Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular vibrations”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor

Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ~5-50 cm -1 . This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effect of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal/mol -1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From Coherence to Function: Exploring the Connection in Chemical Systems

The role of quantum mechanical coherences or coherent superposition states in excited state processes has received considerable attention in the last two decades largely due to advancements in ultrafast laser spectroscopy. These coherence effects hold promise for enhancing the efficiency and robustness of functionally relevant processes, even when confronted with energy disorder and environmental fluctuations. Understanding coherence deeply drives us to unravel mechanisms and dynamics controlled by order and synchronization at a quantum mechanical level, envisioning optical control of coherence to enhance functions or create new ones in molecular and material systems. In this frontier, the interplay between electronic and vibrational dynamics, specifically the influence of vibrations in directing electronic dynamics, has emerged as the leading principle. Here, two energetically disparate quantum degrees of freedom work in-sync to dictate the trajectory of an excited state reaction. Moreover, with the vibrational degree being directly related to the structural composition of molecular or material systems, new molecular designs could be inspired by tailoring certain structural elements. In the realm of chemical kinetics, our understanding of the dynamics of chemical transformations is underpinned by fundamental theories, such as transition state theory, activated rate theory, and Marcus theory. These theories elucidate reaction rates by considering the energy barriers that must be overcome for reactants to transform into products. Those barriers are surmounted by the stochastic nature of energy gap fluctuations within reacting systems, emphasizing that the reaction coordinate, the pathway from reactants to products, is not rigidly defined by a specific vibrational motion but encompasses a diverse array of molecular motions. While less is known about the involvement of specific intramolecular vibrational modes, their significance in certain cases cannot be overlooked. In this Account, we summarize key experimental findings that offer deeper insights into the complex electronic–vibrational trajectories encompassing excited states afforded from state-of-the-art ultrafast laser spectroscopy in three exemplary processes: photoinduced electron transfer, singlet–triplet intersystem crossing, and intramolecular vibrational energy flow in molecular systems. We delve into the rapid decoherence, or loss of phase and amplitude correlations, of vibrational coherences along promoter vibrations during subpicosecond intersystem crossing dynamics in a series of binuclear platinum complexes. This rapid decoherence illustrates the vibration-driven reactive pathways from the Franck–Condon state to the curve crossing region. We also explore the generation of new vibrational coherences induced by impulsive reaction dynamics rather than by the laser pulse in these systems, which sheds light on specific energy dissipation pathways and thereby on the progression of the reaction trajectory in the vicinity of the curve crossing on the product side. Another property of vibrational coherences, amplitude, reveals how energy can flow from one vibration to another in the electronic excited state of a terpyridine–molybdenum complex hosting a nonreactive dinitrogen substrate. In conclusion, a slight change in vibrational energy triggers a quasi-resonant interaction, leading to constructive wavepacket interference and ultimately intramolecular vibrational redistribution from a Franck–Condon active terpyridine vibration to a dinitrogen stretching vibration, energizing the dinitrogen bond.

Electrical energy↗

Experimental Quantification of Spin–Phonon Coupling in Molecular Qubits Using Inelastic Neutron Scattering

Electronic spin superposition states enable nanoscale sensing through their sensitivity to the local environment, yet their sensitivity to vibrational motion also limits their coherence times. In molecular spin systems, chemical tunability and atomicscale resolution are accompanied by a dense, thermally accessible phonon spectrum that introduces efficient spin relaxation pathways. Despite extensive theoretical work, there is little experimental consensus on which vibrational energies dominate spin relaxation or how molecular structure controls spin−phonon coupling (SPC). We present a fully experimental method to quantify SPC coefficients by combining temperature-dependent vibrational spectra from inelastic neutron scattering with spin relaxation rates measured by electron paramagnetic resonance. We apply this framework to two model S = 1/2 systems, copper(II) phthalocyanine (CuPc) and copper(II) octaethylporphyrin (CuOEP). Two distinct relaxation regimes emerge: below 40 K, weakly coupled lattice modes below 50 cm −1 dominate, whereas above 40 K, optical phonons above ∼185 cm −1 become thermally populated and drive relaxation with SPC coefficients nearly 3 orders of magnitude larger. Structural distortions in CuOEP that break planar symmetry soften the crystal lattice and enhance anharmonic scattering but also raise the energy of stretching modes at the molecular core where the spins reside. This redistributes vibrational energy toward the molecular periphery and out of plane, ultimately reducing SPC relative to CuPc and enabling room-temperature spin coherence in CuOEP. Although our method does not provide mode-specific SPC coefficients, it quantifies contributions from distinct spectral regions and establishes a broadly applicable, fully experimental link between crystal structure, lattice dynamics, and spin relaxation.

Lohaus, Stefan H. [California Institute of Technol↗

Insight into the Structural and Emissive Behavior of a Three‐Dimensional Americium(III) Formate Coordination Polymer

Abstract We report the structural, vibrational, and optical properties of americium formate (Am(CHO 2 ) 3 ) crystals synthesized via the in situ hydrolysis of dimethylformamide (DMF). The coordination polymer features Am 3+ ions linked by formate ligands into a three‐dimensional network that is isomorphous to several lanthanide analogs, (e. g., Eu 3+ , Nd 3+ , Tb 3+ ). Structure determination revealed a nine‐coordinate Am 3+ metal center that features a unique local C 3v symmetry. The metal–ligand bonding interactions were investigated by vibrational spectroscopy, natural localized molecular orbital calculations, and the quantum theory of atoms in molecules. The results paint a predominantly ionic bond picture and suggest the metal‐oxygen bonds increase in strength from Nd−O 5 D 1′ → 7 F 0′ emission band is observed and dominates the emission spectrum. This behavior is unusual and is attributed to the C 3v coordination environment of the metal center.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ion Pairing Mediates Molecular Organization Across Liquid/Liquid Interfaces

Liquid/liquid interfaces play a central role in scientific fields ranging from nanomaterial synthesis and soft matter electronics to nuclear waste remediation and chemical separations. This diversity of functions arises from an interface’s ability to respond to changing conditions in its neighboring bulk phases. Understanding what drives this interfacial flexibility can provide novel avenues for designing new functional interfaces. However, limiting this progress is an inadequate understanding of the subtle intermolecular and interphase interactions taking place at the molecular level. Here, we use surface-specific vibrational sum frequency generation spectroscopy combined with atomistic molecular dynamics simulations to investigate the self-assembly and structure of model ionic oligomers consisting of an oligodimethylsiloxane (ODMS) tail covalently attached to a positively charged methyl imidazolium (MIM + ) head group at buried oil/aqueous interfaces. We show how the presence of seemingly innocuous salts can impart dramatic changes to the ODMS tail conformations in the oil phase via specific ion effects and ion-pairing interactions taking place in the aqueous phase. These specific ion interactions are shown to drive enhanced amphiphile adsorption, induce morphological changes, and disrupt emergent hydrogen-bonding structures at the interface. Tuning these interactions allows for independent control over the oligomer structure in the oil phase versus interfacial population changes and represents key mechanistic insight that is needed to control chemical reactions at liquid/liquid interfaces.

36 MATERIALS SCIENCE↗

Hydration structure of flat and stepped MgO surfaces

We investigate the solvation structure of flat and stepped MgO(001) in neutral liquid water using ab initio molecular dynamics based on a hybrid density functional with dispersion corrections. Our simulations show that the MgO surface is covered by a densely packed layer of mixed intact and dissociated adsorbed water molecules in a planar arrangement with strong intermolecular H-bonds. The water dissociation fractions in this layer are >20% and >30% on the flat and stepped surfaces, respectively. Slightly above the first water layer, we observe metastable OH groups perpendicular to the interface, similar to those reported in low temperature studies of water monolayers on MgO. Here, these species receive hydrogen bonds from four nearby water molecules in the first layer and have their hydrophobic H end directed toward bulk water, while their associated protons are bound to surface oxygens. The formation of these OH species is attributed to the strong basicity of the MgO surface and can be relevant for understanding various phenomena from morphology evolution and growth of (nano)crystalline MgO particles to heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Contribution of the Hydroxyl Group on Interfacial Heat Conduction of Monohydric Alcohols: A Molecular Dynamics Study

Monohydric alcohols have been used as promising phase change materials (PCMs) for low-temperature latent heat storage. However, the heat storage/retrieval rates are limited due to the low thermal conductivity of such alcohols. In this work, nonequilibrium molecular dynamics (NEMD) simulations were performed to study the microscopic heat conduction in example monohydric alcohols, i.e., 1-dodecanol (C12H26O), 1-tetradecanol (C14H30O), and 1-hexadecanol (C16H34O). A simplified ideal crystal model was proposed to exploit the potential for improving the thermal conductivity of monohydric alcohols. The effect of ideal crystalline structures, especially the contribution of the hydroxyl group, on the microscopic heat conduction process was analyzed. The thermal conductivity of the ideal crystals of the various monohydric alcohols was predicted to be more than twice as compared to that of their respective solids. The major thermal resistance in the ideal crystals was found around the molecular interfaces, as a result of the excellent heat conduction performance along the linear molecular chains. The calculated vibrational density of states (VDOS) and interfacial heat transfer were then investigated. When the interfaces are surrounded by hydroxyl groups as walls, strong hydrogen bond (HB) interactions were observed. The interfacial heat transfer coefficient of the ideal crystalline structures of 1-tetradecanol was found to reach up to ~735.6 MW/m2 W. It was elucidated that the high interfacial heat transfer rate is clearly related to the stronger intermolecular interactions.

Engineering↗

Simultaneous imaging of vibrational, rotational, and electronic wave-packet dynamics in a triatomic molecule

Light-induced molecular dynamics often involve the excitation of several electronic, vibrational, and rotational states. Since the ensuing electronic and nuclear motion determines the pathways and outcomes of photoinduced reactions, our ability to monitor and understand these dynamics is crucial for molecular physics, physical chemistry, and photobiology. However, characterizing this complex motion represents a significant challenge when different degrees of freedom are strongly coupled. In this Letter, we demonstrate how the interplay between vibrational, rotational, and electronic degrees of freedom governs the evolution of molecular wave packets in the low-lying states of strong-field-ionized sulfur dioxide. Using time-resolved Coulomb explosion imaging (CEI) and quantum mechanical wave packet simulations, we directly map the bending vibrations of the molecule, show how the vibrational wave packet is influenced by molecular alignment, and elucidate the consequences of nuclear motion for the coupling between the two lowest electronic states of the cation. Furthermore, our results demonstrate that multicoincident CEI can be an efficient experimental tool for characterizing coupled electronic and nuclear motion in polyatomic molecules.

Atomic & molecular processes in external fields↗

Atomistic insights into the synergistic effects of tensile strain and hydroxyl group on increasing the thermal conductivity of monohydric alcohols as latent heat storage materials

The low thermal conductivity of linear monohydric alcohols significantly limits their performance when used as latent heat storage materials. It was found that imposing certain mechanical strains on nanomaterials with highly ordered structures can lead to appreciable thermal conductivity enhancement. To explore the potential of enhancing the intrinsic thermal conductivity of monohydric alcohols, a simplified ideal crystal model was employed for molecular arrangement in this work. The variation of atomistic heat transfer as a function of tensile strains was exploited by non-equilibrium molecular dynamics simulations. Furthermore, the influence of stretching on the vibration density of states and the corresponding molecular morphology were revealed. The results suggested that the thermal conductivity of monohydric alcohols with such simplified ideal crystalline structures can increase by about 170 % at the strain of 0.1. The distance between neighboring interfaces was found to determine the energy of inter-molecular interactions at the crystal grain boundaries. The hydrogen bonds energy has not reached the critical value when increasing tensile strains from 0 to 0.1. In contrast, the strongest van der Walls interactions for alkanes were obtained at the strain of 0.06 where the interfacial distances of alkanes have achieved their equilibrium distances. In addition, the interfacial heat transfer coefficient of ideal crystal monohydric alcohols at hydroxyl interfaces was found to be threefold than that between methyl interfaces, in consistent with the strength of inter-molecular interactions between functional groups at the interfaces.

36 MATERIALS SCIENCE↗

Covalent Drug Binding in Live Cells Monitored by Mid-Infrared Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System

The detection of drug-target interactions in live cells enables analysis of therapeutic compounds in a native cellular environment. Recent advances in spectroscopy and molecular biology have facilitated the development of genetically encoded vibrational probes like nitriles that can sensitively report on molecular interactions. Nitriles are powerful tools for measuring electrostatic environments within condensed media like proteins, but such measurements in live cells have been hindered by low signal-to-noise ratios. In this study, we design a spectrometer based on a double-beam quantum cascade laser (QCL)-based transmission infrared (IR) source with balanced detection that can significantly enhance sensitivity to nitrile vibrational probes embedded in proteins within cells compared to a conventional FTIR spectrometer. Here, using this approach, we detect small-molecule binding in Escherichia coli, with particular focus on the interaction between para-Coumaric acid (pCA) and nitrile-incorporated photoactive yellow protein (PYP). This system effectively serves as a model for investigating covalent drug binding in a cellular environment. Notably, we observe large spectral shifts of up to 15 cm –1 for nitriles embedded in PYP between the unbound and drug-bound states directly within bacteria, in agreement with observations for purified proteins. Such large spectral shifts are ascribed to the changes in the hydrogen-bonding environment around the local environment of nitriles, accurately modeled through high-level molecular dynamics simulations using the AMOEBA force field. Our findings underscore the QCL spectrometer’s ability to enhance sensitivity for monitoring drug–protein interactions, offering new opportunities for advanced methodologies in drug development and biochemical research.

chromophores↗

Comparative analysis of internal energy excitation and dissociation of nitrogen predicted by independently developed ab initio potential energy surfaces

In this article we present a comparative atomic level study analyzing the vibrational excitation and dissociation of molecular nitrogen due to N 2 ⁢( 1 Σ g ⁢ + )+N⁢( 4 S u ) and N 2 ⁢( 1 Σ g ⁢ + )+N 2 ⁢( 1 Σ g ⁢+ ) interactions governed by independently developed potential energy surfaces at the University of Minnesota and NASA Ames Research Center. Further, vibrational excitation was studied for N 2 +N 2 interactions from T=10000 to 25000 K and for N 2 +N from T=5000 to 30000 K. Nonequilibrium dissociation is studied from T=10000 to 30000 K under the quasi-steady-state condition for N 2 +N 2 and N 2 +N interactions. Finally, an inviscid Mach 20 dissociating nitrogen flow over a cylinder with a Knudsen number of 0.015 is carried out to study the impact of molecular interactions predicted by independently developed potential energy surfaces on a canonical hypersonic flow.

74 ATOMIC AND MOLECULAR PHYSICS↗

Effect of interfacial vibrational coupling on surface wettability and water transport

Here, we report that the atomic-scale vibrational coupling at the solid-fluid interface can substantially alter the interfacial properties such as wettability and fluid slip. The wettability of water droplets on substrates subjected to various vibrational frequencies is studied using molecular dynamics simulation. The contact angle increases (i.e., becomes more hydrophobic) when the oscillation frequency of the substrate matches the intermolecular bending frequency of liquid water. We investigate the underlying mechanism by examining the dynamics of water molecules at the interface and find that the temporal contact between the solid and fluid is shorter when the frequencies match, resulting in weak solid-fluid adsorption. We further report that the vibrational match at the interface reduces wall-fluid friction and enhances water transport through the nanopore. Our findings demonstrate the importance of the atomic-scale vibrational coupling at the solid-fluid interface on the physicochemical behavior of nanodevices and biological nanochannels.

74 ATOMIC AND MOLECULAR PHYSICS↗

The interplay of excitonic delocalization and vibrational localization in optical lineshapes: A variational polaron approach

The dynamics of molecular excitonic systems are complicated by a competition between electronic coupling (which drives delocalization) and vibrational-electronic (vibronic) interactions (which tend to encourage electronic localization). A particular challenge of molecular systems is that they typically possess a large number of independent vibrations, with frequencies often spanning the entire spectrum of relevant electronic energy gaps. Recent spectroscopic observations and numerical simulations on a water-soluble chlorophyll-binding protein (WSCP) reveal a transition between two regimes of vibronic behavior, a Redfield-like regime in which low-frequency vibrations respond to a delocalized excitonic state, and a Förster-like regime where high-frequency vibrations act as incoherent excitations on individual pigments. Although numerical simulations can reproduce these effects, there is a need for a simple, systematic theory that accurately describes the smooth transition between these two regimes in experimental spectra. Here we address this challenge by generalizing the variational polaron transform approach of [Bloemsma et al., Chem. Phys. 481, 250 (2016)] to include arbitrary bath densities for systems with or without symmetry. We benchmark this theory against both numerical matrix-diagonalization methods and experimental 77 K fluorescence spectra for two WSCP variants, obtaining quite satisfactory agreement in both cases. Here, we apply this theory to offer an explanation for the large loss in apparent electronic coupling in the WSCP Q57K mutant and to examine the likely impact of the interplay between excitonic delocalization and vibrational localization on vibrational sideband shapes and apparent coupling strengths in high-resolution optical spectra for chlorophyll-protein complexes such as WSCP.

14 SOLAR ENERGY↗

First principles simulation of reacting hypersonic flow over a blunt wedge

This article presents molecular-level analysis of a reactive, near-continuum, Mach 21 nitrogen flow over a blunt wedge using the direct molecular simulation (DMS) method. The flow conditions lead to internal energy excitation and dissociation in the flow field, resulting in thermal and chemical nonequilibrium in the flow. Thermal nonequilibrium in the vibrational mode is observed to extend to the molecular level, where the vibrational energy distributions at various points in the flow field are observed to be non-Boltzmann. Furthermore, this is the first reactive DMS calculation where the wall is assumed to be isothermal and full momentum accommodation of the particles is enforced, hence incorporating viscous wall effects. Since the DMS method uses a quantum mechanically generated interaction potential as its only modeling input, all thermochemical and transport properties of the flow field can directly be attributed to the ab initio potential energy surface. Using the DMS solution as a benchmark, this article assesses the performance of Navier–Stokes computational fluid dynamics solutions using lower fidelity two-temperature models. Two models are chosen as points of comparison: the well-known Park two-temperature model and the recently developed modified Marrone and Treanor model.

Mechanics↗

Ab Initio Molecular Dynamics Simulations of Amorphous Calcium Carbonate: Interpretation of Pair Distribution Function and X-Ray Absorption Spectroscopy Data

The structure and transformation of hydrous amorphous calcium carbonate (ACC) are key to understanding biomineralization pathways and their relationship with the properties of the resulting material. Quantitative interpretation of scattering experiments aimed at elucidating the structure of ACC is challenging, due to the amorphous nature of this material, and, therefore, requires models for the structure and the scattering physics. Here, we generate physically realistic ensembles of hydrated ACC structures and their vibrational disorder from ab initio molecular dynamics (AIMD) simulations with an emphasis on enabling the consistent interpretation of the finer details of three complementary structural probes: neutron and x-ray pair distribution experiments and x-ray absorption spectroscopy (XAS). In each case, we simulate the signal directly in reciprocal space and then manipulate it into the real-space pair distribution function (PDF) or spectrum using the same procedures for the experimental and theoretical data. Good agreement with experiment was obtained across the three techniques with the simulations accounting well for all features in the spectra. Remaining small discrepancies pointed to differences between real samples and the idealized simulated systems such as deviations from the nominal CaCO3·nH2O stoichiometry. Additionally, the simulations offered a more accurate description of the local coordination environment of calcium than previous shell-by-shell fits to spectra of synthetic ACC and classical molecular dynamics simulations. This work demonstrates that AIMD is a powerful approach for extracting detailed structural information from neutron PDF, x-ray PDF, and XAS of amorphous carbonate phases.

Prange, Micah P.↗

Attosecond photoionization delays in the vicinity of molecular Feshbach resonances

Temporal delays extracted from photoionization phases are currently determined with attosecond resolution by using interferometric methods. Such methods require special care when photoionization occurs near Feshbach resonances due to the interference between direct ionization and autoionization. Although theory can accurately handle these interferences in atoms, in molecules, it has to face an additional, so far insurmountable problem: Autoionization is slow, and nuclei move substantially while it happens, i.e., electronic and nuclear motions are coupled. Here, we present a theoretical framework to account for this effect and apply it to evaluate time-resolved and vibrationally resolved photoelectron spectra and photoionization phases of N 2 irradiated by a combination of an extreme ultraviolet (XUV) attosecond pulse train and an infrared pulse. We show that Feshbach resonances lead to unusual non–Franck-Condon vibrational progressions and to ionization phases that strongly vary with photoelectron energy irrespective of the vibrational state of the remaining molecular cation.

74 ATOMIC AND MOLECULAR PHYSICS↗

High phase resolution: Probing interactions in complex interfaces with sum frequency generation

An often-quoted statement attributed to Wolfgang Pauli is that God made the bulk, but the surface was invented by the devil. Although humorous, the statement really reflects frustration in developing a detailed picture of a surface. In the last several decades, that frustration has begun to abate with numerous techniques providing clues to interactions and reactions at surfaces. Often these techniques require considerable prior knowledge. Complex mixtures on irregular or soft surfaces—complex interfaces—thus represent the last frontier. Two optical techniques: sum frequency generation (SFG) and second harmonic generation (SHG) are beginning to lift the veil on complex interfaces. Of these techniques, SFG with one excitation in the infrared has the potential to provide exquisite molecular- and moiety-specific vibrational data. This Perspective is intended both to aid newcomers in gaining traction in this field and to demonstrate the impact of high-phase resolution. It starts with a basic description of light-induced surface polarization that is at the heart of SFG. The sum frequency is generated when the input fields are sufficiently intense that the interaction is nonlinear. This nonlinearity represents a challenge for disentangling data to reveal the molecular-level picture. Three, high-phase-resolution methods that reveal interactions at the surface are described.

Biophysics↗

Defects vibrations engineering for enhancing interfacial thermal transport in polymer composites

To push upper boundaries of thermal conductivity in polymer composites, understanding of thermal transport mechanisms is crucial. Despite extensive simulations, systematic experimental investigation on thermal transport in polymer composites is limited. To better understand thermal transport processes, we design polymer composites with perfect fillers (graphite) and defective fillers (graphite oxide), using polyvinyl alcohol (PVA) as a matrix model. Measured thermal conductivities of ~1.38 ± 0.22 W m -1 K -1 in PVA/defective filler composites is higher than those of ~0.86 ± 0.21 W m -1 K -1 in PVA/perfect filler composites, while measured thermal conductivities in defective fillers are lower than those of perfect fillers. We identify how thermal transport occurs across heterogeneous interfaces. Thermal transport measurements, neutron scattering, quantum mechanical modeling, and molecular dynamics simulations reveal that vibrational coupling between PVA and defective fillers at PVA/filler interfaces enhances thermal conductivity, suggesting that defects in polymer composites improve thermal transport by promoting this vibrational coupling.

42 ENGINEERING↗