Source 1primary paper2021Physical Chemistry Chemical Physics
Toolkit/QM calculations
QM calculations
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
QM calculations are a quantum-chemical computational method used to predict conformer energetics, rotational barriers, and infrared spectra of transient glutamine isomers in LOV photoreceptors. In EL222, AsLOV2, and RsLOV, these calculations were used to infer favored glutamine orientations along an assumed light-driven reaction path and to interpret transient infrared behavior.
Usefulness & Problems
Why this is useful
This method is useful for assigning transient glutamine rotamers and tautomers in LOV photoreceptors when intermediates are difficult to characterize directly. It links calculated energetics and predicted infrared spectra to mechanistic interpretation of light-driven structural changes.
Problem solved
It addresses the problem of identifying which transient glutamine isomers are energetically accessible and spectroscopically consistent with observed intermediates in LOV-domain photoreceptors. The reported application specifically examined EL222, AsLOV2, and RsLOV along an assumed reaction path.
Problem links
Need precise spatiotemporal control with light input
DerivedQM calculations are a computational method used to predict the energetics, rotational barriers, and infrared spectra of transient glutamine isomers in LOV photoreceptors. In EL222, AsLOV2, and RsLOV, these calculations were used to infer favored glutamine orientations along an assumed light-driven reaction path and to interpret transient infrared spectra.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
mechanistic inference from calculated energy barriers and theory-spectrum agreementmechanistic inference from energy barriers and theory-experiment spectral agreementquantum-chemical prediction of conformer energeticsquantum-chemical prediction of conformer energeticsquantum-chemical prediction of infrared spectraquantum-chemical prediction of infrared spectrarotamer analysisrotamer and tautomer analysistautomer analysisTechniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: builder
The reported implementation involved quantum-chemical calculations of glutamine rotamer and tautomer energetics, rotational barriers, and infrared spectra. The available evidence does not specify software, level of theory, basis sets, or computational workflow details.
The evidence describes mechanistic inference along an assumed reaction path rather than direct experimental observation of glutamine configurations. Validation in the provided evidence is limited to transient glutamine isomers in three LOV photoreceptors, and no broader benchmarking or independent replication is described.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Calculated energies and rotational barriers for glutamine rotamers and tautomers allowed the authors to postulate the most energetically favoured glutamine orientation for each of EL222, AsLOV2, and RsLOV along the assumed reaction path.
Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path.
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Energetic and spectroscopic analyses converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and, more strongly, for AsLOV2, whereas RsLOV retains the initial glutamine configuration.
both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Approval Evidence
1 source2 linked approval claimsfirst-pass slug qm-calculations
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
Source:
computational predictionsupports
QM calculations were used to predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.
QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
Source:
theory experiment agreementsupports
Constructed infrared difference spectra showed good agreement with experimental transient infrared spectra for EL222 and AsLOV2, permitting assignment of the majority of observed bands.
The good agreement between theory and experiment permitted the assignment of the majority of observed bands
Source:
Comparisons
Source-backed strengths
The method provides both energetic and spectroscopic predictions, enabling convergence between theory and transient infrared interpretation. In the cited study, calculated energies and rotational barriers supported mechanistic proposals including a facile glutamine flip at the adduct intermediate for EL222 and more strongly for AsLOV2, while RsLOV was inferred to retain the initial glutamine configuration.
Compared with mathematical model of light-induced expression kinetics
QM calculations and mathematical model of light-induced expression kinetics address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with model bioinformatics analysis
QM calculations and model bioinformatics analysis address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with molecular dynamics simulations
QM calculations and molecular dynamics simulations address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Relative tradeoffs: appears more independently replicated; looks easier to implement in practice.
Ranked Citations
- 1.