Source 1primary paper2010Journal of Chemical Theory and Computation
Toolkit/SOS-CIS(D) method
SOS-CIS(D) method
Also known as: scaled opposite spin configuration interaction with single substitutions SOS-CIS(D)
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
SOS-CIS(D) is a quantum-chemical excited-state calculation method used to compute vertical excitation energies. In the cited 2010 BLUF photoreceptor study, it was applied to model flavin-associated structural and spectral changes and to evaluate light-induced states.
Usefulness & Problems
Why this is useful
This method is useful for estimating excitation energies relevant to photoreceptor chromophores and for connecting computed spectral shifts to experimentally observed light responses. In the cited study, the resulting molecular structures and spectral shifts were reported to be in excellent agreement with experiment.
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
SOS-CIS(D) helps address the problem of assigning and rationalizing light-induced structural and spectral changes in BLUF photoreceptor proteins at the electronic-structure level. Specifically, it was used to test mechanistic models involving the flavin chromophore environment and a conserved Gln residue.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
The extraction evidence states that vertical excitation energies were calculated with the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method. The available evidence does not specify software, basis sets, solvation treatment, QM/MM setup, or other practical computational parameters.
The supplied evidence only documents use of SOS-CIS(D) for vertical excitation energy calculations in a BLUF photoreceptor context. No evidence is provided here on computational cost, generalizability across systems, benchmarking against alternative methods, 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 source3 linked approval claimsfirst-pass slug sos-cis-d-method
Calculations of the vertical excitation energies were performed with the scaled opposite spin configuration interaction with single substitutions SOS-CIS(D) method
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:
method capabilitysupports
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
Source:
Comparisons
Source-backed strengths
The cited study reports excellent agreement between computed molecular structures and spectral shifts and experimental results. The calculations also provided mechanistic support for a light-induced transformation involving rotation/tautomerization of a conserved Gln residue near the flavin chromophore.
Ranked Citations
- 1.