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1.	Aquilante, Francesco, et al. (författare) Modern quantum chemistry with [Open]Molcas 2020 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21 Tidskriftsartikel (refereegranskat)abstract MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
2.	Delcey, Mickael G., et al. (författare) Exact semi-classical light-matter interaction operator applied to two-photon processes with strong relativistic effects 2020 Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 153:2 Tidskriftsartikel (refereegranskat)abstract X-ray processes involve interactions with high-energy photons. For these short wavelengths, the perturbing field cannot be treated as constant, and there is a need to go beyond the electric-dipole approximation. The exact semi-classical light-matter interaction operator offers several advantages compared to the multipole expansion such as improved stability and ease of implementation. Here, the exact operator is used to model x-ray scattering in metal K pre-edges. This is a relativistic two-photon process where absorption is dominated by electric-dipole forbidden transitions. With the restricted active space state-interaction approach, spectra can be calculated even for the multiconfigurational wavefunctions including second-order perturbation. However, as the operator itself depends on the transition energy, the cost for evaluating integrals for hundreds of thousands unique transitions becomes a bottleneck. Here, this is solved by calculating the integrals in a molecular-orbital basis that only runs over the active space, combined with a grouping scheme where the operator is the same for close-lying transitions. This speeds up the calculations of single-photon processes and is critical for the modeling of two-photon scattering processes. The new scheme is used to model Kα resonant inelastic x-ray scattering of iron-porphyrin complexes with relevance to studies of heme enzymes, for which the total computational time is reduced by several orders of magnitude with an effect on transition intensities of 0.1% or less.
3.	Farahani, Pooria, 1985-, et al. (författare) A combined theoretical and experimental study onthe mechanism of spiro-adamantyl-1,2-dioxetanone decomposition 2017 Ingår i: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 7, s. 17462-17472 Tidskriftsartikel (refereegranskat)abstract 1,2-Dioxetanones have been considered as model compounds for bioluminescence processes. Theunimolecular decomposition of these prototypes leads mainly to the formation of triplet excited stateswhereas in the catalysed decomposition of these peroxides singlet states are formed preferentially.Notwithstanding, these cyclic peroxides are important models to understand the general principles ofchemiexcitation as they can be synthesised, purified and characterised. We report here results ofexperimental and theoretical approaches to investigating the decomposition mechanism of spiroadamantyl-1,2-dioxetanone. The activation parameters in the unimolecular decomposition of thisderivative have been determined by isothermal kinetic measurements (30–70 C) and thechemiluminescence activation energy calculated from the correlation of emission intensities. Theactivation energy for peroxide decomposition proved to be considerably lower than thechemiluminescence activation energy indicating the existence of different reaction pathways for groundand excited state formation. These experimental results are compared with the calculations at thecomplete active space second-order perturbation theory (CASPT2), which reveal a two-step biradicalmechanism starting by weak peroxide bond breakage followed by carbon–carbon elongation. Thetheoretical findings also indicate different transition state energies on the excited and ground statesurfaces during the C–C bond cleavage in agreement with the experimental activation parameters.
4.	Farahani, Pooria, 1985-, et al. (författare) Advances in computationalphotochemistry and chemiluminescenceof biological and nanotechnologicalmolecules 2017. - 44 Ingår i: Photochemistry. - Cambridge, UK : Royal Society of Chemistry. - 1465-1947. ; , s. 16-60, s. 16-60 Bokkapitel (refereegranskat)abstract Recent advances (2014–2015) in computational photochemistry and chemiluminescencederive from the development of theory and from the application of state-of-the-art andnew methodology to challenging electronic-structure problems. Method developmentshave mainly focused, first, on the improvement of approximate and cheap methods toprovide a better description of non-adiabatic processes, second, on the modification ofaccurate methods in order to decrease the computation time and, finally, on dynamicsapproaches able to provide information that can be directly compared with experimentaldata, such as yields and lifetimes. Applications of the ab initio quantum-chemistry methodshave given rise to relevant findings in distinct fields of the excited-state chemistry.We brieflysummarise, in this chapter, the achievements on photochemical mechanisms andchemically-induced excited-state phenomena of interest in biology and nanotechnology.
5.	Galván, Ignacio Fdez., et al. (författare) OpenMolcas : From Source Code to Insight 2019 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964 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.
6.	Manni, Giovanni Li, et al. (författare) The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry 2023 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991 Tidskriftsartikel (refereegranskat)abstract The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
7.	Sankari, Anna, et al. (författare) Non-radiative decay and fragmentation in water molecules after 1a1-14a1 excitation and core ionization studied by electron-energy-resolved electron–ion coincidence spectroscopy 2020 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:7 Tidskriftsartikel (refereegranskat)abstract In this paper, we examine decay and fragmentation of core-excited and core-ionized water molecules combining quantum chemical calculations and electron-energy-resolved electron–ion coincidence spectroscopy. The experimental technique allows us to connect electronic decay from core-excited states, electronic transitions between ionic states, and dissociation of the molecular ion. To this end, we calculate the minimum energy dissociation path of the core-excited molecule and the potential energy surfaces of the molecular ion. Our measurements highlight the role of ultra-fast nuclear motion in the 1a1-14a1 core-excited molecule in the production of fragment ions. OH+ fragments dominate for spectator Auger decay. Complete atomization after sequential fragmentation is also evident through detection of slow H+ fragments. Additional measurements of the non-resonant Auger decay of the core-ionized molecule (1a1-1) to the lower-energy dication states show that the formation of the OH+ + H+ ion pair dominates, whereas sequential fragmentation OH+ + H+ → O + H+ + H+ is observed for transitions to higher dication states, supporting previous theoretical investigations.
8.	Schalk, Oliver, et al. (författare) Competition between ring-puckering and ring-opening excited state reactions exemplified on 5H-furan-2-one and derivatives 2020 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:6 Tidskriftsartikel (refereegranskat)abstract The influence of ring-puckering on the light-induced ring-opening dynamics of heterocyclic compounds was studied on the sample 5-membered ring molecules gamma-valerolactone and 5H-furan-2-one using time-resolved photoelectron spectroscopy and ab initio molecular dynamics simulations. In gamma-valerolactone, ring-puckering is not a viable relaxation channel and the only available reaction pathway is ring-opening, which occurs within one vibrational period along the C-O bond. In 5H-furan-2-one, the C = C double bond in the ring allows for ring-puckering which slows down the ring-opening process by about 150 fs while only marginally reducing its quantum yield. This demonstrates that ring-puckering is an ultrafast process, which is directly accessible upon excitation and which spreads the excited state wave packet quickly enough to influence even the outcome of an otherwise expectedly direct ring-opening reaction.
9.	Ugandi, Mihkel, et al. (författare) Uncontracted basis sets for ab initio calculations of muonic atoms and molecules 2018 Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 118:21 Tidskriftsartikel (refereegranskat)abstract In this work, we investigated muonic atoms and molecules from a quantum chemist's viewpoint by incorporating muons in the CASSCF model. With the aim of predicting muonic X-ray energies, primitive muonic basis sets were developed for a selection of elements. The basis sets were then used in CASSCF calculations of various atoms and molecules to calculate muonic excited states. We described the influence of nuclear charge distribution in predicting muonic X-ray energies. Effects of the electronic wave function on the muonic X-ray energies were also examined. We have computationally demonstrated how the muon can act as a probe for the nuclear charge distribution or electronic wave function by considering lower or higher muonic excited states, respectively.
10.	Vacher, Morgane, et al. (författare) How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield ofDioxetane? 2017 Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8, s. 3790-3794 Tidskriftsartikel (refereegranskat)abstract Chemiluminescence is the emission of light as aresult of a nonadiabatic chemical reaction. The present work isconcerned with understanding the yield of chemiluminescence,in particular how it dramatically increases upon methylation of1,2-dioxetane. Both ground-state and nonadiabatic dynamics(including singlet excited states) of the decomposition reactionof various methyl-substituted dioxetanes have been simulated.Methyl-substitution leads to a significant increase in thedissociation time scale. The rotation around the O−C−C−Odihedral angle is slowed; thus, the molecular system stayslonger in the “entropic trap” region. A simple kinetic model isproposed to explain how this leads to a higher chemiluminescence yield. These results have important implications for the designof efficient chemiluminescent systems in medical, environmental, and industrial applications.
11.	Aquilante, Francesco, et al. (författare) Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry 2017 Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 115:17-18, s. 2052-2064 Tidskriftsartikel (refereegranskat)abstract The density-fitting technique for approximating electron-repulsion integrals relies on the quality of auxiliary basis sets. These are commonly obtained through data fitting, an approach that presents some shortcomings. On the other hand, it is possible to derive auxiliary basis sets by removing elements from the product space of both contracted and primitive orbitals by means of a particular form of inner projection technique that has come to be known as Cholesky decomposition (CD). This procedure allows for on-the-fly construction of auxiliary basis sets that may be used in conjunction with any quantum chemical method, i.e. unbiased auxiliary basis sets. One key feature of these sets is that they represent the electron-repulsion integral matrix in atomic orbital basis with an accuracy that can be systematically improved. Another key feature is represented by the fact that locality of fitting coefficients is obtained even with the long-ranged Coulomb metric, as result of integral accuracy. Here we report on recent advances in the development of the CD-based density fitting technology. In particular, the implementation of analytical gradients algorithms is reviewed and the present status of local formulations - potentially linear scaling - is analysed in detail.
12.	Battaglia, Stefano, et al. (författare) Regularized CASPT2 : an Intruder-State-Free Approach 2022 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:8, s. 4814-4825 Tidskriftsartikel (refereegranskat)abstract In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on sigma p regularization. The resulting sigma(p)-CASPT2 method is compared to previous techniques, namely, the real and imaginary level shifts, on a theoretical basis and by performing a series of systematic calculations. The analysis is focused on two aspects, the effectiveness of sigma(p)-CASPT2 in removing the ISP and the sensitivity of the approach with respect to the input parameter. We found that sigma p- CASPT2 compares favorably with respect to previous approaches and that different versions, sigma(1)-CASPT2 and sigma(2)-CASPT2, have different potential application domains. This analysis also reveals the unsuitability of the real level shift technique as a general way to avoid the intruder-state problem.
13.	Calio, Paul B., et al. (författare) Minimum-Energy Conical Intersections by Compressed Multistate Pair-Density Functional Theory 2024 Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 128:9, s. 1698-1706 Tidskriftsartikel (refereegranskat)abstract Compressed multistate pair-density functional theory (CMS-PDFT) is a multistate version of multiconfiguration pair-density functional theory that can capture the correct topology of coupled potential energy surfaces (PESs) around conical intersections. In this work, we develop interstate coupling vectors (ISCs) for CMS-PDFT in the OpenMolcas and PySCF/mrh electronic structure packages. Yet, the main focus of this work is using ISCs to calculate minimum-energy conical intersections (MECIs) by CMS-PDFT. This is performed using the projected constrained optimization method in OpenMolcas, which uses ISCs to restrain the iterations to the conical intersection seam. We optimize the S1/S0 MECIs for ethylene, butadiene, and benzene and show that CMS-PDFT gives smooth PESs in the vicinities of the MECIs. Furthermore, the CMS-PDFT MECIs are in good agreement with the MECI calculated by the more expensive XMS-CASPT2 method.
14.	Corchado, José C., et al. (författare) Theoretical Study of Solvent Effects on the Ground and Low-Lying Excited Free Energy Surfaces of a Push–Pull Substituted Azobenzene 2014 Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 118:43, s. 12518-12530 Tidskriftsartikel (refereegranskat)abstract The ground and low-lying excited free energy surfaces of 4-amino-4'-cyano azobenzene, a molecule that has been proposed as building block for chiroptical switches, are studied in gas phase and a variety of solvents (benzene, chloroform, acetone, and water). Solvent effects on the absorption and emission spectra and on the cistrans thermal and photo isomerizations are analyzed using two levels of calculation: TD-DFT and CASPT2/CASSCF. The solvent effects are introduced using a polarizable continuum model and a QM/MM method, which permits one to highlight the role played by specific interactions. We found that, in gas phase and in agreement with the results found for other azobenzenes, the thermal cistrans isomerization follows a rotation-assisted inversion mechanism where the inversion angle must reach values close to 180 degrees but where the rotation angle can take almost any value. On the contrary, in polar solvents the mechanism is controlled by the rotation of the CN=NC angle. The change in the mechanism is mainly related to a better solvation of the nitrogen atoms of the azo group in the rotational transition state. The photoisomerization follows a rotational pathway both in gas phase and in polar and nonpolar solvents. The solvent introduces only small modifications in the n pi* free energy surface (S-1), but it has a larger effect on the pi pi* surface (S-2) that, in polar solvents, gets closer to S-1. In fact, the S-2 band of the absorption spectrum is red-shifted 0.27 eV for the trans isomer and 0.17 eV for the cis. In the emission spectrum the trend is similar: only S-2 is appreciably affected by the solvent, but in this case a blue shift is found.
15.	Cuéllar-Zuquin, Juliana, et al. (författare) Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size 2023 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:22, s. 8258-8272 Tidskriftsartikel (refereegranskat)abstract We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
16.	Fernández Galván, Ignacio, 1977-, et al. (författare) Chemiexcitation without the Peroxide Bond? : Replacing oxygen with other heteroatoms 2019 Ingår i: ChemPhotoChem. - : Wiley. - 2367-0932. ; 3:9, s. 957-967 Tidskriftsartikel (refereegranskat)abstract Chemiexcitation is the population of electronic excited states from the electronic ground state via radiationless non-adiabatic transitions upon thermal activation. The subsequent emission of the excess of energy in the form of light is called chemiluminescence or bioluminescence when occurring in living organisms. Key intermediates in these reactions have been shown to contain a high-energy (often cyclic) peroxide which decomposes. The simplest molecules, 1,2-dioxetane and 1,2-dioxetanone, have thus been used extensively both theoretically and experimentally as model systems to understand the underlying mechanisms of chemiexcitation. An outstanding question remains whether the peroxide bond is a necessity and whether equivalent processes could happen in other simple molecules not containing an OO bond. In the present work, the decomposition reactions of four analogs of 1,2-dioxetane not containing a peroxide bond, the 1,2-oxazetidine anion, the 1,2-diazetidine anion, (neutral) 1,2-oxazetidine and 1,2-dithietane, have been studied theoretically using ab initio multicongurational methods. In particular, the reaction energy barriers and spin-orbit coupling strengths were calculated; the electronic degeneracy was studied and compared to the case of 1,2-dioxetane to assess the potentiality of chemiexcitation in the analog molecules.
17.	Fernández Galván, Ignacio, 1977-, et al. (författare) Restricted-Variance Constrained, Reaction Path, and Transition State Molecular Optimizations Using Gradient-Enhanced Kriging 2021 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:1, s. 571-582 Tidskriftsartikel (refereegranskat)abstract Gaussian process regression has recently been explored as an alternative to standard surrogate models in molecular equilibrium geometry optimization. In particular, the gradient-enhanced Kriging approach in association with internal coordinates, restricted-variance optimization, and an efficient and fast estimate of hyperparameters has demonstrated performance on par or better than standard methods. In this report, we extend the approach to constrained optimizations and transition states and benchmark it for a set of reactions. We compare the performance of the newly developed method with the standard techniques in the location of transition states and in constrained optimizations, both isolated and in the context of reaction path computation. The results show that the method outperforms the current standard in efficiency as well as in robustness.
18.	Fernández Galván, Ignacio, 1977-, et al. (författare) Role of conical intersection seam topography in the chemiexcitation of 1,2-dioxetanes 2022 Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:3, s. 1638-1653 Tidskriftsartikel (refereegranskat)abstract Chemiexcitation, the generation of electronic excited states by a thermal reaction initiated on the ground state, is an essential step in chemiluminescence, and it is mediated by the presence of a conical intersection that allows a nonadiabatic transition from ground state to excited state. Conical intersections classified as sloped favor chemiexcitation over ground state relaxation. The chemiexcitation yield of 1,2-dioxetanes is known to increase upon methylation. In this work we explore to which extent this trend can be attributed to changes in the conical intersection topography or accessibility. Since conical intersections are not isolated points, but continuous seams, we locate regions of the conical intersection seams that are close to the configuration space traversed by the molecules as they react on the ground state. We find that conical intersections are energetically and geometrically accessible from the reaction trajectory, and that topographies favorable to chemiexcitation are found in all three molecules studied. Nevertheless, the results suggest that dynamic effects are more important for explaining the different yields than the static features of the potential energy surfaces.
19.	Fernández Galván, Ignacio, 1977-, et al. (författare) Smooth Things Come in Threes : A Diabatic Surrogate Model for Conical Intersection Optimization 2023 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:11, s. 3418-3427 Tidskriftsartikel (refereegranskat)abstract The optimization of conical intersection structures iscomplicatedby the nondifferentiability of the adiabatic potential energy surfaces.In this work, we build a pseudodiabatic surrogate model, based onGaussian process regression, formed by three smooth and differentiablesurfaces that can adequately reproduce the adiabatic surfaces. Usingthis model with the restricted variance optimization method resultsin a notable decrease of the overall computational effort requiredto obtain minimum energy crossing points.
20.	Fernández García-Prieto, F., et al. (författare) Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore 2015 Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:21, s. 5504-5514 Tidskriftsartikel (refereegranskat)abstract Solvent effects on the UV–vis absorption spectra and molecular properties of four models of the photoactive yellow protein (PYP) chromophore have been studied with ASEP/MD, a sequential quantum mechanics/molecular mechanics method. The anionic trans-p-coumaric acid (pCA–), thioacid (pCTA–), methyl ester (pCMe–), and methyl thioester (pCTMe–) derivatives have been studied in gas phase and in water solution. We analyze the modifications introduced by the substitution of sulfur by oxygen atoms and hydrogen by methyl in the coumaryl tail. We have found some differences in the absorption spectra of oxy and thio derivatives that could shed light on the different photoisomerization paths followed by these compounds. In solution, the spectrum substantially changes with respect to that obtained in the gas phase. The n → π1* state is destabilized by a polar solvent like water, and it becomes the third excited state in solution displaying an important blue shift. Now, the π → π1* and π → π2* states mix, and we find contributions from both transitions in S1 and S2. The presence of the sulfur atom modulates the solvent effect and the first two excited states become practically degenerate for pCA– and pCMe– but moderately well-separated for pCTA– and pCTMe–.
21.	Francés-Monerris, Antonio, et al. (författare) Triplet versus singlet chemiexcitation mechanism in dioxetanone : a CASSCF/CASPT2 study 2017 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 136:6 Tidskriftsartikel (refereegranskat)abstract Chemiluminescence is a fundamental process of chemistry consisting in the conversion of chemical energy stored in chemical bonds into light. It is used by nature and by man-made technology, being especially relevant in chemical analysis. The understanding of the phenomenon strongly relies in the study of peroxide models such as 1,2-dioxetanones. In the present contribution, the singlet S2 and the triplet T2 potential energy surfaces of the unimolecular decomposition of 1,2-dioxetanone have been mapped along the O-O and C-C bond coordinates on the grounds of the multiconfigurational CASPT2//CASSCF approach. Results confirm the energy degeneracy between T2, T1, S1, and S0 at the TS region, whereas S2 is unambiguously predicted at higher energies. Triplet-state population is also supported by the spin-orbit couplings between the singlet and triplet states partaking in the process. In particular, the first-principle calculations show that decomposition along the T2 state is a competitive process, having a small (similar to 3 kcal/mol) energy barrier from the ground-state TS structure. The present findings can explain the higher quantum yield of triplet-state population with respect to the excited singlet states recorded experimentally for the uni-molecular decomposition of 1,2-dioxetanone models.
22.	Häse, Florian, et al. (författare) How machine learning can assist the interpretation of ab initio molecular dynamics simulations and conceptual understanding of chemistry 2019 Ingår i: Chemical Science. - : The Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 10:8, s. 2298-2307 Tidskriftsartikel (refereegranskat)abstract Molecular dynamics simulations are often key to the understanding of the mechanism, rate and yield of chemical reactions. One current challenge is the in-depth analysis of the large amount of data produced by the simulations, in order to produce valuable insight and general trends. In the present study, we propose to employ recent machine learning analysis tools to extract relevant information from simulation data without a priori knowledge on chemical reactions. This is demonstrated by training machine learning models to predict directly a specific outcome quantity of ab initio molecular dynamics simulations - the timescale of the decomposition of 1,2-dioxetane. The machine learning models accurately reproduce the dissociation time of the compound. Keeping the aim of gaining physical insight, it is demonstrated that, in order to make accurate predictions, the models evidence empirical rules that are, today, part of the common chemical knowledge. This opens the way for conceptual breakthroughs in chemistry where machine analysis would provide a source of inspiration to humans.
23.	Jorner, Kjell, et al. (författare) Unraveling factors leading to efficient norbornadiene-quadricyclane molecular solar-thermal energy storage systems 2017 Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 5:24, s. 12369-12378 Tidskriftsartikel (refereegranskat)abstract Developing norbornadiene-quadricyclane (NBD-QC) systems for molecular solar-thermal (MOST) energy storage is often a process of trial and error. By studying a series of norbornadienes (NBD-R-2) doubly substituted at the C7-position with R = H, Me, and iPr, we untangle the interrelated factors affecting MOST performance through a combination of experiment and theory. Increasing the steric bulk along the NBD-R-2 series gave higher quantum yields, slightly red-shifted absorptions, and longer thermal lifetimes of the energy-rich QC isomer. However, these advantages are counterbalanced by lower energy storage capacities, and overall R = Me appears most promising for short-term MOST applications. Computationally we find that it is the destabilization of the NBD isomer over the QC isomer with increasing steric bulk that is responsible for most of the observed trends and we can also predict the relative quantum yields by characterizing the S-1/S-0 conical intersections. The significantly increased thermal half-life of NBD-iPr(2) is caused by a higher activation entropy, highlighting a novel strategy to improve thermal half-lives of MOST compounds and other photo-switchable molecules without affecting their electronic properties. The potential of the NBD-R-2 compounds in devices is also explored, demonstrating a solar energy storage efficiency of up to 0.2%. Finally, we show how the insights gained in this study can be used to identify strategies to improve already existing NBD-QC systems.
24.	Khamesian, Marjan, et al. (författare) Spectroscopy of linear and circular polarized light with the exact semiclassical light–matter interaction 2019 Ingår i: Annual Reports in Computational Chemistry. - : Elsevier Ltd. - 1574-1400. - 9780128171196 ; , s. 39-76 Bokkapitel (refereegranskat)abstract We present the theory and the analytical and numerical solution for the calculation of the oscillator and rotatory strengths of molecular systems using a state-specific formalism. For a start, this is done in the context of the exact semiclassical light–matter interaction in association with electronic wave functions expanded in a Gaussian basis. The reader is guided through the standard approximations of the field, e.g., the use of commutators, truncation of Taylor expansions, and the implications of these are discussed in parallel. Expressions for the isotropically averaged values are derived, recovering the isotropic oscillator strength in terms of the transition electric-dipole moment, and the isotropic rotatory strength in terms of the transition electric-dipole and magnetic-dipole moments. This chapter gives a detailed description of the computation of the integrals over the plane wave in association with Gaussian one-particle basis sets. Finally, a brief description is given of how the computed oscillator and rotatory strengths are related to the quantities commonly used and discussed in experimental studies.
25.	Raggi, Gerardo, et al. (författare) Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging 2020 Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:6, s. 3989-4001 Tidskriftsartikel (refereegranskat)abstract Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional-step-restricted second-order truncated expansion-molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In this paper, we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect, the GEK procedure will be used to mimic the behavior of a conventional second-order scheme but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimizations to facilitate restricted-variance optimizations. A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two: the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, full Baker-TS, and S22 test suites, at the density functional theory and second-order Moller-Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected.
26.	Roca-Sanjuán, Daniel, et al. (författare) A Theoretical Analysis of the Intrinsic Light-Harvesting Properties of Xanthopterin 2014 Ingår i: Computational and Theoretical Chemistry. - Netherlands : Elsevier. - 2210-271X .- 2210-2728. ; 1040-1041, s. 230-236 Tidskriftsartikel (refereegranskat)abstract Belonging to the family of pterins, which are common chromophores in several bio-organisms, xanthopterin has been shown experimentally (Plotkin et al., 2010) to have the ability of acting as a light-harvesting molecule. In the present study, multiconfigurational second-order perturbation theory is used to determine the stability of distinct amino/imino and lactam/lactim tautomers and the absorption and emission spectroscopic characteristics, electron donor and acceptor properties and the electron and charge transfer efficiencies via π-stacking. The lactam–lactam form 3H5H (and in a lesser extent 1H5H) is predicted to have the most appropriate intrinsic characteristics for the light-harvesting properties of xanthopterin, since it is the most stable isomer predicted for the gas phase and estimated for polar environments, absorbs solar light at longer wave lengths, has relatively low donor properties and the presence of the keto groups, instead of enol, increases the efficiency for energy transfer through excimer-like interactions.
27.	Vacher, Morgane, et al. (författare) Chemi- and Bioluminescence of Cyclic Peroxides 2018 Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 118:15, s. 6927-6974 Forskningsöversikt (refereegranskat)abstract Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.
28.	Vacher, Morgane, et al. (författare) Dynamical Insights into the Decomposition of 1,2-Dioxetane 2017 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 13:6, s. 2448-2457 Tidskriftsartikel (refereegranskat)abstract Chemiluminescence in 1,2-dioxetane occurs through a thermally activated decomposition reaction into two formaldehyde molecules. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction have been simulated, starting from the first O–O bond-breaking transition structure. The ground-state dissociation occurs between t = 30 fs and t = 140 fs. The so-called entropic trap leads to frustrated dissociations, postponing the decomposition reaction. Specific geometrical conditions are necessary for the trajectories to escape from the entropic trap and for dissociation to be possible. The singlet excited states participate as well in the trapping of the molecule: dissociation including the nonadiabatic transitions to singlet excited states now occurs from t = 30 fs to t = 250 fs and later. Specific regions of the seam of the So/S1 conical intersections that would "retain" the molecule for longer on the excited state have been identified.
29.	Valentini, Alessio, et al. (författare) Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model 2017 Ingår i: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 56:14, s. 3842-3846 Tidskriftsartikel (refereegranskat)abstract The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counter-intuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.

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