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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.

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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Extended Lagrangian Excited State Molecular Dynamics

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Can TDDFT Describe Excited Electronic States of Naphthol Photoacids? A Closer Look with EOM-CCSD

The 1 L b and 1 L a excited states of naphthols are characterized by using time-dependent density functional theory (TDDFT), configuration interaction with singles (CIS), and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) methods. TDDFT fails dramatically at predicting the energy and ordering of the 1 L a and 1 L b excited states as observed experimentally, while EOM-CCSD accurately predicts the excited states as characterized by natural transition orbital analysis. Here, the limitations of TDDFT are attributed to the absence of correlation from doubly excited configurations as well as the inconsistent description of excited electronic states of naphthol photoacids revealed by excitation analysis based on the one-electron transition density matrix.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Energy Decomposition Analysis for Excimers Using Absolutely Localized Molecular Orbitals within Time-Dependent Density Functional Theory and Configuration Interaction with Single Excitations

Here, we present an improved energy decomposition analysis (EDA) scheme for understanding intermolecular interactions in delocalized excited states, especially in excimers. In the EDA procedure, excited states are treated with linear response theory such as configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT), and absolutely localized molecular orbitals (ALMOs) are used to define the intermediate (frozen, excitonic coupling, and polarized) states. The intermolecular interaction energy is thereby separated into frozen, excitonic splitting, polarization, and charge transfer contributions. The excitonic splitting term describes the delocalization effect as two or more degenerate local excitations coupled with each other, which is often an important binding force in excimers. A maximum overlap state-tracking procedure is introduced to connect the initial fragment excitations to the constrained intermediate states and finally to the unconstrained delocalized states of the complex. The EDA scheme is applied to several excimer systems, including the He 2 * and Ne 2 * noble gas excimers, the doubly hydrogen-bonded 2-pyridone dimer, and the aromatic benzene and perylene excimers. We are able to gain some useful insights into the role each term is playing in the formation of these excimers, and the resulting method may also be useful for understanding a range of other complexes in excited states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Nonadiabatic Excited-State Molecular Dynamics for Open-Shell Systems

Nonadiabatic Molecular Dynamics (NAMD) of excited states has been widely used in the simulation of photoinduced phenomena. However, the inability to treat bond breaking and forming processes with single-reference electronic structure methods limits their application in photochemistry for extended molecular systems. In this work, the extension of excited-state NAMD for open-shell systems is developed and implemented in the NEXMD software. We present the spin-unrestricted CIS and TDSCF formalism for the ground and excited states, analytical derivatives, and nonadiabatic derivative couplings for the respective potential energy surfaces. Next, this methodology is employed to study the photochemical reaction of three model molecules. The results demonstrate the advantage of the open-shell approach in modeling photochemical reactions, especially involving bond breaking processes. We find that the open-shell method lowers the reaction barrier at the bond-breaking limits resulting in larger calculated photochemical quantum yields compared to the respective closed-shell results. We also address problems related to spin contamination in the open-shell method, especially when molecular geometries are far from equilibrium.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Development of Glucose Regulated Protein 94-Selective Inhibitors Based on the BnIm and Radamide Scaffold

Glucose regulated protein 94 (Grp94) is the endoplasmic reticulum resident of the heat shock protein 90 kDa (Hsp90) family of molecular chaperones. Grp94 associates with many proteins involved in cell adhesion and signaling, including integrins, Toll-like receptors, immunoglobulins, and mutant myocilin. Grp94 has been implicated as a target for several therapeutic areas including glaucoma, cancer metastasis, and multiple myeloma. While 85% identical to other Hsp90 isoforms, the N-terminal ATP-binding site of Grp94 possesses a unique hydrophobic pocket that was used to design isoform-selective inhibitors. Incorporation of a cis-amide bioisostere into the radamide scaffold led to development of the original Grp94-selective inhibitor, BnIm. Structure–activity relationship studies have now been performed on the aryl side chain of BnIm, which resulted in improved analogues that exhibit better potency and selectivity for Grp94. Furthermore, these analogues also manifest superior antimigratory activity in a metastasis model as well as enhanced mutant myocilin degradation in a glaucoma model compared to BnIm.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Catch and Release: Orbital Symmetry Guided Reaction Dynamics from a Freed “Tension Trapped Transition State”

The dynamics of reactions at or in the immediate vicinity of transition states are critical to reaction rates and product distributions, but direct experimental probes of those dynamics are rare. In this paper, s-trans, s-trans 1,3-diradicaloid transition states are trapped by tension along the backbone of purely cis-substituted gem-difluorocyclopropanated polybutadiene using the extensional forces generated by pulsed sonication of dilute polymer solutions. Once released, the branching ratio between symmetry-allowed disrotatory ring closing (of which the trapped diradicaloid structure is the transition state) and symmetry-forbidden conrotatory ring closing (whose transition state is nearby) can be inferred. Finally, net conrotatory ring closing occurred in 5.0 ± 0.5% of the released transition states, in excellent agreement with ab initio molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Interaction–Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions

The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG + G + TG + G + g – )-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as “preparation energy” or “reorganization energy”. We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme’s efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 310-polyglycine and H+GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction–deletion in 2-nitrobenzene-1,3-diol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Two-Dimensional Projected-Momentum Covariance Mapping for Coulomb Explosion Imaging

We introduce projected-momentum covariance mapping, an extension of recoil-frame covariance mapping for 2D ion imaging studies. By considering the two-dimensional projection of the ion momenta as recorded by the detector, one opens the door to a complex suite of analysis tools adapted from three-dimensional momentum imaging studies. This includes the use of different frames of reference to unravel the dynamics of fragmentation and the application of fragment momentum constraints to isolate specific fragmentation channels. The technique is demonstrated on data from a two-dimensional ion imaging study of the Coulomb explosion of the cis and trans isomers of 1,2-dichloroethene, following strong-field ionization by an intense near-infrared femtosecond laser pulse. Classical simulations are used to guide the interpretation of projected-momentum covariance maps. The results offer a detailed insight into the distinct Coulomb explosion dynamics for this pair of isomers and lay the groundwork for future time-resolved studies of photoisomerization dynamics in this molecular system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Infrared spectroscopy and structure of (NO) n clusters

Nitrogen oxide clusters (NO) n have been studied in He droplets via infrared depletion spectroscopy and by quantum chemical calculations. The ν 1 and ν 5 bands of cis-ON-NO dimer have been observed at 1868.2 and 1786.5 cm –1 , respectively. Furthermore, spectral bands of the trimer and tetramer have been located in the vicinity of the corresponding dimer bands in accord with computed frequencies that place NO-stretch bands of dimer, trimer, and tetramer within a few wavenumbers of each other. In addition, a new line at 1878.1 cm –1 close to the band origin of single molecules was assigned to van der Waals bound dimers of (NO) 2 , which are stabilized due to the rapid cooling in He droplets. Spectra of larger clusters (n > 5), have broad unresolved features in the vicinity of the dimer bands. As a result, experiments and calculations indicate that trimers consist of a dimer and a loosely bound third molecule, whereas the tetramer consists of two weakly bound dimers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Contact Freezing of Water Droplets by Crystalline Organic Acids

The ability of water to freeze into ice crystals in mixed-phase clouds affects physical properties, including particle size, precipitation rates, and radiative properties. The presence of an insoluble particle at the surface of water droplets can promote ice nucleation at temperatures higher than that of pure water, even in the absence of a collision. However, contact freezing remains an underexplored mode of ice nucleation. Here, we present a study of atmospherically relevant organic acids and their role as effective ice-nucleating particles (INP) in contact mode using a Raman-microscope-equipped environmental chamber. We determined contact freezing temperatures induced by solid crystals of docosanol, adipic acid, cis-pinonic acid, fumaric acid, 4-hydroxybenzoic acid, palmitic acid, phthalic acid, sebacic acid, stearic acid, terephthalic acid, and vanillic acid. All solids except fumaric acid promoted contact freezing of water droplets at significantly higher temperatures than pure water in the chamber (−15.0 to −18.5 °C vs −21.3 °C). Physical and chemical properties were identified which correlate with greater effectiveness of INPs in the contact mode, including crystal lattice mismatch with ice, carbon number, and insolubility in water. In conclusion, we suggest that the presence of these organic solids in atmospheric aerosols may promote atmospheric ice nucleation at warm temperatures.

Clouds↗
DOE OSTI2016

Photophysical Properties and Electronic Structure of Porphyrins Bearing Zero to Four meso -Phenyl Substituents: New Insights into Seemingly Well Understood Tetrapyrroles

Six free base porphyrins bearing 0–4 meso substituents have been examined by steady-state and time-resolved absorption and fluorescence spectroscopy in both toluene and N,N-dimethylformamide (DMF). The lifetime of the lowest singlet excited state (S 1 ) decreases with an increase in the number of meso-phenyl groups; the values in toluene are H 2 P-0 (15.5 ns) > H 2 P-1 (14.9 ns) > H 2 P-2c (14.4 ns) > H 2 P-2t (13.8 ns) ~ H 2 P-3 (13.8 ns) > H 2 P-4 (12.8 ns), where “H 2 P” refers to the core free base porphyrin, the numerical suffix indicates the number of meso-phenyl groups, and “c” and “t” refer to cis and trans, respectively. The opposite trend is found for the fluorescence quantum yield; the values in toluene are H 2 P-0 (0.049) < H 2 P-1 (0.063) ~ H 2 P-2c (0.063) < H 2 P-2t (0.071) < H 2 P-3 (0.073) < H 2 P-4 (0.090). Similar trends occur in DMF. All radiative and non-radiative (internal conversion and intersystem crossing) rate constants for S 1 decay increase with increasing number of meso-phenyl groups. The increase in the rate constant for fluorescence parallels an increase in oscillator strength of the S o → S 1 absorption manifold. Here, the trend is reproduced by time-dependent density functional theory calculations. The calculations within the context of the four-orbital model reveal that the enhanced S o → S 1 radiative probabilities derive from a preferential effect of the meso-phenyl groups to raise the energy of the highest occupied molecular orbital, which underpins a parallel bathochromic shift in the S o → S 1 absorption wavelength. Polarizations of the S 1 and S 2 excited states with respect to molecular structural features (e.g., the central proton axis) are analyzed in the context of historical conventions for porphyrins versus chlorins and bacteriochlorins, where some ambiguity exists, including for porphine, one of the simplest tetrapyrroles. Collectively, the study affords fundamental insights into the photophysical properties and electronic structure of meso-phenylporphyrins that should aid their continued widespread use as benchmarks for tetrapyrrole-based architectures in chemical, solar-energy and life-sciences research.

14 SOLAR ENERGY↗
DOE OSTI2016

Implementation of INDO/SCI with COSMO Implicit Solvation and Benchmarking for Solvatochromic Shifts

Accurate and rapid quantum mechanical prediction of solvatochromic shifts, particularly in systems where charge transfer plays a significant role, is important for many aspects of molecular and material design. Although the semiempirical INDO/SCI approach is computationally efficient and performs well for charge-transfer states, the availability of implicit solvent approaches has been limited. As such, we implement the COSMO solvent model with a perturbative state-specific correction to the excited-state energies with the INDO/SCI method. We show that for a series of prototypical π-conjugated molecules, our newly implemented INDO/SCI/COSMO model yields more accurate absorption energies and comparably accurate solvatochromic shifts to those computed using TD-ωB97XD and CIS with COSMO solvation at a substantially lower computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Development of a Systematic and Extensible Force Field for Peptoids (STEPs)

Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. In conclusion, equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains

Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)–to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. Furthermore, these results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Do TFSA anions slither? Pressure exposes the role of TFSA conformational exchange in self-diffusion

Multi-nuclear ( 1 H, 2 H, and 19 F) magnetic resonance spectroscopy techniques as functions of temperature and pressure were applied to the study of selectively deuterated 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (EMIM TFSA) ionic liquid isotopologues and related ionic liquids. For EMIM TFSA, temperature-dependent 2 H T 1 data indicate stronger electric field gradients in the alkyl chain region compared to the imidazolium ring. Most significantly, the pressure dependences of the EMIM and TFSA self-diffusion coefficients revealed that the displacements of the cations and anions are independent, with diffusion of the TFSA anions being slowed much more by increasing pressure than for the EMIM cations, as shown by their respective activation volumes (28.8 ± 2.5 cm³/mol for TFSA vs. 14.6 ± 1.3 cm³/mol for EMIM). Increasing pressure may lower the mobility of the TFSA anion by hindering its interconversion between trans and cis conformers, a process that is coupled to diffusion according to published molecular dynamics simulations. Measured activation volumes (ΔV ‡ ) for ion self-diffusion in EMIM bis(fluoromethylsulfonyl)amide and EMIM tetrafluoroborate support this hypothesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

First-Principles Molecular Dynamics Study of a Deep Eutectic Solvent: Choline Chloride/Urea and Its Mixture with Water

First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom–atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms of urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. Finally, the vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Foldamer architectures of triazine-based sequence-defined polymers investigated with molecular dynamics simulations and enhanced sampling methods

Triazine-based sequence-defined polymers have recently been developed that are biomimetic and robust (Grate \latin{et al.} Angewandte Chemie 2016). In molecular dynamics (MD) simulations, the triazine polymers were shown to form linear nanorod foldamers through hydrogen bonding and $\pi$-$\pi$ interactions. The nanorod foldamers have motifs resembling those of DNA, $\alpha$-helices, and $\beta$-sheets, and have potential to be useful building blocks for new macromolecules and materials. To understand the formation of nanorod foldamers, we investigate how linker structures in the middle of the triazine polymers lead to folding using MD simulations. We found that a variety of linkers can participate in folding, but that specific linker structures are more favorable than others, depending on the polymer length. Folding of hexamers into well-defined nanorod foldamers was most favorable with pentanediamine and \emph{ortho}-xylenediamine linkers in the center of the polymers. Foldamers with \emph{ortho}-xylenediamine linkers in the center were investigated for longer polymers, i.e., octamers and decamers, using two different enhanced sampling methods, since regular MD simulations had failed to show any folding for these longer polymers. In particular, the recently developed concurrent adaptive sampling (CAS) algorithm (Ahn \latin{et al.} J. Chem. Phys. 2017) and replica exchange molecular dynamics (REMD) were used. We found that the two enhanced sampling methods did lead to the observation of foldamers, and that REMD revealed new foldamer architectures where \emph{cis}-\emph{trans} isomerizations had occurred. Foldamer formation, diversity, and the strengths and limitations of simulation techniques are discussed. These findings provide new insights into the diversity of foldamer architectures for a new type of biomimetic synthetic polymer.

Foldamers, Nanorods, Free energy landscapes, Molec↗