 2016
National Category
Theoretical Chemistry Atom and Molecular Physics and Optics Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-132610 (URN)10.1080/00268976.2016.1235736 (DOI)
Available from: 2016-11-16 Created: 2016-11-16 Last updated: 2016-11-17Bibliographically approved

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