29 research outputs found
Electronic Spectra from TDDFT and Machine Learning in Chemical Space
Due to its favorable computational efficiency time-dependent (TD) density
functional theory (DFT) enables the prediction of electronic spectra in a
high-throughput manner across chemical space. Its predictions, however, can be
quite inaccurate. We resolve this issue with machine learning models trained on
deviations of reference second-order approximate coupled-cluster singles and
doubles (CC2) spectra from TDDFT counterparts, or even from DFT gap. We applied
this approach to low-lying singlet-singlet vertical electronic spectra of over
20 thousand synthetically feasible small organic molecules with up to eight
CONF atoms. The prediction errors decay monotonously as a function of training
set size. For a training set of 10 thousand molecules, CC2 excitation energies
can be reproduced to within 0.1 eV for the remaining molecules. Analysis
of our spectral database via chromophore counting suggests that even higher
accuracies can be achieved. Based on the evidence collected, we discuss open
challenges associated with data-driven modeling of high-lying spectra, and
transition intensities
Ab initio simulation of the ultrafast circular dichroism spectrum of provitamin D ring-opening
We present a method to simulate ultrafast pump-probe time-resolved circular
dichroism (TRCD) spectra based on time-dependent density functional theory
trajectory surface hopping. The method is applied to simulate the TRCD spectrum
along the photoinduced ring-opening of provitamin D. Simulations reveal that
the initial decay of the signal is due to excited state relaxation, forming the
rotationally flexible previtamin D. We further show that oscillations in the
experimental TRCD spectrum arise from isomerizations between previtamin D
rotamers with different chirality, which are associated with the helical
conformation of the triene unit. We give a detailed description of the
formation dynamics of different rotamers, playing a key role in the natural
regulation vitamin D photosynthesis. Going beyond the sole extraction of decay
rates, simulations greatly increase the amount of information that can be
retrieved from ultrafast TRCD, making it a sensitive tool to unravel details in
the sub-picosecond dynamics of photoinduced chirality changes
Development of a non-adiabatic ab initio molecular dynamics method and its application to photodynamical processes
Photoprocesses are ubiquitous in nature, science, and engineering. The understanding as well as the optimization of photochemical and photophysical properties of molecular systems requires computational tools that are able to describe the dynamical evolution of the system in electronically excited states. Ab Initio Molecular Dynamics (AIMD) based on Density Functional Theory (DFT) has become an established tool for elucidating mechanisms of chemical reactions that occur in the electronic ground state. However, to describe photoprocesses by AIMD, an underlying electronic-structure method that is able to treat excited states is necessary. This complicates the description of these processes because in the past this implied the use of computationally expensive wavefunction-based methods, which in addition are not straightforward to use. Time-Dependent Density Functional Theory (TDDFT) provides an in principle exact description of electronically excited states, although in practice, approximations have to be introduced. Compared to wavefunction-based methods, TDDFT is computationally less demanding and is relatively straightforward and easy to use. Recently, TDDFT nuclear gradients have become available and allow to carry out AIMD in excited states. In this thesis a TDDFT-based AIMD method that is able to account for non-adiabatic effects is developed and implemented. The non-adiabatic couplings are computed by means of a Kohn-Sham orbital based reconstruction of the many-electron wavefunction for ground and excited states. The non-adiabatic scheme is based on the fewest switches trajectory surface hopping (SH) method introduced by Tully. The method is applied to describe decay processes, such as fragmentation or isomerization, that occur upon photoexcitation of the molecules protonated formaldimine and oxirane. In the case of protonated formaldimine, the results of the TDDFT-SH method are in good agreement with SH simulations based on the state-averaged complete active space (SA-CASSCF) method, both with respect to the observed reaction mechanisms and the excited state life times. In the case of oxirane, the TDDFT-SH simulations confirm the main experimental results and provide an additional refinement of the postulated reaction mechanism. The accuracy of TDDFT is investigated with respect to different issues that are especially important for the proper description of photoprocesses. These aspects include the accuracy of non-adiabatic coupling (NAC) vectors, the description of S1-S0 conical intersections, and the description of locally excited states in systems where charge transfer (CT) states are present, that are affected by the well-known CT failure of TDDFT. Concerning the NAC vectors, a qualitative agreement with SA-CASSCF is found, although magnitudes are underestimated by TDDFT/PBE. Regarding the description of conical intersections to the ground state, we find as expected that TDDFT in the adiabatic approximation (ALDA) is not able to predict an intersection that is strictly conical. However, we find that TDDFT is able to approximate a conical intersection that has a similar shape as the one predicted by SA-CASSCF. For an electron donor-bridge-acceptor molecule it is shown that the CT failure of TDDFT can also considerably affect properties of non-CT states. The use of TDDFT using conventional exchange-correlation functionals is thus not recommended for the description of such systems. Using the second-order approximate coupled cluster (CC2) method in conjunction with a high quality basis set, an accurate and balanced description of both locally excited and CT states can be made. The use of CC2 with large basis sets for AIMD simulations is however still computationally unaffordable for larger systems. TDDFT is still in its infancy and several attempts to cure some of its defiencies have already been made. These attempts mainly concern improvements of the approximations of the exchange-correlation functionals and associated TDDFT kernels. The TDDFT-SH method that has been developed in this thesis can in principle be applied in combination with any approximation for the exchange correlation functional, provided that nuclear gradients for this approximation are available and the computational cost remains acceptable. In this way, the method developed here is able to directly profit from the ongoing improvements in the active research field of exchange-correlation functionals and kernels
Molecular Dynamics Simulation of Apolipoprotein E3 Lipid Nanodiscs
Nanodiscs are binary discoidal complexes of a phospholipid bilayer
circumscribed by belt-like helical scaffold proteins. Using coarse-grained and
all-atom molecular dynamics simulations, we explore the stability, size, and
structure of nanodiscs formed between the N-terminal domain of apolipoprotein
E3 (apoE3-NT) and variable number of
1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) molecules. We study both
parallel and antiparallel double-belt configurations, consisting of four
proteins per nanodisc. Our simulations predict nanodiscs containing between 240
and 420 DMPC molecules to be stable. The antiparallel configurations exhibit an
average of 1.6 times more amino acid interactions between protein chains and 2
times more ionic contacts, compared to the parallel configuration. With one
exception, DMPC order parameters are consistently larger in the antiparallel
configuration than in the parallel one. In most cases, the root mean square
deviation of the positions of the protein backbone atoms is smaller in the
antiparallel configuration. We further report nanodisc size, thickness, radius
of gyration, and solvent accessible surface area. Combining all investigated
parameters, we hypothesize the antiparallel protein configuration leading to
more stable and more rigid nanodiscs than the parallel one
Calculation of vibrationally resolved absorption spectra of acenes and pyrene
The absorption spectra of naphthalene, anthracene, pentacene and pyrene in the ultraviolet-visible (UV-Vis) range have been simulated by using an efficient real-time generating function method that combines calculated adiabatic electronic excitation energies with vibrational energies of the excited states. The vertical electronic excitation energies have been calculated at the density functional theory level using the PBE0 functional and at the second-order approximate coupled-cluster level (CC2). The absorption spectra have been calculated at the PBE0 level for the studied molecules and at the CC2 level for naphthalene. The transition probabilities between vibrationally resolved states were calculated by using the real-time generating function method employing the full Duschinsky formalism. The absorption spectrum for naphthalene calculated at the PBE0 and CC2 levels agrees well with the experimental one after the simulated spectra have been blue-shifted by 0.48 eV and 0.12 eV at the PBE0 and CC2 level, respectively. The absorption spectra for anthracene, pentacene and pyrene simulated at the PBE0 level agree well with the experimental ones when they are shifted by 0.49 eV, 0.57 eV and 0.46 eV, respectively. The strongest transitions of the main vibrational bands have been assigned.Peer reviewe
TURBOMOLE: Today and Tomorrow
TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light–matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE’s functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree–Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties
Applicability of the thawed Gaussian wavepacket dynamics to the calculation of vibronic spectra of molecules with double-well potential energy surfaces
Simulating vibrationally resolved electronic spectra of anharmonic systems,
especially those involving double-well potential energy surfaces, often
requires expensive quantum dynamics methods. Here, we explore the applicability
and limitations of the recently proposed single-Hessian thawed Gaussian
approximation for the simulation of spectra of systems with double-well
potentials, including 1,2,4,5-tetrafluorobenzene, ammonia, phosphine, and
arsine. This semiclassical wavepacket approach is shown to be more robust and
to provide more accurate spectra than the conventional harmonic approximation.
Specifically, we identify two cases in which the Gaussian wavepacket method is
especially useful due to the breakdown of the harmonic approximation: (i) when
the nuclear wavepacket is initially at the top of the potential barrier but
delocalized over both wells, e.g., along a low-frequency mode, and (ii) when
the wavepacket has enough energy to classically go over the low potential
energy barrier connecting the two wells. The method is efficient and requires
only a single classical ab initio molecular dynamics trajectory, in addition to
the data required to compute the harmonic spectra. We also present an improved
algorithm for computing the wavepacket autocorrelation function, which
guarantees that the evaluated correlation function is continuous for arbitrary
size of the time step.Comment: v2: Modified abstract, added finite-temperature and Herzberg-Teller
results for TFB in the Supporting Information and their discussion in the
main text; last 15 pages contain the Supporting Informatio