| 1. |
- Aquilante, Francesco, et al.
(författare)
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Modern quantum chemistry with [Open]Molcas
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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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.
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| 2. |
- Aquilante, Francesco, et al.
(författare)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541
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Tidskriftsartikel (refereegranskat)abstract
- In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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| 3. |
- Delcey, Mickael G., et al.
(författare)
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Exact semi-classical light-matter interaction operator applied to two-photon processes with strong relativistic effects
- 2020
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 153:2
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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.
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| 4. |
- Farahani, Pooria, 1985-, et al.
(författare)
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A combined theoretical and experimental study onthe mechanism of spiro-adamantyl-1,2-dioxetanone decomposition
- 2017
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Ingår i: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 7, s. 17462-17472
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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.
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| 5. |
- Farahani, Pooria, 1985-, et al.
(författare)
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Advances in computationalphotochemistry and chemiluminescenceof biological and nanotechnologicalmolecules
- 2017. - 44
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Ingår i: Photochemistry. - Cambridge, UK : Royal Society of Chemistry. - 1465-1947. ; , s. 16-60, s. 16-60
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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.
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| 6. |
- 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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| 7. |
- Manni, Giovanni Li, et al.
(författare)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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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.
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| 8. |
- Sankari, Anna, et al.
(författare)
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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
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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.
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| 9. |
- Schalk, Oliver, et al.
(författare)
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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.
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| 10. |
- Ugandi, Mihkel, et al.
(författare)
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Uncontracted basis sets for ab initio calculations of muonic atoms and molecules
- 2018
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 118:21
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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.
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| 11. |
- Vacher, Morgane, et al.
(författare)
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How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield ofDioxetane?
- 2017
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8, s. 3790-3794
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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.
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| 12. |
- Augusto, Felipe A., et al.
(författare)
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Mechanism of activated chemiluminescence of cyclic peroxides : 1,2-dioxetanes and 1,2-dioxetanones
- 2017
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 19:5, s. 3955-3962
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Tidskriftsartikel (refereegranskat)abstract
- Almost all chemiluminescent and bioluminescent reactions involve cyclic peroxides. The structure of the peroxide and reaction conditions determine the quantum efficiency of light emission. Oxidizable fluorophores, the so-called activators, react with 1,2-dioxetanones promoting the former to their first singlet excited state. This transformation is inefficient and does not occur with 1,2-dioxetanes; however, they have been used as models for the efficient firefly bioluminescence. In this work, we use the SA-CASSCF/CASPT2 method to investigate the activated chemiexcitation of the parent 1,2-dioxetane and 1,2-dioxetanone. Our findings suggest that ground state decomposition of the peroxide competes efficiently with the chemiexcitation pathway, in agreement with the available experimental data. The formation of non-emissive triplet excited species is proposed to explain the low emission efficiency of the activated decomposition of 1,2-dioxetanone. Chemiexcitation is rationalized considering a peroxide/activator supermolecule undergoing an electron-transfer reaction followed by internal conversion.
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| 13. |
- Battaglia, Stefano, et al.
(författare)
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Multiconfigurational quantum chemistry: The CASPT2 method
- 2023
-
Ingår i: Theoretical and Computational Photochemistry. - Amsterdam : Elsevier. ; , s. 135-162
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Bokkapitel (refereegranskat)abstract
- This chapter presents the theory behind the CASPT2 method and its adaptation to a multistate formalism. The chapter starts with an introduction to the theory of the CASPT2 method—an application of the Rayleigh-Schrödinger perturbation theory applied to the multiconfigurational reference function—as it was originally presented. In particular, we discuss the nature of the reference Hamiltonian and the first-order interacting space. This is followed by some detailed discussion with respect to the intruder state problem and various shift techniques to address this problem. Afterward, a longer review on alternative reference Hamiltonians, which to some degree or completely remove the intruder state problem, is put forward. Subsequently, the presently proposed multistate versions of the CASPT2 method are discussed in some detail. The chapter is concluded with a review of different benchmark assessments of the accuracy of the method and a qualified suggestion on the future development potentials of the approach.
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| 14. |
- Doloczki, Susanne, et al.
(författare)
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Photophysical characterization and fluorescence cell imaging applications of 4-N-substituted benzothiadiazoles
- 2022
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Ingår i: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 12:23, s. 14544-14550
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Tidskriftsartikel (refereegranskat)abstract
- In this work, a series of fluorescent 2,1,3-benzothiadiazole derivatives with various N-substituents in the 4- position was synthesized and photophysically characterized in various solvents. Three compounds emerged as excellent fluorescent probes for imaging lipid droplets in cancer cells. A correlation between their high lipophilicity and lipid droplet specificity could be found, with log P ≥ 4 being characteristic for lipid droplet accumulation.
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| 15. |
- Fernández García-Prieto, F., et al.
(författare)
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Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore
- 2015
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:21, s. 5504-5514
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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–.
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| 16. |
- Garcia-Prieto, Francisco F., et al.
(författare)
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QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore
- 2017
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Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 13:2, s. 737-748
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Tidskriftsartikel (refereegranskat)abstract
- Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the transcis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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| 17. |
- Hase, Florian, et al.
(författare)
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Machine learning for analysing ab initio molecular dynamics simulations
- 2020
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Ingår i: 31St International Conference On Photonic, Electronic And Atomic Collisions (Icpeac Xxxi). - : IOP PUBLISHING LTD.
-
Konferensbidrag (refereegranskat)abstract
- Post-calculation analyses are often required to extract physical insights from ab initio molecular dynamics simulations. In the present work, we use different machine learning classifiers to take a new perspective on the decomposition reaction of dioxetane. Upon thermally activated decomposition, dioxetane can form products in an electronically excited state and can thus chemiluminesce. Simulated dynamics trajectories exhibit both successful and frustrated dissociations. As an exhaustive and systematic study of the decomposition mechanism "by hand" is beyond feasibility, machine learning models have been employed to study the relevant nuclear distortions governing molecular dissociation. According to all classifiers used in the study, the two sets of geometries differ by the in-phase planarisation of the two formaldehyde moieties. New insights are obtained from this analysis: if both moieties are not planar enough when the dissociation is attempted, it is frustrated and the molecule remains trapped. The postponing of the decomposition reaction by the so-called entropic trap enhances the chemiexcitation efficiency.
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| 18. |
- Lindh, Roland, et al.
(författare)
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Molecular structure optimizations with Gaussian process regression
- 2023
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Ingår i: Quantum Chemistry in the Age of Machine Learning. - Amsterdam : Elsevier. ; , s. 391-428
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Bokkapitel (refereegranskat)abstract
- Molecular structure optimization is one of the most common tasks performed in computational chemistry. Many applications require locating special points in a potential energy surface: minima, saddle points, and others. Given that the calculation of energies and gradients with accurate quantum chemical methods is quite computationally demanding, one is often interested in finding these special points with a minimal number of energy evaluations. During the last decades, optimization methods and strategies based on a second-order expansion of the potential energy surface have been developed and perfectioned, reaching a high level of efficiency and robustness. These “conventional” methods are briefly described in this chapter. More recently, alternative models and methods applying machine learning techniques (and most significantly Gaussian process regression) are being proposed and developed, and already show superior characteristics with respect to the established methods. These new approaches are discussed, in particular the restricted variance optimization method is described in some detail. Practical examples include optimization of stable structures and transition states.
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| 19. |
- Martín, M. Elena, et al.
(författare)
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Accelerating QM/MM Calculations by Using the Mean Field Approximation
- 2015
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Ingår i: Quantum Modeling of Complex Molecular Systems. - Cham : Springer. - 9783319216256 - 9783319216263 ; , s. 135-152
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- It is well known that solvents can modify the frequency and intensity of the solute spectral bands, the thermodynamics and kinetics of chemical reactions, the strength of molecular interactions or the fate of solute excited states. The theoretical study of solvent effects is quite complicated since the presence of the solvent introduces additional difficulties with respect to the study of analogous problems in gas phase. The mean field approximation (MFA) is used for many of the most employed solvent effect theories as it permits to reduce the computational cost associated to the study of processes in solution. In this chapter we revise the performance of ASEP/MD, a quantum mechanics/molecular mechanics method developed in our laboratory that makes use of this approximation. It permits to combine state of the art calculations of the solute electron distribution with a detailed, microscopic, description of the solvent. As examples of application of the method we study solvent effects on the absorption spectra of some molecules involved in photoisomerization processes of biological systems.
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| 20. |
- Pedersen, Thomas Bondo, et al.
(författare)
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The versatility of the Cholesky decomposition in electronic structure theory
- 2024
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The resolution-of-the-identity (RI) or density fitting (DF) approximation for the electron repulsion integrals (ERIs) has become a standard component of accelerated and reduced-scaling implementations of first-principles Gaussian-type orbital electronic-structure methods. The Cholesky decomposition (CD) of the ERIs has also become increasingly deployed across quantum chemistry packages in the last decade, even though its early applications were mostly limited to high-accuracy methods such as coupled-cluster theory and multiconfigurational approaches. Starting with a summary of the basic theory underpinning both the CD and RI/DF approximations, thus underlining the extremely close relation of the CD and RI/DF techniques, we provide a brief and largely chronological review of the evolution of the CD approach from its birth in 1977 to its current state. In addition to being a purely numerical procedure for handling ERIs, thus providing robust and computationally efficient approximations to the exact ERIs that have been found increasingly useful on modern computer platforms, CD also offers highly accurate approaches for generating auxiliary basis sets for the RI/DF approximation on the fly due to the deep mathematical connection between the two approaches. In this review, we aim to provide a concise reference of the main techniques employed in various CD approaches in electronic structure theory, to exemplify the connection between the CD and RI/DF approaches, and to clarify the state of the art to guide new implementations of CD approaches across electronic structure programs.
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| 21. |
- Sanchez, M. Luz, et al.
(författare)
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A new QM/MM method oriented to the study of ionic liquids
- 2015
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 36:25, s. 1893-1901
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Tidskriftsartikel (refereegranskat)abstract
- The interest on room temperature ionic liquids has grown in the last decades because of their use as all-purpose solvent and their low environmental impact. In the present work, a new theoretical procedure is developed to study pure ionic liquids within the framework of the quantum mechanics/molecular mechanics method. Each type of ion (cation or anion) is considered as an independent entity quantum mechanically described that follows a differentiated path in the liquid. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate. It was found that, similar to non-polar liquids and as a consequence of the low value of the reaction field, the cation and anion charge distributions are hardly polarized by the rest of molecules in the liquid. Their structure is characterized by an alternance between anion and cation shells as evidenced by the coincidence of the first maximum of the anion-anion and cation-cation radial distribution functions with the first minimum of the anion-cation. Some degree of stacking between the cations is also found.
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| 22. |
- Sethio, Daniel, et al.
(författare)
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A Story of Three Levels of Sophistication in SCF/KS-DFT Orbital Optimization Procedures
- 2024
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 128:12, s. 2472-2486
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Tidskriftsartikel (refereegranskat)abstract
- In this work, three versions of self-consistent field/Kohn-Sham density functional theory (SCF/KS-DFT) orbital optimization are described and benchmarked. The methods are a modified version of the geometry version of the direct inversion in the iterative subspace approach (which we call r-GDIIS), the modified restricted step rational function optimization method (RS-RFO), and the novel subspace gradient-enhanced Kriging method combined with restricted variance optimization (S-GEK/RVO). The modifications introduced are aimed at improving the robustness and computational scaling of the procedures. In particular, the subspace approach in S-GEK/RVO allows the application to SCF/KS-DFT optimization of a machine learning technique that has proven to be successful in geometry optimizations. The performance of the three methods is benchmarked for a large number of small- to medium-sized organic molecules, at equilibrium structures and close to a transition state, and a second set of molecules containing closed- and open-shell transition metals. The results indicate the importance of the resetting technique in boosting the performance of the r-GDIIS procedure. Moreover, it is demonstrated that already at the inception of the subspace version of GEK to optimize SCF wave functions, it displays superior and robust convergence properties as compared to those of the standard state-of-the-art SCF/KS-DFT optimization methods.
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| 23. |
- Slanina, Tomáš, et al.
(författare)
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Impact of Excited-State Antiaromaticity Relief in a Fundamental Benzene Photoreaction Leading to Substituted Bicyclo[3.1.0]hexenes
- 2020
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 142:25, s. 10942-10954
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Tidskriftsartikel (refereegranskat)abstract
- Benzene exhibits a rich photochemistry which can provide access to complex molecular scaffolds that are difficult to access with reactions in the electronic ground state. While benzene is aromatic in its ground state, it is antiaromatic in its lowest ππ∗ excited states. Herein, we clarify to what extent relief of excited-state antiaromaticity (ESAA) triggers a fundamental benzene photoreaction: the photoinitiated nucleophilic addition of solvent to benzene in acidic media leading to substituted bicyclo[3.1.0]hex-2-enes. The reaction scope was probed experimentally, and it was found that silyl-substituted benzenes provide the most rapid access to bicyclo[3.1.0]hexene derivatives, formed as single isomers with three stereogenic centers in yields up to 75% in one step. Two major mechanism hypotheses, both involving ESAA relief, were explored through quantum chemical calculations and experiments. The first mechanism involves protonation of excited-state benzene and subsequent rearrangement to bicyclo[3.1.0]hexenium cation, trapped by a nucleophile, while the second involves photorearrangement of benzene to benzvalene followed by protonation and nucleophilic addition. Our studies reveal that the second mechanism is operative. We also clarify that similar ESAA relief leads to puckering of S1-state silabenzene and pyridinium ion, where the photorearrangement of the latter is of established synthetic utility. Finally, we identified causes for the limitations of the reaction, information that should be valuable in explorations of similar photoreactions. Taken together, we reveal how the ESAA in benzene and 6π-electron heterocycles trigger photochemical distortions that provide access to complex three-dimensional molecular scaffolds from simple reactants.
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| 24. |
- Stenrup, Michael, et al.
(författare)
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Constrained numerical gradients and composite gradients : Practical tools for geometry optimization and potential energy surface navigation
- 2015
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 36:22, s. 1698-1708
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Tidskriftsartikel (refereegranskat)abstract
- A method is proposed to easily reduce the number of energy evaluations required to compute numerical gradients when constraints are imposed on the system, especially in connection with rigid fragment optimization. The method is based on the separation of the coordinate space into a constrained and an unconstrained space, and the numerical differentiation is done exclusively in the unconstrained space. The decrease in the number of energy calculations can be very important if the system is significantly constrained. The performance of the method is tested on systems that can be considered as composed of several rigid groups or molecules, and the results show that the error with respect to conventional optimizations is of the order of the convergence criteria. Comparison with another method designed for rigid fragment optimization proves the present method to be competitive. The proposed method can also be applied to combine numerical and analytical gradients computed at different theory levels, allowing an unconstrained optimization with numerical differentiation restricted to the most significant degrees of freedom. This approach can be a practical alternative when analytical gradients are not available at the desired computational level and full numerical differentiation is not affordable. (c) 2015 Wiley Periodicals, Inc.
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