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Data from: Implications of Byproduct Chemistry in Nanoparticle Synthesis

Component

Figure 5

File Size
  • 529 MB
File Format
  • ZIP Format
Description

TD-DFT calculated absorption spectra of selected MES oxidation byproducts with transitions in the UV range. (a) reduced molecular weight species, (b) Au(I) complexes, (c) dimer-type species, (d) radical cations, and (e) trimer-type species. The grey area lies outside the range of the UV-vis spectrometer. R represents ethylsulfonate, and X in (c) and (e) represents compound 5 bonded through the β-carbon.

Scope And Content

Contains panels A-E with pertinent molecules within, as relevant to the figure.

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Figure 6

File Size
  • 811 MB
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  • ZIP Format
Description

Comparison of experimental spectrum of the filtrate at 110 min (black) to TD-DFT simulated spectra of 28 with PCM solvent model (red), with 50 water molecules after 250 frames of the MD run with the TIP3P water model (blue), and 500 frames of the MD run with SPC (green). The inset shows 28 surrounded by 50 water molecules after 500 frames using SPC.

Scope And Content

Contains simulations based on TIP3P and SPC molecular dynamics methods. Contains PCM reference spectrum, also available in other components, for your convenience.

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Figure S24

File Size
  • 140 MB
File Format
  • ZIP Format
Description

Calculated absorption spectra of organic molecules derived from one MES molecule. ‘S’ and ‘C’ refer to situations where the sulfonate tail is either straight or curled, respectively. ‘0’ and ‘1-‘ refer to the overall charge of the molecule as a result of protonation of the nitrogen.

Scope And Content

Contains panels A-I with pertinent molecules and their various charge states, as applicable.

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Figure S25

File Size
  • 139 MB
File Format
  • ZIP Format
Description

Calculated absorption spectra of Au(I)-complexes with amines related to MES or its oxidation products. In (g) and (h), the inorganic ligand is either water (solid) or chloride (dashed).

Scope And Content

Contains panels A-H with pertinent molecules and their various charge states, as applicable.

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Figure S26

File Size
  • 1.42 GB
File Format
  • ZIP Format
Description

Calculated absorption spectra of organic molecules derived from two or three MES molecules. In (a), both the s-trans (black) and s-cis (magenta) conformations are shown. In (e), ‘a’ and ‘e’ refer to situations where either the amine or enamine is protonated, respectively. Labels ranging from ‘1+’ to ‘3-‘ refer to the overall charge of the molecules as a result of protonation of nitrogen atoms, except for (m) where ‘1-‘ and ‘2-‘ indicate the radical cation and diradical dication, respectively.

Scope And Content

Contains panels A-N with pertinent molecules and their various charge states, as applicable.

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Figure S27

File Size
  • 95 MB
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  • ZIP Format
Description

Effect of curling of sulfonate tails in compound 28. The spectra of conformers with two straight (S-S, solid), one straight and one curled (S-C, dashed), and two curled (C-C, dotted) sulfonate tails are almost identical.

Scope And Content

Contains simulations showing the effect of curling the sulfonate groups in molecule 27.

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Figure S28

File Size
  • 61.5 MB
File Format
  • ZIP Format
Description

Comparison of (a) basis sets, and (b) functionals for compound 18. Functionals were compared with def2tzvpp basis set.

Scope And Content

Contains panels A and B showing the effect of basis set and functional for compound 18.

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Figure S29

File Size
  • 134 MB
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  • ZIP Format
Description

The effect of the solvent model on the predicted spectra was examined for (a) the dimer 18, and (b) the dimer radical 28.

Scope And Content

Contains panels A and B showing the effect of continuum solvation models for compounds 18 and 28.

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Figure S30

File Size
  • 139 MB
File Format
  • ZIP Format
Description

The effect of including explicit water molecules in the modelling of absorption spectra of the dimer radical 28 by hand. (a) Calculated spectra of 28 with increasing number of water molecules (indicated in the legend). (b) Peak position as function of number of explicit water molecules for the UV peak (black) and visible peak (red). Solvent model is PCM.

Scope And Content

Contains simulations showing the effect of 0 to 3 "hand placed" water molecules near the central pi system of compound 28.

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Figure S31

File Size
  • 1.28 GB
File Format
  • ZIP Format
Description

The effect of including explicit water molecules in the modelling of absorption spectra of the dimer radical 28 employing molecular dynamics simulations. (a) Calculated spectra of 28 with 16 water molecules after 1 (black), 250 (red), and 500 (blue) frames with SPC methods. (b) Peak positions in (a) as function of frame for the UV peak (black) and visible peak (red). (c) Calculated spectra of 28 with 16 water molecules after 1 (black), 250 (red), and 500 (blue) frames with TIP3P methods. (d) Peak positions in (c) as function of frame for the UV peak (black) and visible peak (red). Dashed lines in (a) and (c) refer to simulations including the full set of 50 water mole-cules. Labels in (b) and (d) indicate the peak extinction coefficient of the visible transition.

Scope And Content

Contains simulations for panels A and C, SPC and TIP3P, respectively. Each subfolder contains the .xyz file with the coordinates of the 50 closest waters for all 500 frames, in addition to 2 folders "water_16" and "water_50." Within "water_16" are 3 simulations, using frames 1, 250, and 500. "Water_50" contains the simulation with all 50 waters from the best-fitting frame in "water_16."

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Cite This Work

Stappen, Frederick N.; Enemark-Rasmussen, Kasper; Junor, Glen P.; Clausen, Mads H.; Zhang, Jingdong; Engelbrekt, Christian (2019). Data from: Implications of Byproduct Chemistry in Nanoparticle Synthesis. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0GB228D

Description

Abstract: Byproducts in metal nanoparticle synthesis can interfere with nanomaterial formation and self-assembly, as well as the perceived nanomaterial properties. Such syntheses go through a complicated series of intermediates, making it difficult to predict byproduct chemistry and challenging to determine experimentally. By a combined experimental and theoretical approach, the formation of organic byproducts is mapped out for the synthesis of gold nanoparticles with Good’s buffer 2-(N-morpholino)ethanesulfonic acid. Comprehensive nuclear magnetic resonance studies supported by mass spectrometry, ultraviolet–visible spectroscopy, and density functional theory reveal a number of previously unidentified byproducts formed by oxidation, C–N bond cleavage, and C–C bond formation. A reaction mechanism involving up to four consecutive oxidations is proposed. Oligomeric products with electronic transitions in the visible range are suggested. This approach can be extended broadly and lead to a more informed synthesis design and material characterization.

Scope And Content

Data pertaining to each figure can be downloaded. Folders pertaining to Panels within the figure contain folders with individual molecules, charge states, and calculation types (TDDFT and Frequency), as necessary. Some figures will contain the same files as other figures, but names are changed for clarity in each respective figure.

Creation Date
  • 2016 to 2018
Date Issued
  • 2019
Authors
Principal Investigator
Technical Details

Gaussian 09, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.

AMBER 16: D.A. Case, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, W.M. Botello-Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao and P.A. Kollman (2016), AMBER 2016, University of California, San Francisco.

Funding

Financial support from the Independent Research Fund Denmark to JZ (DFF-1335-00330 and DFF 4093-00297), CE (DFF-5054-00107) and MHC (DFF-7017-00026B), the Lundbeck Foundation to JZ (R141-2013-13273), and the Alfred P. Sloan Foundation University Center for Exemplary Mentoring to GPJ is greatly appreciated. The 800 MHz and 600 MHz NMR data were recorded at the NMR Center at DTU supported by the Villum Foundation. We acknowledge the computational resources made available by the W. M. Keck Foundation. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. (DGE-1650112; G.P.J.). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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  • No linguistic content; Not applicable
Identifier

Identifier: Christian Engelbrekt: https://orcid.org/0000-0003-3679-3666

Identifier: Frederick N. Stappen: https://orcid.org/0000-0002-8337-2664

Identifier: Glen P. Junor: https://orcid.org/0000-0002-6733-3577

Identifier: Jingdong Zhang: https://orcid.org/0000-0002-0889-7057

Identifier: Kasper Enemark-Rasmussen: https://orcid.org/0000-0001-7455-7512

Identifier: Mads H. Clausen: https://orcid.org/0000-0001-9649-1729

Doi: https://doi.org/10.6075/J0GB228D

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Last Modified

2023-06-06