Designing all-graphene nanojunctions by covalent functionalization

We investigated theoretically the effect of covalent edge functionalization, with organic functional groups, on the electronic properties of graphene nanostructures and nano-junctions. Our analysis shows that functionalization can be designed to tune electron affinities and ionization potentials of graphene flakes, and to control the energy alignment of frontier orbitals in nanometer-wide graphene junctions. The stability of the proposed mechanism is discussed with respect to the functional groups, their number as well as the width of graphene nanostructures. The results of our work indicate that different level alignments can be obtained and engineered in order to realize stable all-graphene nanodevices

Estudio teórico de la interacciones de los brasinoesteroides con el medio biológico

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química Física Aplicada. Fecha de lectura: 28-09-201

Molecular modelling on cyclodextrin inclusion complexes

Es wurden ab initio und Dichtefunktionaltheorie-Berechnungen auf entsprechend hohem theoretischen Niveau an Cyclodextrinen und Cyclodextrin-Komplexen durchgeführt. Als Ergebnis einer Untersuchung über den Einfluss der verwendeten Theorie auf die Größe der BSSE (basis set superposition error)-Korrektur auf die berechneten Energien im Modellsystem Wasser-Methanol konnte gezeigt werden, dass die Korrektur-Energie mit Verbesserung des Basissatzes abnimmt. Systematische Untersuchungen der Abhängigkeit bestimmter geometrischer Parameter von Malonaldehyd im Hinblick auf das Niveau der verwendeten Theorie ergaben, dass Optimierungen mit den theoretischen Modellen DFT B3LYP/6-31G(d,p) und MP2/6-311+G(d,p) Geometrien ergeben, die in ausgezeichneter Übereinstimmung mit den gefundenen experimentellen Ergebnissen stehen. Eine Untersuchung der Komplexbildung zwischen β-Cyclodextrin und der Aminosäure Alanin mittels DFT B3LYP/6-31G(d,p)-Rechnungen bestätigte die Annahme, dass β-Cyclodextrin als chiraler Selektor der beiden enantiomeren Formen des Alanins fungieren kann. Als wichtigstes Ergebnis einer Untersuchung verschiedener neutraler und anionischer Einschlussverbindungen von Meloxicam und β-Cyclodextrin mittels DFT B3LYP/6-31G(d,p)-Rechnungen wurde gefunden, dass Wasserstoffbrückenbindungs-Wechselwirkungen an der Komplexbildung beteiligt sind und maßgeblich zur Stabilisierung der jeweiligen Komplexe beitragen. Die Ergebnisse all dieser Untersuchungen wurden in den folgenden fünf Veröffentlichungen zusammengefasst und angewendet: “Homodromic Hydrogen Bonds in Low-Energy Conformations of Single Molecule CDs”, “On the Structure of Anhydrous β-CD”, “Density Functional Calculations on CDs”, “Molecular Dynamics Simulations and Quantum Chemical Calculations on β-CD-Spironolactone Complex”, und “Density functional calculations on meloxicam-β-cyclodextrin Inclusion Complexes”Ab initio and Density Functional Theory (DFT) computations at an appropriate high level of theory have been performed on cyclodextrins (CDs) and CD complexes. As a result of an investigation of the impact of the theory used on the magnitude of the basis set superposition error (BSSE) correction energy on the calculated energies of the model system water-methanol-dimer it could be shown that as the basis set is improved the BSSE energy is reduced. Systematic investigations on the dependence of several geometric parameters of malonaldehyde on the level of theory used led to the outcome that optimizations with DFT B3LYP/6-31G(d) and MP2/6-311+G(d,p) model chemistries yield a resulting geometry which is in excellent agreement with the experimental findings. A DFT B3LYP/6-31G(d,p) computational investigation of the complexation process between β-cylodextrin and the amino acid alanine confirmed that β-CD can act as a chiral selector between the two enantiomeric forms of alanine. As a main result of the investigation of several neutral and anionic inclusion complexes of meloxicam with β-CD using DFT B3LYP/6-31G(d,p) calculations it was found that hydrogen bonding interactions are involved in the complexation process and support considerably the stabilization of the respective complexes. The results of all these investigations have been summarized in the following five papers: “Homodromic Hydrogen Bonds in Low-Energy Conformations of Single Molecule CDs”, “On the Structure of Anhydrous β-CD”, “Density Functional Calculations on CDs”, “Molecular Dynamics Simulations and Quantum Chemical Calculations on β-CD-Spironolactone Complex”, and “Density functional calculations on meloxicam-β-cyclodextrin Inclusion Complexes

Use of Molecular Modelling for the Understanding of Self-Assembly Processes in Supramolecular Polymers

There is an increasing need to further improve and obtain new materials for biomedical and technological applications. The tools and intricacies of material discovery and design have been exponentially multiplying, especially in recent years, opening the way for new discoveries for next generation materials. This thesis investigates in silico conjugated organic supramolecular assemblies with the use of selected tools at the molecular level. The computational examination entails the geometrical and architectural design of the assemblies, and the study of their energetic details. A directed focus on OPE oligo(p-phenyleneethynylene)s, a photoisomerizing wire aggregate, and a series of porphyrinic assemblies is made in the evolution of this examination. These are versatile structures for supramolecular assembly, able to bind via a combination of non-covalent interactions, with interesting applications. The OPEs form 1D (one dimensional) wires with notable electronic properties. Furthermore, photoisomerizing aggregates have sparked abundant interest due to the control of assembly via light induction. Lastly, porphyrins are highly conjugated and readily functionalised molecules with the ability to form supramolecular assemblies from one to three dimensions. Porphyrin aggregates are also offered in crucial applications such as in photodynamic therapy, as well as an immensely wide and versatile spectrum of applications in further scientific sectors. The first part of this thesis assesses the recent relevant computational methods through a benchmark study for their accuracy and computational cost for their predictivity of conjugated organic self-assemblies. Subsequently, the chosen assessed method is further evaluated by comparison with a set of published experimental data of OPE assemblies. The newly published method, GFN2-xTB, is then evaluated as the most efficient for this type of entitiy. The aggregation motifs and polymer properties two of two OPEs and a photoisomerizing 1D wire assembly are initially studied. Subsequently, a set of porphyrinic supramolecular aggregations first in the 1D, and then in 3D are studied by utilising reference experimental data for further validation of the predictive capacity of GFN2-xTB. Lastly, for the first-time, chemical tuning recommendations are presented for promoting specific aggregations motifs. The combined results produce structure-property trends that purvey model assembly suggestions for supramolecular architectural synthesis and design

Simulation and Modeling of Nanomaterials

This Special Issue focuses on computational detailed studies (simulation, modeling, and calculations) of the structures, main properties, and peculiarities of the various nanomaterials (nanocrystals, nanoparticles, nanolayers, nanofibers, nanotubes, etc.) based on various elements, including organic and biological components, such as amino acids and peptides. For many practical applications in nanoelectronics., such materials as ferroelectrics and ferromagnetics, having switching parameters (polarization, magnetization), are highly requested, and simulation of dynamics and kinetics of their switching are a very important task. An important task for these studies is computer modeling and computational research of the properties on the various composites of the other nanostructures with polymeric ferroelectrics and with different graphene-like 2-dimensional structures. A wide range of contemporary computational methods and software are used in all these studies

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

2nd International Conference on Nanomaterials Science and Mechanical Engineering: book of abstracts

2nd International Conference on Nanomaterials Science and Mechanical Engineering: book of abstracts - University of Aveiro, Portugal July 9-12, 2019.publishe

Molecular machinery and manufacturing with applications to computation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Architecture, 1991.Vita.Includes bibliographical references (p. 469-487).by K. Eric Drexler.Ph.D