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DOE OSTI2021

Universality in Quantum Gravity. Final Technical Report

This is the final technical report for the DOE Early Career Award to PI Thomas Hartman at Cornell University, outlining the goals of the research project and summarizing its main technical achievements. These include the discovery of new constraints on quantum field theory, new theoretical methods that allow for a direct derivation of emergent spacetime from conformal field theory in certain settings, and the discovery of fundamental bounds on the dynamics of quantum information.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1993

Prediction of nonlinear optical properties of organic materials. General theoretical considerations

The prediction of nonlinear optical properties of organic materials is geared to assist materials scientists in the selection of good candidate molecules. A brief summary of the quantum mechanical methods used for estimating hyperpolarizabilities will be presented. The advantages and limitations of each technique will be discussed. Particular attention will be given to the finite-field method for calculating first and second order hyperpolarizabilities, since this method is better suited for large molecules. Corrections for dynamic fields and bulk effects will be discussed in detail, focusing on solvent effects, conformational isomerization, core effects, dispersion, and hydrogen bonding. Several results will be compared with data obtained from third-harmonic-generation (THG) and dc-induced second harmonic generation (EFISH) measurements. These comparisons will demonstrate the qualitative ability of the method to predict the relative strengths of hyperpolarizabilities of a class of compounds. The future application of molecular mechanics, as well as other techniques, in the study of bulk properties and solid state defects will be addressed. The relationship between large values for nonlinear optical properties and large conjugation lengths is well known, and is particularly important for third-order processes. For this reason, the materials with the largest observed nonresonant third-order properties are conjugated polymers. An example of this type of polymer is polydiacetylene. One of the problems in dealing with polydiacetylene is that substituents which may enhance its nonlinear properties may ultimately prevent it from polymerizing. A model which attempts to predict the likelihood of solid-state polymerization is considered, along with the implications of the assumptions that are used. Calculations of the third-order optical properties and their relationship to first-order properties and energy gaps will be discussed. The relationship between monomeric and polymeric third-order optical properties will also be considered.

Cardelino, B.↗

NASA NTRS1998

Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A molecular dynamics study

The undecamer of poly-L-leucine at the water-hexane interface is studied by molecular dynamics simulations. This represents a simple model relevant to folding and insertion of hydrophobic peptides into membranes. The peptide, initially placed in a random coil conformation on the aqueous side of the system, rapidly translocates toward the hexane phase and undergoes interfacial folding into an alpha-helix in the subsequent 36 ns. Folding is nonsequential and highly dynamic. The initially formed helical segment at the N-terminus of the undecamer becomes transiently broken and, subsequently, reforms before the remainder of the peptide folds from the C-terminus. The formation of intramolecular hydrogen bonds during the folding of the peptide is preceded by a dehydration of the participating polar groups, as they become immersed in hexane. Folding proceeds through a short-lived intermediate, a 3(10)-helix, which rapidly interconverts to an alpha-helix. Both helices contribute to the equilibrium ensemble of folded structures. The helical peptide is largely buried in hexane, yet remains adsorbed at the interface. Its preferred orientation is parallel to the interface, although the perpendicular arrangement with the N-terminus immersed in hexane is only slightly less favorable. In contrast, the reversed orientation is highly unfavorable, because it would require dehydration of C-terminus carbonyl groups that do not participate in intramolecular hydrogen bonding. For the same reason, the transfer of the undecamer from the interface to the bulk hexane is also unfavorable. The results suggest that hydrophobic peptides fold in the interfacial region and, simultaneously, translocate into the nonpolar side of the interface. It is further implied that peptide insertion into the membrane is accomplished by rotating from the parallel to the perpendicular orientation, most likely in such a way that the N-terminus penetrates the bilayer.

NASA Discipline Exobiology↗

DOE OSTI2024

Distinct binding conformations of epinephrine with α- and β-adrenergic receptors

Abstract Agonists targeting α 2 -adrenergic receptors (ARs) are used to treat diverse conditions, including hypertension, attention-deficit/hyperactivity disorder, pain, panic disorders, opioid and alcohol withdrawal symptoms, and cigarette cravings. These receptors transduce signals through heterotrimeric Gi proteins. Here, we elucidated cryo-EM structures that depict α 2A -AR in complex with Gi proteins, along with the endogenous agonist epinephrine or the synthetic agonist dexmedetomidine. Molecular dynamics simulations and functional studies reinforce the results of the structural revelations. Our investigation revealed that epinephrine exhibits different conformations when engaging with α-ARs and β-ARs. Furthermore, α 2A -AR and β 1 -AR (primarily coupled to Gs, with secondary associations to Gi) were compared and found to exhibit different interactions with Gi proteins. Notably, the stability of the epinephrine–α 2A -AR–Gi complex is greater than that of the dexmedetomidine–α 2A -AR–Gi complex. These findings substantiate and improve our knowledge on the intricate signaling mechanisms orchestrated by ARs and concurrently shed light on the regulation of α-ARs and β-ARs by epinephrine.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Variable-Temperature Scattering and Spectroscopy Characterizations for Temperature-Dependent Solution Assembly of PffBT4T-Based Conjugated Polymers

The solution structure of conjugated polymers (CPs) from which the films are cast is critical for tailoring the thin-film morphology thus device performance. Here, we used multimodal variable-temperature scattering and spectroscopy tools to fully quantify the solution assembly of poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3'''-dialkyl-2,2';5',2'';5'',2'''-quaterthiophen-5,5'''-diyl)] (PffBT4T) polymers with varying side-chain lengths at different assembly temperatures. The conformational and aggregation behaviors for PffBT4T-based CPs were found to be very sensitive to both temperature and side chain length using ultraviolet–visible (UV–vis) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and small-angle neutron scattering (SANS). We found that with slightly increasing side chain length from 2-octyldodecyl (C8C12) to 2-nonyltridecyl (C9C13), PffBT4T-based CPs show a significant decrease in aggregation-to-dissolved chain transition temperature (10 °C), degree of aggregation, enthalpy change of aggregation, and size of the aggregates in solution. At room temperature, PffBT4T polymer strongly aggregated to form fabric structure with the film thickness of a few nanometers in thickness and hundreds of nanometers in length, as probed by atomic force microscopy (AFM), transmission electronic microscopy (TEM), and dynamic light scattering (DLS). At the elevated temperature above the aggregation-to-dissolved chain transition temperature, PffBT4T is fully dissolved and adopts a semiflexible coil conformation with the persistence length of 3.1 nm for PffBT4T-C8C12 and a slightly increased persistence length of 3.4 nm for PffBT4T-C9C13, according to temperature-dependent SANS measurements. Longer side chains of PffBT4T-C9C13 also lead to less aggregation enthalpy gain compared with PffBT4T-C8C12. This work provides a solution structure manipulating strategy of CPs and thus will inspire the molecular design and processing protocols of CPs toward higher performance electronic devices.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Electron Binding Energy Spectra of Al n Pt – Clusters—A Combined Experimental and Computational Study

Results of size-selected electron photo-detachment experiments and density functional theory calculations on anionic Al n Pt – , n = 1–7, clusters are presented and analyzed. The measured and calculated spectra of electron binding energies are, overall, in excellent accord with each other. The analysis reveals the general importance of accounting for the multiplicity of structural forms of a given-size cluster that can contribute to its measured spectrum, especially when the clusters are fluxional and/or the conditions of the experiment allow for structural transitions. Here, we show that for the systems studied here, the size-specific peculiarities of the measured spectra can be understood in terms of the combined contributions of corresponding different accessible stable equilibrium conformations, bona-fide transition-state configurations, and electronic-crossing structures that may play the role of effective barriers in electronically nonadiabatic dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Mechanism of Peptide Agonist Binding in CXCR4 Chemokine Receptor

Chemokine receptors are key G-protein-coupled receptors (GPCRs) that control cell migration in immune system responses, development of cardiovascular and central nervous systems, and numerous diseases. In particular, the CXCR4 chemokine receptor promotes metastasis, tumor growth and angiogenesis in cancers. CXCR4 is also used as one of the two co-receptors for T-tropic HIV-1 entry into host cells. Therefore, CXCR4 serves as an important therapeutic target for treating cancers and HIV infection. Apart from the CXCL12 endogenous peptide agonist, previous studies suggested that the first 17 amino acids of CXCL12 are sufficient to activate CXCR4. Two 17-residue peptides with positions 1–4 mutated to RSVM and ASLW functioned as super and partial agonists of CXCR4, respectively. However, the mechanism of peptide agonist binding in CXCR4 remains unclear. Here, we have investigated this mechanism through all-atom simulations using a novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method. The Pep-GaMD simulations have allowed us to explore representative binding conformations of each peptide and identify critical low-energy states of CXCR4 activated by the super versus partial peptide agonists. Our simulations have provided important mechanistic insights into peptide agonist binding in CXCR4, which are expected to facilitate rational design of new peptide modulators of CXCR4 and other chemokine receptors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

DOE OSTI2023

Uncertainty-driven dynamics for active learning of interatomic potentials

Machine learning (ML) models, if trained to data sets of high-fidelity quantum simulations, produce accurate and efficient interatomic potentials. Active learning (AL) is a powerful tool to iteratively generate diverse data sets. In this approach, the ML model provides an uncertainty estimate along with its prediction for each new atomic configuration. If the uncertainty estimate passes a certain threshold, then the configuration is included in the data set. Here we develop a strategy to more rapidly discover configurations that meaningfully augment the training data set. The approach, uncertainty-driven dynamics for active learning (UDD-AL), modifies the potential energy surface used in molecular dynamics simulations to favor regions of configuration space for which there is large model uncertainty. The performance of UDD-AL is demonstrated for two AL tasks: sampling the conformational space of glycine and sampling the promotion of proton transfer in acetylacetone. The method is shown to efficiently explore the chemically relevant configuration space, which may be inaccessible using regular dynamical sampling at target temperature conditions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

PotLib 2023: New version of a potential energy surface library for chemical systems

POTLIB is a library of global and semiglobal potential energy surface subprograms. The library currently features 410 entries, including both single-state entries and multi-state entries. When one calls the routine of a single-state entry, it returns the ground-electronic-state adiabatic potential energy surface at the input geometry. In addition, some entries also return the gradient of the surface. Further, when one calls a multi-state entry, it returns a diabatic potential energy matrix (DPEM). If the entry also has the gradient of the DPEM, one can compute adiabatic surfaces, their gradients, and the nonadiabatic coupling vectors (NACs) from the DPEM and its gradient by diagonalization. Some but not all the routines conform to one of a set of standard interfaces. The goal is to facilitate chemical dynamics research by collecting and disseminating a comprehensive collection of state-of-the-art potential energy routines (developed by a wide, international group of researchers) with systematic and well-defined interfaces for use with chemical dynamics programs. Systems in the library include CHArO 2 , CHN 2 O + , CH 2 O, CH 2 O 2 , CH 3 N 2 , CH 3 O, CH 4 , CH 4 Br, CH 4 Cl, CH 4 F, CH 4 O, CH 4 OCl, CH 4 OF, CH 4 OH, CH 5 , CH$^{+}_{5}$, CH 5 N, CH 5 O 2 , CH 8 O 2 , C 2 H 2 N 2 O, C 2 H 2 O, C 2 H 4 N, C 2 H 4 O 4 , C 2 H 6 Cl, C 2 H 6 F, C 2 H 6 H, C 2 H 6 O, C 2 H 6 OH, C 2 H 7 , C 2 O 2 , C 3 H 4 O 2 , C 3 H 7 NO, C 6 H 6 O, C 6 H 6 S, C 7 H8S, HBrCl, HCl 2 , HF 2 , HI 2 , HLiF, HNaF, HO 2 , HO 3 , HOBr, HSiO, H 2 Br, H 2 ClO, H 2 F, H 2 F 2 , H 2 FO, H 2 Na, H 2 O, H 2 O 2 , H 2 OBr, H 3 , H 3 Cl, H 3 ClN, H 3 ClO, H 3 N, H 3 O, H 3 O 2 , H$^{+}_{3}$, H 3 S, H 4 ClSi, H 4 N, H 4 NO, H 4 O 2 , H 5 GeO, H 5 Si, H$^{+}_{7}$, Al m H n , Al n , Ar N O, K 2 Rb 2 , NO 2 , N 2 O, N 2 O 2 , N 3 , N 4 , O 3 , and O 4 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗

DOE OSTI2024

Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Abstract Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Elucidation of the physical factors that control activated transport of penetrants in chemically complex glass-forming liquids

Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S 0 ( T ) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S 0 ( T ) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S 0 ( T ) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.

Science & Technology - Other Topics↗

DOE OSTI2020

Global Phase Diagram of a Spin-Orbital Kondo Impurity Model and the Suppression of Fermi-Liquid Scale

Many correlated metallic materials are described by Landau Fermi-liquid theory at low energies, but for Hund metals the Fermi-liquid coherence scale $T_{FL}$ is found to be surprisingly small. In this Letter, we study the simplest impurity model relevant for Hund metals, the three-channel spin-orbital Kondo model, using the numerical renormalization group (NRG) method and compute its global phase diagram. In this framework, $T_{FL}$ becomes arbitrarily small close to two new quantum critical points that we identify by tuning the spin or spin-orbital Kondo couplings into the ferromagnetic regimes. We find quantum phase transitions to a singular Fermi-liquid or a novel non-Fermi-liquid phase. The new non-Fermi-liquid phase shows frustrated behavior involving alternating overscreenings in spin and orbital sectors, with universal power laws in the spin (ω -1/5 ), orbital (ω 1/ 5 ) and spin-orbital (ω 1 ) dynamical susceptibilities. These power laws, and the NRG eigenlevel spectra, can be fully understood using conformal field theory arguments, which also clarify the nature of the non-Fermi-liquid phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1975

A generalized tensor formulation of atmosphere and seas dynamics

A generalized mathematical model was developed for simulation of the dynamics and transport of both the atmosphere and seas. A nearly horizontal bottom coordinate surface conforms to the land-to-air interface and the sea-floor-to-water interface, which simplifies computations. General vertical motion of the other quasi-horizontal coordinate surfaces is allowed; external gravity waves can be represented by the top coordinate surface, and meteorological fronts and inversion layers in the atmosphere and refractive layers in the seas can be represented with enhanced resolution by the internal quasi-horizontal coordinate surfaces. A tensor reformulation of the standard subgrid mixing theory departs significantly from the standard theory in allowing, as a solution under adiabatic conditions, rigid-body rotation of the atmosphere.

Avis, L. M.↗