About

Ivan J. Dmochowski is the Alan MacDiarmid Term Professor of Chemistry at the University of Pennsylvania. His research focuses on a broad range of areas including Biological, Biophysical Chemistry, Chemical Biology, Chemical Physics and Physical Chemistry, Inorganic, and Materials Chemistry. He is based in room 348 N with laboratory spaces in rooms 332, 334, 336, and 338 N. The information provided highlights his interdisciplinary approach, integrating multiple chemistry subfields to advance understanding and innovation in these areas.

Research topics

• Chemistry
• Nuclear magnetic resonance
• Combinatorial chemistry
• Physical chemistry
• Physics
• Materials science
• Biochemistry
• Crystallography
• Biology
• Genetics
• Organic chemistry
• Stereochemistry
• Nanotechnology

Selected publications

• Cavity acidification limits ferritin iron biomineralization

  Journal of Inorganic Biochemistry · 2026-01-22

  articleOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• Unusually air-stable copper(<scp>i</scp>) complexes showing high selectivity for carbon monoxide

  Chemical Science · 2025-01-01 · 1 citations

  articleOpen accessSenior authorCorresponding

  . Spectroscopy, electrochemical, and X-ray crystal structure analyses indicate that the phenyl rotators of the capsule select for small axial ligands.

  PublisherOA PDFDOI

• siRNA-Mimetic Ratiometric pH (sMiRpH) Probes for Improving Cell Delivery and mRNA Knockdown

  ACS Chemical Biology · 2025-02-05 · 1 citations

  articleSenior authorCorresponding

  Second-generation siRNA-mimetic ratiometric pH probes (sMiRpH-2) were developed by hybridizing a 3'-FAM-labeled 2'-OMe RNA strand with a 3'-Cy5-labeled 25mer RNA strand. These duplexes demonstrated the silencing of cytoplasmic mRNA targets in HeLa cells as measured by RT-qPCR and supported by western blot analysis. Fluorescence intensity and lifetime measurements revealed that a single guanosine (G) positioned adjacent to FAM achieves substantial static quenching at pH 5, with additional collisional quenching rendering the dye almost nonemissive. A FAM-G π-π stacking interaction was evidenced by a red-shifted absorbance spectrum for FAM. Decreased quenching at near-neutral pH enhances the FAM dynamic range in the physiologic pH window and improves the differentiation in cells between endocytic entrapment and cytoplasmic release. Flow cytometric analysis of intracellular pH and uptake using sMiRpH-2 was corroborated by live cell confocal microscopy and found to be predictive of knockdown efficacy. A sMiRpH-2 probe successfully predicted the relative efficacy of two transfection agents in more challenging SK-OV-3 cells, which highlights its use for the rapid assessment of nonviral siRNA delivery vectors.

  PublisherDOI

• Correction: Charge engineering controls cooperative assembly and loading in protein host–guest complexes

  Journal of Materials Chemistry B · 2025-01-01 · 1 citations

  erratumOpen accessSenior authorCorresponding

  Correction for ‘Charge engineering controls cooperative assembly and loading in protein host–guest complexes’ by Zhiheng Wang et al. , J. Mater. Chem. B , 2025, https://doi.org/10.1039/D5TB01202C.

  PublisherOA PDFDOI

• Exosome-Mediated Mitochondrial Delivery of Antisense Oligonucleotides

  Nucleic Acid Therapeutics · 2025-06-25

  articleOpen accessSenior author

  -methyl (2'-OMe) RNA oligonucleotides (oligos) to mitochondria for antisense applications, with potential for implementation in other mitochondrial DNA (mtDNA)-targeted therapies. Exosomes, which are nanoscale, naturally occurring extracellular vesicles (EVs), have been employed for biotechnology applications in oligonucleotide delivery in recent years. We discovered that exosomes from fetal bovine serum (FBS) can be used as a simple and biologically compatible delivery agent of 2'-OMe RNA antisense oligonucleotides to cellular mitochondria, leading to target protein knockdown. While most RNA interference and antisense mechanisms occur in the cytoplasm or nucleus, the need for mitochondrial targeting has become increasingly apparent. Mitochondrial disease describes a variety of currently incurable syndromes that especially affect organs requiring significant energy including the muscles, heart, and brain. Many of these syndromes result from mutations in mtDNA, which codes for the 13 proteins of the oxidative phosphorylation system and are thus often implicated in inherited metabolic disorders.

  PublisherOA PDFDOI

• Correction: Interfacial rheology of lanthanide binding peptide surfactants at the air–water interface

  Soft Matter · 2025-01-01

  erratumOpen access

  Correction for ‘Interfacial rheology of lanthanide binding peptide surfactants at the air–water interface’ by Stephen A. Crane et al. , Soft Matter , 2024, 20 , 9161–9173, https://doi.org/10.1039/D4SM00493K.

  PublisherOA PDFDOI

• RIBOsensor for FRET-based, real-time ribose measurements in live cells

  Chemical Science · 2025-01-01 · 2 citations

  articleOpen accessSenior authorCorresponding

  d-Ribose is a building block of many essential biomolecules, including all nucleic acids, and its supplementation can enhance energy production, particularly under stress conditions such as ischemia and heart failure. The distribution, biosynthesis, and regulation of ribose in mammalian systems remain poorly understood. To explore intracellular ribose dynamics, we developed a genetically encoded fluorescence resonance energy transfer (FRET) sensor using ribose binding protein (RBP) and enhanced cyan and yellow fluorescent proteins (FPs). The RIBOsensor, which positions one FP near the active site of RBP, achieves the necessary sensitivity for cellular imaging by increasing the FRET signal upon ribose binding, compared to traditional N- and C-terminal FP orientations. This sensor rapidly, reversibly, and selectively detects labile ribose in live cells-enabling longitudinal studies-and can be employed for intracellular ribose quantitation, which provides a valuable tool for investigating ribose transport and metabolism in normal and disease states.

  PublisherOA PDFDOI

• Charge engineering controls cooperative assembly and loading in protein host–guest complexes

  Journal of Materials Chemistry B · 2025-01-01 · 1 citations

  articleOpen accessSenior author

  ferritin. Guided by molecular dynamics (MD) simulations and computational protein design, experiments confirmed that GFP charge magnitude and distribution dictate capsule assembly and loading efficiency. These data provide the first example of cooperative assembly with a ferritin capsule. Finally, we established a strategy for generating stoichiometric 1 : 1 protein host-guest complexes, confirmed by time-resolved fluorescence anisotropy. This provides a blueprint for designing ferritin host-guest complexes with enhanced homogeneity and functionality.

  PublisherOA PDFDOI

• Continuous Delivery of Hyperpolarized Xenon-129 Gas Using a “Stopped-Flow” Clinical-Scale Cryogen-Free Hyperpolarizer

  Analytical Chemistry · 2025-02-04

  articleOpen access

  In 2022, the FDA approved hyperpolarized (HP) 129Xe gas as an inhalable contrast agent for functional lung imaging. For clinical imaging, HP 129Xe is usually given as a bolus inhalation. However, for preclinical applications (e.g., pulmonary imaging in small rodents), the continuous delivery of HP 129Xe is greatly desired to enable MRI scanning under conditions of physiological continuous animal breathing patterns. Moreover, HP 129Xe gas can be utilized for other applications including materials science and bioanalytical chemistry, where a continuous flow of hyperpolarized gas through an NMR sample over several minutes is also desired for sensing of 129Xe inside an NMR spectrometer. 129Xe is often hyperpolarized using continuous-flow spin-exchange optical pumping, which employs a lean (1–2%) mixture of Xe and a carrier gas (e.g., He and N2). The low Xe concentration in the produced output reduces the NMR detection sensitivity, and thus, Xe cryo-collection is typically employed to achieve near-100% pure gas-phase Xe before administration to the sample or subject. However, the need for cryo-collection undermines a key advantage of continuous-flow production, i.e., the continuous flowing in a hyperpolarizer HP 129Xe gas is trapped inside the hyperpolarizer, and the produced HP 129Xe gas is released at once when the production cycle (30–60 min) is completed. An alternative HP 129Xe production technology employs a “stopped-flow” approach, where a batch of HP gas is hyperpolarized over time and quickly released from a hyperpolarizer. Here, a clinical-scale “stopped-flow” 129Xe hyperpolarizer was employed to hyperpolarize a 1.3 L-atm batch of 50:50 Xe:N2 gas mixture inside a glass cell with an ultralong lifetime of the HP 129Xe state (T1 > 2 h). The produced HP 129Xe gas was slowly delivered into a 5 mm NMR tube via PEEK tubing under a wide range of gas flow rates: 3–180 standard cubic centimeters per minute (sccm). The polarization of the gas ejected from the hyperpolarizer was quantified using in situ low-field NMR polarimetry and additionally verified using a 0.35 T clinical MRI scanner. Continuous-flow delivery of HP 129Xe was demonstrated for up to 15 min with a gas flow rate of 45–150 sccm over a 2.5-m length of PEEK tubing, suffering only small losses in 129Xe polarization. These observations are additionally supported by 129Xe relaxation measurements inside the PEEK tubing employed for gas delivery and the 5 mm NMR tube employed for polarimetry. 129Xe polarization of 16–19% was obtained in the delivered gas, starting with an “in-polarizer” 129Xe polarization of 19%. We envision that this method can be employed for on-demand cryogen-free delivery of hyperpolarized gas using “stopped-flow” 129Xe hyperpolarizers for a broad range of applications, from preclinical imaging to biosensors, and to spectroscopy of materials surfaces.

  PublisherOA PDFDOI

• Improved Large-Scale Synthesis of Acridonylalanine for Diverse Peptide and Protein Applications

  Bioconjugate Chemistry · 2024-11-12 · 4 citations

  articleOpen access

  Fluorescent unnatural amino acids give biochemists, biophysicists, and bioengineers new ways to probe the properties of proteins and peptides. Here, the synthesis of acridon-2-ylalanine (Acd) is optimized for large-scale production to enable ribosomal incorporation through genetic code expansion (GCE), and fluorenylmethoxycarbonyl (Fmoc)-protected Acd is prepared for solid-phase peptide synthesis (SPPS). We demonstrate the utility of Acd in several applications: first, Acd quenching by Tyr is used in the design of fluorescent protease sensors made by SPPS. Second, we demonstrate Acd incorporation into a lanthanide-binding peptide that is generated either by GCE or by SPPS and demonstrate the utility of Acd for sensitizing the emission of Eu3+. Finally, Acd is inserted into the intrinsically disordered protein, α-synuclein, using GCE and used to study ion binding and aggregation.

  PublisherOA PDFDOI

Recent grants

• NIH Grant S10RR023444

  NIH · $308k · 2009

• Computationally designed synergistic protein-nanoparticle assemblies

  NSF · $545k · 2015–2018

• MRI: Acquisition of Tri-Institutional, Cyber-Enabled Chemistry MALDI-TOF Mass Spectrometer

  NSF · $435k · 2008–2011

• NIH Grant S10RR021113

  NIH · $995k · 2008

• Light-activated oligonucleotides for biological applications

  NIH · $3.0M · 2008–2019

Frequent coauthors

• Serge D. Zemerov

  University of Pennsylvania

  51 shared

• P. Aru Hill

  Denison University

  30 shared

• Benjamin W. Roose

  Merck & Co., Inc., Rahway, NJ, USA (United States)

  30 shared

• Teresa L. Rapp

  University of Washington

  26 shared

• Jeffery G. Saven

  University of Pennsylvania

  25 shared

• Michael R. Gau

  24 shared

• Yanfei Wang

  23 shared

• Katherine W. Pulsipher

  University of Pennsylvania

  21 shared

Awards & honors

• Caltech Herbert Newby McCoy Award (2000)
• Helen Hay Whitney Postdoctoral Fellow, Biophysics, Caltech (…
• Camille and Henry Dreyfus New Faculty Award (2003)
• National Science Foundation CAREER Award (2005)
• Camille and Henry Dreyfus Teacher-Scholar Award (2007)