Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

lamaGOET: an interface for quantum crystallography.

ABSTRACT: In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.

SUBMITTER: Malaspina LA

PROVIDER: S-EPMC8202027 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

lamaGOET: an interface for quantum crystallography.

Malaspina Lorraine A LA Genoni Alessandro A Grabowsky Simon S

Journal of applied crystallography 20210416 Pt 3

In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the sp ...[more]

PMID: 34188618

Similar Datasets

Quantum crystallography.

Project description:Approximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated tool. The development of quantum crystallographic research is reviewed. Some results obtained by quantum crystallography illustrate the potential and limitations of this field.

| S-EPMC5576428 | biostudies-literature

Aurophilic Interactions Studied by Quantum Crystallography.

Project description:This is the first use of a wave-function-based crystallographic method to characterize aurophilic interactions from X-ray diffraction data. Theoretical calculations previously suggested the importance of electron correlation and dispersion forces, but no influence of relativistic corrections to the Au...Au interaction energy was found. In this study, we confirm the importance of relativistic corrections in the characterization of aurophilic interactions in addition to electron correlation and dispersion.

| S-EPMC8924918 | biostudies-literature

Further Validation of Quantum Crystallography Approaches.

Project description:Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data.

| S-EPMC8233966 | biostudies-literature

Fault-tolerant interface between quantum memories and quantum processors.

Project description:Topological error correction codes are promising candidates to protect quantum computations from the deteriorating effects of noise. While some codes provide high noise thresholds suitable for robust quantum memories, others allow straightforward gate implementation needed for data processing. To exploit the particular advantages of different topological codes for fault-tolerant quantum computation, it is necessary to be able to switch between them. Here we propose a practical solution, subsystem lattice surgery, which requires only two-body nearest-neighbor interactions in a fixed layout in addition to the indispensable error correction. This method can be used for the fault-tolerant transfer of quantum information between arbitrary topological subsystem codes in two dimensions and beyond. In particular, it can be employed to create a simple interface, a quantum bus, between noise resilient surface code memories and flexible color code processors.

| S-EPMC5674034 | biostudies-literature

The advanced treatment of hydrogen bonding in quantum crystallography.

Project description:Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.

| S-EPMC8202034 | biostudies-literature

Orbital angular momentum photonic quantum interface.

Project description:Light-carrying orbital angular momentum (OAM) has great potential in enhancing the information channel capacity in both classical and quantum optical communications. Long distance optical communication requires the wavelengths of light are situated in the low-loss communication windows, but most quantum memories currently being developed for use in a quantum repeater work at different wavelengths, so a quantum interface to bridge the wavelength gap is necessary. So far, such an interface for OAM-carried light has not been realized yet. Here, we report the first experimental realization of a quantum interface for a heralded single photon carrying OAM using a nonlinear crystal in an optical cavity. The spatial structures of input and output photons exhibit strong similarity. More importantly, single-photon coherence is preserved during up-conversion as demonstrated.

| S-EPMC6059842 | biostudies-literature

Quantum Capacitance of a Topological Insulator-Ferromagnet Interface.

Project description:We study the quantum capacitance in a topological insulator thin film system magnetized in the in-plane direction in the presence of an out-of-plane magnetic field and hexagonal warping. To first order, the modification in quantum capacitance due to hexagonal warping compared to the clean case, where both the in-plane magnetization and hexagonal warping are absent, is always negative, and increases in magnitude monotonically with the energy difference from the charge neutrality point. In contrast, the change in the quantum capacitance due to in-plane magnetization oscillates with the energy in general, except when a certain relation between the inter-surface coupling, out of plane Zeeman energy splitting and magnetic field strength is satisfied. In this special case, the quantum capacitance remains unchanged by the in-plane magnetization for all energies.

| S-EPMC5364463 | biostudies-literature

Quantum-enabled operation of a microwave-optical interface.

Project description:Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only [Formula: see text] microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with [Formula: see text]), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago.

| S-EPMC8917169 | biostudies-literature

Cavity piezo-mechanics for superconducting-nanophotonic quantum interface.

Project description:Hybrid quantum systems are essential for the realization of distributed quantum networks. In particular, piezo-mechanics operating at typical superconducting qubit frequencies features low thermal excitations, and offers an appealing platform to bridge superconducting quantum processors and optical telecommunication channels. However, integrating superconducting and optomechanical elements at cryogenic temperatures with sufficiently strong interactions remains a tremendous challenge. Here, we report an integrated superconducting cavity piezo-optomechanical platform where 10 GHz phonons are resonantly coupled with photons in a superconducting cavity and a nanophotonic cavity at the same time. Taking advantage of the large piezo-mechanical cooperativity (Cem ~7) and the enhanced optomechanical coupling boosted by a pulsed optical pump, we demonstrate coherent interactions at cryogenic temperatures via the observation of efficient microwave-optical photon conversion. This hybrid interface makes a substantial step towards quantum communication at large scale, as well as novel explorations in microwave-optical photon entanglement and quantum sensing mediated by gigahertz phonons.

| S-EPMC7320138 | biostudies-literature

Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography.

Project description:Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine. The application of quantum crystallography, including aspherical atom refinement, has enriched the depiction of electron density in the studied systems and non-covalent interactions, providing more details than previous studies. Our experimental results, combined with a topological analysis of the electron density and its Laplacian, provided detailed descriptions of how protonation changes the electron density distribution around the amine group and water molecule, concurrently decreasing the electron density at bond critical points of N/O-H bonds. Protonation also alters the molecular architecture of the systems under investigation. This is reflected in different proportions of the N⋯H and O⋯H intermolecular contacts for the neutral and protonated forms. Periodic DFT calculations of the cohesive energies of the crystal lattice, as well as computed interaction energies between molecules in the crystal, confirm that protonation stabilises the crystal structure due to a positive synergy between strong halogen and hydrogen bonds. Our findings highlight the potential of quantum crystallography in predicting crystal structure properties and point to its possible applications in developing new formulations for poorly soluble drugs.

| S-EPMC10859733 | biostudies-literature