| 1. |
- Creutzberg, Joel, et al.
(författare)
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A method to capture the large relativistic and solvent effects on the UV-vis spectra of photo-activated metal complexes
- 2023
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 25:8, s. 6153-6163
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Tidskriftsartikel (refereegranskat)abstract
- We have recently developed a method based on relativistic time-dependent density functional theory (TD-DFT) that allows the calculation of electronic spectra in solution (Creutzberg, Hedegård, J. Chem. Theory Comput.18, 2022, 3671). This method treats the solvent explicitly with a classical, polarizable embedding (PE) description. Furthermore, it employs the complex polarization propagator (CPP) formalism which allows calculations on complexes with a dense population of electronic states (such complexes are known to be problematic for conventional TD-DFT). Here, we employ this method to investigate both the dynamic and electronic effects of the solvent for the excited electronic states of trans-trans-trans-[Pt(N3)2(OH)2(NH3)2] in aqueous solution. This complex decomposes into species harmful to cancer cells under light irradiation. Thus, understanding its photo-physical properties may lead to a more efficient method to battle cancer. We quantify the effect of the underlying structure and dynamics by classical molecular mechanics simulations, refined with a subsequent DFT or semi-empirical optimization on a cluster. Moreover, we quantify the effect of employing different methods to set up the solvated system, e.g., how sensitive the results are to the method used for the refinement, and how large a solvent shell that is required. The electronic solvent effect is always included through a PE potential.
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| 2. |
- Creutzberg, Joel
(författare)
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Extending relativistic linear response theory to address solvent effects
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The central aim of this thesis is to derive, implement and test new methods to calculate various types of spectroscopies of compounds containing heavy elements in an aqueous environment. Methods that can target such systems have to consider the following:(i) It is crucial to take relativistic effects into account.(ii) Modeling of larger systems is expensive in quantum chemistry. Thus, cheaper options need to be consideredfor the water solvent.(iii) Methods to calculate electronic spectra have to be able to model electronic excitations properly.(i) The relativistic effects can be obtained by solving the Dirac equation. This yields a four-component wave function, but methods based on only two-components have been developed in this thesis. (ii) Larger systems can be tackled by dividing them into a region that is treated by methods from electronic structure theory, and a larger environment that is treated classically as a collection of localized static multipole moments (charges, dipole moments, etc.). In most such hybrid schemes (called QM/MM) we only take into account how the static multipole moments in the environment influence the wave function in the QM region. In this thesis, however, we allow mutual polarization of the regions through the polarizable embedding (PE) model. (iii) We calculate excited state properties through linear response theory. This has been developed to work with a variety of approximate state wave functions and has been extended to a relativistic framework. Moreover, it has been combined with PE. Yet, regular linear response theory suffers from problems in non-resonant regions of spectra. For this, we consider a variant of linear response theory, called the complex polarization propagator. Here, the life-times of the excited states are included in the response equations. This allows the calculation of spectra in regions that are problematic in regular response theory. In this thesis, we have devised a method that combines relativistic CPP within a polarizable embedding framework. We employ the method on light-activated platinum complexes with application in chemotheraphy. Here, both relativistic and solvent effects are crucial to model the excitation processes. Moreover, we also consider the calculation of electronic circular dichroism for chiral organic molecules that contain heavy elements like iodine.
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| 3. |
- Creutzberg, Joel, et al.
(författare)
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Investigating the influence of relativistic effects on absorption spectra for platinum complexes with light-activated activity against cancer cells
- 2020
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 22:46, s. 27013-27023
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Tidskriftsartikel (refereegranskat)abstract
- We report the first systematic investigation of relativistic effects on the UV-vis spectra of two prototype complexes for so-called photo-activated chemotherapy (PACT), trans-trans-trans-[Pt(N3)2(OH)2(NH3)2] and cis-trans-cis-[Pt(N3)2(OH)2(NH3)2]. In PACT, design of new drugs requires in-depth understanding of the photo-activation mechanisms. A first step is usually to rationalize their UV-vis spectra for which time-dependent density functional theory (TD-DFT) is an indispensable tool. We carried out TD-DFT calculations with a systematic series of non-relativistic (NR), scalar-relativistic (SR), and four-component (4c) Hamiltonians. As expected, large differences are found between spectra calculated within 4c and NR frameworks, while the most intense features (found at higher energies below 300 nm) can be reasonably well reproduced within a SR framework. It is also shown that effective core potentials (ECPs) yield essentially similar results as all-electron SR calculations. Yet the underlying transitions can be strongly influenced by spin-orbit coupling, which is only present in the 4c framework: While this can affect both intense and less intense transitions in the spectra, the effect is most pronounced for weaker transitions at lower energies, above 300 nm. Since the investigated complexes are activated with light of wavelengths above 300 nm, employing a method with explicit inclusion of spin-orbit coupling may be crucial to rationalize the activation mechanism.
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| 4. |
- Creutzberg, Joel, et al.
(författare)
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Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks
- 2022
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:6, s. 3671-3686
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Tidskriftsartikel (refereegranskat)abstract
- Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and [Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods.
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| 5. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Tidskriftsartikel (refereegranskat)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 6. |
- Hedegård, Erik Donovan, et al.
(författare)
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New relativistic quantum chemical methods for understanding light-induced therapeutics
- 2022
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 51:42, s. 16055-16064
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Forskningsöversikt (refereegranskat)abstract
- The inorganic platinum complexes currently in clinical use for cancer treatment have severe side effects, and complexes with fewer side effects are required. One option is to use complexes that are inactive until they are light-activated. Theoretical chemistry can contribute to the design of these complexes, but most current theoretical methods lack explicit treatment of relativistic effects (since the target complexes often contain heavy elements). In particular, spin-orbit coupling is required for accurate predictions of the complexes’ photo-physical properties. In this perspective, we summarize relativistic methods developed in recent years that can contribute to our understanding of light-induced reactivity and thereby help predict new, suitable complexes.
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| 7. |
- Mcevoy, Aina, et al.
(författare)
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The role of the active site tyrosine in the mechanism of lytic polysaccharide monooxygenase
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 12:1, s. 352-362
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Tidskriftsartikel (refereegranskat)abstract
- Catalytic breakdown of polysaccharides can be achieved more efficiently by means of the enzymes lytic polysaccharide monooxygenases (LPMOs). However, the LPMO mechanism has remained controversial, preventing full exploitation of their potential. One of the controversies has centered around an active site tyrosine, present in most LPMO classes. Recent investigations have for the first time obtained direct (spectroscopic) evidence for the possibility of chemical modification of this tyrosine. However, the spectroscopic features obtained in the different investigations are remarkably different, with absorption maximum at 420 and 490 nm, respectively. In this paper we use density functional theory (DFT) in a QM/MM formulation to reconcile these (apparently) conflicting results. By modeling the spectroscopy as well as the underlying reaction mechanism we can show how formation of two isomers (both involving deprotonation of tyrosine) explains the difference in the observed spectroscopic features. Both isomers have a [TyrO-Cu-OH]+ moiety with the OH in either the cis- or trans-position to a deprotonated tyrosine. Although the cis-[TyrO-Cu-OH]+ moiety is well positioned for oxidation of the substrate, preliminary calculations with the substrate reveal that the reactivity is at best moderate, making a protective role of tyrosine more likely.
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