August 2023

Tuesday 1^st July

I’ve booked the spectrometers for a couple of hours this afternoon. I think that if the TCSPC is going to be in competition, I should just focus on UV-vis and fluorescence for now and do a bit of photon counting when the resources are available (or when the spectrometers get booked out ).

I really need to spend some time trying to push through more calcs, but it’s so painful…

I didn’t end up doing that^, but I did collect a few spectra…

Wednesday 2^nd July

Meeting Notes:

• EFP from MD structures - static shell size - cpcm outer?
• For BPA - try the truncated Dunnings accpvtz (the calendar revisions)
• Multiple levels of xtb for a couple of fluorophores
  • FAT
  • NDA
  • Maybe BOD493
• HF small basis with different solvent models to compare the influence of the model on the geometry.
• Scrap R800 from the computational dataset for now.

Thursday/Friday 4-5^th July

I’ve been helping a former student of Toby’s, Ash these past couple of days. We’re both studying BODIPY 493/503, and I was able to help him with my spectra, to produce some single point quantum yields, to determine an molar extinction coefficient and use it to obtain a LogP for the dye. I think it was actually a really fun and useful thing to do with my time

Monday 7^th July

I got some improved xtb calcs going over the weekend. I decided to use the density of n-hexane to figure out how many molecules to put in a region, and then I confined them in xtb using a force field. I decided to test out GFN-FF as well as GFN-1 and GFN-2, since it’s so much faster, and while I haven’t done any quantitative analysis, they seem to be pretty good?

For BPA CASSCF, the cc-pvtz job finished with minimal iterations, but it’s right on the edge of active space occupation, so I’m running a (14,14) single point as well

I’m trying Katya’s advice and going for a slightly less augmented Dunnings basis set, with jul-cc-pv(t+d)z for both (12,12) and (14,14).

Tuesday-Friday 8-11^th July

This week I’ve focused on three main things:

1. Getting more of the experimental dataset finalised - This has been tricky given how many of these solvents are VOCs, so I don’t want to spend too long each day working with them.
2. Trying to push through the XTB AIMD runs and see how I can analyse them - I’ve yet to figure out how to generate an RDF or SDF of these through… I think I might need to be more specific in my atom definitions within the PDBs I’m using for topology definition, but
3. Trying to get the BPA CASSCF jobs sorted - This has also meant trying to figure out MO rotations, which I’m still really unsure of

Wednesday 16^th July

From meeting:

• Extract some clusters and determine dispersion by the perturbation method described below:

$$ \begin{gather} \Delta E_{Int}=E_{Cluster}-E_{Solvent Sphere}-E_{Solute}\ \Delta E_{Disp}=\Delta E_{Int}^{DFT}-\Delta E_{Int}^{HF} \end{gather} $$ * Use NTOs to determine where the BPA transitions are located. This should help determine which \(\pi\) orbitals to include in the active space for BPA * We have an issue… While the primary transition (94%) for s1 is all localised to the naphthalene core, the second contribution (2%) extends out through the ethyne and phenyl rings, meaning that we don’t really know which \(\pi\) orbitals are going to be the important ones to include. Realistically, we probably need them all.

From	To

* Also focus on non-augmented basis sets for now.

Saturday 19^th July

Soooooo… M3 seems to be stalled. I’ve tried to clean up as much as I can, but I’mma need to wait for things to come back up before I resubmit my jobs

Monday 21^st July

Teaching day, but I also made a presentation for group meeting.

Tuesday 22^nd July

Got a bit more lab work done today. Started on the THF series.

Thursday 24^th July

Burnout…

I’m taking a month off from today in order to fix some burnout prevention. I don’t think I’ll be back to my PhD from this.

Idea for freqs/deconv

What if instead of starting with a random guess, we make a function that has a fixed number of Gaussians at a fixed spacing from each other, and we fit them with an offset parameter. We could use the frequencies to dictate the distribution of the Gaussians and and only have the amplitude and sigma as free parameters

func(shift: float, amps: list[float], sigma: list[float] cen_FIXED: list[float])

Important Questions:

• Can we use the difference between TDDFT Eq and nEq energies to figure out the stokes correction to the 0-0 energy in abs and fluor
• Can we use the shape of the Theoretical PES to determine what the width of the deconvoluting Gaussians should be for fitting?

Experimental work

Problematic spectra:

• Collecting:
  • AZ lifetimes - all solvents. No solvatochromic shift on s2 → s0
  • Solvent excitation issues
    • DMSO with azulene
    • Anisole with azulene
• Difficulty fitting
  • TCSPC
    • DAA/nhex
    • BSC/etoh

Experimental to-do:

UV/FL

	nhex	tol	ans	ether	chcl3	thf	dcm	c80h	etoh	acn	dmf	dmso
nr			Issues with ex/em
nda
r800	insol
c153
bod493
az
aaq
dapi	insol		insol
daa
bsc
fno
bpa
fat

TCSPC

	nhex	tol	ans	ether	chcl3	thf	dcm	c80h	etoh	acn	dmf	dmso
nr
nda
r800	insol
c153
bod493
az	-	-	-	-	-	-	-	-	-	-	-	-
aaq
dapi	insol
daa
bsc
fno
bpa
fat

Job Matrix

CAS (M3)

State	Active Spaces	CASSCF/aug-cc-pvdz	QD-NEVPT2/aug-cc-pvdz
s0
s1+2

DFT - Gas (MonARCH)

State	Functional	Opt	Freq	Pol	Ex/Em	ESD
s0	ωB97X-D
s1+2	ωB97X-D
s0	CAM-B3LYP			N/A
s1+2	CAM-B3LYP			N/A

DFT - solv (MonARCH)

State	Functional	Opt	Freq	Pol	SS	VEM	ESD
s0	ωB97X-D
s1+2	ωB97X-D
s0	CAM-B3LYP
s1+2	CAM-B3LYP

To do:

• Jobs to figure out
  • Test QChem to figure out how to do VEM/cLR/LR/IBSF emission
• Code
  • Write energy extractors
    • pullQChem_Freq
      • \(\Delta E_{ZPVE}\)
      • \(\Delta E_{elec}\)
      • Number of -ve freqs
      • Extend and test for CASSCF
    • Q-chem ex/em extractors
      • ss-ex
      • ss-em
      • lr-ex
      • lr-em

GANTT Chart

gantt
    dateFormat D/M/YY
    title Adrea's PhD Plan
    %%excludes    weekends

    section Preparation
    Preliminary reading                     :active,                    5/4/22,     10/2/23
    Method "Play"                               :done,                      5/4/22,     10/6/22
    Software comparisons                    :done,                      10/6/22,    13/7/22
    Preliminary benchmarking            :done,                      12/7/22,    27/10/22
    Christmas break                             :crit,                      22/12/22,   3/1/23
    Dataset design                              :active,                    12/7/22,    18/12/22
    Experimental design                     :active,                    28/11/22,   27/1/23



    section Chapter 2
    Data collection                             :dc,                            23/2/23,    16/8/23
    Data processing                             :                                   23/2/23,    23/8/23
    Writeup                                             :w,               after dc, 8w
  R&R break                                         :crit,            after w,  2w

    section Chapter 3
  Computation & Analysis                :comp,                      1/10/22,      58w
  Writeup                                               :                 after comp,   10w
  Christmas break                               :crit,                      22/12/23,   3w

  section Chapter 4
  Computation & Analysis                :c4,                            26/2/24,    20w
  Writeup                                               :w4,                            after c4, 6w
  R&R break                                         :crit,                      after w4,   2w


  section Chapter 5
  Computation & Analysis                :c5,                            after w4, 20w
  Christmas break                               :crit,                      20/12/24,   2w
  Writeup                                               :w5,                            after c5, 6w

    section Milestones and Thesis
    IPR writeup                   :ipr,                         19/12/22, 10/2/23
    IPR                           :milestone, ipr,  23/2/23,    0d

    Confirmation writeup                    :                                   19/6/23,    11/7/23
    Confirmation                                    :crit, milestone, 19/7/23,  0d

  Progress review writeup               :                                   23/4/24,    9/5/24
    Progress review                             :milestone,             23/5/24,    0d

    Final review writeup                    :                                   28/3/25,    9/5/25
    Final review                                    :milestone,             23/5/25,    0d

    Drop everyhting for thesis      :                                   25/4/25,    25/7/25
    Thesis submission                           :crit, milestone,   22/8/25,    0d

    section Conferences
    APC 2023                      :                 27/11/23, 1/12/23
    APATCC-11 Kobe                :                 01/09/24, 30/11/24
    WATOC Oslo                    :                 22/6/25,  6d

Code Object Structure

flowchart LR
    subgraph Legend
    1((Entity))
    3[[module]]
    4[(database)]
    5[/Data Types/]
    6[Hidden Code\n12000+ lines]:::backend
    7[User Facing Code\n3000+ lines]:::ui
    end

    classDef backend fill:#bfbdbd;
    classDef ui fill:#fa4ba0;
    classDef db fill:#00f2ff;

flowchart TD
    a -- Output Files --> g
    g -- SLURM Scripts -->  
    a((HPC Clusters))
    subgraph Backend Code
    s[/Spectrum Object/]:::backend
    m[/Fluorophores/]:::backend
    n[/Solvents/]:::backend
    o[/PCM Models/]:::backend
    p[/Software/]:::backend
    r[/Methods/]:::backend
    q[/Basis Sets/]:::backend
    s & m & n & o & p & r & q -.-> l[[Data Types]]:::backend -.- w
    g[[HPC Manager]]:::backend -.- w
    w[[Resources module]]:::backend
    end

    c <-- Job Status --> v
    c -- QM Properties --> k

    subgraph Databases
    j[DB Manager]:::ui -.- b & e & k
    e[(ΔE/λ/Φ/τ DB)]:::backend
    b[(Spectra DB)]:::backend 
    k[(Computational Results DB)]:::backend
    v[(Computational Progress DB)]:::backend
    v <--> j
    end

    subgraph Experiment
    h[Spectra Importer]:::ui 
    i[Spectra Analyser/Plotter]:::ui
    t -- .txt files --> h
    d -- .csv files --> h
  t((TCSPC))
    d((UV-Vis/Fl)) 
    end


    c[Job Manager]:::ui 
    b <-- Fitted spectra --> i

    h -.- i -- Spectral Features --> e
    b <-- Fitted spectra --> h

    w -. Jobs -.- c
    w -.- j



    k & e --> u[Stats Scripts]:::ui


    classDef backend fill:#bfbdbd;
    classDef ui fill:#fa4ba0;
    classDef db fill:#00f2ff;