Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nonadiabatic dynamics of cobalt tricarbonyl nitrosyl for ligand dissociation induced by electronic excitation.

ABSTRACT: We utilize real-time time-dependent density functional theory and Ehrenfest dynamics scheme to investigate excited-state nonadiabatic dynamics of ligand dissociation of cobalt tricarbonyl nitrosyl, Co(CO)₃NO, which is a precursor used for cobalt growth in advanced technologies, where the precursor's reaction is enhanced by electronic excitation. Based on the first-principles calculations, we demonstrate two dissociation pathways of the NO ligand on the precursor. Detailed electronic structures are further analyzed to provide an insight into dynamics following the electronic excitations. This study sheds light on computational demonstration and underlying mechanism of the electronic-excitation-induced dissociation, especially in molecules with complex chemical bonds such as the Co(CO)₃NO.

SUBMITTER: Lee Y

PROVIDER: S-EPMC8076320 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Nonadiabatic dynamics of cobalt tricarbonyl nitrosyl for ligand dissociation induced by electronic excitation.

Lee Yeonghun Y Kolesov Grigory G Yao Xiaolong X Kaxiras Efthimios E Cho Kyeongjae K

Scientific reports 20210426 1

We utilize real-time time-dependent density functional theory and Ehrenfest dynamics scheme to investigate excited-state nonadiabatic dynamics of ligand dissociation of cobalt tricarbonyl nitrosyl, Co(CO)<sub>3</sub>NO, which is a precursor used for cobalt growth in advanced technologies, where the precursor's reaction is enhanced by electronic excitation. Based on the first-principles calculations, we demonstrate two dissociation pathways of the NO ligand on the precursor. Detailed electronic s ...[more]

PMID: 33903609

Similar Datasets

Detailed glycan structural characterization by electronic excitation dissociation.

Project description:The structural complexity and diversity of glycans parallel their multilateral functions in living systems. To better understand the vital roles glycans play in biological processes, it is imperative to develop analytical tools that can provide detailed glycan structural information. This was conventionally achieved by multistage tandem mass spectrometry (MS(n)) analysis using collision-induced dissociation (CID) as the fragmentation method. However, the MS(n) approach lacks the sensitivity and throughput needed to analyze complex glycan mixtures from biological sources, often available in limited quantities. We define herein the critical parameters for a recently developed fragmentation technique, electronic excitation dissociation (EED), which can yield rich structurally informative fragment ions during liquid chromatographic (LC)-MS/MS analysis of glycans. We further demonstrate that permethylation, reducing end labeling and judicious selection of the metal charge carrier, can greatly facilitate spectral interpretation. With its high sensitivity, throughput, and compatibility with online chromatographic separation techniques, EED appears to hold great promise for large-scale glycomics studies.

| S-EPMC3851312 | biostudies-literature

Dissociation and Isomerization Following Ionization of Ethylene: Insights from Nonadiabatic Dynamics Simulations.

Project description:Photoionized and electronically excited ethylene C2H4+ can undergo H-loss, H2-loss, and ethylene-ethylidene isomerization, where the latter entails a hydrogen migration. Recent pioneering experiments with few-femtosecond extreme ultraviolet pulses and complementary theoretical studies have shed light on the photodynamics of this prototypical organic cation. However, no theoretical investigation based on dynamics simulations reported to date has described the mechanisms and time scales of dissociation and isomerization. Herein, we simulate the coupled electron-nuclear dynamics of ethylene following vertical ionization and electronic excitation to its four lowest-lying cationic states. The electronic structure is treated at the CASSCF level, with an active space large enough to describe bond breaking and formation. The simulations indicate that dissociation and isomerization take place mainly on the cationic ground state and allow the probing of previous hypotheses concerning the correlation between the photochemical outcome and the traversed conical intersections. The results, moreover, support the long-standing view that H2-loss may occur from the ethylidene form. However, the ethylene-ethylidene isomerization time predicted by the simulations is considerably longer than those previously inferred from indirect experimental measurements.

| S-EPMC10911106 | biostudies-literature

Nonadiabatic dissociation dynamics in H2O: Competition between rotationally and nonrotationally mediated pathways.

Project description:The photochemistry of H(2)O in the VUV region is important in interstellar chemistry. Whereas previous studies of the photodissociation used excitation via unbound states, we have used a tunable VUV photolysis source to excite individual levels of the rotationally structured C state near 124 nm. The ensuing OH product state distributions were recorded by using the H-atom Rydberg tagging technique. Experimental results indicate a dramatic variation in the OH product state distributions and its stereodynamics for different resonant states. Photodissociation of H(2)O(C) in rotational states with k'(a) = 0 occurs exclusively through a newly discovered homogeneous coupling to the A state, leading to OH products that are vibrationally hot (up to v = 13), but rotationally cold. In contrast, for H(2)O in rotationally excited states with k'(a) > 0, an additional pathway opens through Coriolis-type coupling to the B state surface. This yields extremely rotationally hot and vibrationally cold ground state OH(X) and electronically excited OH(A) products, through 2 different mechanisms. In the case of excitation via the 1(10) <-- 0(00) transition the H atoms for these 2 product channels are ejected in completely different directions. Quantum dynamical models for the C-state photodissociation clearly support this remarkable dynamical picture, providing a uniquely detailed illustration of nonadiabatic dynamics involving at least 4 electronic surfaces.

| S-EPMC2614730 | biostudies-literature

Mechanistic Study on Electronic Excitation Dissociation of the Cellobiose-Na(+) Complex.

Project description:The recent development of electron activated dissociation (ExD) techniques has opened the door for high-throughput, detailed glycan structural elucidation. Among them, ExD methods employing higher-energy electrons offer several advantages over low-energy electron capture dissociation (ECD), owing to their applicability towards chromophore-labeled glycans and singly charged ions, and ability to provide more extensive structural information. However, a lack of understanding of these processes has hindered rational optimization of the experimental conditions for more efficient fragmentation as well as the development of informatics tools for interpretation of the complex glycan ExD spectra. Here, cellobiose-Na(+) was used as the model system to investigate the fragmentation behavior of metal-adducted glycans under irradiation of electrons with energy exceeding their ionization potential, and served as the basis on which a novel electronic excitation dissociation (EED) mechanism was proposed. It was found that ionization of the glycan produces a mixture of radical cations and ring-opened distonic ions. These distonic ions then capture a low-energy electron to produce diradicals with trivial singlet-triplet splitting, and subsequently undergo radical-induced dissociation to produce a variety of fragment ions, the abundances of which are influenced by the stability of the distonic ions from which they originate. Graphical Abstract ᅟ.

| S-EPMC4724539 | biostudies-literature

Restoring electronic coherence/decoherence for a trajectory-based nonadiabatic molecular dynamics.

Project description:By utilizing the time-independent semiclassical phase integral, we obtained modified coupled time-dependent Schrödinger equations that restore coherences and induce decoherences within original simple trajectory-based nonadiabatic molecular dynamic algorithms. Nonadiabatic transition probabilities simulated from both Tully's fewest switches and semiclassical Ehrenfest algorithms follow exact quantum electronic oscillations and amplitudes for three out of the four well-known model systems. Within the present theory, nonadiabatic transitions estimated from statistical ensemble of trajectories accurately follow those of the modified electronic wave functions. The present theory can be immediately applied to the molecular dynamic simulations of photochemical and photophysical processes involving electronic excited states.

| S-EPMC4827081 | biostudies-literature

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study.

Project description:The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.

| S-EPMC5389128 | biostudies-literature

De Novo Glycan Sequencing by Electronic Excitation Dissociation and Fixed-Charge Derivatization.

Project description:Detailed glycan structural characterization is frequently achieved by collisionally activated dissociation (CAD) based sequential tandem mass spectrometry (MS n) analysis of permethylated glycans. However, it is challenging to implement MS n ( n > 2) during online glycan separation, and this has limited its application to analysis of complex glycan mixtures from biological samples. Further, permethylation can reduce liquid chromatographic (LC) resolution of isomeric glycans. Here, we studied the electronic excitation dissociation (EED) fragmentation behavior of native glycans with a reducing-end fixed charge tag and identified key spectral features that are useful for topology and linkage determination. We also developed a de novo glycan sequencing software that showed remarkable accuracy in glycan topology elucidation based on the EED spectra of fixed charge-derivatized glycans. The ability to obtain glycan structural details at the MS2 level, without permethylation, via a combination of fixed charge derivatization, EED, and de novo spectral interpretation, makes the present approach a promising tool for comprehensive and rapid characterization of glycan mixtures.

| S-EPMC6521716 | biostudies-literature

Multisecond ligand dissociation dynamics from atomistic simulations.

Project description:Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and rate-limiting steps in protein-ligand unbinding is crucial for modern drug discovery. To achieve the enhanced sampling, we perform dissipation-corrected targeted molecular dynamics simulations, which yield free energy and friction profiles of molecular processes under consideration. Subsequently, we use these fields to perform temperature-boosted Langevin simulations which account for the desired kinetics occurring on multisecond timescales and beyond. Adopting the dissociation of solvated sodium chloride, trypsin-benzamidine and Hsp90-inhibitor protein-ligand complexes as test problems, we reproduce rates from molecular dynamics simulation and experiments within a factor of 2-20, and dissociation constants within a factor of 1-4. Analysis of friction profiles reveals that binding and unbinding dynamics are mediated by changes of the surrounding hydration shells in all investigated systems.

| S-EPMC7286908 | biostudies-literature

Comparison of Matrix Product State and Multiconfiguration Time-Dependent Hartree Methods for Nonadiabatic Dynamics of Exciton Dissociation.

Project description:The excited-state dynamics of organic molecules, molecular aggregates, and donor-acceptor clusters is typically governed by the interplay of electronic excitations and, due to their flexibility and soft bonding, by the interaction with their vibrations. This interaction in these systems can be characterized by a few relevant electronic states that are coupled to numerous vibrational normal modes, encompassing a vast configurational space of the molecules. The full quantum simulation of these type of systems has been long dominated by the multiconfiguration time-dependent Hartree (MCTDH) approach and its multilayer variants, which are considered the gold standard in the presence of electron-vibration coupling with a large number of modes. Recently, also the matrix product state ansatz (MPS) with appropriate time-evolution schemes has been applied to these types of Hamiltonians. In this article, we provide a numerical comparison of excited-state dynamics between the MCTDH and MPS approaches for two electron-vibration coupled systems. Notably, we consider two models for exciton dissociation at a P3HT:PCBM heterojunction, comprising two electronic states and 100 vibrational modes, and 26 electronic states and 113 vibrational modes, respectively. While both methods agree very well for the first model, more pronounced deviations are found for the second model. We trace back the divergence between the methods to the different way entanglement is treated.

| S-EPMC11500411 | biostudies-literature

Characterization of Isomeric Glycans by Reversed Phase Liquid Chromatography-Electronic Excitation Dissociation Tandem Mass Spectrometry.

Project description:The occurrence of numerous structural isomers in glycans from biological sources presents a severe challenge for structural glycomics. The subtle differences among isomeric structures demand analytical methods that can provide structural details while working efficiently with on-line glycan separation methods. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool for mixture analysis, the commonly utilized collision-induced dissociation (CID) method often does not generate a sufficient number of fragments at the MS2 level for comprehensive structural characterization. Here, we studied the electronic excitation dissociation (EED) behaviors of metal-adducted, permethylated glycans, and identified key spectral features that could facilitate both topology and linkage determinations. We developed an EED-based, nanoscale, reversed phase (RP)LC-MS/MS platform, and demonstrated its ability to achieve complete structural elucidation of up to five structural isomers in a single LC-MS/MS analysis. Graphical Abstract.

| S-EPMC6004250 | 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