The application of calorimetry for the characterization of chemical and physical processes in supramolecular systems

Kalorimetrija je eksperimentalna metoda kojom je moguće izmjeriti toplinu tijekom kemijskog ili fizikalnog procesa. Cilj ovog rada je objasniti teorijsku osnovu kalorimetrijskih mjerenja te opisati najčešće korištene kalorimetrijske metode. Također, želi se pokazati opseg strukturnih i termodinamičkih karakteristika supramolekulskih i biokemijskih sustava do kojih je moguće doći na temelju eksperimentalnih podataka. Naglasak ovog rada je na praktičnoj primjeni kalorimetrijskih mjerenja u svrhu opisa procesa uzrokovanih supramolekulskim, odnosno nekovalentnim interakcijama, budući da su te interakcije osnova i većine biokemijskih procesa u kojima je bitan proces molekulskog prepoznavanja. Kalorimetrijskim metodama moguće je okarakterizirati i fizikalne procese koji se zbivaju u biološkim sustavima. Jedan od tih procesa je fazna transformacija lipidnih dvosloja, koji služe kao modelni sustavi bioloških membrana. Također, kalorimetrija je pogodna metoda za određivanje uvjeta pri kojima molekule proteina zadržavaju svoju nativnu konformaciju, odnosno za termodinamičku karakterizaciju procesa denaturacije proteina. Primjenom kalorimetrije stječe se uvid u termodinamičke karakteristike supramolekulskih veznih interakcija između makromolekula i različitih liganada, odnosno međusobnog vezanja više makromolekula kao što je to slučaj kod interakcija proteina i molekule DNA. Osim što omogućuju termodinamičku karakterizaciju, kalorimetrijska mjerenja omogućuju i razumijevanje mehanizama procesa molekulskog prepoznavanja u supramolekulskim i biokemijskim sustavima. Uz poznavanje mehanizama navedenih procesa, moguće je dizajnirati ligande s takvim strukturnim karakteristikama koje omogućuju vezanje tih molekula na željeno vezno mjesto makromolekule. Takav postupak bitan je u farmakologiji prilikom razvoja novih lijekova koji se direktno vežu na molekule koje sudjeluju u biokemijskih procesima unutar organizma

On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface.

In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation

Highly Ordered Co-Assembly of Bisurea Functionalized Molecular Switches at the Solid-Liquid Interface

Immobilization of stimulus-responsive systems on solid surfaces is beneficial for controlled signal transmission and adaptive behavior while allowing the characterization of the functional interface with high sensitivity and high spatial resolution. Positioning of the stimuli-responsive units with nanometer-scale precision across the adaptive surface remains one of the bottlenecks in the extraction of cooperative function. Nanoscale organization, cooperativity, and amplification remain key challenges in bridging the molecular and the macroscopic worlds. Here we report on the design, synthesis, and scanning tunneling microscopy (STM) characterization of overcrowded alkene photoswitches merged in self-assembled networks physisorbed at the solid-liquid interface. A detailed anchoring strategy that ensures appropriate orientation of the switches with respect to the solid surface through the use of bis-urea groups is presented. We implement a co-assembly strategy that enables the merging of the photoswitches within physisorbed monolayers of structurally similar 'spacer' molecules. The self-assembly of the individual components and the co-assemblies was examined in detail using (sub)molecular resolution STM which confirms the robust immobilization and controlled orientation of the photoswitches within the spacer monolayers. The experimental STM data is supported by detailed molecular mechanics (MM) simulations. Different designs of the switches and the spacers were investigated which allowed us to formulate guidelines that enable the precise organization of the photoswitches in crystalline physisorbed self-assembled molecular networks.</p