Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics.

ABSTRACT: Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxation to the singlet ground state and instead privileges transitions from the low-lying n?* state (S1) to a ??* triplet state (T2) followed by rapid internal conversion to the lowest triplet state.

SUBMITTER: Richter M

PROVIDER: S-EPMC4391640 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics.

Richter Martin M Richter Martin M Mai Sebastian S Marquetand Philipp P González Leticia L

Physical chemistry chemical physics : PCCP 20141101 44

Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxa ...[more]

PMID: 25301389

Similar Datasets

Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water

Project description:Rationalizing the

| S-EPMC9327080 | biostudies-literature

Intersystem crossing-branched excited-state intramolecular proton transfer for o-nitrophenol: An ab initio on-the-fly nonadiabatic molecular dynamic simulation.

Project description:The 6SA-CASSCF(10, 10)/6-31G (d, p) quantum chemistry method has been applied to perform on-the-fly trajectory surface hopping simulation with global switching algorithm and to explore excited-state intramolecular proton transfer reactions for the o-nitrophenol molecule within low-lying electronic singlet states (S0 and S1) and triplet states (T1 and T2). The decisive photoisomerization mechanisms of o-nitrophenol upon S1 excitation are found by three intersystem crossings and one conical intersection between two triplet states, in which T1 state plays an essential role. The present simulation shows branch ratios and timescales of three key processes via T1 state, non-hydrogen transfer with ratio 48% and timescale 300 fs, the tunneling hydrogen transfer with ratios 36% and timescale 10 ps, and the direct hydrogen transfer with ratios 13% and timescale 40 fs. The present simulated timescales might be close to low limit of the recent experiment results.

| S-EPMC4879701 | biostudies-literature

Mechanism of Ultrafast Intersystem Crossing in 2-Nitronaphthalene.

Project description:Nitronaphthalene derivatives efficiently populate their electronically excited triplet states upon photoexcitation through ultrafast intersystem crossing (ISC). Despite having been studied extensively by time-resolved spectroscopy, the reasons behind their ultrafast ISC remain unknown. Herein, we present the first ab initio nonadiabatic molecular dynamics study of a nitronaphthalene derivative, 2-nitronaphthalene, including singlet and triplet states. We find that there are two distinct ISC reaction pathways involving different electronic states at distinct nuclear configurations. The high ISC efficiency is explained by the very small electronic and nuclear alterations that the chromophore needs to undergo during the singlet-triplet transition in the dominating ISC pathway after initial dynamics in the singlet manifold. The insights gained in this work are expected to shed new light on the photochemistry of other nitro polycyclic aromatic hydrocarbons that exhibit ultrafast intersystem crossing.

| S-EPMC5947663 | biostudies-literature

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.

Project description:We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.

| S-EPMC8197069 | biostudies-literature

TAO-DFT-Based <i>Ab Initio</i> Molecular Dynamics.

Project description:Recently, AIMD (ab initio molecular dynamics) has been extensively employed to explore the dynamical information of electronic systems. However, it remains extremely challenging to reliably predict the properties of nanosystems with a radical nature using conventional electronic structure methods (e.g., Kohn-Sham density functional theory) due to the presence of static correlation. To address this challenge, we combine the recently formulated TAO-DFT (thermally-assisted-occupation density functional theory) with AIMD. The resulting TAO-AIMD method is employed to investigate the instantaneous/average radical nature and infrared spectra of n-acenes containing n linearly fused benzene rings (n = 2-8) at 300 K. According to the TAO-AIMD simulations, on average, the smaller n-acenes (up to n = 5) possess a nonradical nature, and the larger n-acenes (n = 6-8) possess an increasing radical nature, showing remarkable similarities to the ground-state counterparts at 0 K. Besides, the infrared spectra of n-acenes obtained with the TAO-AIMD simulations are in qualitative agreement with the existing experimental data.

| S-EPMC7674663 | biostudies-literature

Ab initio molecular dynamics: concepts, recent developments, and future trends.

Project description:The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given.

| S-EPMC1100773 | biostudies-literature

Ultrafast intersystem-crossing in platinum containing ?-conjugated polymers with tunable spin-orbit coupling.

Project description:The development of efficient organic light-emitting diodes (OLED) and organic photovoltaic cells requires control over the dynamics of spin sensitive excitations. Embedding heavy metal atoms in ?-conjugated polymer chains enhances the spin-orbit coupling (SOC), and thus facilitates intersystem crossing (ISC) from the singlet to triplet manifolds. Here we use various nonlinear optical spectroscopies such as two-photon absorption and electroabsorption in conjunction with electronic structure calculations, for studying the energies, emission bands and ultrafast dynamics of spin photoexcitations in two newly synthesized ?-conjugated polymers that contain intrachain platinum (Pt) atoms separated by one (Pt-1) or three (Pt-3) organic spacer units. The controllable SOC in these polymers leads to a record ISC time of <~1?ps in Pt-1 and ~6?ps in Pt-3. The tunable ultrafast ISC rate modulates the intensity ratio of the phosphorescence and fluorescence emission bands, with potential applications for white OLEDs.

| S-EPMC3772376 | biostudies-literature

Assessment of ab initio models of protein complexes by molecular dynamics.

Project description:Determining how proteins interact to form stable complexes is of crucial importance, for example in the development of novel therapeutics. Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding partners, such as RosettaDock, might potentially emerge to become a promising alternative to traditional structure determination methods. However, while models virtually identical to the correct experimental structure can in some cases be generated, the main difficulty remains to discriminate correct or approximately correct models from decoys. This is due to the ruggedness of the free-energy landscape, the approximations intrinsic in the scoring functions, and the intrinsic flexibility of proteins. Here we show that molecular dynamics simulations performed starting from a number top-scoring models can not only discriminate decoys and identify the correct structure, but may also provide information on an initial map of the free energy landscape that elucidates the binding mechanism.

| S-EPMC6002105 | biostudies-literature

Insights into H2 formation in space from ab initio molecular dynamics.

Project description:Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley-Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley-Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account.

| S-EPMC3637713 | biostudies-literature

Mechanoelectric Response of Single-Crystal Rubrene from Ab Initio Molecular Dynamics.

Project description:A robust understanding of the mechanoelectric response of organic semiconductors is crucial for the development of materials for flexible electronics. In particular, the prospect of using external mechanical strain to induce a controlled modulation in the charge mobility of the material is appealing. Here we develop an accurate computational protocol for the prediction of the mechanical strain dependence of charge mobility. Ab initio molecular dynamics simulations with a van der Waals density functional are carried out to quantify the off-diagonal electronic disorder in the system as a function of strain by the explicit calculation of the thermal distributions of electronic coupling matrix elements. The approach is applied to a representative molecular organic semiconductor, single-crystal rubrene. We find that charge mobility along the high-mobility direction a⃗ increases with compressive strain, as one might expect. However, the increase is larger when compressive strain is applied in the perpendicular direction than in the parallel direction with respect to a⃗, in agreement with experimental reports. We show that this seemingly counterintuitive result is a consequence of a significantly greater suppression of electronic coupling fluctuations in the range of 50-150 cm-1, when strain is applied in the perpendicular direction. Thus our study highlights the importance of considering off-diagonal electron-phonon coupling in understanding the mechanoelectric response of organic semiconducting crystals. The computational approach developed here is well suited for the accurate prediction of strain-charge mobility relations and should provide a useful tool for the emerging field of molecular strain engineering.

| S-EPMC8256417 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data