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At least 73 records · Page 4

Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy

The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accelerating and stabilizing the convergence of vibrational self-consistent field calculations via the direct inversion of the iterative subspace (vDIIS) algorithm

The vibrational self-consistent field (VSCF) method yields anharmonic states and spectra for molecular vibrations, and it serves as the starting point for more sophisticated correlated-vibration methods. Convergence of the iterative, non-linear optimization in VSCF calculations can be erratic or altogether unsuccessful, particularly for chemical systems involving low-frequency motions. In this work, a vibrational formulation of the Direct Inversion of the Iterative Subspace method of Pulay is presented and investigated. This formulation accounts for distinct attributes of the vibrational and electronic cases, including the expansion of each single-mode vibrational wavefunction in its own basis set. The resulting Direct Inversion of the Iterative Subspace method is shown to substantially accelerate VSCF convergence in all convergent cases as well as rectify many cases where Roothaan-based methods fail. Performance across systems ranging from small, rigid molecules to weakly bound molecular clusters is investigated in this analysis.

Chemistry↗

Quantum dynamical effects of vibrational strong coupling in chemical reactivity

Abstract Recent experiments suggest that ground state chemical reactivity can be modified when placing molecular systems inside infrared cavities where molecular vibrations are strongly coupled to electromagnetic radiation. This phenomenon lacks a firm theoretical explanation. Here, we employ an exact quantum dynamics approach to investigate a model of cavity-modified chemical reactions in the condensed phase. The model contains the coupling of the reaction coordinate to a generic solvent, cavity coupling to either the reaction coordinate or a non-reactive mode, and the coupling of the cavity to lossy modes. Thus, many of the most important features needed for realistic modeling of the cavity modification of chemical reactions are included. We find that when a molecule is coupled to an optical cavity it is essential to treat the problem quantum mechanically to obtain a quantitative account of alterations to reactivity. We find sizable and sharp changes in the rate constant that are associated with quantum mechanical state splittings and resonances. The features that emerge from our simulations are closer to those observed in experiments than are previous calculations, even for realistically small values of coupling and cavity loss. This work highlights the importance of a fully quantum treatment of vibrational polariton chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatially dependent H-bond dynamics at interfaces of water/biomimetic self-assembled lattice materials

Significance It is challenging to develop biomimetic lattice self-assemblies because such materials need to resemble the flexibility and crystallinity of their biological analog. We show that these materials exhibit unique micro- and mesoscopic-ordered ultrafast hydrogen-bond dynamics, which could be a key feature in the lattice self-assembly: the ultrafast dynamics ensure flexibility, whereas the domain-level ordering reflects crystallinity. This scientific insight cannot be revealed without the ultrafast transient vibrational sum-frequency generation microscope, which integrates ultrafast interfacial spectroscopy with interfacial molecular vibrational imaging––a state-of-the-art development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Laboratory simulation of interstellar grain chemistry and the production of complex organic molecules

During the past 15 years considerable progress in observational techniques has been achieved in the middle infrared (5000 to 500 cm(-1), 2 to 20 microns m), the spectral region most diagnostic of molecular vibrations. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds, are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. By comparing these astronomical spectra with the spectra of laboratory ices one can determine the composition and abundance of the icy materials frozen on the cold (10K) dust grains present in the interior of molecular clouds. These grains and their ice mantles may well be the building blocks from which comets are made. As an illustration of the processes which can take place as an ice is irradiated and subsequently warmed, researchers present the infrared spectra of the mixture H2O:CH3OH:CO:NH3:C6H14 (100:50:10:10:10). Apart from the last species, the ratio of these compounds is representative of the simplest ices found in interstellar clouds. The last component was incorporated into this particular experiment as a tracer of the behavior of a non-aromatic hydrocarbon. The change in the composition that results from ultraviolet photolysis of this ice mixture using a UV lamp to simulate the interstellar radiation field is shown. Photolysis produces CO, CO2, CH4, HCO, H2CO, as well as a family of moderately volatile hydrocarbons. Less volatile carbonaceous materials are also produced. The evolution of the infrared spectrum of the ice as the sample is warmed up to room temperature is illustrated. Researchers believe that the changes are similar to those which occur as ice is ejected from a comet and warmed up by solar radiation. The warm-up sequence shows that the nitrile or iso-nitrile bearing compound produced during photolysis evaporates between 200 and 250K, suggesting that it is carried by a small molecular species. These molecules could be similar to the source material in Comet Halley that is ejected in grains into the coma, freed by sublimation, and photolyzed by solar radiation to produce the observed jets.

Allamandola, L. J.↗

The Origins of Polycyclic Aromatic Hydrocarbons: Are They Everywhere?

During the past 15 years considerable progress in observational techniques has been achieved in the middle-infrared region (5000-500 per centimeter, 2-20 micron), the region where most diagnostic molecular vibrations occur. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds and others at their edges, are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas and solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. The two lectures will focus on the evidence that polycyclic aromatic hydrocarbons (PAHs) are an important, ubiquitous and abundant interstellar species. PAHs are. extremely stable species which can range in size from a few angstroms across to several hundred angstroms (PAHs are also the building blocks of amorphous carbon particles). This identification rests on the suggestive agreement between the laboratory spectra of PAHs with a set of IR emission bands which emanate from many different sources where ultraviolet starlight impinges on a "dusty" region. The picture is that individual PAHs are first pumped into highly vibrationally excited states and relax by fluorescence at their fundamental vibrational frequencies. That PAHs are a ubiquitous interstellar component has serious ramifications in other spectral regions as well, including the strong extinction in the ultraviolet, and the classic visible diffuse interstellar bands discovered more than 50 years ago (but unexplained to this day) The first part of the course will focus on the interpretation of astronomical spectra. The second lecture will start by showing how recent laboratory data on PAHs taken under realistic interstellar conditions has con borated the PAH hypothesis and led to great insight into the conditions in the PAH containing regions. This lecture will end by reviewing the ever-increasing evidence for interstellar PAHs in meteorites and interplanetary dust particles. This in conjunction with the recent suggestion that PAHs are abundant in Jupiter's atmosphere will make the point that "PAHs are Everywhere".

Allamandola, L. J.↗

The nature of interstellar/pre-cometary dust

During the past 15 years considerable progress in observational techniques has been achieved in the middle-infrared region (5000-500/cm, 2-20 microns), the region where most diagnostic molecular vibrations occur. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds and others obscured only by dust in the diffuse interstellar medium are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas and solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. By comparing these spectra with laboratory spectra one can determine the composition and abundance of the icy material frozen on the cold (- 10K) dust in the dark interior of molecular clouds and of the hydrocarbon component of dust in the diffuse interstellar medium. As these are the building blocks of comets, the work described here also gives insight into the nature of comets.

Allamandola, Louis↗

Analysis of vibronic coupling in a 4f molecular magnet with FIRMS

Vibronic coupling, the interaction between molecular vibrations and electronic states, is a fundamental effect that profoundly affects chemical processes. In the case of molecular magnetic materials, vibronic, or spin-phonon, coupling leads to magnetic relaxation, which equates to loss of magnetic memory and loss of phase coherence in molecular magnets and qubits, respectively. The study of vibronic coupling is challenging, and most experimental evidence is indirect. Here we employ far-infrared magnetospectroscopy to directly probe vibronic transitions in [Yb(trensal)] (where H 3 trensal = 2,2,2-tris(salicylideneimino)trimethylamine). We find intense signals near electronic states, which we show arise due to an “envelope effect” in the vibronic coupling Hamiltonian, which we calculate fully ab initio to simulate the spectra. We subsequently show that vibronic coupling is strongest for vibrational modes that simultaneously distort the first coordination sphere and break the C 3 symmetry of the molecule. With this knowledge, vibrational modes could be identified and engineered to shift their energy towards or away from particular electronic states to alter their impact. Hence, these findings provide new insights towards developing general guidelines for the control of vibronic coupling in molecules.

36 MATERIALS SCIENCE↗

Vibrational Signatures of Electronic Properties in Renewable-Energy Catalysis

The objective of this research program is to discover and develop new approaches for ab initio computational simulations of molecular motion. Specifically, this program aims to decipher the connection between the underlying electronic structure and the accordant molecular vibrations in reactive ions and radicals for renewable-energy purposes. Recent experimental progress in ion sources and optical spectroscopies has unearthed considerable new inner-sphere detail for these complexes, but the connection between these spectral signatures and mechanistic information often remains elusive, to the continued frustration of experimentalists. For this purpose, new anharmonic vibrational frequency methods, along with a publicly deployed software package, will be developed. Working closely with committed experimental collaborators, this conceptual and computational framework will be used to explain the results of new spectroscopy experiments, focusing specifically on the inner-shell mechanisms of renewable-energy catalysis. The oxidation half of catalytic water-splitting chemistry will be a central focus, along with fundamental studies of the manner in which strong ions and radicals activate solvent as a chemical species. The resulting products of the research program will include openly available software and algorithms for the ab initio simulation of challenging vibrational spectra, as well as critical mechanistic insight into energy-focused catalytic processes that are opaque to other existing analytical techniques.

42 ENGINEERING↗

Thermal-infrared emission spectroscopy of natural surfaces: Application to coated surfaces

Thermal-infrared vibrational spectroscopy has great potential for remotely determining the composition of planetary surface materials by taking advantage of fundamental molecular vibrational modes that produce spectral features in the range from approximately 3 to greater than 50 microns. Much of the current interest in the thermal infrared wavelength region stems from the deployment of multispectral scanners, such as the Thermal Infrared Multispectral Scanner (TIMS) and the Mars Observer Thermal Emission Spectrometer (TES). In order to support these missions, it is necessary to develop an appropriate library of laboratory measurements. The purpose of this work was to develop a technique which, with a very limited set of assumptions, can be used to determine the emissivity of natural surfaces directly by using emitted energy.

Christensen, Philip R.↗

Conversion of laser energy to gas kinetic energy

Techniques for the gas phase absorption of laser radiation for conversion to gas kinetic energy are discussed. Absorption by inverse Bremsstrahlung, in which laser energy is converted at a gas kinetic rate in a spectrally continuous process, is briefly described, and absorption by molecular vibrational rotation bands is discussed at length. High pressure absorption is proposed as a means of minimizing gas bleaching and dissociation, the major disadvantages of the molecular absorption process. A band model is presented for predicting the molecular absorption spectra in the high pressure absorption region and is applied to the CO molecule. Use of a rare gas seeded with Fe(CO)5 for converting vibrational modes to translation modes is described.

Caledonia, G. E.↗

The Interference of the Dynamically Squeezed Vibrational Wave Packets

An electronic excitation of a molecule by a sequence of two femtosecond phase-locked laser pulses is considered. In this case the interference between the vibrational wave packets induced by each of the subpulses within a single molecule takes place. It is shown that due to the dynamical squeezing effect of a molecular vibrational state the interference of the vibrational wave packets allows one to measure the duration of a femtosecond laser pulse. This can be achieved experimentally by measuring the dependence of the integral fluorescence of the excited molecule on the delay time between the subpulses. The interference can lead to a sharp peak (or to a down-fall) in that dependence, the width of which is equal to the duration of the laser pulse. It is shown that finite temperature of the medium is favorable for such an experiment.

Vinogradov, An. V.↗

Thermalization of the Kerr index of refraction in acetone and methanol using femtosecond pump-probe scattering spectroscopy

Femtosecond time-resolved pump-probe scattering is used to temporally investigate the index thermalization Δn(t) of the molecular motions associated with the Kerr nonlinear index n 2 . This is done using an intense 300 fs 1034 nm pump pulse and temporally probed by a 517 nm and supercontinuum pulse in acetone and methanol. The optically pumped molecular states change the index of refraction and through the processes of Raman and Rayleigh scattering are shown to engage in a 4-step energy relaxation process. Here, the pump first initiates the Kerr effect as well as populate resonant vibrational molecular motions, which act as a “mother” energy state. The electronic component of the Kerr effect is shown to couple with these vibrational modes through the process of Born-Oppenheimer coupling, which can be measured through the Raman scattering of the probe. The “mother” coupled state then decays into “daughter” anharmonic non-resonant states, which then further decay into “granddaughter” and thermal bath states. The population of these states alter the index of refraction in time, Δn(t), and can be measured through the changing in the probe beam’s Rayleigh scattering. This thermalization process takes ~5.5 ps in acetone and ~3.7 ps in methanol. The scattering signals from each Δn(t) thermalization stage in the localized region, (“mother”, to “daughter”, to “granddaughter”, to the bath states, to the ground state), are fitted to theoretical decay equations that show the rise and fall times of the energy decay routes.

47 OTHER INSTRUMENTATION↗

Concordant Mode Approach (CMA): Vibrational Analysis of New and Upgraded Intermolecular Benchmarks for Noncovalent Bonding

The Concordant Mode Approach (CMA) is a novel method that offers tremendous potential for increasing the system size and the level of theory attainable in quantum chemical computations of molecular vibrational frequencies. To investigate the extension of CMA to intermolecular vibrations, computations with coupled cluster singles and doubles with perturbative triples theory [CCSD(T)] using two augmented correlation-consistent polarized-valence triple-ζ basis sets (aug-cc-pVTZ or h-aug-ccpVTZ) were performed on 17 prototypical loosely bound complexes of hydrogen-bonded, dispersion, and mixed character. These Level A results provide new and upgraded benchmarks for noncovalent bonding and a severe test for CMA vibrational analyses. The Level A target frequencies were recovered remarkably well using second-order Møller−Plesset perturbation theory (MP2) with h-aug-cc-pVTZ for generating the underlying (Level B) normal modes of the CMA scheme. Employing this Level B within the lowest-rung CMA-0A method reproduces the 435 benchmark frequencies with a mean absolute error (MAE) of 0.23 cm −1 and a corresponding standard deviation (σ) of 0.84 cm −1 ; strikingly, the corresponding subset of 106 interfragment frequencies exhibits MAE = 0.34 cm −1 and σ = 0.90 cm −1 . Subsequent application of the higher-rung CMA-2A scheme eliminates all outliers and reduces the overall MAE to a minuscule 0.08 cm −1 with the inclusion of only 3.0% of the off-diagonal couplings not accounted for by CMA-0A. Accordingly, the highly efficient CMA methodology proves to be robust even for vibrations on flat potential energy surfaces.

Aromatic compounds↗