Carbon Nanodots from an In Silico Perspective

Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications

Molecular Dynamics Simulation

Condensed matter systems, ranging from simple fluids and solids to complex multicomponent materials and even biological matter, are governed by well understood laws of physics, within the formal theoretical framework of quantum theory and statistical mechanics. On the relevant scales of length and time, the appropriate ‘first-principles’ description needs only the Schroedinger equation together with Gibbs averaging over the relevant statistical ensemble. However, this program cannot be carried out straightforwardly—dealing with electron correlations is still a challenge for the methods of quantum chemistry. Similarly, standard statistical mechanics makes precise explicit statements only on the properties of systems for which the many-body problem can be effectively reduced to one of independent particles or quasi-particles. [...

Vývoj a aplikace molekulové dynamiky pro molekulovou spektroskopii

This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...Katedra fyzikální a makromol. chemieDepartment of Physical and Macromolecular ChemistryFaculty of SciencePřírodovědecká fakult

A theoretical approach to the engineering of bioinspired systems: design, applications & information management

Premi extraordinari doctorat curs 2010-2011, àmbit d’Enginyeria Enginyeria IndustrialL’enginyeria de sistemes bioinspirats ha crescut en importància i nombre d’aplicacions en el últims anys, atraient l’atenció dels científics sobre els seus usos potencials en camps com ara la bionanotecnologia, la nanomedicina i la ciència de materials. En aquesta tesis, es presenta una aproximació mitjançant mètodes computacionals a l’enginyeria de sistemes biomimètics. Em posat la nostra èmfasi en l’estudi teòric basat en principis fonamentals de sistemes peptídics, això vol dir des de mètodes mecànic quàntics d’alt nivell per als elements més bàsics fins a la simulació de tot o part del sistema en un ambient més realista a partir de diferents aproximacions computacionals. Un altre objectiu del present treball és la recopilació exhaustiva de la informació derivada dels estudis fets així com dels potencials usos en un sistema informàtic orientat a l’usuari d’emmagatzemament de dades. S’han caracteritzat anàlegs conformacionalment restringits de l’arginina, prolina i fenilalanina a través de càlculs mecànic quàntics d’alt nivell. Aquest aminoàcids no codificats (és a dir que no estan entre els 20 aminoàcids naturals) han demostrat la seva capacitat de modulació del perfil conformacional dels pèptids a on són introduïts. A més a més, indueixen resistència a l’acció de les proteases a banda d’introduir noves propietats electròniques i espectroscòpiques útils en aplicacions tals com els sistemes de diagnòstic, alliberadors de fàrmacs i del camp de l’enginyeria de materials. Els aminoàcids obtinguts són emprats per a modificar pèptids de “homing”, blocs proteics autoagregants i superfícies actives recobertes de pèptids. La remarcable quantitat d’informació sobre aminoàcids no codificats accessible en publicacions científiques expressa la necessitat urgent de sistemes que, basant-se en ordinadors recopilin, organitzin i ofereixin aquesta informació de manera intel·ligible per a l’usuari final. Una base de dades ha estat dissenyada, creada i posada en funcionament per tal d’emmagatzemar dades conformacionals teòriques sobre aminoàcids no codificats. La base de dades també conté, en cas que la informació sigui accessible, dades experimentals referents a aplicacions, caracterització estructural i propietats espectroscòpiques. En resum, aquests treball ofereix un nou enfoc a l’enginyeria assistida per ordinador i la gestió de la informació de sistemes bioinspirats des de les seves unitats més elementals fins al disseny de les aplicacions de major complexitatThe engineering of systems inspired by biochemical molecules has grown in importance and number of applications in the recent years, focusing the researchers’ attention in its potential uses in fields such as nanotechnology, bionanotechnology, nanomedicine and material sciencie. A computational approach to engineering of biomimetic systems is presented in this work. Our emphasis is put on theoretical studies of some peptidic systems from scratch, this means from the use high level quantum mechanics studies of their primary building blocks to the simulation using different computational approaches of their behavior as part of an entire system in a more realistic environment. The thorough compilation of the derived information and its potential uses in a proper user-friendly data-storage support is also a question dealt in the thesis. Conformationaly restricted analogues of arginine, proline and phenylalanine amino acids are designed and fully characterized using high level quantum mechanics methods. These new non-coded amino acids (non-naturally occurring amino acids in proteins) demonstrate to modulate the conformational profile of peptides where they are inserted. Furthermore, they induce resistance to proteolysis altogether with new electronic and spectroscopic features useful in diagnostics, drug delivery and material engineering. The developed non-coded amino acids are used to engineer systems such as homing peptides, self-aggregating protein building blocks and peptide-coated active surfaces. The remarkable amount of information available about non-coded amino acids in scientific publications stressed out the dire need of computer-based systems to gather, to organize and to display in a user-friendly way the information about these compounds. A data base has been designed, implemented and run to store theoretically-obtained conformational information on non-coded amino acids. The data bases also contains, if available, experimentallyacquired knowledge such us structural and spectroscopic characterizations and reported applications. To conclude, this thesis offers a successful approach to the computer-aided engineering and information management of bioinspired systems from their basics to high complexity design.Award-winningPostprint (published version