Source 1primary paper2010Journal of Chemical Theory and Computation
Toolkit/QM(B3LYP/cc-pVDZ)/MM(AMBER) approach
QM(B3LYP/cc-pVDZ)/MM(AMBER) approach
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The QM(B3LYP/cc-pVDZ)/MM(AMBER) approach is a hybrid quantum mechanics/molecular mechanics computational method used for geometry optimization and vibrational frequency calculations in flavin-binding photoreceptor proteins. In the cited BLUF photoreceptor study, it was used to model light-induced structural changes and associated spectral shifts.
Usefulness & Problems
Why this is useful
This approach is useful for connecting atomistic structural models to spectroscopic observables in light-responsive flavoproteins. The cited study reports that the computed molecular structures and spectral shifts were in excellent agreement with experimental results, supporting its value for mechanistic interpretation.
Source:
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
Problem solved
It addresses the problem of identifying the molecular basis of light-induced structural changes in BLUF photoreceptors. Specifically, the calculations were used to evaluate whether transformations of a conserved Gln residue near the flavin chromophore can explain the observed spectral changes.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
gln rotationgln side-chain rotationgln tautomerizationlight-induced structural change modelingTechniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
The reported implementation used a QM/MM partition with QM(B3LYP/cc-pVDZ) and MM(AMBER). The evidence specifically states that the approach was used for geometry optimization and vibrational frequency calculations in flavin-binding photoreceptor proteins; no further setup details are provided here.
The provided evidence is limited to a single 2010 study in BLUF flavin-binding photoreceptors. No evidence here describes computational cost, generalization to other protein classes, benchmarking against alternative QM/MM schemes, or independent replication.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
absorption red shift 12-16 nmC4=O flavin vibrational downshift 25 cm(-1)
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
The SOS-CIS(D) method enables efficient treatment of excited states in large molecular systems.
the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems
Approval Evidence
1 source2 linked approval claimsfirst-pass slug qm-b3lyp-cc-pvdz-mm-amber-approach
Geometry optimization and calculations of vibrational frequencies were carried out with the QM(B3LYP/cc-pVDZ)/MM(AMBER) approach
Source:
agreement with experimentsupports
The computed molecular structures and spectral shifts are in excellent agreement with experimental results.
The computed molecular structures as well as the spectral shifts (the red shift by 12–16 nm in absorption and the downshift by 25 cm(-1) for the C4═O flavin vibrational mode) are in excellent agreement with the experimental results
Source:
mechanistic supportsupports
Quantum chemical calculations support a mechanism of light-induced changes in BLUF photoreceptor proteins involving rotation/tautomerization transformations of a conserved Gln residue near the flavin chromophore.
To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore, we performed accurate quantum chemical calculations
Source:
Comparisons
Source-backed strengths
The method combines QM treatment at the B3LYP/cc-pVDZ level with MM treatment using AMBER, and it was applied to both geometry optimization and vibrational frequency analysis. In the cited work, its predictions were reported to agree excellently with experiment and to support a specific mechanistic model involving conserved Gln rotation/tautomerization.
Ranked Citations
- 1.