Department of Chemistry

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Chemical Physics Letter

<a href="https://www.sciencedirect.com/science/article/pii/S0009261422002809">Structural changes of interfacial water upon fluid-ripple-gel phase transitions of bilayers</a>

Journal of Molecular Structure

Diorganostannoxanes Stabilized by Intramolecular N→ Sn Coordination Approach: Synthesis, Structure, TD-DFT and Hirshfeld Surface Analysis

A Non-Football Cage Type Dodecanuclear Organostannoxane: Synthesis, Structure and NDR Behaviour

Organic \& Biomolecular Chemistry

Stereoselective synthesis of tri-substituted tetrahydrothiophenes and their in silico binding against mycobacterial protein tyrosine phosphatase B

ACS omega

Designing a Redox Noninnocent Phenalenyl-Based Copper (II) Complex: An Autotandem Catalyst for the Selective Oxidation of Polycyclic Aromatic Hydrocarbons (PAHs)

Recently, there has been substantial interest in the fluorination of nanomaterials-based thin films used in various optoelectronic devices for optimum charge transport across semiconducting layers. The discovery of electrophilic fluorinating agents such as Selectfluor (R) (F-TEDA) has led to the development of novel methods for fluorination of metal oxides such as tin oxide (SnO2) in this work. Herein, we elucidate the fluorination of SnO2 thin films using X-ray photoelectron spectroscopy (XPS) depth profiling. The interaction of the F-TEDA molecule with the SnO2 surface occurs via N-F bonds. Fluorine is found to occupy interstices and substitutional sites in the SnO2 lattice. The interstitial fluorine (1.21 at\%) decays off by a depth of 61 nm in the SnO2 film. The substitutional fluorine (1.28 at\%) in SnO2 results in remarkable changes in its electronic structure due to the lowering of oxygen defects by similar to 80\%. The electrical properties of the F-SnO2 film is examined by impedance spectroscopy analysis. F-SnO2 exhibits an increase in electrical conductivity by similar to 1-2 orders of magnitude and an increase in electron density by similar to 65\%, making it suitable as a charge transport layer in photoelectrochemical cells (PECs). The PEC in aqueous medium at neutral pH with F-SnO2 as the charge transport layer shows similar to 81\% increase in the photocurrent density (at 1.6 V versus RHE) and decrease in charge transfer resistance by similar to 36\%. Thus, the efficient transport of photogenerated charge carriers is observed in PECs with minimal recombination losses for the fluorinated SnO2 films. This study helps in understanding the role of defect passivation via single-step fluorination of metal-oxide for charge transport layers which can be extended to perovskite solar cells in the future.

JOURNAL OF MATERIALS CHEMISTRY A

Chemical insights into electrophilic fluorination of SnO2 for photoelectrochemical applications

The role of second-order saddle in the isomerization dynamics was investigated by considering the E-Z isomerization of guanidine. The potential energy profile for the reaction was mapped using the ab initio wavefunction method. The isomerization path involved a torsional motion about the imine (C-N) bond in a clockwise or an anticlockwise fashion resulting in two degenerate transition states corresponding to a barrier of 23.67 kcal/mol.An alternative energetically favorable path (~1 kcal/mol higher than the transition states) by an in-plane motion of the imine (N-H) bond via a second-order saddle point on the potential energy surface was also obtained. The dynamics of the isomerization was investigated by ab initio classical trajectory simulations. The trajectories reveal that isomerization happens via the transition states as well as the second-order saddle. The dynamics was found to be nonstatistical with trajectories exhibiting recrossing and the higher energy second-order saddle pathway preferred over the traditional transition state pathway. Wavelet based time-frequency analysis of internal coordinates indicate regular dynamics and existence of long-lived quasi-periodic trajectories in the phase space. © 2021, Pleiades Publishing, Ltd.

Regular and Chaotic Dynamics

Second-order Saddle Dynamics in Isomerization Reaction

Abstract: The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data. Graphic Abstract: [Figure not available: see fulltext.] © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC part of Springer Nature.

Journal of Membrane Biology

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα-1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα-0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature. © 2021 Author(s).

Fulltext

Journal of Chemical Physics

Dehydration induced dynamical heterogeneity and ordering mechanism of lipid bilayers

Molecular design, synthesis, and biological evaluation of tubulysin analogues, linker-drugs, and antibody-drug conjugates are described. Among the new discoveries reported is the identification of new potent analogues within the tubulysin family that carry a C11 alkyl ether substituent, rather than the usual ester structural motif at that position, a fact that endows the former with higher plasma stability than that of the latter. Also described herein are X-ray crystallographic analysis studies of two tubulin-tubulysin complexes formed within the α/β interface between two tubulin heterodimers and two highly potent tubulysin analogues, one of which exhibited a different binding mode to the one previously reported for tubulysin M. The X-ray crystallographic analysis-derived new insights into the binding modes of these tubulysin analogues explain their potencies and provide inspiration for further design, synthesis, and biological investigations within this class of antitumor agents. A number of these analogues were conjugated as payloads with appropriate linkers at different sites allowing their attachment onto targeting antibodies for cancer therapies. A number of such antibody-drug conjugates were constructed and tested, both in vivo and in vitro, leading to the identification of at least one promising ADC (Herceptin-LD3), warranting further investigations. © 2021 American Chemical Society.

Journal of Organic Chemistry

Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding Derived from X-ray Crystallographic Analysis