Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In Search of the Reason for the Breathing Effect of MIL53 Metal-Organic Framework: An ab Initio Multiconfigurational Study.

ABSTRACT: Multiconfigurational methods are applied to study electronic properties and structural changes in the highly flexible metal-organic framework MIL53(Cr). Via calculated bending potentials of angles, that change the most during phase transition, it is verified that the high flexibility of this material is not a question about special electronic properties in the coordination chemistry, but about overall linking of the framework. The complex posseses a demanding electronic structure with delocalized spin density, antifferomagnetic coupling and high multi-state character requiring multiconfigurational methods. Calculated properties are in good agreement with known experimental values confirming our chosen methods.

SUBMITTER: Weser O

PROVIDER: S-EPMC5723392 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

In Search of the Reason for the Breathing Effect of MIL53 Metal-Organic Framework: An ab Initio Multiconfigurational Study.

Weser Oskar O Veryazov Valera V

Frontiers in chemistry 20171205

Multiconfigurational methods are applied to study electronic properties and structural changes in the highly flexible metal-organic framework MIL53(Cr). Via calculated bending potentials of angles, that change the most during phase transition, it is verified that the high flexibility of this material is not a question about special electronic properties in the coordination chemistry, but about overall linking of the framework. The complex posseses a demanding electronic structure with delocalize ...[more]

PMID: 29259969

Similar Datasets

The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution.

Project description:We demonstrate that "brute force" quantum-mechanics/molecular-mechanics computations based on ab initio (i.e., first principles) multiconfigurational perturbation theory can reproduce the absorption maxima of a set of modified bovine rhodopsins with an accuracy allowing for the analysis of the factors determining their colors. In particular, we show that the theory accounts for the changes in excitation energy even when the proteins display the same charge distribution. Three color-tuning mechanisms, leading to changes of close magnitude, are demonstrated to operate in these conditions. The first is based on the change of the conformation of the conjugated backbone of the retinal chromophore. The second operates through the control of the distance between the positive charge residing on the chromophore and the carboxylate counterion. Finally, the third mechanism operates through the changes in orientation of the chromophore relative to the protein. These results offer perspectives for the unbiased computational design of mutants or chemically modified proteins with wanted optical properties.

| S-EPMC1859901 | biostudies-literature

A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction.

Project description:Protein structure prediction is computationally a very challenging problem. A large number of existing search algorithms attempt to solve the problem by exploring possible structures and finding the one with the minimum free energy. However, these algorithms perform poorly on large sized proteins due to an astronomically wide search space. In this paper, we present a multipoint spiral search framework that uses parallel processing techniques to expedite exploration by starting from different points. In our approach, a set of random initial solutions are generated and distributed to different threads. We allow each thread to run for a predefined period of time. The improved solutions are stored threadwise. When the threads finish, the solutions are merged together and the duplicates are removed. A selected distinct set of solutions are then split to different threads again. In our ab initio protein structure prediction method, we use the three-dimensional face-centred-cubic lattice for structure-backbone mapping. We use both the low resolution hydrophobic-polar energy model and the high-resolution 20 × 20 energy model for search guiding. The experimental results show that our new parallel framework significantly improves the results obtained by the state-of-the-art single-point search approaches for both energy models on three-dimensional face-centred-cubic lattice. We also experimentally show the effectiveness of mixing energy models within parallel threads.

| S-EPMC3976798 | biostudies-other

Relativistic Multiconfigurational <i>Ab Initio</i> Calculation of Uranyl 3d4f Resonant Inelastic X-ray Scattering.

Project description:We applied relativistic multiconfigurational all-electron ab initio calculations including the spin-orbit interaction to calculate the 3d4f resonant inelastic X-ray scattering (RIXS) map (3d3/2 → 5f5/2 U M4 absorption edge and 4f5/2 → 3d3/2 U Mβ emission) of uranyl (UO22+). The calculated data are in excellent agreement with experimental results and allow a detailed understanding of the observed features and an unambiguous assignment of all involved intermediate and final states. The energies corresponding to the maxima of the resonant emission and the non-resonant (normal) emission were determined with high accuracy, and the corresponding X-ray absorption near edge structure spectra extracted at these two positions were simulated and agree well with the measured data. With the high quality of our theoretical data, we show that the cause of the splitting of the three main peaks in emission is due to the fine structure splitting of the 4f orbitals induced through the trans di-oxo bonds in uranyl and that we are able to obtain direct information about the energy differences between the 5f and 4f orbitals: Δ5f δ/ϕ - 4f δ/ϕ, Δ5f π* - 4f π, and Δ5f σ* - 4f σ from the 3d4f RIXS map. RIXS maps contain a wealth of information, and ab initio calculations facilitate an understanding of their complex structure in a clear and transparent way. With these calculations, we show that the multiconfigurational protocol, which is nowadays applied as a standard tool to study the X-ray spectra of transition metal complexes, can be extended to the calculation of RIXS maps of systems containing actinides.

| S-EPMC8693175 | biostudies-literature

Electrically Induced Breathing of the MIL-53(Cr) Metal-Organic Framework.

Project description:The breathing behavior of the MIL-53(Cr) metal-organic framework (MOF) has been explored previously upon guest-adsorption and thermal and mechanical stimuli. Here, advanced molecular simulations based on the use of an accurate force field to describe the flexibility of this porous framework demonstrate that the application of an electrical field induces the structural switching of this MOF leading to a first-order transition and a volume change of more than 40%. This motivated us to electrically tune the pore size of MIL-53(Cr) with the idea to propose a new concept to selectively capture CO2 over CH4 via a molecular sieving that paves the way toward the optimization of current separation-based processes.

| S-EPMC5445524 | biostudies-literature

Breathing-Dependent Redox Activity in a Tetrathiafulvalene-Based Metal-Organic Framework.

Project description:"Breathing" metal-organic frameworks (MOFs) that involve changes in their structural and physical properties upon an external stimulus are an interesting class of crystalline materials due to their range of potential applications including chemical sensors. The addition of redox activity opens up a new pathway for multifunctional "breathing" frameworks. Herein, we report the continuous breathing behavior of a tetrathiafulvalene (TTF)-based MOF, namely MUV-2, showing a reversible swelling (up to ca. 40% of the volume cell) upon solvent adsorption. Importantly, the planarity of the TTF linkers is influenced by the breathing behavior of the MOF, directly impacting on its electrochemical properties and thus opening the way for the development of new electrochemical sensors. Quantum chemical calculations and Raman spectroscopy have been used to provide insights into the tunability of the oxidation potential.

| S-EPMC6166999 | biostudies-literature

A Novel Framework for Ab Initio Coarse Protein Structure Prediction.

Project description:Hydrophobic-Polar model is a simplified representation of Protein Structure Prediction (PSP) problem. However, even with the HP model, the PSP problem remains NP-complete. This work proposes a systematic and problem specific design for operators of the evolutionary program which hybrids with local search hill climbing, to efficiently explore the search space of PSP and thereby obtain an optimum conformation. The proposed algorithm achieves this by incorporating the following novel features: (i) new initialization method which generates only valid individuals with (rather than random) better fitness values; (ii) use of probability-based selection operators that limit the local convergence; (iii) use of secondary structure based mutation operator that makes the structure more closely to the laboratory determined structure; and (iv) incorporating all the above-mentioned features developed a complete two-tier framework. The developed framework builds the protein conformation on the square and triangular lattice. The test has been performed using benchmark sequences, and a comparative evaluation is done with various state-of-the-art algorithms. Moreover, in addition to hypothetical test sequences, we have tested protein sequences deposited in protein database repository. It has been observed that the proposed framework has shown superior performance regarding accuracy (fitness value) and speed (number of generations needed to attain the final conformation). The concepts used to enhance the performance are generic and can be used with any other population-based search algorithm such as genetic algorithm, ant colony optimization, and immune algorithm.

| S-EPMC6031167 | biostudies-literature

Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite.

Project description:Today's fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future, and therefore effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end, we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate (GP) and inositol hexaphosphate (IHP)) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite-IHP/GP-water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the 3M motif being most stable. The order of goethite-IHP/GP interaction energies is GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite-IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature.

| S-EPMC7795625 | biostudies-literature

Dual Metal-Organic Framework Heterointerface.

Project description:Herein, a core-shell dual metal-organic framework (MOF) heterointerface is synthesized. The Prussian blue (PB) MOF acts as a core for the growth of a porphyrin-doped MOF which is named PB@MOF. Porphyrins can significantly enhance the transfer of photoinspired electrons from PB and suppress the recombination of electrons and holes, thus enhancing the photocatalytic properties and consequently promoting the yields of singlet oxygen rapidly under 660 nm illumination. PB@MOF can exhibit a better photothermal conversion efficiency up to 29.9% under 808 nm near-infrared irradiation (NIR). The PB@MOF heterointerface can possess excellent antibacterial efficacies of 99.31% and 98.68% opposed to Staphylococcus aureus and Escherichia coli, separately, under the dual light illumination of 808 nm NIR and 660 nm red light for 10 min. Furthermore, the trace amount of Fe and Zr ions can trigger the immune system to favor wound healing, promising that PB@MOF achieves the rapid therapy of bacterial infected wounds and environmental disinfection.

| S-EPMC6764158 | biostudies-literature

Ab Initio Calculation of Surface Thermochemistry for Popular Solid Transition Metal-Based Species

Project description:This

| S-EPMC8427637 | biostudies-literature

Accurate ab Initio Spin Densities.

Project description:We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of ? and ? electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

| S-EPMC3373140 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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