Stanford Advisors

All Publications

  • Complex Formation and Dissociation Dynamics on Amorphous Silica Surfaces. The journal of physical chemistry. B Yamada, S. A., Hung, S. T., Shin, J. Y., Fayer, M. D. 2021


    Benzene complex formation and dissociation dynamics with silanols on the amorphous silica surfaces of nanoporous SiO2, from a benzene/carbon tetrachloride solution, were measured by the growth of off-diagonal peaks in the two-dimensional infrared (2D IR) chemical exchange spectrum of the isolated Si-OD stretch. The presence of two types of isolated silanols, termed type I and II, was revealed, with dissociation time constants of 82 and 4.0 ps, respectively. The type I silanols are associated with the main IR absorption feature in the Si-OD stretching region, while the type II silanols give rise to a broader shoulder to lower frequency. Polarization selective pump-probe (PSPP) measurements provided the vibrational lifetimes and orientational relaxation rates of the two silanols in the CCl4 (free) and benzene (complex) environments. The type II silanols constitute roughly 30% of the isolated silanol population and exhibit a substantially faster rate of vibrational relaxation, making the type I dynamics the dominant contribution to the PSPP and 2D IR signals. From the measured dissociation times, the enthalpies of formation for the two surface complexes were obtained, with the formation of the type I complex being significantly more exothermic. As the type II site is preferentially removed from the amorphous silica surface with increasing activation temperature, the results provide a reasonable explanation for the increased exothermicity of benzene adsorption on silica with increasing activation temperature in previous calorimetry experiments.

    View details for DOI 10.1021/acs.jpcb.1c01225

    View details for PubMedID 33890776

  • Orientational Pair Correlations and Local Structure of Benzonitrile from Molecular Dynamics Simulations with Comparisons to Experiments. The journal of physical chemistry. B Sha, M., Yamada, S. A., Fayer, M. D. 2021


    We present an experimentally parametrized molecular dynamics study of single-molecule and collective orientational relaxation in neat benzonitrile through the analysis of the reorientational anisotropy and polarizability anisotropy time correlation function (PA-TCF). The simulations show that the PA-TCF is dominated by collective reorientation after 20 ps. Collective reorientation is found to be slower than single-molecule reorientation by a factor of 1.67, consistent with recent experiments. The simulations provide direct evidence of local antiparallel benzonitrile configurations. These structures, which have been the center of some debate, are responsible for the slower rate of collective versus single-molecule reorientation in the liquid. Further structural analysis indicates that significant Coulombic interactions between the nitrile group and hydrogen atoms on adjacent molecules play a role in the formation of the antiparallel structures. The single-molecule dynamics reflected in the anisotropy are complex and consist of a ballistic regime, restricted angular diffusion, and spatially anisotropic free diffusion. The principal components of the rotational diffusion tensor are independently obtained and shown to reproduce the free diffusion regime of the anisotropy for each principal axis according to the predictions of a previous theory.

    View details for DOI 10.1021/acs.jpcb.0c11148

    View details for PubMedID 33730488

  • Effects of pore size on water dynamics in mesoporous silica. The Journal of chemical physics Yamada, S. A., Hung, S. T., Thompson, W. H., Fayer, M. D. 2020; 152 (15): 154704


    Water confined in mesoporous silica plays a central role in its many uses ranging from gas sorption to nanoconfined chemical reactions. Here, the influence of pore diameter (2.5-5.4 nm) on water hydrogen bond (H-bond) dynamics in MCM41 and SBA15 mesoporous silicas is investigated using femtosecond infrared vibrational spectroscopy and molecular dynamics simulations on selenocyanate (SeCN-) anions dissolved in the pores. As shown recently, SeCN- spectral diffusion is a reliable probe of surrounding water H-bond structural motions. Additionally, the long CN stretch vibrational lifetime facilitates measurement of the full range of confined dynamics, which are much slower than in bulk water. The simulations shed light on quantitative details that are inaccessible from the spatially averaged observables. The dependence of SeCN- orientational relaxation and that of spectral diffusion on the distance from the silica interface are quantitatively described with an exponential decay and a smoothed step-function, respectively. The distance-dependence of both quantities is found to be independent of the diameter of the pores, and the spatial distribution of SeCN- is markedly non-uniform, reaching a maximum between the interface and the pore center. The results indicate that the commonly invoked two-state, or core-shell, model is a more appropriate description of spectral diffusion. Using these insights, we model the full time-dependence of the measured dynamics for all pore sizes and extract the "core" and "shell" dynamical correlation functions and SeCN- spatial probability distributions. The results are critically compared to those for water confined in reverse micelles.

    View details for DOI 10.1063/1.5145326

    View details for PubMedID 32321257

  • Enhanced Menshutkin SN2 Reactivity in Mesoporous Silica: The Influence of Surface Catalysis and Confinement. Journal of the American Chemical Society Zheng, W., Yamada, S. A., Hung, S. T., Sun, W., Zhao, L., Fayer, M. D. 2020


    A significant enhancement in the Menshutkin SN2 reaction between 1-methylimidazole (MeIm) and methyl thiocyanate (MeSCN) is observed when the reaction is confined in the nanoscale silica pores of MCM41 and SBA15. The experiments in the silica pores are conducted without the surrounding bulk reaction mixture. The influences of temperature, pore radius, and surface chemistry on the kinetics of the confined reaction are analyzed with time-dependent infrared spectroscopy, molecular dynamics simulations, and ab initio calculations. The rate constant of the pseudo-first order reaction increases with decreasing pore size, and the activation energy is found to decrease by 5.6 kJ/mol in the smallest pore studied (2.8 nm) relative to the bulk reaction. The rate constant dependence on pore size is accurately described by a two-state model in which molecules within the 4.6 A interfacial layer experience a 2.4-fold rate constant increase relative to those reacting at the bulk rate further away from the interface. The removal of polar silanol groups from the silica surface via passivation with trimethylsilyl chloride results in bulk-like kinetics despite a reduction in the pore diameter, demonstrating the role of silanols as catalytic sites. Electronic structure calculations of the energy profile on a model silica surface confirm that silanol groups, particularly those of the vicinal type, can reduce the activation energy and reaction endothermicity through the donation of hydrogen bonds to the reactant, transition state, and product complexes.

    View details for DOI 10.1021/jacs.9b12666

    View details for PubMedID 32077695

  • Water Dynamics in Nanoporous Silica: Ultrafast Vibrational Spectroscopy and Molecular Dynamics Simulations JOURNAL OF PHYSICAL CHEMISTRY C Yamada, S. A., Shin, J., Thompson, W. H., Fayer, M. D. 2019; 123 (9): 5790–5803
  • Imidazole and 1-Methylimidazole Hydrogen Bonding and Nonhydrogen Bonding Liquid Dynamics: Ultrafast IR Experiments. The journal of physical chemistry. B Shin, J. Y., Wang, Y., Yamada, S. A., Hung, S. T., Fayer, M. D. 2019


    The dynamics of imidazole (IM) and 1-methylimidazole (1-MeIM) in the liquid phase at 95 °C were studied by IR polarization selective pump-probe and two-dimensional IR (2D IR) spectroscopies. The two molecules are very similar structurally except that IM can be simultaneously a hydrogen bond donor and acceptor and therefore forms extended hydrogen-bonded networks. The broader IR absorption spectrum and a shorter vibrational lifetime of the vibrational probe, selenocyanate anion (SeCN-), in IM vs 1-MeIM indicate that stronger hydrogen bonding exists between SeCN- and IM. Molecular dynamics (MD) simulations support the strong hydrogen bond formation between SeCN- and IM via the HN moiety. SeCN- makes two H-bonds with IM; it is inserted in the IM H-bonded chains rather than being a chain terminator. The strong hydrogen bonding influenced the reorientation dynamics of SeCN- in IM, leading to a more restricted short time angular sampling (wobbling-in-a-cone). The complete orientational diffusion time in IM is 1.7 times slower than in 1-MeIM, but the slow down is less than expected, considering the 3-fold larger viscosity of IM. The jump reorientation mechanism accounts for the anomalously fast orientational relaxation in IM, and the MD simulations determined the average jump angle of the probe between hydrogen bonding sites. Spectral diffusion time constants obtained from the 2D IR experiments are only modestly slower in IM than in 1-MeIM in spite of the significant increase in viscosity. The results indicate that the spectral diffusion sensed by the SeCN- has IM hydrogen bond dynamics contributions not present in 1-MeIM.

    View details for PubMedID 30727725

  • Orientational Pair Correlations in a Dipolar Molecular Liquid: Time-Resolved Resonant and Nonresonant Pump-Probe Spectroscopies. The journal of physical chemistry. B Yamada, S. A., Bailey, H. E., Fayer, M. D. 2018


    Orientational pair correlations (OPCs), when they are sufficiently strong in a liquid, contain information on the interplay between structure and dynamics that arise from intermolecular interactions. Consequently, the quantification of OPCs remains a subject of substantial interest in current experimental and theoretical works. In the case of benzonitrile, the importance of OPCs remains ambiguous, owing to the use of model-dependent analyses or reliance on a single spectroscopic technique. Here, IR polarization-selective pump-probe (PSPP) and optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments were used to quantify OPCs in benzonitrile. These methods measure single molecule and collective orientational relaxation dynamics, respectively. A comparison of the orientational correlation function (PSPP) of the naturally abundant 13CN stretching mode and the polarizability anisotropy relaxation (OHD-OKE) of the liquid revealed that the collective reorientation time was a factor of 1.56 ± 0.08 slower than the single molecule reorientation time. The two types of measurements on dilute benzonitrile in carbon tetrachloride were the same within experimental error. These results support the proposition that OPCs exist and arise from the formation of parallel-aligned intermolecular structures in the neat liquid.

    View details for PubMedID 30411625

  • Influence of Water on Carbon Dioxide and Room Temperature Ionic Liquid Dynamics: Supported Ionic Liquid Membrane vs the Bulk Liquid JOURNAL OF PHYSICAL CHEMISTRY B Shin, J., Yamada, S. A., Fayer, M. D. 2018; 122 (8): 2389–95


    The influence of water on the dynamics of a room temperature ionic liquid (RTIL), 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2), and CO2 in the RTIL was studied in the bulk liquid and a supported ionic liquid membrane (SILM) using two-dimensional infrared (IR) and IR polarization selective pump-probe spectroscopies. In the water-saturated bulk EmimNTf2, the complete orientational randomization and structural spectral diffusion (SSD) of CO2 became faster than in the dry EmimNTf2. In the poly(ether sulfone) SILM, only the longer time components of the SSD became faster in the water-saturated RTIL; the complete orientational randomization remained similar to the dry RTIL in the SILM. The implication is that the presence of water in EmimNTf2 contained in the SILM facilitates the fluctuation of globally modified RTIL structure in the pores, but the local RTIL environments are relatively unaffected.

    View details for PubMedID 29412666

  • Dynamics in a Room-Temperature Ionic Liquid from the Cation Perspective: 2D IR Vibrational Echo Spectroscopy. Journal of the American Chemical Society Yamada, S. A., Bailey, H. E., Tamimi, A., Li, C., Fayer, M. D. 2017; 139 (6): 2408-2420


    The dynamics of the room-temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf2) were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy and polarization selective pump-probe (PSPP) experiments. The CN stretch frequency of a modified Bmim(+) cation (2-SeCN-Bmim(+)), in which a SeCN moiety was substituted onto the C-2 position of the imidazolium ring, was used as a vibrational probe. A major result of the 2D IR experiments is the observation of a long time scale structural spectral diffusion component of 600 ps in addition to short and intermediate time scales similar to those measured for selenocyanate anion (SeCN(-)) dissolved in BmimNTf2. In contrast to 2-SeCN-Bmim(+), SeCN(-) samples its inhomogeneous line width nearly an order of magnitude faster than the complete structural randomization time of neat BmimNTf2 liquid (870 ± 20 ps) measured with optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments. The orientational correlation function obtained from PSPP experiments on 2-SeCN-Bmim(+) exhibits two periods of restricted angular diffusion (wobbling-in-a-cone) followed by complete orientational randomization on a time scale of 900 ± 20 ps, significantly slower than observed for SeCN(-) but identical within experimental error to the complete structural randomization time of BmimNTf2. The experiments indicate that 2-SeCN-Bmim(+) is sensitive to local motions of the ionic region that influence the spectral diffusion and reorientation of small, anionic, and neutral molecules as well as significantly slower, longer-range fluctuations that are responsible for complete randomization of the liquid structure.

    View details for DOI 10.1021/jacs.6b12011

    View details for PubMedID 28099808

  • Dynamics of a Room Temperature Ionic Liquid in Supported Ionic Liquid Membranes vs the Bulk Liquid: 2D IR and Polarized IR Pump-Probe Experiments JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Shin, J. Y., Yamada, S. A., Fayer, M. D. 2017; 139 (1): 311-323


    Supported ionic liquid membranes (SILMs) are membranes that have ionic liquids impregnated in their pores. SILMs have been proposed for advanced carbon capture materials. Two-dimensional infrared (2D IR) and polarization selective IR pump-probe (PSPP) techniques were used to investigate the dynamics of reorientation and spectral diffusion of the linear triatomic anion, SeCN(-), in poly(ether sulfone) (PES) membranes and room-temperature ionic liquid (RTIL), 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2). The dynamics in the bulk EmimNTf2 were compared to its dynamics in the SILM samples. Two PES membranes, PES200 and PES30, have pores with average sizes, ∼300 nm and ∼100 nm, respectively. Despite the relatively large pore sizes, the measurements reveal that the reorientation of SeCN(-) and the RTIL structural fluctuations are substantially slower in the SILMs than in the bulk liquid. The complete orientational randomization, slows from 136 ps in the bulk to 513 ps in the PES30. 2D IR measurements yield three time scales for structural spectral diffusion (SSD), that is, the time evolution of the liquid structure. The slowest decay constant increases from 140 ps in the bulk to 504 ps in the PES200 and increases further to 1660 ps in the PES30. The results suggest that changes at the interface propagate out and influence the RTIL structural dynamics even more than a hundred nanometers from the polymer surface. The differences between the IL dynamics in the bulk and in the membranes suggest that studies of bulk RTIL properties may be poor guides to their use in SILMs in carbon capture applications.

    View details for DOI 10.1021/jacs.6b10695

    View details for Web of Science ID 000392036900049

    View details for PubMedID 27973786

  • Water-anion hydrogen bonding dynamics: Ultrafast IR experiments and simulations. The Journal of chemical physics Yamada, S. A., Thompson, W. H., Fayer, M. D. 2017; 146 (23): 234501


    Many of water's remarkable properties arise from its tendency to form an intricate and robust hydrogen bond network. Understanding the dynamics that govern this network is fundamental to elucidating the behavior of pure water and water in biological and physical systems. In ultrafast nonlinear infrared experiments, the accessible time scales are limited by water's rapid vibrational relaxation (1.8 ps for dilute HOD in H2O), precluding interrogation of slow hydrogen bond evolution in non-bulk systems. Here, hydrogen bonding dynamics in bulk D2O were studied from the perspective of the much longer lived (36.2 ps) CN stretch mode of selenocyanate (SeCN(-)) using polarization selective pump-probe (PSPP) experiments, two-dimensional infrared (2D IR) vibrational echo spectroscopy, and molecular dynamics simulations. The simulations make use of the empirical frequency mapping approach, applied to SeCN(-) for the first time. The PSPP experiments and simulations show that the orientational correlation function decays via fast (2.0 ps) restricted angular diffusion (wobbling-in-a-cone) and complete orientational diffusive randomization (4.5 ps). Spectral diffusion, quantified in terms of the frequency-frequency correlation function, occurs on two time scales. The initial 0.6 ps time scale is attributed to small length and angle fluctuations of the hydrogen bonds between water and SeCN(-). The second 1.4 ps measured time scale, identical to that for HOD in bulk D2O, reports on the collective reorganization of the water hydrogen bond network around the anion. The experiments and simulations provide details of the anion-water hydrogen bonding and demonstrate that SeCN(-) is a reliable vibrational probe of the ultrafast spectroscopy of water.

    View details for PubMedID 28641416

  • Carbon Dioxide in a Supported Ionic Liquid Membrane: Structural and Rotational Dynamics Measured with 2D IR and Pump-Probe Experiments. Journal of the American Chemical Society Shin, J. Y., Yamada, S. A., Fayer, M. D. 2017


    Supported ionic liquid membranes (SILMs) are porous membranes impregnated with ionic liquids (ILs) and used as advanced carbon capture materials. Here, two-dimensional infrared (2D IR) and IR polarization selective pump-probe (PSPP) spectroscopies were used to investigate CO2 reorientation and spectral diffusion dynamics in SILMs. The SILM contained 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonly)imide in the poly(ether sulfone) membrane with average pore size of ~350 nm. Two ensembles of CO2 were observed in the SILM, one in the IL phase in the membrane pores and the other in the supporting membrane polymer. CO2 in the polymer displayed a red-shifted IR absorption spectrum and a shorter vibrational lifetime of the asymmetric stretch mode compared to the IL phase. Despite the relatively large pore sizes, the complete orientational randomization of CO2 and structural fluctuations of the IL (spectral diffusion) in the pores are slower than in the bulk IL by ~2-fold. The implication is that the IL structural change induced by the polymer interface can propagate out from the interface more than a hundred nanometers, influencing the dynamics. The dynamics in the polymer are even slower. This study demonstrates that there are significant differences in the dynamics of ILs in SILMs on a molecular level compared to the bulk IL, and the study of dynamics in SILMs can provide important information for the design of SILMs for CO2 capture.

    View details for PubMedID 28723129

  • Structural and Rotational Dynamics of Carbon Dioxide in 1-Alkyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquids: The Effect of Chain Length JOURNAL OF PHYSICAL CHEMISTRY B Giammanco, C. H., Yamada, S. A., Kramer, P. L., Tamimi, A., Fayer, M. D. 2016; 120 (27): 6698-6711


    Ionic liquids (ILs) have been proposed as possible carbon dioxide (CO2) capture media; thus, it is useful to understand the dynamics of both the dissolved gas and its IL environment as well as how altering an IL affects these dynamics. With increasing alkyl chain length, it is well-established that ILs obtain a mesoscopic structural feature assigned to polar-apolar segregation, and the change in structure with chain length affects the dynamics. Here, the dynamics of CO2 in a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ILs, in which the alkyl group is ethyl, butyl, hexyl, or decyl, were investigated using ultrafast infrared spectroscopy by measuring the reorientation and spectral diffusion of carbon dioxide in the ILs. It was found that reorientation of the carbon dioxide occurs on three time scales, which correspond to two different time scales of restricted wobbling-in-a-cone motions and a long-time complete diffusive reorientation. Complete reorientation slows with increasing chain length but less than the increases in viscosity of the bulk liquids. Spectral diffusion, measured with two-dimensional IR spectroscopy, is caused by a combination of the liquids' structural fluctuations and reorientation of the CO2. The data were analyzed using a recent theory that takes into account both contributions to spectral diffusion and extracts the structural spectral diffusion. Different components of the structural fluctuations have distinct dependences on the alkyl chain length. All of the dynamics are fast compared to the complete orientational randomization of the bulk ILs, as measured with optical heterodyne-detected optical Kerr effect measurements. The results indicate a hierarchy of constraint releases in the liquids that give rise to increasingly slower dynamics.

    View details for DOI 10.1021/acs.jpcb.6b03971

    View details for Web of Science ID 000379991000024

    View details for PubMedID 27264965

  • 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)


    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 Web of Science ID 000372974600024

  • 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 PubMedID 26731088