All Publications

  • Pendant Group Functionalization of Cyclic Olefin for High Temperature and High-Density Energy Storage. Advanced materials (Deerfield Beach, Fla.) Shukla, S., Wu, C., Mishra, A., Pan, J., Charnay, A. P., Khomane, A., Deshmukh, A., Zhou, J., Mukherjee, M., Gurnani, R., Rout, P., Casalini, R., Ramprasad, R., Fayer, M. D., Vashishta, P., Cao, Y., Sotzing, G. 2024: e2402133


    High-temperature flexible polymer dielectrics are critical for high-power-density energy storage and conversion under harsh operating conditions. These types of dielectrics will need to simultaneously possess a high bandgap, dielectric constant and glass transition temperature - a substantial challenge when designing novel dielectric polymers. In this work, by varying halogen substituents of an aromatic pendant hanging off a bicyclic mainchain polymer, a class of high-temperature olefins with adjustable thermal stability are obtained, all with uncompromised large bandgaps. Halogens substitution of the pendant groups at para or ortho position of polyoxanorborneneimides (PONB) imparts it with tunable high glass transition temperature from ∼220 to 245 °C, while with also moderate dielectric constant of ∼ 2.8-3.0 and high breakdown strength of ∼625-800 MV/m. A high energy density of 7.1 J/cc at 200 °C is achieved with p-POClNB, representing the highest reported energy density among all-organic homo-polymer dielectrics. Molecular dynamic simulations and ultrafast infrared spectroscopy were used to probe the free volume element distribution and chain relaxations of the polymers to provide insights to the dielectric thermal properties. An increase in free volume element is observed with the change in the pendant group from fluorine to bromine at the para position; however, a decrease in free volume element is observed as we change the pendant group from fluorine to chlorine at the ortho position because of the steric hindrance. Overall, the dielectric constant and band gap remain stable while the glass transition temperature changes more obviously. Consequently, by proper designing the pendant groups, the thermal stability of PONB can be improved for harsh condition electrification. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1002/adma.202402133

    View details for PubMedID 38767177

  • Restricted Orientation Anisotropy Method for FVE Radii Characterization: Confirmed and Refined via the Study of Six Vibrational Probes MACROMOLECULES Pan, J., Charnay, A. P., Fica-Contreras, S. M., Fayer, M. D. 2024; 57 (3): 903-915
  • Influence of Internal Bond Rotation on Ultrafast IR Anisotropy Measurements and the Internal Rotational Potential. The journal of physical chemistry. B Charnay, A. P., Pan, J., Fayer, M. D. 2023


    Measurement of molecular orientation relaxation using ultrafast infrared (IR) pump-probe experiments is widely used to understand the properties of liquids and other systems. In the simplest situation, the anisotropy decay is a single exponential reflecting diffusive orientational relaxation. However, the anisotropy decay is frequently biexponential. The faster component is caused by solvent caging restricting angular sampling until constraint release permits all angles to be sampled. Here, we describe another mechanism that limits the range of sampling, i.e., sampling of a restricted range of angles via internal bond reorientation on a rotational potential surface with barriers. If the internal angular sampling occurs faster than the entire molecule's diffusive orientational relaxation, it will produce a fast component of anisotropy decay with a cone angle determined by the shape of the internal rotation potential. We studied four molecules to illustrate the effects of internal bond rotations on anisotropy decay. The molecules are p-chlorobenzonitrile, phenylselenocyanate, phenylthiocyanate, and 2-nitrophenylselenocyante in the solvent N,N-dimethylformamide. The CN stretch is used as the IR chromophore. p-Chlorobenzonitrile does not have internal rotation; its anisotropy decays as a single exponential. The other three have bent geometries and internal rotation of the moieties containing the CN occurs; the anisotropies decay as biexponentials. The faster of the two decays can be understood in terms of motions on the rotational potential surface. A method is developed for extracting the intramolecular rotational potential surface by employing a modification of the harmonic cone model, and the results are compared to density functional theory calculations.

    View details for DOI 10.1021/acs.jpcb.3c07080

    View details for PubMedID 38150550

  • Synthetically tunable polymers, free volume element size distributions, and dielectric breakdown field strengths MATERIALS TODAY Fica-Contreras, S. M., Li, Z., Alamri, A., Charnay, A. P., Pan, J., Wu, C., Lockwood, J. R., Yassin, O., Shukla, S., Sotzing, G., Cao, Y., Fayer, M. D. 2023; 67: 57-67
  • Rethinking Vibrational Stark Spectroscopy: Peak Shifts, Line Widths, and the Role of Non-Stark Solvent Coupling. The journal of physical chemistry. B Fica-Contreras, S. M., Charnay, A. P., Pan, J., Fayer, M. D. 2023


    A vibration's transition frequency is partly determined by the first-order Stark effect, which accounts for the electric field experienced by the mode. Using ultrafast infrared pump-probe and FT-IR spectroscopies, we characterized both the 0 1 and 1 2 vibrational transitions' field-dependent peak positions and line widths of the CN stretching mode of benzonitrile (BZN) and phenyl selenocyanate (PhSeCN) in ten solvents. We present a theoretical model that decomposes the observed line width into a field-dependent Stark contribution and a field-independent non-Stark solvent coupling contribution (NSC). The model demonstrates that the field-dependent peak position is independent of the line width, even when the NSC dominates the latter. Experiments show that when the Stark tuning rate is large compared to the NSC (PhSeCN), the line width has a field dependence, albeit with major NSC-induced excursions from linearity. When the Stark tuning rate is small relative to the NSC (BZN), the line width is field-independent. BZN's line widths are substantially larger for the 1 2 transition, indicating a 1 2 transition enhancement of the NSC. Additionally, we examine, theoretically and experimentally, the difference in the 0 1 and 1 2 transitions' Stark tuning rates. Second-order perturbation theory combined with density functional theory explain the difference and show that the 1 2 transition's Stark tuning rate is 10% larger. The Stark tuning rate of PhSeCN is larger than BZN's for both transitions, consistent with the theoretical calculations. This study provides new insights into vibrational line shape components and a more general understanding of the vibrational response to external electric fields.

    View details for DOI 10.1021/acs.jpcb.2c06071

    View details for PubMedID 36629314

  • Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis. The journal of physical chemistry. B Fica-Contreras, S. M., Daniels, R., Yassin, O., Hoffman, D. J., Pan, J., Sotzing, G., Fayer, M. D. 2021


    Ultrafast infrared vibrational spectroscopy is widely used for the investigation of dynamics in systems from water to model membranes. Because the experimental observation window is limited to a few times the probe's vibrational lifetime, a frequent obstacle for the measurement of a broad time range is short molecular vibrational lifetimes (typically a few to tens of picoseconds). Five new long-lifetime aromatic selenocyanate vibrational probes have been synthesized and their vibrational properties characterized. These probes are compared to commercial phenyl selenocyanate. The vibrational lifetimes range between 400 and 500 ps in complex solvents, which are some of the longest room-temperature vibrational lifetimes reported to date. In contrast to vibrations that are long-lived in simple solvents such as CCl4, but become much shorter in complex solvents, the probes discussed here have 400 ps lifetimes in complex solvents and even longer in simple solvents. One of them has a remarkable lifetime of 1235 ps in CCl4. These probes have a range of molecular sizes and geometries that can make them useful for placement into different complex materials due to steric reasons, and some of them have functionalities that enable their synthetic incorporation into larger molecules, such as industrial polymers. We investigated the effect of a range of electron-donating and electron-withdrawing para-substituents on the vibrational properties of the CN stretch. The probes have a solvent-independent linear relationship to the Hammett substituent parameter when evaluated with respect to the CN vibrational frequency and the ipso 13C NMR chemical shift.

    View details for DOI 10.1021/acs.jpcb.1c04939

    View details for PubMedID 34339200

  • Distinguishing steric and electrostatic molecular probe orientational ordering via their effects on reorientation-induced spectral diffusion. The Journal of chemical physics Hoffman, D. J., Fica-Contreras, S. M., Pan, J., Fayer, M. D. 2021; 154 (24): 244104


    The theoretical framework for reorientation-induced spectral diffusion (RISD) describes the polarization dependence of spectral diffusion dynamics as measured with two-dimensional (2D) correlation spectroscopy and related techniques. Generally, RISD relates to the orientational dynamics of the molecular chromophore relative to local electric fields of the medium. The predictions of RISD have been shown to be very sensitive to both restricted orientational dynamics (generally arising from steric hindrance) and the distribution of local electric fields relative to the probe (electrostatic ordering). Here, a theory that combines the two effects is developed analytically and supported with numerical calculations. The combined effects can smoothly vary the polarization dependence of spectral diffusion from the purely steric case (least polarization dependence) to the purely electrostatic case (greatest polarization dependence). Analytic approximations of the modified RISD equations were also developed using the orientational dynamics of the molecular probe and two order parameters describing the degree of electrostatic ordering. It was found that frequency-dependent orientational dynamics are a possible consequence of the combined electrostatic and steric effects, providing a test for the applicability of this model to experimental systems. The modified RISD equations were then used to successfully describe the anomalous polarization-dependent spectral diffusion seen in 2D infrared spectroscopy in a polystyrene oligomer system that exhibits frequency-dependent orientational dynamics. The degree of polarization-dependent spectral diffusion enables the extent of electrostatic ordering in a chemical system to be quantified and distinguished from steric ordering.

    View details for DOI 10.1063/5.0053308

    View details for PubMedID 34241361

  • Free Volume Element Sizes and Dynamics in Polystyrene and Poly(methyl methacrylate) Measured with Ultrafast Infrared Spectroscopy. Journal of the American Chemical Society Fica-Contreras, S. M., Hoffman, D. J., Pan, J., Liang, C., Fayer, M. D. 2021


    The size, size distribution, dynamics, and electrostatic properties of free volume elements (FVEs) in polystyrene (PS) and poly(methyl methacrylate) (PMMA) were investigated using the Restricted Orientation Anisotropy Method (ROAM), an ultrafast infrared spectroscopic technique. The restricted orientational dynamics of a vibrational probe embedded in the polymer matrix provides detailed information on FVE sizes and their probability distribution. The probe's orientational dynamics vary as a function of its frequency within the inhomogeneously broadened vibrational absorption spectrum. By characterizing the degree of orientational restriction at different probe frequencies, FVE radii and their probability distribution were determined. PS has larger FVEs and a broader FVE size distribution than PMMA. The average FVE radii in PS and PMMA are 3.4 and 3.0 A, respectively. The FVE radius probability distribution shows that the PS distribution is non-Gaussian, with a tail to larger radii, whereas in PMMA, the distribution is closer to Gaussian. FVE structural dynamics, previously unavailable through other techniques, occur on a 150 ps time scale in both polymers. The dynamics involve FVE shape fluctuations which, on average, conserve the FVE size. FVE radii were associated with corresponding electric field strengths through the first-order vibrational Stark effect of the CN stretch of the vibrational probe, phenyl selenocyanate (PhSeCN). PMMA displayed unique measured FVE radii for each electric field strength. By contrast, PS showed that, while larger radii correspond to unique and relatively weak electric fields, the smallest measured radii map onto a broad distribution of strong electric fields.

    View details for DOI 10.1021/jacs.0c13397

    View details for PubMedID 33630576

  • Pulse-shaped chopping: Eliminating and characterizing heat effects in ultrafast infrared spectroscopy. The Journal of chemical physics Hoffman, D. J., Fica-Contreras, S. M., Pan, J., Fayer, M. D. 2020; 153 (20): 204201


    The infrared pulses used to generate nonlinear signals from a vibrational probe can cause heating via solvent absorption. Solvent absorption followed by rapid vibrational relaxation produces unwanted heat signals by creating spectral shifts of the solvent and probe absorptions. The signals are often isolated by "chopping," i.e., alternately blocking one of the incident pulses. This method is standard in pump-probe transient absorption experiments. As less heat is deposited into the sample when an incident pulse is blocked, the heat-induced spectral shifts give rise to artificial signals. Here, we demonstrate a new method that eliminates heat induced signals using pulse shaping to control pulse spectra. This method is useful if the absorption spectrum of the vibrational probe is narrow compared to the laser bandwidth. By using a pulse shaper to selectively eliminate only frequencies of light resonant with the probe absorption during the "off" shot, part of the pulse energy, and the resulting heat, is delivered to the solvent without generating the nonlinear signal. This partial heating reduces the difference heat signal between the on and off shots. The remaining solvent heat signal can be eliminated by reducing the wings of the on shot spectrum while still resonantly exciting the probe; the heat deposition from the on shot can be matched with that from the off shot, eliminating the solvent heat contribution to the signal. Modification of the pulse sequence makes it possible to measure only the heat signal, permitting the kinetics of heating to be studied.

    View details for DOI 10.1063/5.0031581

    View details for PubMedID 33261482

  • NMR Structural Analysis of Isolated Shaker Voltage-Sensing Domain in LPPG Micelles BIOPHYSICAL JOURNAL Chen, H., Pan, J., Gandhi, D. M., Dockendorff, C., Cui, Q., Chanda, B., Henzler-Wildman, K. A. 2019; 117 (2): 388–98


    The voltage-sensing domain (VSD) is a conserved structural module that regulates the gating of voltage-dependent ion channels in response to a change in membrane potential. Although the structures of many VSD-containing ion channels are now available, our understanding of the structural dynamics associated with gating transitions remains limited. To probe dynamics with site-specific resolution, we utilized NMR spectroscopy to characterize the VSD derived from Shaker potassium channel in 1-palmitoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) (LPPG) micelles. The backbone dihedral angles predicted based on secondary chemical shifts using torsion angle likeliness obtained from shift (TALOS+) showed that the Shaker-VSD shares many structural features with the homologous Kv1.2/2.1 chimera, including a transition from α-helix to 310 helix in the C-terminal portion of the fourth transmembrane helix. Nevertheless, there are clear differences between the Shaker-VSD and Kv1.2/2.1 chimera in the S2-S3 linker and S3 transmembrane region, where the organization of secondary structure elements in Shaker-VSD appears to more closely resemble the KvAP-VSD. Comparison of microsecond-long molecular dynamics simulations of Kv 1.2-VSD in LPPG micelles and a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayer showed that LPPG micelles do not induce significant structural distortion in the isolated voltage sensor. To assess the integrity of the tertiary fold, we directly probed the binding of BrMT analog 2-[2-({[3-(2-amino-ethyl)-6-bromo-1H-indol-2-yl]methoxy}k7methyl)-6-bromo-1H-indol-3-yl]ethan-1-amine (BrET), a gating modifier toxin, and identified the location of the putative binding site. Our results suggest that the Shaker-VSD in LPPG micelles is in a native-like fold and is likely to provide valuable insights into the dynamics of voltage-gating and its regulation.

    View details for DOI 10.1016/j.bpj.2019.06.020

    View details for Web of Science ID 000476709900019

    View details for PubMedID 31301804

  • Specificity landscapes unmask submaximal binding site preferences of transcription factors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bhimsaria, D., Rodriguez-Martinez, J. A., Pan, J., Roston, D., Korkmaz, E., Cui, Q., Ramanathan, P., Ansari, A. Z. 2018; 115 (45): E10586–E10595


    We have developed Differential Specificity and Energy Landscape (DiSEL) analysis to comprehensively compare DNA-protein interactomes (DPIs) obtained by high-throughput experimental platforms and cutting edge computational methods. While high-affinity DNA binding sites are identified by most methods, DiSEL uncovered nuanced sequence preferences displayed by homologous transcription factors. Pairwise analysis of 726 DPIs uncovered homolog-specific differences at moderate- to low-affinity binding sites (submaximal sites). DiSEL analysis of variants of 41 transcription factors revealed that many disease-causing mutations result in allele-specific changes in binding site preferences. We focused on a set of highly homologous factors that have different biological roles but "read" DNA using identical amino acid side chains. Rather than direct readout, our results indicate that DNA noncontacting side chains allosterically contribute to sculpt distinct sequence preferences among closely related members of transcription factor families.

    View details for DOI 10.1073/pnas.1811431115

    View details for Web of Science ID 000449459000011

    View details for PubMedID 30341220

    View details for PubMedCentralID PMC6233140