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Hillers-Bendtsen, A. E., Todarwal, Y., Norman, P. & Mikkelsen, K. V. (2024). Dynamical Effects of Solvation on Norbornadiene/Quadricyclane Systems. Journal of Physical Chemistry A, 128(13), 2602-2610
Open this publication in new window or tab >>Dynamical Effects of Solvation on Norbornadiene/Quadricyclane Systems
2024 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 128, no 13, p. 2602-2610Article in journal (Refereed) Published
Abstract [en]

Molecules that can undergo reversible chemical transformations following the absorption of light, the so-called molecular photoswitches, have attracted increasing attention in technologies, such as solar energy storage. Here, the optical and thermochemical properties of the photoswitch are central to its applicability, and these properties are influenced significantly by solvation. We investigate the effects of solvation on two norbornadiene/quadricyclane photoswitches. Emphasis is put on the energy difference between the two isomers and the optical absorption as these are central to the application of the systems in solar energy storage. Using a combined classical molecular dynamics and quantum mechanical/molecular mechanical computational scheme, we showcase that the dynamic effects of solvation are important. In particular, it is found that standard implicit solvation models generally underestimate the energy difference between the two isomers and overestimate the strength of the absorption, while the explicit solvation spectra are also less red-shifted than those obtained using implicit solvation models. We also find that the absorption spectra of the two systems are strongly correlated with specific dihedral angles. Altogether, this highlights the importance of including the dynamic effects of solvation.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-345571 (URN)10.1021/acs.jpca.4c00045 (DOI)001189782700001 ()38511966 (PubMedID)2-s2.0-85188552902 (Scopus ID)
Note

QC 20240412

Available from: 2024-04-12 Created: 2024-04-12 Last updated: 2024-04-12Bibliographically approved
Ahmadzadeh, K., Li, X., Rinkevicius, Z., Norman, P. & Zaleśny, R. (2024). Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation. Journal of Physical Chemistry Letters, 15(4), 969-974
Open this publication in new window or tab >>Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation
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2024 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 15, no 4, p. 969-974Article in journal (Refereed) Published
Abstract [en]

In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
National Category
Theoretical Chemistry Organic Chemistry
Identifiers
urn:nbn:se:kth:diva-343471 (URN)10.1021/acs.jpclett.3c03513 (DOI)001156015800001 ()38252270 (PubMedID)2-s2.0-85184138546 (Scopus ID)
Note

QC 20240215

Available from: 2024-02-15 Created: 2024-02-15 Last updated: 2024-02-26Bibliographically approved
Minh, N. N., Begum, A., Zhang, J., Leira, P., Todarwal, Y., Linares, M., . . . Koenig, C. (2023). Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study. Journal of Physical Chemistry B, 127(30), 6628-6635
Open this publication in new window or tab >>Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study
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2023 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 127, no 30, p. 6628-6635Article in journal (Refereed) Published
Abstract [en]

Misfolding and aggregation of transthyretin (TTR) causeseveralamyloid diseases. Besides being an amyloidogenic protein, TTR hasan affinity for bicyclic small-molecule ligands in its thyroxine (T4)binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbenescaffold is also widely applied for amyloid fibril-specific ligandsused as fluorescence probes and as positron emission tomography tracersfor amyloid detection and diagnosis of amyloidosis. We have shownthat native tetrameric TTR binds to amyloid ligands based on the trans-stilbenescaffold providing a platform for the determination of high-resolutionstructures of these important molecules bound to protein. In thisstudy, we provide spectroscopic evidence of binding and X-ray crystallographicstructure data on tetrameric TTR complex with the fluorescent salicylicacid-based pyrene amyloid ligand (Py1SA), an analogue of the Congored analogue X-34. The ambiguous electron density from the X-ray diffraction,however, did not permit Py1SA placement with enough confidence likelydue to partial ligand occupancy. Instead, the preferred orientationof the Py1SA ligand in the binding pocket was determined by moleculardynamics and umbrella sampling approaches. We find a distinct preferencefor the binding modes with the salicylic acid group pointing intothe pocket and the pyrene moiety outward to the opening of the T4binding site. Our work provides insight into TTR binding mode preferencefor trans-stilbene salicylic acid derivatives as well as a frameworkfor determining structures of TTR-ligand complexes.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-333782 (URN)10.1021/acs.jpcb.3c02147 (DOI)001033885300001 ()37477604 (PubMedID)2-s2.0-85166442446 (Scopus ID)
Note

QC 20230810

Available from: 2023-08-10 Created: 2023-08-10 Last updated: 2024-01-08Bibliographically approved
Björk, L., Shirani, H., Todarwal, Y., Linares, M., Vidal, R., Ghetti, B., . . . Nilsson, K. P. (2023). Distinct Heterocyclic Moieties Govern the Selectivity of Thiophene‐Vinylene‐Based Ligands towards Aβ or Tau Pathology in Alzheimer's Disease. European Journal of Organic Chemistry, 26(41), e202300583
Open this publication in new window or tab >>Distinct Heterocyclic Moieties Govern the Selectivity of Thiophene‐Vinylene‐Based Ligands towards Aβ or Tau Pathology in Alzheimer's Disease
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2023 (English)In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 26, no 41, p. e202300583-Article in journal (Refereed) Published
Abstract [en]

Distinct aggregated proteins are correlated with numerous neurodegenerative diseases and the development of ligands that selectively detect these pathological hallmarks is vital. Recently, the synthesis of thiophene-based optical ligands, denoted bi-thiophene-vinyl-benzothiazoles (bTVBTs), that could be utilized for selective assignment of tau pathology in brain tissue with Alzheimer's disease (AD) pathology, was reported. Herein, we investigate the ability of these ligands to selectively distinguish tau deposits from aggregated amyloid-β (Aβ), the second AD associated pathological hallmark, when replacing the terminal thiophene moiety with other heterocyclic motifs. The selectivity for tau pathology was reduced when introducing specific heterocyclic motifs, verifying that specific molecular interactions between the ligands and the aggregates are necessary for selective detection of tau deposits. In addition, ligands having certain heterocyclic moieties attached to the central thiophene-vinylene building block displayed selectivity to aggregated Aβ pathology. Our findings provide chemical insights for the development of ligands that can distinguish between aggregated proteinaceous species consisting of different proteins and might also aid in creating novel agents for clinical imaging of tau pathology in AD.

Place, publisher, year, edition, pages
Wiley, 2023
Keywords
Alzheimer's disease, amyloid-β, fluorescent ligands, protein aggregates, tau
National Category
Theoretical Chemistry
Research subject
Chemistry
Identifiers
urn:nbn:se:kth:diva-341948 (URN)10.1002/ejoc.202300583 (DOI)2-s2.0-85172707759 (Scopus ID)
Note

QC 20240108

Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-08Bibliographically approved
Fransson, T., Delcey, M. G., Brumboiu, I. E., Hodecker, M., Li, X., Rinkevicius, Z., . . . Norman, P. (2023). eChem: A Notebook Exploration of Quantum Chemistry. Journal of Chemical Education, 100(4), 1664-1671
Open this publication in new window or tab >>eChem: A Notebook Exploration of Quantum Chemistry
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2023 (English)In: Journal of Chemical Education, ISSN 0021-9584, E-ISSN 1938-1328, Vol. 100, no 4, p. 1664-1671Article in journal (Refereed) Published
Abstract [en]

The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
Keywords
chemistry education, computational chemistry, interactive, Jupyter, notebook, Python, theoretical chemistry, visualization
National Category
Chemical Sciences Learning
Identifiers
urn:nbn:se:kth:diva-331091 (URN)10.1021/acs.jchemed.2c01103 (DOI)000954538900001 ()2-s2.0-85150424886 (Scopus ID)
Note

QC 20230705

Available from: 2023-07-05 Created: 2023-07-05 Last updated: 2024-03-15Bibliographically approved
Brand, M., Dreuw, A., Norman, P. & Li, X. (2023). Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator. Journal of Chemical Theory and Computation, 20(1), 103-113
Open this publication in new window or tab >>Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator
2023 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 103-113Article in journal (Refereed) Published
Abstract [en]

We present the implementation of an efficient matrix-folded formalism for the evaluation of complex response functions and the calculation of transition properties at the level of the second-order algebraic-diagrammatic construction (ADC(2)) scheme. The underlying algorithms, in combination with the adopted hybrid MPI/OpenMP parallelization strategy, enabled calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1032 contracted basis functions, thereby utilizing vast computational resources from up to 32,768 CPU cores. Further analysis of the convergence behavior of the involved iterative subspace algorithms revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window, including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electronic circular dichroism spectrum calculated with a complex polarization propagator approach at the ADC(2) level of theory.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-342465 (URN)10.1021/acs.jctc.3c01065 (DOI)001139474200001 ()38117937 (PubMedID)2-s2.0-85181012222 (Scopus ID)
Note

QC 20240122

Available from: 2024-01-22 Created: 2024-01-22 Last updated: 2024-01-22Bibliographically approved
Arja, K., Selegård, R., Paloncyova, M., Linares, M., Lindgren, M., Norman, P., . . . Nilsson, K. P. (2023). Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides. ChemPlusChem, 88(1), Article ID e202200262.
Open this publication in new window or tab >>Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides
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2023 (English)In: ChemPlusChem, E-ISSN 2192-6506, Vol. 88, no 1, article id e202200262Article in journal (Refereed) Published
Abstract [en]

Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene−porphyrin derivatives and random coil synthetic peptides. The photo-physical- and structural properties of the materials were assessed by absorption-, fluorescence- and circular dichroism spectroscopy, as well as dynamic light scattering, scanning electron microscopy and theoretical calculations. The materials display a three-dimensional ordered helical structure and optical activity that are observed due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chemical composition of the oligothiophene−porphyrin derivative, as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications. 

Place, publisher, year, edition, pages
Wiley, 2023
Keywords
circular dichroism, oligothiophene, porphyrin, self-assembly, synthetic peptides
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-328109 (URN)10.1002/cplu.202200262 (DOI)000861449900001 ()36173143 (PubMedID)2-s2.0-85138863227 (Scopus ID)
Note

QC 20230602

Available from: 2023-06-02 Created: 2023-06-02 Last updated: 2023-06-02Bibliographically approved
De Oliveira, D. H., Biler, M., Mim, C., Nilebäck, L., Kvick, M., Norman, P., . . . Hedhammar, M. (2023). Silk Assembly against Hydrophobic Surfaces?Modeling and Imaging of Formation of Nanofibrils. ACS Applied Bio Materials, 6(3), 1011-1018
Open this publication in new window or tab >>Silk Assembly against Hydrophobic Surfaces?Modeling and Imaging of Formation of Nanofibrils
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2023 (English)In: ACS Applied Bio Materials, E-ISSN 2576-6422, Vol. 6, no 3, p. 1011-1018Article in journal (Refereed) Published
Abstract [en]

A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, fi-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of similar to 7 nm and a width of similar to 11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2023
Keywords
spider silk, spidroin, MaSp, hydrophobic surfaces, nanofibrils self-assembly, atomic force microscope, cryo-electron microscopy, molecular dynamics modeling
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-326055 (URN)10.1021/acsabm.2c00878 (DOI)000956123600001 ()36791416 (PubMedID)2-s2.0-85148431162 (Scopus ID)
Note

QC 20230425

Available from: 2023-04-25 Created: 2023-04-25 Last updated: 2023-11-15Bibliographically approved
Scheurer, M., Papapostolou, A., Fransson, T., Norman, P., Dreuw, A. & Rehn, D. R. (2023). Solving response expressions in the ADC/ISR framework. Journal of Chemical Physics, 158(8), 084105, Article ID 084105.
Open this publication in new window or tab >>Solving response expressions in the ADC/ISR framework
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2023 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 158, no 8, p. 084105-, article id 084105Article in journal (Refereed) Published
Abstract [en]

We present an implementation for the calculation of molecular response properties using the algebraic-diagrammatic construction (ADC)/intermediate state representation approach. For the second-order ADC model [ADC(2)], a memory-efficient ansatz avoiding the storage of double excitation amplitudes is investigated. We compare the performance of different numerical algorithms for the solution of the underlying response equations for ADC(2) and show that our approach also strongly improves the convergence behavior for the investigated algorithms compared with the standard implementation. All routines are implemented in an open-source Python library.

Place, publisher, year, edition, pages
AIP Publishing, 2023
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-324999 (URN)10.1063/5.0139721 (DOI)000937824600018 ()36859074 (PubMedID)2-s2.0-85149323360 (Scopus ID)
Note

QC 20230404

Available from: 2023-03-27 Created: 2023-03-27 Last updated: 2023-04-04Bibliographically approved
Gonzalez-Sanchez, M., Mayoral, M. J., Vazquez-Gonzalez, V., Paloncyova, M., Sancho-Casado, I., Aparicio, F., . . . Gonzalez-Rodriguez, D. (2023). Stacked or Folded?: Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers. Journal of the American Chemical Society, 145(32), 17805-17818
Open this publication in new window or tab >>Stacked or Folded?: Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers
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2023 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 32, p. 17805-17818Article in journal (Refereed) Published
Abstract [en]

Self-assembled nanotubesexhibit impressive biologicalfunctionsthat have always inspired supramolecular scientists in their effortsto develop strategies to build such structures from small moleculesthrough a bottom-up approach. One of these strategies employs moleculesendowed with self-recognizing motifs at the edges, which can undergoeither cyclization-stacking or folding-polymerizationprocesses that lead to tubular architectures. Which of these self-assemblypathways is ultimately selected by these molecules is, however, oftendifficult to predict and even to evaluate experimentally. We showhere a unique example of two structurally related molecules substitutedwith complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway takenis determined by chelate cooperativity, that is, by their propensityto assemble in specific cyclic structures through Watson-Crickpairing. Because of chelate cooperativities that differ in severalorders of magnitude, these molecules exhibit distinct supramolecularscenarios prior to their polymerization that generate self-assemblednanotubes with different internal monomer arrangements, either stackedor coiled, which lead at the same time to opposite helicities andchiroptical properties.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Materials Chemistry
Identifiers
urn:nbn:se:kth:diva-334764 (URN)10.1021/jacs.3c04773 (DOI)001041604900001 ()37531225 (PubMedID)
Note

QC 20230824

Available from: 2023-08-24 Created: 2023-08-24 Last updated: 2024-03-18Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-1191-4954

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