Dynamics of self-assembled monolayers of molecular machines on the water/air interface

master's thesis

• Title (croatian): Dinamika samoudruženih monoslojeva molekularnih strojeva na međupovršini voda/zrak
• Author: Lujo Matasović
• Mentor: Jiří Kaleta https://orcid.org/0000-0002-5561-7580 (mentor)
• Committee member: Ivana Biljan (predsjednik povjerenstva)
• Committee member: Vladimir Stilinović (član povjerenstva)
• Committee member: Davor Kovačević (član povjerenstva)
• Committee member: Ivan Kodrin (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Defense date and country: 2022-07-06, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Chemistry

Abstract

We present a computational study of self-assembled monolayers (SAMs) of several functional
molecules which share a triptycene core and differ in the number of anchoring groups and
functional mounts (photoswitches or light-driven motors). Structural properties of different
SAMs on the water-air interface are explored by nanoscale molecular dynamics carried out in
the tight-binding DFT formalism, as well as by static meta-GGA DFT calculations. Both
approaches give similar results, revealing that tilting and bending in SAMs is significant in all
investigated systems. Molecular dynamics shows that SAMs tilt collectively, although the
motion of individual machines is not strongly correlated. Functional heads, triptycenes and
anchoring groups are found to strongly affect SAM properties, and a structure bearing two
triptycene units and three anchoring groups is identified as the most promising future synthetic
target. Finally, the computational results are validated by comparing them with previously
performed experiments (anisotropic spectroscopy and ellipsometry).

Abstract (croatian)

U ovom radu računalnim su metodama istraženi samoudruženi monoslojevi (SAM) niza
funkcionalnih molekula koje se razlikuju po funkcionalnoj jedinici (sklopka ili svjetlom
upogonjeni motor) i broju veznih skupina, a dijele tripticensku jezgru. Strukturna svojstva
različitih SAM-ova na međupovršini voda-zrak istražena su nanosekundnom molekulskom
dinamikom provedenom u formalizmu DFT modela čvrste veze, te meta-GGA DFT statičkim
izračunima. Oba pristupa daju slične rezultate i otkrivaju da su, u svim proučavanim sustavima,
molekule značajno nagnute i savinute. Rezultati molekulske dinamike pokazuju da je nagibanje
SAM-ova kolektivan proces, iako gibanje individualnih strojeva nije korelirano. Također,
potvrđeno je da funkcionalne glave, tripticeni i vezne skupine značajno utječu na svojstva
monoslojeva, te je kao glavni kandidat za sintezu novih funkcionalnih materijala identificiran
molekulski sustav s dvije tripticenske jedinice i tri vezne skupine. Usporedbom s prethodno
provedenim eksperimentima (anizotropnom spektroskopijom i elipsometrijom) potvrđeni su
računalni rezultati.

• Keywords: IR reflection adsorption spectroscopy; meta-GGA DFT; molecular dynamics; molecular machines; self assembled monolayers; tight-binding DF
• Keywords (english): DFT model čvrste veze; IR refleksijska adsorpcijska spektroskopija; metaGGA DFT; molekulska dinamika; molekulski strojevi; samoudruženi monoslojevi
• Language: english
• URN:NBN: urn:nbn:hr:217:196352
• Study programme: Title: Graduate university studies in chemistry; specializations in: Research programme; Course: Research programme; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra kemije (magistar/magistra kemije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access; Embargo expiration date: 2024-07-06
• Created on: 2022-07-12 12:30:46