02399nas a2200169 4500008004100000022001400041245008200055210006900137260000800206300001600214490000700230520181800237100001902055700002102074700002002095856011402115 2023 eng d a1463-907600aMolecular mechanisms underlying nanowire formation in pristine phthalocyanine0 aMolecular mechanisms underlying nanowire formation in pristine p cNOV a30259-302680 v253 a

Understanding the molecular processes of nanowire self-assembly is crucial for designing and controlling nanoscale structures that could lead to breakthroughs in functional materials. In this work, we focus on pristine phthalocyanines as a representative example of mesogenic supramolecular assemblies and have analyzed the formation of nanowires using classical molecular dynamics simulations. In the simulations, the molecules spontaneously form multi-columnar structures resembling supramolecular polymers that subsequently grow into more ordered aggregates. These self-assemblies are concentration dependent, leading to the formation of multi-columnar, dynamic aggregates at higher concentrations and nanowires at lower concentrations. The multi-columnar assemblies on a whole are more disordered than the nanowires, but have locally ordered domains of parallel facing molecules that can fluctuate while maintaining their overall shape. The nanowire formation at lower concentrations involves the initial interaction and clustering of randomly oriented phthalocyanine molecules, followed by the merging of small clusters into elongated segments and the eventual formation of a stable nanowire. We observe three main conformers in these self-assemblies, the parallel, T-shaped and edge-to-edge stacking of the phthalocyanine dimers. We calculate the underlying free energy landscape and show that the parallel conformers form the most stable configuration which is followed by the T-shaped and edge-to-edge dimer configurations. The findings provide insights into the mechanisms and pathways of nanowire formation and a step towards the understanding of self-assembly processes in supramolecular mesogens. Understanding the molecular processes of nanowire self-assembly of phthalocyanine molecules.

1 aPinjari, Aadil1 aSaraf, Deepashri1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-mechanisms-underlying-nanowire-formation-pristine-phthalocyanine02172nas a2200265 4500008004100000022001400041245007500055210006900130260000900199300001100208490000800219520135600227653001101583653001201594653003101606653002301637653001801660653002001678100002101698700002001719700001901739700002401758700002001782856010401802 2023 eng d a0167-732200aSurface-induced demixing of self-assembled isomeric mixtures of citral0 aSurfaceinduced demixing of selfassembled isomeric mixtures of ci cJUL  a1218030 v3813 a

The self-assembly of organic molecules and their interactions with metal surfaces have been of considerable interest, both for developing novel functional materials and for understanding fundamental design principles of nanostructures. In this study, we investigate the solution and surface-induced self-assembly of two stereoisomers of citral molecules (geranial and neral) using atomistic molecular dynamics simulations. We demonstrate that the morphology of the aggregates in water is concentration dependent (ranging from distorted spherical to slab-like aggregates) but independent of isomer effects. The isomeric mixtures of citral indicate homogeneous mixing based on differential density maps and high values of Shannon entropy. Interestingly, surface-confinement of citral aggregates on a Cu(111) surface leads to phase segregation and demixing of the two isomers that is more apparent in the surface-bound monolayer in comparison to the adjacent layers. Positional ordering and formation of domains are observed over a series of isomeric citral mixtures with varying compositions, as indicated by high differential density and low values of Shannon entropy. Our work provides new insights into molecular self-assembly of organic molecules in nanostructures and metal-organic overlayers.(c) 2023 Elsevier B.V. All rights reserved.

10aCitral10aIsomers10aMetal-organic interactions10amolecular dynamics10aSelf-assembly10aShannon entropy1 aSaraf, Deepashri1 aPrakash, Shikha1 aPinjari, Aadil1 aPujari, Bhalchandra1 aSengupta, Durba uhttps://library.ncl.res.in/content/surface-induced-demixing-self-assembled-isomeric-mixtures-citral02516nas a2200217 4500008004100000022001400041245007100055210006900126260000800195300001400203490000700217520182800224100001702052700002302069700002002092700002102112700001902133700002302152700002002175856010302195 2025 eng d a1463-907600aAnomalous membrane organization by omega-6 and omega-9 fatty acids0 aAnomalous membrane organization by omega6 and omega9 fatty acids cMAR a6235-62480 v273 a

Omega fatty acids are currently being marketed as healthy food supplements as they have been implicated in multiple pathophysiological conditions, such as reducing plaque formation of A beta peptide and inhibiting SARS-CoV-2 infection. Their mode of action has been hypothesized to be via membrane reorganization by the unsaturated acyl chains, leading to the modulation of lipid-protein cross-talk. However, the lack of molecular details led us to evaluate the molecular effect of omega-6 (linolenic acid) and omega-9 (oleic acid) fatty acids on membrane organization using a consolidated approach of fluorescence spectroscopy and all-atom molecular dynamics simulation. Our results show that the effect of these omega fatty acids is sensitive to their protonation states. Contrary to the accepted notion that chain unsaturation causes membrane disordering, both experimental and simulation results demonstrate that protonated linoleic acid promotes membrane ordering, despite having two unsaturations at the fatty acyl chain. However, protonated oleic fatty acid, with reduced unsaturation, disordered the acyl chain area of the lipid membranes. Equally surprisingly, deprotonated oleic acid orders, whereas deprotonated linoleic acid disorders, the membrane core region. Interestingly, while the lipid order parameter measurements from simulations did not capture these subtle differences, the calculated rotational autocorrelation function of a membrane dye was in line with experimentally measured apparent rotational correlation times. Our work provides a comprehensive revised molecular picture of the effect of omega fatty acids on membranes and highlights the importance of rigorous comparative approaches, as experimental and simulation studies in isolation can sometimes lead to inconsistent results.

1 aPorte, Sudha1 aPandia, Swaratmika1 aJoardar, Ankita1 aSaraf, Deepashri1 aPinjari, Aadil1 aChakraborty, Hirak1 aSengupta, Durba uhttps://library.ncl.res.in/content/anomalous-membrane-organization-omega-6-and-omega-9-fatty-acids