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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
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
Fransson, T., Delcey, M. G., Brumboiu, I. E., Hodecker, M., Li, X., Rinkevicius, Z., . . . Norman, P. (2022). Computational Chemistry from Laptop to HPC: A notebook exploration of quantum chemistry (1ed.). Stockholm: KTH Royal Institute of Technology
Open this publication in new window or tab >>Computational Chemistry from Laptop to HPC: A notebook exploration of quantum chemistry
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2022 (English)Book (Other academic)
Abstract [en]

Quantum chemistry is a powerful tool. It is now possible to model complex chemical processes even on a laptop getting insights into matter at its fundamental scale.

But quantum chemistry is also very complex. Answering a chemical question requires selecting parameters among a wide variety of choices. Choosing a model system, an electronic structure method, a basis set, a set of properties, and a wide array of parameters which can affect the results in small but sometimes meaningful way… It can be a very daunting task, even for veterans of the field.

Similarly, for those who wish to get a deeper understanding of a method, going through the pages of equation often riddled with inconsistent notations and formulations is very challenging. And at the end, the link between the equation and the computer implementation found in existing softwares can be vague at best.

We believe that a core issue is that humans are not good at learning in abstract terms. We can get very far with a lecture or a textbook, but we will never build as much intuition about how a clock work as by simply breaking one apart and rebuilding it from scratch.

This is exactly the aim of this page, allowing a hands-on approach to computational chemistry. Together we will dismantle the black box that a computational chemistry code often seems to be, go through all the cogs and gears, and build back together some of the main computational methods of modern computational chemistry. We will do this by presenting the underlying equations, all expressed with consistent notations, as well as by suggesting a simple python implementation, to really display in action how the theory is implemented into a practical tool. Additionally, we will put these methods in context by showing how they can be used to address concrete chemical questions, discussing the strengths and weaknesses of each method and how to best use them to solve practical problems.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2022 Edition: 1
Keywords
theoretical chemistry; spectroscopy; computational chemistry; molecular physics
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-316346 (URN)10.30746/978-91-988114-0-7 (DOI)978-91-988114-0-7 (ISBN)
Note

QC 20220819

Available from: 2022-08-15 Created: 2022-08-15 Last updated: 2022-11-11Bibliographically approved
Ahmadzadeh, K., Li, X., Rinkevicius, Z. & Norman, P. (2022). Efficient Kohn-Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions. Electronic Structure, 4(4), Article ID 044004.
Open this publication in new window or tab >>Efficient Kohn-Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions
2022 (English)In: Electronic Structure, E-ISSN 2516-1075, Vol. 4, no 4, article id 044004Article in journal (Refereed) Published
Abstract [en]

For general exchange-correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only similar to 25% (one-photon off-resonance regions) and similar to 50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.

Place, publisher, year, edition, pages
IOP Publishing, 2022
Keywords
density functional theory, response theory, nonlinear optics
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-324057 (URN)10.1088/2516-1075/aca859 (DOI)000919217600001 ()2-s2.0-85145257235 (Scopus ID)
Note

QC 20230222

Available from: 2023-02-22 Created: 2023-02-22 Last updated: 2023-10-03Bibliographically approved
Wang, J.-X., Li, X. & Li, C. (2021). Constructing photochromic diarylethene with NIR-absorption beyond 800 nm. Dyes and pigments, 189, Article ID 109273.
Open this publication in new window or tab >>Constructing photochromic diarylethene with NIR-absorption beyond 800 nm
2021 (English)In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 189, article id 109273Article in journal (Refereed) Published
Abstract [en]

Near-infrared (NIR) absorbing dyes have received increasing attention due to their ability of NIR radiation absorption and efficient light-to-heat conversion. NIR absorbing photochromic diarylethene (DAE) materials, which could modulate NIR absorption upon light stimulation, provide a convenient route to fabricate smart NIR absorbers. In this study, we constructed a new NIR absorbing photochromic DAE system, of which NIR absorption stems from closed isomer bearing triarylamine (TAA) radical (TDEc-ox). Upon 365/440 nm light irradiation, the open isomer TDEo undergoes photo-oxidation and cyclization to yield TDEc-ox, which exhibited NIR absorption at 928 nm in chloroform. TDEc-ox possesses a photo-inactive feature facilitating non-destructive readout of NIR absorption and high stability (lifetime time ? 3 days). Contrary to TDEo, the closed isomer TDEc cannot be directly photo-oxidized to give TDEc-ox. This discrepancy makes TDEc a ?photogenerated TAA radical reservoir?: after cycles of photoisomerization, a controllable accumulation of NIR absorbing TDEc-ox can be achieved.

Place, publisher, year, edition, pages
Elsevier BV, 2021
Keywords
Photochromism, Diarylethenes, NIR absorption, Photogenerated triarylamine radical, Non-destructive readout
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-293646 (URN)10.1016/j.dyepig.2021.109273 (DOI)000634733200006 ()2-s2.0-85101959210 (Scopus ID)
Note

QC 20210430

Available from: 2021-04-30 Created: 2021-04-30 Last updated: 2022-06-25Bibliographically approved
Ahmadzadeh, K., Scott, M., Brand, M., Vahtras, O., Li, X., Rinkevicius, Z. & Norman, P. (2021). Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation. Journal of Chemical Physics, 154(2), Article ID 024111.
Open this publication in new window or tab >>Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation
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2021 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 2, article id 024111Article in journal (Refereed) Published
Abstract [en]

Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only similar to 3.3% (one-photon off-resonance regions) and similar to 10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than similar to 5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

Place, publisher, year, edition, pages
AIP Publishing, 2021
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-289893 (URN)10.1063/5.0031851 (DOI)000609824200001 ()33445884 (PubMedID)2-s2.0-85099407136 (Scopus ID)
Note

QC 20210215

Available from: 2021-02-15 Created: 2021-02-15 Last updated: 2023-10-03Bibliographically approved
Yang, S., Zhao, C.-X., Crespi, S., Li, X., Zhang, Q., Zhang, Z.-Y., . . . Qu, D.-H. (2021). Reversibly modulating a conformation-adaptive fluorophore in [2]catenane. Chem, 7(6), 1544-1556
Open this publication in new window or tab >>Reversibly modulating a conformation-adaptive fluorophore in [2]catenane
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2021 (English)In: Chem, ISSN 2451-9308, E-ISSN 2451-9294, Vol. 7, no 6, p. 1544-1556Article in journal (Refereed) Published
Abstract [en]

Tuning molecular emission by chemicalmeans has long been a fundamental topic, because the emerging methodologies and mechanisms of this topic usually bring a lot of opportunities in many multi-disciplinary applications. Here, we demonstrate the reversible switching of a conformation-adaptive fluorophore, 9,14-diphenyl-9,14-dihydrodibenzo[ a,c]phenazine (DPAC), by incorporating this fluorescent unit into a mechanically interlocked [2]catenane. Taking advantage of the mechanical bond of [2]catenane, the conformational freedom of the DPAC-macrocycle can be modulated by the co-conformational state of the [2]catenane, thus enabling the reversible switching of the fluorescent properties of DPAC. Owing to the mechanically interlocked structure, this fluorescent molecular system can be switched in a dual-mode (wavelength or intensity), visually recognizable, and highly reversible manner. This work provides a distinctmechanism of switchingmolecular emission by modulating conformation-adaptive fluorescent systems in mechanically interlocked structures.

Place, publisher, year, edition, pages
Elsevier BV, 2021
National Category
Biochemistry and Molecular Biology Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-298870 (URN)10.1016/j.chempr.2021.02.019 (DOI)000660002500017 ()2-s2.0-85105731708 (Scopus ID)
Note

QC 20210720

Available from: 2021-07-20 Created: 2021-07-20 Last updated: 2022-06-25Bibliographically approved
Brand, M., Ahmadzadeh, K., Li, X., Rinkevicius, Z., Saidi, W. A. & Norman, P. (2021). Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations. Journal of Chemical Physics, 154(7), Article ID 074304.
Open this publication in new window or tab >>Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations
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2021 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 7, article id 074304Article in journal (Refereed) Published
Abstract [en]

While the anomalous non-additive size-dependencies of static dipole polarizabilities and van der Waals C-6 dispersion coefficients of carbon fullerenes are well established, the widespread reported scalings for the latter (ranging from N-2.2 to N-2.8) call for a comprehensive first-principles investigation. With a highly efficient implementation of the linear complex polarization propagator, we have performed Hartree-Fock and Kohn-Sham density functional theory calculations of the frequency-dependent polarizabilities for fullerenes consisting of up to 540 carbon atoms. Our results for the static polarizabilities and C-6 coefficients show scalings of N-1.2 and N-2.2, respectively, thereby deviating significantly from the previously reported values obtained with the use of semi-classical/empirical methods. Arguably, our reported values are the most accurate to date as they represent the first ab initio or first-principles treatment of fullerenes up to a convincing system size.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2021
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-292491 (URN)10.1063/5.0040009 (DOI)000630521400004 ()33607910 (PubMedID)2-s2.0-85100915441 (Scopus ID)
Note

QC 20210412

Available from: 2021-04-12 Created: 2021-04-12 Last updated: 2022-10-17Bibliographically approved
Wang, Q., Zhang, Q., Zhang, Q.-W. -., Li, X., Zhao, C.-X. -., Xu, T.-Y. -., . . . Tian, H. (2020). Color-tunable single-fluorophore supramolecular system with assembly-encoded emission. Nature Communications, 11(1), Article ID 158.
Open this publication in new window or tab >>Color-tunable single-fluorophore supramolecular system with assembly-encoded emission
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2020 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 158Article in journal (Refereed) Published
Abstract [en]

Regulating the fluorescent properties of organic small molecules in a controlled and dynamic manner has been a fundamental research goal. Although several strategies have been exploited, realizing multi-color molecular emission from a single fluorophore remains challenging. Herein, we demonstrate an emissive system by combining pyrene fluorophore and acylhydrazone units, which can generate multi-color switchable fluorescent emissions at different assembled states. Two kinds of supramolecular tools, amphiphilic self-assembly and γ-cyclodextrin mediated host-guest recognition, are used to manipulate the intermolecular aromatic stacking distances, resulting in the tunable fluorescent emission ranging from blue to yellow, including a pure white-light emission. Moreover, an external chemical signal, amylase, is introduced to control the assembly states of the system on a time scale, generating a distinct dynamic emission system. The dynamic properties of this multi-color fluorescent system can be also enabled in a hydrogel network, exhibiting a promising potential for intelligent fluorescent materials.

Place, publisher, year, edition, pages
Nature Research, 2020
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-267775 (URN)10.1038/s41467-019-13994-6 (DOI)000511898900009 ()31919416 (PubMedID)2-s2.0-85077733109 (Scopus ID)
Note

QC 20200304

Available from: 2020-03-04 Created: 2020-03-04 Last updated: 2023-03-28Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-6508-8355

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