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On the inter-ring torsion potential of regioregular P3HT: a first principles reexamination with explicit side chains
Get PDFPoly(3-alkylthiophene) is a family of conjugated semicrystalline polymers for organic electronic applications. Crucial for the fine-tuning of such systems is a detailed understanding of the correlation between molecular structure/morphology and electronic properties. However, a series of a priori assumptions is commonly made in order to deduce macromolecular-scale geometric and energetic features from those of rather small homologous molecular systems. Alkyl side chains are routinely shortened (if not systematically removed) during such high-accuracy ab initio calculations in order to reduce their conformational space. We will show through first principles calculations on a monosubstituted bithiophene molecule how a full-length alkyl fragment can influence both side chain energetics and backbone flexibility in alkylthiophene-based polymers and copolymers. Folded side chains, characterized by a gauche arrangement of the second torsion angle from the ring, are found to be substantially favoured over extended ones, thanks to a network of CH–π hydrogen-bond-like interactions with both aromatic rings. Trans-planar (conjugated) arrangements of limit-ordered crystalline models, and cisoid sequences suitable for the investigation of chain-folding phenomena, are also discussed in detail
Exploring short intramolecular interactions in alkylaromatic substrates
Get PDFFrom proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues
Unusual crystallization mode of tubular helical 2,3-exo-disyndiotactic polynorbornene: a combined X ray diffraction / molecular modelling study
No full textThis contribution reports the study of the peculiar crystalline structure of the 2,3-exo-disyndiotactic polynorbornene (dsPNB) obtained by polymerization with a TiCl4 based catalysts. Using X-ray diffraction data (Fig. 1a) combined with molecular modelling studies (including the use of molecular mechanics and dynamics together with quantum mechanical methods), the stereochemistry was proved with stereoregular chains adopting an unusual tubular helical conformation in the crystalline state [1,2]. Interestingly, the estimated coherence length along the backbone axis is much higher than the value predicted by the average degree of polymerisation thus suggesting that a sequence of oligomers can packs along the chain axis. The resulting helices three dimensional assembly generates an empty accessible core, in which guest molecules (e.g. toluene, see Fig. 1b) or chain terminals can be easily hosted. A guest like I2 influences substantially the relative intensities of the diffraction patterns while leaving peak positions unchanged as expected for a unique polymer conformation in which I2 replaces guest molecules inside dsPNB channels [2]. Molecular modelling confirms the stability of empty and host-guest crystalline structures. MD simulations rationalises the guest exchange mechanism and the role of chain tails in the crystalline structure. In particular, it has been demonstrated that chain ends of dsPNB has a sufficient mobility to “fill” the empty cavities of the structure even at room temperature [3]
The structure of 2,3-exo-disyndiotactic polynorbornene: a combined X-ray diffraction / molecular modelling study
No full textThe present communication reports studies of modulations of the crystalline structure of 2,3-exo-disyndiotactic polynorbornene (dsPNB) obtained by catalysts based on TiCl4. Using X-ray patterns analysis (see Fig. 1a) combined with molecular modelling methods, the 2,3-exodisyndiotactic
stereochemistry por this polymer has been established,
with stereoregular chains adopting an unusual tubular helical
conformation in the crystalline state [1]. The helices’ packing leaves empty accessible channels, in which guest molecules can be hosted (see the case of toluene in Fig. 1b). Modulations are apparent as different guests alter the diffraction patterns of dsPNB. For example, a
guest like I2 influences very substantially the relative intensities while leaving peak positions invariant as expected for a polymer structure in which I2 replaces toluene inside the dsPNB channels [2]. Molecular modelling, including molecular mechanics and dynamics and quantum mechanics calculations specific for solid state phases may help to evaluate relative stabilities of of different host/guest crystals. Developments can be envisaged both in a fundamental perspective and
for applications in sensing and in recognition/separation technologies
2,3-EXO-DISYNDIOTACTIC POLYNORBORNENE: A CRYSTALLINE POLYMER WITH TUBULAR HELICAL MOLECULAR STRUCTURE
No full textThe present communication reports the study of the crystalline structure of the 2,3-exodisyndiotactic
polynorbornene obtained by catalysts based on TiCl4. Using molecular modelling
methods combined with powder X-ray diffraction patterns analysis the 2,3-exo-disyndiotactic
stereochemistry was proved with stereoregular polynorbornene (dsPNB) chains adopting an
unusual conformation in the crystalline state. The helices packing leave an empty accessible
tubular channel at the core, in which guest molecules like toluene can be hosted. Molecular
modelling, including also quantum mechanics calculations specific for solid state phases,
demonstrated the stability of empty and host guest crystalline structures
A Molecular Modelling Study of 2,3-exo-disyndiotactic Polynorbornene
Get PDFThe present contribution reports a detailed molecular modelling study of the peculiar crystalline structure of the 2,3-exo-disyndiotactic polynorbornene (dsPNB) obtained by polymerization with a TiCl4 based catalysts. Molecular mechanics and dynamics have been used together with quantum mechanical methods specific for solid crystalline phases. Using the low energy models obtained and data from X-ray diffraction experiments, the stereochemistry was proved revealing macromolecular chains, in the crystalline state, with an unusual tubular helical (12 units) conformation (Figure 1) [1]. Interestingly, the estimated coherence length (obtained by X-ray diffraction analysis) along the backbone axis is higher than the value predicted by the average degree of polymerisation of the system thus suggesting that a single chain is plausibly a sequence of oligomers. Moreover, the hexagonal packing of the helices (Figure 1) generates an empty accessible core in which guest molecules (toluene or I2 molecules) and also chain terminals can be easily hosted by reversible processes. Experimental study demonstrated that a guest like I2 influences very substantially the relative intensities of the diffraction patterns while leaving peak positions unchanged as expected for a unique polymer conformation in which I2 replaces molecular guests inside dsPNB channels [2]. Molecular modelling methods confirmed the stability of empty and host-guest crystalline structures. In particular, molecular dynamics simulations rationalises both the guest exchange mechanism and the key role of chain tails in the crystalline structure [3]
Unusual crystallization mode of tubular helical 2,3- exo-disyndiotactic polynorbornene
No full textThe present contribution reports the study of the peculiar crystalline structure of the 2,3-exo-disyndiotactic polynorbornene (dsPNB) obtained by polymerization with a TiCl4 based catalysts. Using X-ray diffraction measurements (Fig. 1a) combined with molecular modelling approaches (including molecular mechanics and dynamics together with quantum mechanical methods), the stereochemistry was proved with stereoregular chains adopting an unusual tubular helical conformation in the crystalline state [1]. Interestingly, the estimated coherence length along the backbone axis is much higher than the value predicted by the average degree of polymerisation suggesting that what is modelled as a single chain is plausibly a sequence of oligomers. Moreover, the helices packing generates an empty accessible core, in which guest molecules (e.g. toluene) and chain terminals can be easily hosted (Fig. 1b). A guest like I2 influences very substantially the relative intensities of the diffraction patterns while leaving peak positions unchanged as expected for a unique polymer conformation in which I2 replaces toluene or other hydrocarbon guests inside dsPNB channels [2]. Molecular modelling confirms the stability of empty and host-guest crystalline structures. In particular, MD simulations rationalises both the guest exchange mechanism and the role of chain tails in the crystalline structure
Polymer-Mediated Adhesion: Nanoscale Surface Morphology and Failure Mechanisms
Get PDFWe present coarse-grained molecular dynamics simulations of polymer-mediated adhesion between chemically heterogeneous surfaces. Our surface models exhibit weakly and strongly absorbing sites in 1:1 proportion but are characterized by different degrees of segregation among these sites. When the surfaces are pulled apart, we observe systematic variations in the stress–strain curves, indicating a significant weakening of the adhesive layer on moving from finely interdispersed to more segregated morphologies. In our model systems, the macroscopic failure of the sandwiched polymer films always appears to be cohesive but, at the nanoscale, there is, in fact, a gradual transition from a cohesive to a mixed cohesive–adhesive mechanism
Organic Peracids: A Structural Puzzle for 17O NMR and Ab InitioChemical Shift Calculations
No full textWe have applied 17O NMR spectroscopy to investigate the structure of the organic peracids formed by reaction of acetic acid (AA) or lactic acid (LA) with aqueous hydrogen peroxide (HP), which are used in several “green chemistry” applications. The interpretation of the experimental spectra has been supported by ab initio calculations of the 17O chemical shifts for several possible species, using a continuum representation of the solvent. The combined use of these tools has also allowed us to discuss the decomposition mechanism of LA/HP solutions. The calculated electric field gradients for water, HP, and CO2 (a decomposition product of LA) correlate well with the experimental 17O line widths
Monomer conformations for poly(3-alkylthiophene) atomistic models
No full textIn existing poly(3-alkylthiophenes) atomistic models, an extended conformation of the side chain is usually assumed. [1-5] We report a first principle study of the side-chain energetics of 3-hexylthiophene, with the constraint of compatibility with crystal packing requirements. The first two torsion angles of the side chain closest to the ring were considered. Dispersion contributions are shown to be of great relevance in the assessment of the relative stability of folded conformers against extended ones. The roles of local charge-transfer, rehybridization, steric repulsion, and basis set superposition error, were all considered in the rationalization of our results.[6] We extend our analysis to the thiophene/methane complex [7] in order to elucidate the main differences between inter- and intramolecular CH/pi phenomena. While in the non-covalent complex a single C–H bond mediates the interaction, folded arrangements of 3-alkylthiophenes require the collective effort of several aliphatic bonds
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