Jun Nishida is a PhD student at Department of Chemistry, Stanford University. He studied Chemistry at University of Tokyo, Japan, as an undergraduate student (2007-2011), and also at National Chiao Tung University, Taiwan, as an exchange student (2010-2011). At Stanford, he is currently working on the development of experimental and theoretical methods to characterize ultrafast dynamics of molecules at interfaces.

Honors & Awards

  • Stanford Graduate Fellowship, Stanford Japanese Association Fellow, Stanford University/ Stanford Japanese Association (2013.9-2016.9)
  • Study Encouragement Award, University of Tokyo, School of Science (2011.4)

Education & Certifications

  • B.S., University of Tokyo, School of Science, Chemistry (2011)

All Publications

  • Orientational Dynamics of a Functionalized Alkyl Planar Monolayer Probed by Polarization-Selective Angle-Resolved Infrared Pump-Probe Spectroscopy. Journal of the American Chemical Society Nishida, J., Yan, C., Fayer, M. D. 2016: -?


    Polarization-selective angle-resolved infrared pump-probe spectroscopy was developed and used to study the orientational dynamics of a planar alkylsiloxane monolayer functionalized with a rhenium metal carbonyl headgroup on an SiO2 surface. The technique, together with a time-averaged infrared linear dichroism measurement, characterized picosecond orientational relaxation of the headgroup occurring at the monolayer-air interface by employing several sets of incident angles of the infrared pulses relative to the sample surface. By application of this method and using a recently developed theory, it was possible to extract both the out-of-plane and "mainly"-in-plane orientational correlation functions in a model-independent manner. The observed correlation functions were compared with theoretically derived correlation functions based on several dynamical models. The out-of-plane correlation function reveals the highly restricted out-of-plane motions of the head groups and also suggests that the angular distribution of the transition dipole moments is bimodal. The mainly-in-plane correlation function, for the sample studied here with the strongly restricted out-of-plane motions, essentially arises from the purely in-plane dynamics. In contrast to the out-of-plane dynamics, significant in-plane motions occurring over various time scales were observed including an inertial motion, a restricted wobbling motion of ∼3 ps, and complete randomization occurring in ∼25 ps.

    View details for PubMedID 27668512

  • Water of Hydration Dynamics in Minerals Gypsum and Bassanite: Ultrafast 2D IR Spectroscopy of Rocks. Journal of the American Chemical Society Yan, C., Nishida, J., Yuan, R., Fayer, M. D. 2016; 138 (30): 9694-9703


    Water of hydration plays an important role in minerals, determining their crystal structures and physical properties. Here ultrafast nonlinear infrared (IR) techniques, two-dimensional infrared (2D IR) and polarization selective pump-probe (PSPP) spectroscopies, were used to measure the dynamics and disorder of water of hydration in two minerals, gypsum (CaSO4·2H2O) and bassanite (CaSO4·0.5H2O). 2D IR spectra revealed that water arrangement in freshly precipitated gypsum contained a small amount of inhomogeneity. Following annealing at 348 K, water molecules became highly ordered; the 2D IR spectrum became homogeneously broadened (motional narrowed). PSPP measurements observed only inertial orientational relaxation. In contrast, water in bassanite's tubular channels is dynamically disordered. 2D IR spectra showed a significant amount of inhomogeneous broadening caused by a range of water configurations. At 298 K, water dynamics cause spectral diffusion that sampled a portion of the inhomogeneous line width on the time scale of ∼30 ps, while the rest of inhomogeneity is static on the time scale of the measurements. At higher temperature, the dynamics become faster. Spectral diffusion accelerates, and a portion of the lower temperature spectral diffusion became motionally narrowed. At sufficiently high temperature, all of the dynamics that produced spectral diffusion at lower temperatures became motionally narrowed, and only homogeneous broadening and static inhomogeneity were observed. Water angular motions in bassanite exhibit temperature-dependent diffusive orientational relaxation in a restricted cone of angles. The experiments were made possible by eliminating the vast amount of scattered light produced by the granulated powder samples using phase cycling methods.

    View details for DOI 10.1021/jacs.6b05589

    View details for PubMedID 27385320

  • Unraveling the dynamics and structure of functionalized self-assembled monolayers on gold using 2D IR spectroscopy and MD simulations PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Yan, C., Yuan, R., Pfalzgraff, W. C., Nishida, J., Wang, L., Markland, T. E., Fayer, M. D. 2016; 113 (18): 4929-4934


    Functionalized self-assembled monolayers (SAMs) are the focus of ongoing investigations because they can be chemically tuned to control their structure and dynamics for a wide variety of applications, including electrochemistry, catalysis, and as models of biological interfaces. Here we combine reflection 2D infrared vibrational echo spectroscopy (R-2D IR) and molecular dynamics simulations to determine the relationship between the structures of functionalized alkanethiol SAMs on gold surfaces and their underlying molecular motions on timescales of tens to hundreds of picoseconds. We find that at higher head group density, the monolayers have more disorder in the alkyl chain packing and faster dynamics. The dynamics of alkanethiol SAMs on gold are much slower than the dynamics of alkylsiloxane SAMs on silica. Using the simulations, we assess how the different molecular motions of the alkyl chain monolayers give rise to the dynamics observed in the experiments.

    View details for DOI 10.1073/pnas.1603080113

    View details for Web of Science ID 000375395700026

    View details for PubMedID 27044113

  • Carbon dioxide in an ionic liquid: Structural and rotational dynamics. journal of chemical physics Giammanco, C. H., Kramer, P. L., Yamada, S. A., Nishida, J., Tamimi, A., Fayer, M. D. 2016; 144 (10): 104506-?


    Ionic liquids (ILs), which have widely tunable structural motifs and intermolecular interactions with solutes, have been proposed as possible carbon capture media. To inform the choice of an optimal ionic liquid system, it can be useful to understand the details of dynamics and interactions on fundamental time scales (femtoseconds to picoseconds) of dissolved gases, particularly carbon dioxide (CO2), within the complex solvation structures present in these uniquely organized materials. The rotational and local structural fluctuation dynamics of CO2 in the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2) were investigated by using ultrafast infrared spectroscopy to interrogate the CO2 asymmetric stretch. Polarization-selective pump probe measurements yielded the orientational correlation function of the CO2 vibrational transition dipole. It was found that reorientation of the carbon dioxide occurs on 3 time scales: 0.91 ± 0.03, 8.3 ± 0.1, 54 ± 1 ps. The initial two are attributed to restricted wobbling motions originating from a gating of CO2 motions by the IL cations and anions. The final (slowest) decay corresponds to complete orientational randomization. Two-dimensional infrared vibrational echo (2D IR) spectroscopy provided information on structural rearrangements, which cause spectral diffusion, through the time dependence of the 2D line shape. Analysis of the time-dependent 2D IR spectra yields the frequency-frequency correlation function (FFCF). Polarization-selective 2D IR experiments conducted on the CO2 asymmetric stretch in the parallel- and perpendicular-pumped geometries yield significantly different FFCFs due to a phenomenon known as reorientation-induced spectral diffusion (RISD), revealing strong vector interactions with the liquid structures that evolve slowly on the (independently measured) rotation time scales. To separate the RISD contribution to the FFCF from the structural spectral diffusion contribution, the previously developed first order Stark effect RISD model is reformulated to describe the second order (quadratic) Stark effect-the first order Stark effect vanishes because CO2 does not have a permanent dipole moment. Through this analysis, we characterize the structural fluctuations of CO2 in the ionic liquid solvation environment, which separate into magnitude-only and combined magnitude and directional correlations of the liquid's time dependent electric field. This new methodology will enable highly incisive comparisons between CO2 dynamics in a variety of ionic liquid systems.

    View details for DOI 10.1063/1.4943390

    View details for PubMedID 26979696

  • Coupling of Carbon Dioxide Stretch and Bend Vibrations Reveals Thermal Population Dynamics in an Ionic Liquid JOURNAL OF PHYSICAL CHEMISTRY B Giammanco, C. H., Kramer, P. L., Yamada, S. A., Nishida, J., Tamimi, A., Fayer, M. D. 2016; 120 (3): 549-556


    The population relaxation of carbon dioxide dissolved in the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2) was investigated using polarization-selective ultrafast infrared pump-probe spectroscopy and two-dimensional infrared (2D IR) spectroscopy. Due to the coupling of the bend with the asymmetric stretch, excitation of the asymmetric stretch of a molecule with a thermally populated bend leads to an additional peak, a hot band, which is red-shifted from the main asymmetric absorption band by the combination band shift. This hot band peak exchanges population with the main peak through the gain and loss of bend excitation quanta. The isotropic pump-probe signal originating from the unexcited bend state displays a fast, relatively small amplitude, initial growth followed by a longer time scale exponential decay. The signal is analyzed over its full time range using a kinetic model to determine both the vibrational lifetime (the final decay) and rate constant for the loss of the bend energy. This bend relaxation manifests as the fast initial growth of the stretch/no bend signal because the hot band (stretch with bend) is "over pumped" relative to the ground state equilibrium. The nonequilibrium pumping occurs because the hot band has a larger transition dipole moment than the stretch/no bend peak. The system is then prepared, utilizing an acousto-optic mid-infrared pulse shaper to cut a hole in the excitation pulse spectrum, such that the hot band is not pumped. The isotropic pump-probe signal from the stretch/no bend state is altered because the initial excited state population ratio has changed. Instead of a growth due to relaxation of bend quanta, a fast initial decay is observed because of thermal excitation of the bend. Fitting this curve gives the rate constant for thermal excitation of the bend and the lifetime, which agree with those determined in the pump-probe experiments without frequency-selective pumping.

    View details for DOI 10.1021/acs.jpcb.5b11454

    View details for Web of Science ID 000369116000018

    View details for PubMedID 26731088

  • Separation of experimental 2D IR frequency-frequency correlation functions into structural and reorientation-induced contributions. journal of chemical physics Kramer, P. L., Nishida, J., Fayer, M. D. 2015; 143 (12): 124505-?


    A vibrational transition frequency can couple to its environment through a directional vector interaction. In such cases, reorientation of the vibrational transition dipole (molecular orientational relaxation) and its frequency fluctuations can be strongly coupled. It was recently shown [Kramer et al., J. Chem. Phys. 142, 184505 (2015)] that differing frequency-frequency correlation function (FFCF) decays, due to reorientation-induced spectral diffusion (RISD), are observed with different two-dimensional infrared polarization configurations when such strong coupling is present. The FFC functional forms were derived for the situation in which all spectral diffusion is due to reorientational motion. We extend the previous theory to include vibrational frequency evolution (spectral diffusion) caused by structural fluctuations of the medium. Model systems with diffusive reorientation and several regimes of structural spectral diffusion rates are analyzed for first order Stark effect interactions. Additionally, the transition dipole reorientational motion in complex environments is frequently not completely diffusive. Several periods of restricted angular motion (wobbling-in-a-cone) may precede the final diffusive orientational randomization. The polarization-weighted FFCF decays are presented in this case of restricted transition dipole wobbling. With these extensions to the polarization-dependent FFCF expressions, the structural spectral diffusion dynamics of methanol in the room temperature ionic liquid 1-hexyl-3-methylimidazolium hexafluorophosphate can be separated quantitatively from RISD using the experimental center line slope data. In addition, prior results on the spectral diffusion of water, methanol, and ethanol in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide are re-examined to elucidate the influence of reorientation on the data, which were interpreted in terms of structural fluctuations.

    View details for DOI 10.1063/1.4931402

    View details for PubMedID 26429022

  • Structural Influences on the Fast Dynamics of Alkylsiloxane Monolayers on SiO2 Surfaces Measured with 2D IR Spectroscopy JOURNAL OF PHYSICAL CHEMISTRY C Yan, C., Yuan, R., Nishida, J., Fayer, M. D. 2015; 119 (29): 16811-16823
  • Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy. journal of chemical physics Kramer, P. L., Nishida, J., Giammanco, C. H., Tamimi, A., Fayer, M. D. 2015; 142 (18): 184505-?


    In nearly all applications of ultrafast multidimensional infrared spectroscopy, the spectral degrees of freedom (e.g., transition frequency) and the orientation of the transition dipole are assumed to be decoupled. We present experimental results which confirm that frequency fluctuations can be caused by rotational motion and observed under appropriate conditions. A theory of the frequency-frequency correlation function (FFCF) observable under various polarization conditions is introduced, and model calculations are found to reproduce the qualitative trends in FFCF rates. The FFCF determined with polarization-selective two-dimensional infrared (2D IR) spectroscopy is a direct reporter of the frequency-rotational coupling. For the solute methanol in a room temperature ionic liquid, the FFCF of the hydroxyl (O-D) stretch decays due to spectral diffusion with different rates depending on the polarization of the excitation pulses. The 2D IR vibrational echo pulse sequence consists of three excitation pulses that generate the vibrational echo, a fourth pulse. A faster FFCF decay is observed when the first two excitation pulses are polarized perpendicular to the third pulse and the echo, 〈XXY Y〉, than in the standard all parallel configuration, 〈XXXX〉, in which all four pulses have the same polarization. The 2D IR experiment with polarizations 〈XY XY〉 ("polarization grating" configuration) gives a FFCF that decays even more slowly than in the 〈XXXX〉 configuration. Polarization-selective 2D IR spectra of bulk water do not exhibit polarization-dependent FFCF decays; spectral diffusion is effectively decoupled from reorientation in the water system.

    View details for DOI 10.1063/1.4920949

    View details for PubMedID 25978898

  • Structural dynamics inside a functionalized metal-organic framework probed by ultrafast 2D IR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America Nishida, J., Tamimi, A., Fei, H., Pullen, S., Ott, S., Cohen, S. M., Fayer, M. D. 2014; 111 (52): 18442-18447


    The structural elasticity of metal-organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer.

    View details for DOI 10.1073/pnas.1422194112

    View details for PubMedID 25512539

  • Theory of third-order spectroscopic methods to extract detailed molecular orientational dynamics for planar surfaces and other uniaxial systems JOURNAL OF CHEMICAL PHYSICS Nishida, J., Fayer, M. D. 2014; 140 (14)

    View details for DOI 10.1063/1.4870436

    View details for Web of Science ID 000334836600028

  • Dynamics of Molecular Monolayers with Different Chain Lengths in Air and Solvents Probed by Ultrafast 2D IR Spectroscopy JOURNAL OF PHYSICAL CHEMISTRY C Nishida, J., Yan, C., Fayer, M. D. 2014; 118 (1): 523-532

    View details for DOI 10.1021/jp410683h

    View details for Web of Science ID 000329678200056

  • Structural Dynamics at Monolayer-Liquid Interfaces Probed by 2D IR Spectroscopy JOURNAL OF PHYSICAL CHEMISTRY C Rosenfeld, D. E., Nishida, J., Yan, C., Kumar, S. K., Tamimi, A., Fayer, M. D. 2013; 117 (3): 1409-1420

    View details for DOI 10.1021/jp311144b

    View details for Web of Science ID 000314205100023

  • Anharmonic coupling of the CH-stretch and CH-bend vibrations of chloroform as studied by near-infrared electroabsorption spectroscopy JOURNAL OF CHEMICAL PHYSICS Nishida, J., Shigeto, S., Yabumoto, S., Hamaguchi, H. 2012; 137 (23)


    Combination bands that involve CH- or OH-stretch vibrations appear in the near-infrared (NIR) region (4000-10 000 cm(-1)). Because they arise from anharmonic coupling between the component fundamentals, detailed analysis of the frequency and intensity of NIR combination bands allows one to elucidate the mechanisms behind the vibrational coupling in the condensed phase in terms of mechanical and electrical anharmonicities. Nevertheless, little has been studied, in particular experimentally, on the origin of the combination band intensity. Here, we show that NIR electroabsorption (EA) spectroscopy, which directly probes the effects of an externally applied electric field on a combination band, can shed new light on anharmonic vibrational coupling through determination of the direction of the transition moment for the combination band. We studied the combination band of the CH-stretch (ν(1)) and CH-bend (ν(4)) modes of liquid chloroform. The electric-field induced absorbance change of the ν(1) + ν(4) combination band caused by reorientation of the chloroform molecule was measured at various χ angles, where χ is the angle between the direction of the applied electric field and the polarization of the incident IR light. We were able to detect an absorbance change as small as 5 × 10(-8) for the combination band. Using the NIR EA spectra of the combination band together with those of the CH-stretch and bend fundamentals, the angle between the transition moment for the combination band and the permanent dipole moment was determined experimentally for the first time to be (79 ± 14)°. The present investigation indicates that the contribution of the CH-stretch mode to the mechanical anharmonicity is minor and that the CH-bend mode plays a dominant role in the mechanical part of the vibrational coupling between the two fundamentals. Furthermore, density functional theory calculations show that both the mechanical anharmonicity of the CH-bend mode and the electrical anharmonicity may contribute equally to the anharmonic coupling.

    View details for DOI 10.1063/1.4770264

    View details for Web of Science ID 000312780300028

    View details for PubMedID 23267490

  • Dynamics of Functionalized Surface Molecular Monolayers Studied with Ultrafast Infrared Vibrational Spectroscopy JOURNAL OF PHYSICAL CHEMISTRY C Rosenfeld, D. E., Nishida, J., Yan, C., Gengeliczki, Z., Smith, B. J., Fayer, M. D. 2012; 116 (44): 23428-23440


    The structural dynamics of thin films consisting of tricarbonyl (1,10-phenanthroline)rhenium chloride (RePhen(CO)(3)Cl) linked to an alkyl silane monolayer through a triazole linker synthesized on silica-on-calcium-fluoride substrates are investigated using ultrafast infrared (IR) techniques. Ultrafast 2D IR vibrational echo experiments and polarization selective heterodyne detected transient grating (HDTG) measurements, as well as polarization dependent FT-IR and AFM experiments are employed to study the samples. The vibrational echo experiments measure spectral diffusion, while the HDTG experiments measure the vibrational excited state population relaxation and investigate the vibrational transition dipole orientational anisotropy decay. To investigate the anticipated impact of vibrational excitation transfer, which can be caused by the high concentration of RePhen(CO)(3)Cl in the monolayer, a concentration dependence of the spectral diffusion is measured. To generate a range of concentrations, mixed monolayers consisting of both hydrogen terminated and triazole/RePhen(CO)(3)Cl terminated alkyl silanes are synthesized. It is found that the measured rate of spectral diffusion is independent of concentration, with all samples showing spectral diffusion of 37 ± 6 ps. To definitively test for vibrational excitation transfer, polarization selective HDTG experiments are conducted. Excitation transfer will cause anisotropy decay. Polarization resolved heterodyne detected transient grating spectroscopy is sensitive to anisotropy decay (depolarization) caused by excitation transfer and molecular reorientation. The HDTG experiments show no evidence of anisotropy decay on the appropriate time scale, demonstrating the absence of excitation transfer the RePhen(CO)(3)Cl. Therefore the influence of excitation transfer on spectral diffusion is inconsequential in these samples, and the vibrational echo measurements of spectral diffusion report solely on structural dynamics. A small amount of very fast (~2 ps time scale) anisotropy decay is observed. The decay is concentration independent, and is assigned to wobbling-in-a-cone orientational motions of the RePhen(CO)(3)Cl. Theoretical calculations reported previously for experiments on a single concentration of the same type of sample suggested the presence of some vibrational excitation transfer and excitation transfer induced spectral diffusion. Possible reasons for the experimentally observed lack of excitation transfer in these high concentration samples are discussed.

    View details for DOI 10.1021/jp307677b

    View details for Web of Science ID 000310769300031

    View details for PubMedID 23259027