Final Report Summary - INTECHSE (International Network on Integrated Techniques in Structural Elucidation)
Research collaborations among synthetic, spectroscopic and theoretical chemists have been established to exchange staff among the different participating groups to solve structure elucidation issues in a more effective way by combining the skills and facilities of all members.
To reach these objectives, we have proposed a research program that resides in three major topics. The first is centered in nuclear magnetic resonance (workpackage 1), principally involving preparation and testing of novel NMR alignment media and the development of new software for structural analysis automation procedures. Shape-persistent acetylenic macrocycles and polyaromatic structures can provide ordered systems in which constitution, physical properties, and chemical reactivity can be controlled in exquisite detail. Thus, in workpackage 2, synthesis and structural elucidation of π-conjugated systems tailored to exhibit specific properties will be addressed involving information gathered from NMR, chiroptical and electrochemical analyses. The third topic focuses on the analysis of chiroptical properties (workpackage 3): ORD, ECD and VCD data will be used with the help of quantum mechanics not only for conformational and configurational characterization in combination with NMR, but also to elucidate the origin of the observed chirality.
Thus, we had prepared several anthraquinone and chromonic derivatives with different alkyl chains successfully and prepared the data set of our candidates for the further studies regarding the integration of modelling techniques in the interpretation of spectroscopic measurements. We have studied the gelation properties of the prepared 1,5-dialkoxyanthraquinones and chromoglicic derivatives. Some of the compounds rendered crystalline fibers and did not show gelating behaviour in the tested solvents (ethanol, 1-decanol, p-xylene, nitro-toluene, chloroform, etc.). The study of chromolyn solutions with or without dopping agents as liquid crystals in structural determination has been developed. Interestingly, these solutions have shown different diffusion coeficients in the z direction and the xy plane. Further studies are undergoing to establish the supramolecular rearrangement of the liquid crystal.
We have developed a prototype code in Python capable to do automatic assignment of relative configuration, starting from 2D structure, by using proton-carbon residual dipolar couplings.
We have prepared and characterized several allenophanes (allenoacetylenic macrocycles). In addition, three-fold symmetric keto-bridged triarylamines were functionalized with perfluorinated alkyl chains of different lengths capable to undergo non-covalent interactions and were further studied in terms of their self-assembly behavior and chemical reactivity on different metal and insulator surfaces. Scanning probe microscopy and spectroscopy techniques in combination with computational studies revealed complex interplay between the molecular structure, intermolecular, and molecule-substrate interactions enabling to tune the self-assembly from porous and compact networks to upright standing - stacked aggregates. The obtained insights enable us in many cases to design a particular molecular building block for desired type of the self-assembled or even covalent nanostructures on various surfaces.
Our attempts to fuse the arylvinylidene-bridged triphenylamines to the corresponding N-centered PAHs were hitherto not completely successful. Regardless of the precursor or reaction conditions used, complex mixtures containing partially cyclized species aside from large amounts of unidentifiable products were obtained, which were often difficult to analyze owing to their poor solubility. Therefore, we have in the meanwhile changed the molecular design of the nitrogen-centered precursors and introduced electron-withdrawing n-heptafluoropropyl and pentafluorophenyl moieties for stabilization in combination with thiophene-containing bridging units which are known to facilitate photochemical cyclodehydrogenation. As a complementary method to solution chemistry we currently study by means of STM the ability of various arylvinylidene-bridged precursors to undergo the desired cyclodehydrogenation on metal surfaces in ultrahigh vacuum.
In addition, the synthesis of a series of N,N’-dialkyldiazapicenium salts, a new family of charged nitrogen-doped PAHs, with various n-alkyl chains and different counterions was accomplished. The ability of these quaternary ammonium salts to exfoliate graphite in ethanol as a function of the alkyl chain length and the anion size was studied. While the n-dodecyl-substituted compound was found to be most suitable for this purpose owing to its superior solubility, no influence of different counterions could be observed. The resulting hybrid systems were studied by diverse spectroscopy techniques to reveal the p-type character of prepared few-layer graphene. These findings show that are compounds can even act as supramolecular dopants for graphene to tune its electronic structure.
We conducted a collaborative work to elucidate the conformational equilibria in macrocycles 2,6 pyridoallenophanes and their dependence on the solvent. Conformational distributions were characterized both at computational (DFT) and NMR level, and allowed to identify three main conformers, namely twist, chair and boat, but not to establish their relative population. In order to determine the latter we compared experimental and computational one-photon photon absorption and electronic circular dichroism (ECD) and their non-linear (two-photon) analogues. Comparison of the observed and predicted vibronic lineshapes of one-photon spectra allowed to exclude that boat conformer is dominant and indicated that twist and chair are both populated at room temperature with the population of the former increasing when moving from hexane to chloroform, due to the establishment of solute-solvent specific interactions. The picture arising from the analysis of one-photon spectra was further confirmed by the comparison of observed and simulated two-photon spectra.
Work currently under development concerns the establishment of reliable models to investigate the ECD response of species exhibiting different conformations separated by very low energy barriers, since in this case the usual approximation of treating the contributions of each conformer separately may break down. To achieve this goal, the development of hybrid quantum/classical protocols is needed.
We faced with the problem of the computation of the vibronic structure associated to the ECD spectrum of exciton dimers. This is a typical example for which a nonadiabatic treatment is needed and the coupling between the two local excitations must be explicitly taken into account. We have presented a computational protocol based on harmonic Hamiltonian for local excitations and quantum dynamical (QD) simulations on the coupled states. QD simulations exploit the definition of effective coordinates rigorously designed to represent accurately the short-time dynamics (i.e. the low resolution ECD spectra) of the systems. This strategy allowed us to surpass the original idea to include in the model few, qualitatively chosen, nuclear coordinates, permitting us to work directly with a protocol that adopts rigorously selected effective modes. Then, the computational protocol for dimers was further developed to derive transition electric and magnetic dipoles for local excitation from ab initio calculations and be able to compute the ECD/absorption dissymetry g factor. This updated protocol is currently adopted to simulate the ECD vibronic spectra of polythiophenes aggregates on the ground of simple molecular models comprising two stacked oligothiophenes of variable length and mutual orientation.
We focused on the simulation of the ECD vibronic shapes arising from stacked trimers and tetramers (3 and 4 coupled electronic states, respectively). A rigorous strategy is available to generate, also for oligomers, a number of effective coordinates able to describe accurately the low-resolution spectra of the full-dimensionality system. We further developed a computational model to derive the vertical transition energies and couplings of the local excitations from data obtainable by a single TD-DFT calculation. Application of these models to the study of the ECD vibronic shapes of polythiophenes aggregates is currently under development with the final goal to establish the effects that determine the vibronic shapes of oligomers (or polymers) organized to form a supramolecular helical structure.
This Network offered a unique opportunity for the synthetic chemists to learn basic aspects of structural information obtained by magnetic and optical spectroscopies, in which experimental measurements are colligated with theoretical calculations. Theoretical chemists have benefited from the experimental chemists in gaining understanding on the mechanisms responsible of chiroptical responses and appropriated methodologies for structural characterization. The expected outcome of this collaborative research is a new set of protocols ready for the use of the synthetic organic chemists in the structural determination of complex structures that are still under development.
The development of computational tools and the popularization of their use will contribute to enhance the education of chemists in the mathematical and physical fundamentals of the discipline, leading to a more meaningful interpretation of the observed chemical phenomena.
This improved structural analysis will also facilitate the design of new systems with desired molecular properties. Particularly, systems with tailored chiroptical responses could be designed upon the understanding of the origin of their optical activity for potential applications, such as chemical sensors, or amplification of chirality in nano-structured systems in order to enable a custom-design of functional materials.
We have boosted our capabilities to recruit students in PhD and Master degree program at the respective participant institutions, with obvious positive effects on revenue and also on the education of new generation of scientists. This network has benefited the educational capacity of all the involved groups, providing early stage researchers and experienced researcher with training in interdisciplinary and collaborative research, and with valuable international experience.
We have developed a website (http://magcid.uvigo.es/~armando/intechse/intechse.html(odnośnik otworzy się w nowym oknie)) to facilitate the communication within the network, whose logo is.
To reach these objectives, we have proposed a research program that resides in three major topics. The first is centered in nuclear magnetic resonance (workpackage 1), principally involving preparation and testing of novel NMR alignment media and the development of new software for structural analysis automation procedures. Shape-persistent acetylenic macrocycles and polyaromatic structures can provide ordered systems in which constitution, physical properties, and chemical reactivity can be controlled in exquisite detail. Thus, in workpackage 2, synthesis and structural elucidation of π-conjugated systems tailored to exhibit specific properties will be addressed involving information gathered from NMR, chiroptical and electrochemical analyses. The third topic focuses on the analysis of chiroptical properties (workpackage 3): ORD, ECD and VCD data will be used with the help of quantum mechanics not only for conformational and configurational characterization in combination with NMR, but also to elucidate the origin of the observed chirality.
Thus, we had prepared several anthraquinone and chromonic derivatives with different alkyl chains successfully and prepared the data set of our candidates for the further studies regarding the integration of modelling techniques in the interpretation of spectroscopic measurements. We have studied the gelation properties of the prepared 1,5-dialkoxyanthraquinones and chromoglicic derivatives. Some of the compounds rendered crystalline fibers and did not show gelating behaviour in the tested solvents (ethanol, 1-decanol, p-xylene, nitro-toluene, chloroform, etc.). The study of chromolyn solutions with or without dopping agents as liquid crystals in structural determination has been developed. Interestingly, these solutions have shown different diffusion coeficients in the z direction and the xy plane. Further studies are undergoing to establish the supramolecular rearrangement of the liquid crystal.
We have developed a prototype code in Python capable to do automatic assignment of relative configuration, starting from 2D structure, by using proton-carbon residual dipolar couplings.
We have prepared and characterized several allenophanes (allenoacetylenic macrocycles). In addition, three-fold symmetric keto-bridged triarylamines were functionalized with perfluorinated alkyl chains of different lengths capable to undergo non-covalent interactions and were further studied in terms of their self-assembly behavior and chemical reactivity on different metal and insulator surfaces. Scanning probe microscopy and spectroscopy techniques in combination with computational studies revealed complex interplay between the molecular structure, intermolecular, and molecule-substrate interactions enabling to tune the self-assembly from porous and compact networks to upright standing - stacked aggregates. The obtained insights enable us in many cases to design a particular molecular building block for desired type of the self-assembled or even covalent nanostructures on various surfaces.
Our attempts to fuse the arylvinylidene-bridged triphenylamines to the corresponding N-centered PAHs were hitherto not completely successful. Regardless of the precursor or reaction conditions used, complex mixtures containing partially cyclized species aside from large amounts of unidentifiable products were obtained, which were often difficult to analyze owing to their poor solubility. Therefore, we have in the meanwhile changed the molecular design of the nitrogen-centered precursors and introduced electron-withdrawing n-heptafluoropropyl and pentafluorophenyl moieties for stabilization in combination with thiophene-containing bridging units which are known to facilitate photochemical cyclodehydrogenation. As a complementary method to solution chemistry we currently study by means of STM the ability of various arylvinylidene-bridged precursors to undergo the desired cyclodehydrogenation on metal surfaces in ultrahigh vacuum.
In addition, the synthesis of a series of N,N’-dialkyldiazapicenium salts, a new family of charged nitrogen-doped PAHs, with various n-alkyl chains and different counterions was accomplished. The ability of these quaternary ammonium salts to exfoliate graphite in ethanol as a function of the alkyl chain length and the anion size was studied. While the n-dodecyl-substituted compound was found to be most suitable for this purpose owing to its superior solubility, no influence of different counterions could be observed. The resulting hybrid systems were studied by diverse spectroscopy techniques to reveal the p-type character of prepared few-layer graphene. These findings show that are compounds can even act as supramolecular dopants for graphene to tune its electronic structure.
We conducted a collaborative work to elucidate the conformational equilibria in macrocycles 2,6 pyridoallenophanes and their dependence on the solvent. Conformational distributions were characterized both at computational (DFT) and NMR level, and allowed to identify three main conformers, namely twist, chair and boat, but not to establish their relative population. In order to determine the latter we compared experimental and computational one-photon photon absorption and electronic circular dichroism (ECD) and their non-linear (two-photon) analogues. Comparison of the observed and predicted vibronic lineshapes of one-photon spectra allowed to exclude that boat conformer is dominant and indicated that twist and chair are both populated at room temperature with the population of the former increasing when moving from hexane to chloroform, due to the establishment of solute-solvent specific interactions. The picture arising from the analysis of one-photon spectra was further confirmed by the comparison of observed and simulated two-photon spectra.
Work currently under development concerns the establishment of reliable models to investigate the ECD response of species exhibiting different conformations separated by very low energy barriers, since in this case the usual approximation of treating the contributions of each conformer separately may break down. To achieve this goal, the development of hybrid quantum/classical protocols is needed.
We faced with the problem of the computation of the vibronic structure associated to the ECD spectrum of exciton dimers. This is a typical example for which a nonadiabatic treatment is needed and the coupling between the two local excitations must be explicitly taken into account. We have presented a computational protocol based on harmonic Hamiltonian for local excitations and quantum dynamical (QD) simulations on the coupled states. QD simulations exploit the definition of effective coordinates rigorously designed to represent accurately the short-time dynamics (i.e. the low resolution ECD spectra) of the systems. This strategy allowed us to surpass the original idea to include in the model few, qualitatively chosen, nuclear coordinates, permitting us to work directly with a protocol that adopts rigorously selected effective modes. Then, the computational protocol for dimers was further developed to derive transition electric and magnetic dipoles for local excitation from ab initio calculations and be able to compute the ECD/absorption dissymetry g factor. This updated protocol is currently adopted to simulate the ECD vibronic spectra of polythiophenes aggregates on the ground of simple molecular models comprising two stacked oligothiophenes of variable length and mutual orientation.
We focused on the simulation of the ECD vibronic shapes arising from stacked trimers and tetramers (3 and 4 coupled electronic states, respectively). A rigorous strategy is available to generate, also for oligomers, a number of effective coordinates able to describe accurately the low-resolution spectra of the full-dimensionality system. We further developed a computational model to derive the vertical transition energies and couplings of the local excitations from data obtainable by a single TD-DFT calculation. Application of these models to the study of the ECD vibronic shapes of polythiophenes aggregates is currently under development with the final goal to establish the effects that determine the vibronic shapes of oligomers (or polymers) organized to form a supramolecular helical structure.
This Network offered a unique opportunity for the synthetic chemists to learn basic aspects of structural information obtained by magnetic and optical spectroscopies, in which experimental measurements are colligated with theoretical calculations. Theoretical chemists have benefited from the experimental chemists in gaining understanding on the mechanisms responsible of chiroptical responses and appropriated methodologies for structural characterization. The expected outcome of this collaborative research is a new set of protocols ready for the use of the synthetic organic chemists in the structural determination of complex structures that are still under development.
The development of computational tools and the popularization of their use will contribute to enhance the education of chemists in the mathematical and physical fundamentals of the discipline, leading to a more meaningful interpretation of the observed chemical phenomena.
This improved structural analysis will also facilitate the design of new systems with desired molecular properties. Particularly, systems with tailored chiroptical responses could be designed upon the understanding of the origin of their optical activity for potential applications, such as chemical sensors, or amplification of chirality in nano-structured systems in order to enable a custom-design of functional materials.
We have boosted our capabilities to recruit students in PhD and Master degree program at the respective participant institutions, with obvious positive effects on revenue and also on the education of new generation of scientists. This network has benefited the educational capacity of all the involved groups, providing early stage researchers and experienced researcher with training in interdisciplinary and collaborative research, and with valuable international experience.
We have developed a website (http://magcid.uvigo.es/~armando/intechse/intechse.html(odnośnik otworzy się w nowym oknie)) to facilitate the communication within the network, whose logo is.