About

Maria Kamenetska is an Associate Professor in the departments of Chemistry and Physics at Boston University, with joint appointments in Material Science & Engineering and the Nanotechnology Innovation Center. She holds a PhD with distinction in Applied Physics from Columbia University, where she worked with Latha Venkataraman, and completed her undergraduate studies at MIT. Prior to joining BU in 2017, she was a Postdoctoral Associate in Chemistry at Yale University working with Ziad Ganim and an NSF Postdoctoral Fellow in Biophysics and Biochemistry at Yale. Her research focuses on condensed matter experiment, biophysics, and nano-devices, particularly exploring the properties of matter confined in one or two dimensions at the nanometer scale. Her group develops experimental approaches to probe the atomic structure and function of single molecule systems, utilizing techniques such as Scanning Tunneling Microscopy Break Junction, Atomic Force Microscopy, Optical Tweezers, and Raman Spectroscopy. Her work aims to understand electron charge transport in metal-molecule-metal junctions, the influence of interfaces on DNA-protein complexes, and the integration of single-molecule spectroscopy with nanomanipulation and force measurements. Her contributions advance the understanding of nanoscale physics and chemistry, with applications in biological and semiconducting materials.

Research topics

• Chemistry
• Physical chemistry
• Crystallography
• Nanotechnology
• Chemical physics
• Materials science
• Condensed matter physics
• Computational chemistry
• Organic chemistry
• Stereochemistry

Selected publications

• Metallophilicity Enhances Electron Transport through Parallel Organometallic 1D Chains Formed in Situ

  Journal of the American Chemical Society · 2026-02-18

  articleSenior authorCorresponding

  We reveal the role of aurophilic interactions in the formation and conductance of gold cyanide molecular wires of variable length-to-width ratios assembled at the tip of an STM break junction in ambient conditions. Specifically, we identify electron transport signatures through 1D single chains containing variable number of monomeric repeats of gold cyanide AuCN, linked in series (AuCN)n, and through adjacent molecular wires linked in parallel. When bound in series, destructive quantum interference causes an exponential decay of conductance in (AuCN)n 1D wires for n = 1–3. But when bound in parallel, aurophilic coupling through the gold atoms of neighboring chains reorders electronic states and results in significant enhancement of conductance. Our work reveals that metallophilicity can play a significant role in junction assembly and electron transport characteristics.

  PublisherDOI

• Single Molecule Force Measurements Reveal Energy Stabilization of Theophylline Aptamer RNA Switch Required for Gene Control

  ACS Physical Chemistry Au · 2026-01-02

  articleOpen accessSenior authorCorresponding

  RNA aptamers play essential roles in gene regulation, sensing, and therapeutics, relying on ligand-induced kinetic changes for function. The theophylline aptamer has been engineered to regulate synthetic gene networks in response to the presence of the theophylline small molecule ligand, but the thermodynamic and kinetic parameters behind theophylline’s unique function are not known. Here, we use optical tweezers single-molecule force spectroscopy to measure the folding dynamics of the theophylline aptamer in the presence and absence of ligand. We find that theophylline binding does not affect folding rates but significantly slows unfolding by stabilizing the aptamer by ∼3.6 kBT, or ∼2.1 kcal/mol. These results support a conformational selection model of ligand binding and reveal no evidence of large structural rearrangement upon ligand association. Our findings suggest that theophylline-induced stabilization, rather than structural remodeling, drives aptamer function in synthetic biology applications to regulate gene expression. This kinetic stabilization supports prior work proposing a kinetic trap mechanism, in which the long-lived, folded ligand-bound state delays ribosome binding and translation. These insights emphasize the kinetic basis of RNA-mediated regulation and inform the future design of ptamer-based tools in synthetic biology and therapeutics.

  PublisherDOI

• Abstract 4077 Single molecule force measurements reveal energy stabilization of theophylline aptamer RNA switch required for gene control

  Journal of Biological Chemistry · 2026-05-01

  articleOpen accessSenior author
  PublisherDOI

• Metallophilicity Enhances Electron Transport through Parallel Organometallic 1D Chain Junctions Formed In Situ

  ArXiv.org · 2025-08-02

  preprintOpen accessSenior author

  We reveal the role of aurophilic interactions in the formation and conductance of gold cyanide molecular wires of variable length-to-width ratios assembled at the tip of an STM break junction in ambient conditions. Specifically, we identify electron transport signatures through 1D single chains containing variable number of monomeric repeats of gold cyanide AuCN, linked in series (AuCN)n, and through adjacent molecular wires linked in parallel. When bound in series, destructive quantum interference causes an exponential decay of conductance in (AuCN)n 1D wires for n=1-3. But when bound in parallel, aurophilic coupling through the gold atoms of neighboring chains reorders electronic states and results in significant enhancement of conductance. Our work reveals that metallophilicity can play a significant role in junction assembly and electron transport characteristics.

  PublisherOA PDFDOI

• Controlled Incorporation of Silver Atoms into Coordination Chain Single-Molecule Junctions Formed on Gold Electrodes

  Nano Letters · 2025-08-15

  articleSenior authorCorresponding

  Enhancing the functionality of molecular junctions through control over the electrode composition, molecular anchor groups, and metal–molecule coupling remains a central goal in advancing molecular electronics. Here, we introduce silver species onto gold electrodes to construct bimetallic coordination bridges of the form (Im––M)n (n = 1 and 2), where M = Ag or Au, using imidazolate (Im–) ligands, and to investigate their transport properties. Through electrochemical control, we systematically modulate the incorporation of silver and observe a corresponding conductance suppression with an increasing concentration of Ag+. Our experimental measurements and density functional theory (DFT)-based calculations reveal that the decreased density of d-states on silver reduces the orbital coupling between the molecular HOMO and silver-tipped gold electrodes, leading to lower transport. Overall, this work determines that weakened metal–molecule coupling is responsible for conductance reduction of imine-terminated molecules on silver and establishes a generalizable approach for incorporating transition metal atoms into molecular circuits in ambient environments.

  PublisherDOI

• Conductance and assembly of quasi-1D coordination chain molecular junctions with triazole derivatives

  Dalton Transactions · 2024-01-01 · 5 citations

  articleOpen accessSenior authorCorresponding

  Binding site electron density in σ-type molecular orbitals is the decisive factor in the in situ assembly of quasi-1D coordination chains using triazole (Tr) isomer ligands in molecular junctions.

  PublisherOA PDFDOI

• Making the Most of Nothing: One-Class Classification for Single-Molecule Transport Studies

  ACS Nanoscience Au · 2024-06-06 · 3 citations

  articleOpen accessCorresponding

  Single-molecule experiments offer a unique means to probe molecular properties of individual molecules-yet they rest upon the successful control of background noise and irrelevant signals. In single-molecule transport studies, large amounts of data that probe a wide range of physical and chemical behaviors are often generated. However, due to the stochasticity of these experiments, a substantial fraction of the data may consist of blank traces where no molecular signal is evident. One-class (OC) classification is a machine learning technique to identify a specific class in a data set that potentially consists of a wide variety of classes. Here, we examine the utility of two different types of OC classification models on four diverse data sets from three different laboratories. Two of these data sets were measured at cryogenic temperatures and two at room temperature. By training the models solely on traces from a blank experiment, we demonstrate the efficacy of OC classification as a powerful and reliable method for filtering out blank traces from a molecular experiment in all four data sets. On a labeled 4,4'-bipyridine data set measured at 4.2 K, we achieve an accuracy of 96.9 ± 0.3 and an area under the receiver operating characteristic curve of 99.5 ± 0.3 as validated over a fivefold cross-validation. Given the wide range of physical and chemical properties that can be probed in single-molecule experiments, the successful application of OC classification to filter out blank traces is a major step forward in our ability to understand and manipulate molecular properties.

  PublisherOA PDFDOI

• Tunable growth of a single high-density ZIF nanoshell on a gold nanoparticle isolated in an optical trap

  Nanoscale · 2024-01-01

  articleOpen accessSenior authorCorresponding

  darkfield spectroscopy. Our single particle approach allows us to localize an individual NP within a microscope slide chamber containing ZIF precursors at the focus of an optical microscope and initiate growth through localized heating without affecting the bulk system. Darkfield spectroscopy is used to characterize changes to the localized surface plasmon resonance (LSPR) of the AuNP resulting from refractive index changes as the ZIF crystal grows on the surface. We show that the procedure can be generalized to grow various types of ZIF crystals, such as ZIF-8, ZIF-11, and a previously undocumented ZIF variety. Utilizing both computational models and experimental methods, we identify the thickness of ZIF layers to be self-limiting to ∼50 nm or less, depending on the trapping laser power. Critically, the refractive index of the shells here was found to be above 1.6, indicating the formation of high-density crystals, previously accessible only through slow atomic layer deposition and not through a bulk heating process. The single particle method developed here opens the door for bottom-up controllable growth of custom nanostructures with tunable optical properties.

  PublisherOA PDFDOI

• Extreme anti-ohmic conductance enhancement in neutral diradical acene-like molecular junctions

  arXiv (Cornell University) · 2024-03-07 · 1 citations

  preprintOpen accessSenior author

  We achieve, at room temperature, conductance enhancements over two orders of magnitude in single molecule circuits formed with polycyclic benzoquinoidal (BQn) diradicals upon increasing molecular length by ~0.5 nm. We find that this extreme and atypical anti-ohmic conductance enhancement at longer molecular lengths is due to the diradical character of the molecules, which can be described as a topologically non-trivial electronic state. We adapt the 1D-SSH model originally developed to examine electronic topological order in linear carbon chains to the polycyclic systems studied here and find that it captures the anti-ohmic trends in this molecular series. The mechanism of conductance enhancement with length is revealed to be constructive quantum interference (CQI) between the frontier orbitals with non-trivial topology, which is present in acene-like, but not in linear, molecular systems. Importantly, we predict computationally and measure experimentally that anti-ohmic trends can be engineered through synthetic adjustments of the diradical character of the acene-like molecules. Overall, we achieve an experimentally unprecedented anti-ohmic enhancement and mechanistic insight into electronic transport in a class of materials that we identify here as promising candidates for creating highly conductive and tunable nanoscale wires.

  PublisherOA PDFDOI

• Autoregressive HMM resolves biomolecular transitions from passive optical tweezer force measurements

  Biophysical Journal · 2024-11-29 · 1 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

Recent grants

• NSF Postdoctoral Fellowship in Biology for FY 2011

  NSF · $123k · 2012–2013

• CAREER: Probing and Manipulating Electronic and Spin Degrees of Freedom in Paramagnetic Single Molecule Circuits

  NSF · $702k · 2022–2027

Frequent coauthors

• Latha Venkataraman

  Columbia University

  62 shared

• Mark S. Hybertsen

  Brookhaven National Laboratory

  54 shared

• Michael L. Steigerwald

  Columbia University

  42 shared

• Colin Nuckolls

  Columbia University

  41 shared

• Adam C. Whalley

  University of Vermont

  29 shared

• Jeffrey B. Neaton

  University of California, Berkeley

  21 shared

• Young S. Park

  20 shared

• Su Ying Quek

  National University of Singapore

  19 shared

Education

• Ph.D., Physics

  Massachusetts Institute of Technology

  2006

• M.S., Physics

  Massachusetts Institute of Technology

  2003

• B.S., Physics

  University of Chicago

  2001