A5031929282- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- RNA modifications and cancer
- Nanopore and Nanochannel Transport Studies
- RNA Research and Splicing
- Covalent Organic Framework Applications
- Enzyme Structure and Function
- Force Microscopy Techniques and Applications
- Luminescence and Fluorescent Materials
- RNA Interference and Gene Delivery
- HIV/AIDS drug development and treatment
- Bacterial Genetics and Biotechnology
- Metal-Organic Frameworks: Synthesis and Applications
- Advanced biosensing and bioanalysis techniques
- Electrostatics and Colloid Interactions
- Bacteriophages and microbial interactions
- Lipid Membrane Structure and Behavior
- Per- and polyfluoroalkyl substances research
- HIV Research and Treatment
- DNA Repair Mechanisms
- Supramolecular Chemistry and Complexes
- Spectroscopy and Quantum Chemical Studies
- Bone Tissue Engineering Materials
- Metal and Thin Film Mechanics
New York University
2018-2025
Courant Institute of Mathematical Sciences
2025
Smart Material (Germany)
2025
New York University Abu Dhabi
2015-2024
New Mexico Consortium
2014-2017
Los Alamos National Laboratory
2014-2015
The University of Texas at Austin
2005-2014
Syracuse University
2007
Texas A&M Health Science Center
2007
Sabancı Üniversitesi
2003
A bowl-shaped calix[4]arene with its exciting host–guest chemistry is a versatile supramolecular building block for the synthesis of distinct coordination cages or metal–organic frameworks. However, utility in crystalline covalent organic frameworks (COFs) remains challenging, presumably due to conformational flexibility. Here, we report periodic 2D extended network calix[4]arenes joined by linear benzidine linker via dynamic imine bonds. By tuning interaction among neighboring calixarene...
Abstract Controlling the number of molecular switches and their relative positioning within porous materials is critical to functionality properties. The proximity many one another can hinder or completely suppress response. Herein, a synthetic strategy involving mixed linkers used control distribution spiropyran-functionalized in covalent organic framework (COF). COF contains spiropyran each pore which exhibits excellent reversible photoswitching behavior its merocyanine form solid state...
A strategy that can be used to develop metal–organic frameworks (MOFs) capture per- and poly-fluoroalkyl substances (PFAS) from water is functionalizing them with fluorine moieties. We investigated different fluorine-functionalization strategies their performance in removing PFAS using molecular simulations. Perfluorooctanoic acid (PFOA), one of the most widely encountered sources, was as probe molecule. Our simulations show functionalization by incorporating fluorinated anions bridging...
Amyloid proteins and peptides are a major contributing factor to the development of various neurodegenerative disorders, including Alzheimer’s prion diseases. Previously, designed cell-penetrating peptide (CPP) comprising hydrophobic signal sequence followed by protein (PrP)-derived polycationic (PrP23–28: KKRPKP) was shown have potent anti-prion properties. Here, we extend this approach toward amyloid-beta (Aβ) amyloid formation, which is associated with disease. We characterized...
On account of its nonbiodegradable nature and persistence in the environment, perfluorooctanoic acid (PFOA) accumulates water resources poses serious environmental issues many parts world. Here, we present development two fluorine-rich calix[4]arene-based porous polymers, FCX4-P FCX4-BP, demonstrate their utility for efficient removal PFOA from water. These materials featured Brunauer–Emmett–Teller (BET) surface areas up to 450 m2 g–1, which is slightly lower than nonfluorinated counterparts...
The high proliferation rate of tumor cells demands energy and metabolites that are sustained by a glycolytic flux known as the 'Warburg effect'. activation further metabolism glucose is initiated hexokinase, focal point metabolic regulation. human hexokinase 2 (HK2) overexpressed in all aggressive tumors predominantly found on outer mitochondrial membrane, where interactions through its N-terminus initiates maintains tumorigenesis. Here, we report structure HK2 complex with...
Abstract Visual sensing of humidity and temperature by solids plays an important role in the everyday life industrial processes. Due to their hydrophobic nature, most covalent organic framework (COF) sensors often exhibit poor optical response when exposed moisture. To overcome this challenge, is set out improve, moisture incorporating H‐bonding ionic functionalities into COF network. A highly sensitive COF, consisting guanidinium diformylpyridine linkers (TG‐DFP), capable detecting changes...
The method of Directional Milestoning is revisited. We start from an exact and more general expression state the conditions validity memory-loss approximation. An algorithm to compute a reaction coordinate data presented. calculated as set discrete jumps between Milestones that maximizes flux two stable states. As application we consider conformational transition in solvated adenosine. compare long molecular dynamic trajectory with discuss differences maximum path minimum energy coordinates.
Abstract Owing to their chemical and thermal stabilities, high uptake capacities, easy recyclability, covalent organic polymers (COPs) have shown promise as pollutant sponges. Herein, we describe the use of diazo coupling synthesize two cationic COPs, COP1 ++ COP2 , that incorporate a viologen‐based molecular switch an macrocycle, calix[4]arene. The COPs form nanosheets height profiles 6.00 nm 8.00 nm, respectively, based on AFM measurements. sheets remain morphologically intact upon one‐ or...
Azacalix[n]arenes (ACAs) are lesser-known cousins of calix[n]arenes that contain amine bridges instead methylene bridges, so they generally have higher flexibility due to enlarged cavities. Herein, we report a highly substituted cationic azacalix[4]arene-based covalent organic framework (ACA-COF) synthesized by the Zincke reaction under microwave irradiation. The current work is rare example synthetic strategy utilizes chemical functionalization an macrocycle constrain its conformational...
Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures monovalent and divalent considered explicitly. Studies tightly bound diffusive (but bound) 25 base pairs conducted in explicit solvent. Replica exchange simulations provide equilibrium with moderate computing resources (20 ns simulation using 64 replicas). The show distinct behavior single double charged cations. Binding Mg2+ ion includes tight binding to specific sites while Na+ binds only...
Remarkable new insight has emerged into the biological role of RNA in cells. folding and dynamics enable many these newly discovered functions, calling for an understanding self-assembly conformational dynamics. Because RNAs pass through multiple structures as they fold, ensemble perspective is required to visualize flow fleetingly populated sets states. Here, we combine microfluidic mixing technology small angle X-ray scattering (SAXS) measure Mg-induced a domain, tP5abc three helix...
Calixarenes are a common motif in supramolecular chemistry but have rarely been incorporated structurally well-defined covalent 2D materials. Such task is challenging, especially without template, because of the nonplanar configuration and conformational flexibility calixarene ring. Here, we report first-of-a-kind solvothermal synthesis calix[4]arene-based polymer (CX4-NS) that porous, covalent, isolated as few-layer thick (3.52 nm) nanosheets. Experimental theoretical characterization...
Abstract Since their initial presentation in 2005 by Yaghi and co-workers, covalent organic frameworks (COFs) have been the focus of much development. Here we introduce mechanical bonds into COFs employing a method that involves supramolecular self-assembly, dynamic imine-bond formation, liquid-liquid interfacial condensation produces continuous 2D polyrotaxaneted film. A diamino-viologen linker is complexed with macrocycle cucurbit[7]uril (CB[7]) to form pseudorotaxanes then condense an...
Abstract Probing the role of surface structure in electrostatic interactions, we report first observation sequence-dependent dsDNA condensation by divalent alkaline earth metal cations. Disparate behaviors were found between two repeating sequences with 100% AT content, a poly(A)-poly(T) duplex (AA-TT) and poly(AT)-poly(TA) (AT-TA). While AT-TA exhibits non-distinguishable from random-sequence genomic DNA, AA-TT condenses all ions. We characterized these interactions experimentally...
The structural diversity of nucleic acid duplexes reflects the critical roles sequence, ions, and waters.
Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem systematically determining proper reaction coordinate (RC) specific process terms set putative can be achieved using committor analysis (CA). Identifying essential degrees freedom that govern such CA remains elusive because high...
Abstract SARS-CoV-2 depends on −1 programmed ribosomal frameshifting (−1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating PRF is thus an attractive drug target. However, the structural models of this obtained from cryo-EM and crystallography differ in some important features, leaving structure unclear. We measured solution using small-angle X-ray scattering (SAXS). profile did not agree with profiles computed previously solved structures. Beginning each...