Study R02
In progressWater and prefilter selectivity
How does water affect the relative binding of formaldehyde and ethanol on functionalized carbon prefilter models?
- Method
- Density functional theory (DFT); r2SCAN-3c pilot in ORCA 6.1.1
- Summary updated
Why this study
Investigate whether water changes the relative binding of formaldehyde and ethanol. Comparing functionalized and unmodified carbon models would help frame hypotheses for prefilter testing.
Current methodological pilot
Before any calculation on formaldehyde, water, or functionalized carbon, the computational method is being tested on a reference system with published data.
Why a reference system first
The reference system is ethanol on coronene (C₂₄H₁₂), a small, flat model of graphene-like carbon. Published interaction data make it possible to test the method before building conclusions on the systems R02 is intended to study. If the method does not give a comparable value, that can be identified before the target calculations begin.
What has been done
Key milestones; the dated record follows below.
Pilot method and search rules fixed
The pilot method and one-search rules were fixed before launch; the method is not yet qualified for final R02 accuracy.
Read the related note →Candidate and repeatability recorded
The 45-atom search ended after 95 cycles with 4 of 5 printed conditions met. A separate force repeatability check passed; the structure remains a candidate.
Read the related note →Candidate frequencies classified
Two frequency calculations and a bound signed in advance classify 119 vibrations as clearly positive, none as clearly negative, and the ten softest as undetermined. The candidate is not yet a confirmed minimum.
Read the related note →References optimized and final-energy rules fixed
Ethanol in two conformations and coronene were optimized. Acceptance rules, including how to choose the reference ethanol conformation, were signed before any final energy was calculated.
Revised isolated-coronene reference accepted
At the updated r2SCAN/def2-TZVPP geometry without D4/gCP, the focused rule accepts all 102 internal modes. The original rule applied to the same two Hessians leaves 99 positive and 3 undetermined. The refinement was fixed between the two checks and does not confirm the pair.
Read the related note →Candidate admitted to a limited energy route
Targeted scans of ten soft directions supported limited use of the existing candidate. Its ten curvatures remain unresolved. Mode combinations, points beyond the selected amplitudes and radial grid convergence were not tested.
Read the related note →Numerical route and local geometry rule checked
Energy/derivative consistency, prescribed grid response and the local geometry-budget rule passed. These checks establish the specified numerical consistency, not physical method accuracy or an unrestricted geometry-error bound.
Read the related note →Nine final single-point calculations accepted
The prescribed nine calculations for the existing candidate and its references were accepted on 6 October. Their completion does not establish agreement with literature or qualify later target-material comparisons.
Read the related note →
What has not been done yet
No formaldehyde, water, or functionalized-carbon calculations have been run. No binding energies are published, and no selectivity ranking exists.
Review status
The project records technical checks and acceptance by the project lead. Scientific acceptance is an internal decision by the project lead; independent external scientific review of the computational work has not been performed. Signed and time-stamped decision records are available for verification on request. The coronene error-rule refinement was fixed after its first check and before its second; this differs from declaring a rule before both checks.
Published reference
Lazar, P. et al. “Adsorption of Small Organic Molecules on Graphene.” Journal of the American Chemical Society 135 (2013): 6372–6377.
DOI 10.1021/ja403162r ↗ (opens in a new tab)Approach
Evaluate the pilot method against a published ethanol–coronene reference before extending the work to the target systems.
Calculate formaldehyde and ethanol binding with and without water using DFT on classical computers.
Compare the binding rankings and test whether they hold as the model and assumptions change.
Intended output
Rank formaldehyde and ethanol binding with and without water, compare with unmodified carbon controls, and test whether the ranking holds as the model and assumptions change.
Binding rankings from molecular models would inform hypotheses for physical testing; they do not establish cartridge performance.
Progress updates
Correction: the comparison criterion was not published when promised
The literature-comparison criterion was signed on 12 September, before the final-energy calculations. This page promised to publish the acceptance band before the comparison. The comparison was completed on 6 October, but that promised advance publication did not take place, so the criterion was not publicly preregistered. We plan to disclose the signed criterion with the numerical comparison report, subject to a disclosure decision; no publication date has been set.
Five-start follow-up launched under its signed protocol
After preparatory stops, the five-start follow-up was launched under its signed protocol. The original three positions × two ethanol conformers define the set. No reviewed result has been recorded yet; launch is not acceptance of a scientific outcome.
Plain-language continuation published
Story 02 explains the revised isolated-coronene reference and why its acceptance does not confirm the pair.
Supporting material →
Show 10 older updates ↓Hide older updates ↑
Numerical route and nine final calculations accepted
The prescribed numerical checks, local geometry-budget rule and nine final single-point calculations have been accepted. Literature agreement remains a separate question; the defined follow-up has no reviewed outcome yet.
Supporting material →Limited energy use of the candidate accepted
The ten-direction energy scan passed under its signed rules. The candidate is admitted to a limited energy route, without confirmation of a minimum or stationarity, combinations of modes, points outside tested amplitudes or radial grid convergence.
Supporting material →Updated free-coronene reference recorded
The project lead recorded the revised reference accepted under the focused rule: 102 positive internal modes. The original rule on the same Hessian pair still gives 99 positive and 3 undetermined; neither result changes the pair’s classification.
Supporting material →Reference structures optimized
Isolated ethanol (anti and gauche) and coronene were optimized with the pilot method for later interaction-energy calculations. ORCA reported 5 of 5 printed conditions met for each ethanol search and 4 of 5 for coronene.
Acceptance rules for final energies signed
The rules for accepting the pilot's final energies were signed before any final energy was calculated. The reference ethanol conformation is the lower-energy of anti and gauche at the more accurate PBE0-D4 level.
Candidate frequencies evaluated
Full analytic frequencies were calculated at the working settings and again at tighter numerical settings. After translation and rotation were removed, both gave 129 real vibrations, the lowest near 21 cm⁻¹; the ten softest differ by at most 2.2 cm⁻¹. A rule signed before either run classifies 119 as clearly positive, none as clearly negative, and the ten softest, below about 191 cm⁻¹, as undetermined. The candidate is not yet a confirmed minimum.
Supporting material →Search method and completion rules fixed
The pilot r2SCAN-3c method in ORCA 6.1.1 on cloud resources, one-search scope, 100-cycle limit, and outcome rules were authorized before launch. No automatic restart or additional calculation was allowed; the method is not yet qualified for final R02 accuracy.
Supporting material →First geometry search completed
The 45-atom ethanol–coronene search ended after 95 cycles with 4 of 5 printed conditions met. Ethanol moved sideways by more than 1 Å and changed orientation; the movement was recorded and the same trajectory continued. The structure remains a candidate requiring review, and no frequency calculation followed automatically.
Repeatability check passed
Two separately started energy-and-force calculations differed by 6.7 × 10⁻¹¹ hartree/bohr in the largest force component and passed the pre-declared tolerances. This checks repeatability, not accuracy or software superiority.
Supporting material →R02 work started
Preparation began under the agreed R02 plan. The exact search method and completion rules had not yet been fixed.
Related research
Classical preparation connects this work to R04. A limited quantum hardware pilot can begin once its own model and classical comparison are ready, without waiting for the full R02 study.
R04 · Molecular binding on IBM Quantum →
Related notes
Coronene as a Reference: Two Frequency Checks, Two Error Rules →Method note
Using a Candidate Structure Without Calling It a Minimum →Method note
Are the Softest Vibrations Real? A Pre-Declared Error Bound for R02 Frequencies →Method note
Deciding in Advance What Counts as a Result →Method note
Same Input, Same Answer? A Repeatability Check for R02 Calculations →Repeatability note
Ethanol Interference in Formaldehyde Sensors: What the Evidence Supports →Literature review