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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A nitrogen- and carbonyl-rich conjugated small-molecule organic cathode for high-performance sodium-ion batteries

Organic-based cathode materials have attracted considerable attention for sustainable Na-ion batteries due to their great promise to overcome the issues arising from the insertion of large Na + into the rigid structures of conventional transition-metal-containing inorganic electrodes. The structural flexibility as a result of weak intermolecular interactions and simple electron- and ion-storage mechanisms found in organic compounds ensure facile and reversible transport of Na ions. In order to address the general drawbacks of small-molecule organic electrodes such as material dissolution in commonly used organic electrolytes and poor electronic conductivity, we report the use of a nitrogen- and carbonyl-rich highly extended π-conjugated small molecule, hexaazatrianthranylene (HATA) embedded quinone (HATAQ), as a cathode for sodium-ion batteries. The unique hydrogen bonds between highly functionalized conjugated HATAQ molecules allow supramolecular graphite-like 2D layered arrangements in the solid state which help facilitate the structural stability during long-term cycling and promote charge transfer. The compound delivers a capacity as high as 460 mA h g -1 at 500 mA g -1 and an excellent capacity retention of 99% (~138 mA h g -1 ) after 5000 cycles at an extremely high rate of 60 A g -1 . The reaction kinetics and redox mechanism of the material have been elucidated by several characterization techniques together with density functional theory (DFT) studies. The insights gained in this work could pave the way for ultra-high-performance small-molecule organic cathodes for sustainable energy storage.

25 ENERGY STORAGE↗
DOE OSTI2026

Advancing density functional tight-binding method for large organic molecules through equivariant neural networks

Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.

Medrano Sandonas, Leonardo [Technische Universität↗
DOE OSTI2019

Dissecting the cytochrome c2–reaction centre interaction in bacterial photosynthesis using single molecule force spectroscopy

The reversible docking of small, diffusible redox proteins onto a membrane protein complex is a common feature of bacterial, mitochondrial and photosynthetic electron transfer (ET) chains. Spectroscopic studies of ensembles of such redox partners have been used to determine ET rates and dissociation constants. Here, we report a single-molecule analysis of the forces that stabilise transient ET complexes. We examined the interaction of two components of bacterial photosynthesis, cytochrome c 2 and the reaction centre (RC) complex, using dynamic force spectroscopy and PeakForce quantitative nanomechanical imaging. RC–LH1–PufX complexes, attached to silicon nitride AFM probes and maintained in a photo-oxidised state, were lowered onto a silicon oxide substrate bearing dispersed, immobilised and reduced cytochrome c 2 molecules. Microscale patterns of cytochrome c 2 and the cyan fluorescent protein were used to validate the specificity of recognition between tip-attached RCs and surface-tethered cytochrome c 2 . Following the transient association of photo-oxidised RC and reduced cytochrome c 2 molecules, retraction of the RC-functionalised probe met with resistance, and forces between 112 and 887 pN were required to disrupt the post-ET RC– c 2 complex, depending on the retraction velocities used. If tip-attached RCs were reduced instead, the probability of interaction with reduced cytochrome c 2 molecules decreased 5-fold. Thus, the redox states of the cytochrome c 2 haem cofactor and RC ‘special pair’ bacteriochlorophyll dimer are important for establishing a productive ET complex. The millisecond persistence of the post-ET cytochrome c 2 [oxidised]–RC[reduced] ‘product’ state is compatible with rates of cyclic photosynthetic ET, at physiologically relevant light intensities.

Biochemistry & Molecular Biology↗
DOE OSTI2011

The Charmonium-molecule hybrid structure of the X(3872)

We propose that the X(3872) has the charmonium and the DD*-bar hadronic molecule hybrid structure. We study the structure of the X(3872) using the schematic model with the separable interaction. The strengths of the couplings between the charmonium state and the hadronic molecule states are determined so as to reproduce the observed mass of the the X(3872). The isospin symmetry breaking is introduced by the mass differences of the neutral and charged D mesons. The obtained structure of the X(3872) is about 9% of cc-bar charmonium, 75% of the isoscalar DD*-bar molecule and 16percent; of the isovector DD*-bar molecule which explains observed properties of the X(3872) well.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Polyad quantum numbers and multiple resonances in anharmonic vibrational studies of polyatomic molecules

In the theory of anharmonic vibrations of a polyatomic molecule, mixing the zero-order vibrational states due to cubic, quartic and higher-order terms in the potential energy expansion leads to the appearance of more-or-less isolated blocks of states (also called polyads), connected through multiple resonances. Such polyads of states can be characterized by a common secondary integer quantum number. This polyad quantum number is defined as a linear combination of the zero-order vibrational quantum numbers, attributed to normal modes, multiplied by non-negative integer polyad coefficients, which are subject to definition for any particular molecule. According to Kellman's method [J. Chem. Phys. 93, 6630 (1990)], the corresponding formalism can be conveniently described using vector algebra. In the present work, a systematic consideration of polyad quantum numbers is given in the framework of the canonical Van Vleck perturbation theory (CVPT) and its numerical-analytic operator implementation for reducing the Hamiltonian to the quasi-diagonal form, earlier developed by the authors. It is shown that CVPT provides a convenient method for the systematic identification of essential resonances and the definition of a polyad quantum number. The method presented is generally suitable for molecules of significant size and complexity, as illustrated by several examples of molecules up to six atoms. The polyad quantum number technique is very useful for assembling comprehensive basis sets for the matrix representation of the Hamiltonian after removal of all non-resonance terms by CVPT. In addition, the classification of anharmonic energy levels according to their polyad quantum numbers provides an additional means for the interpretation of observed vibrational spectra.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Imaging photoelectron circular dichroism of chiral molecules by femtosecond multiphoton coincidence detection

Here, we provide a detailed account of novel experiments employing electron-ion coincidence imaging to discriminate chiral molecules. The full three-dimensional angular scattering distribution of electrons is measured after photoexcitation with either left or right circular polarized light. The experiment is performed using a simplified photoelectron-photoion coincidence imaging setup employing only a single particle imaging detector. Results are reported applying this technique to enantiomers of the chiral molecule camphor after three-photon ionization by circularly polarized femtosecond laser pulses at 400 nm and 380 nm. The electron-ion coincidence imaging provides the photoelectron spectrum of mass-selected ions that are observed in the time-of-flight mass spectra. The coincident photoelectron spectra of the parent camphor ion and the various fragment ions are the same, so it can be concluded that fragmentation of camphor happens after ionization. We discuss the forward-backward asymmetry in the photoelectron angular distribution which is expressed in Legendre polynomials with moments up to order six. Furthermore, we present a method, similar to one-photon electron circular dichroism, to quantify the strength of the chiral electron asymmetry in a single parameter. The circular dichroism in the photoelectron angular distribution of camphor is measured to be 8% at 400 nm. The electron circular dichroism using femtosecond multiphoton excitation is of opposite sign and about 60% larger than the electron dichroism observed before in near-threshold one-photon ionization with synchrotron excitation. We interpret our multiphoton ionization as being resonant at the two-photon level with the 3s and 3p Rydberg states of camphor. Theoretical calculations are presented that model the photoelectron angular distribution from a prealigned camphor molecule using density functional theory and continuum multiple scattering X alpha photoelectron scattering calculations. Qualitative agreement is observed between the experimental results and the theoretical calculations of the Legendre moments representing the angular distribution for the two enantiomers. The electron-ion coincidence technique using multiphoton ionization opens new directions in table-top analytical mass-spectrometric applications of mixtures of chiral molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Noncovalent π⋅⋅⋅π interaction between graphene and aromatic molecule: Structure, energy, and nature

Noncovalent π⋅⋅⋅π interactions between graphene and aromatic molecules have been studied by using density functional theory with empirical dispersion correction (ωB97X-D) combined with zeroth-order symmetry adapted perturbation theory (SAPT0). Excellent agreement of the interaction energies computed by means of ωB97X-D and spin component scaled (SCS) SAPT0 methods, respectively, shows great promise for the two methods in the study of the adsorption of aromatic molecules on graphene. The other important finding in this study is that, according to SCS-SAPT0 analyses, π⋅⋅⋅π interactions between graphene and aromatic molecules are largely dependent on both dispersion and electrostatic type interactions. It is also noticed that π⋅⋅⋅π interactions become stronger and more dispersive (less electrostatic) upon substitution of the very electronegative fluorine atoms onto the aromatic molecules.

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

Adsorbed states of chlorophenol on Cu(110) and controlled switching of single-molecule junctions

A molecular junction of substituted benzene (chlorophenol) is fabricated and controlled by using a scanning tunneling microscope (STM). Prior to the junction formation, the bonding geometry of the molecule on the surface is characterized by STM and electron energy loss spectroscopy (EELS). EELS shows that the OH group of chlorophenol is dissociated on Cu(110) and that the molecule is bonded nearly flat to the surface via an O atom, with the Cl group intact. We demonstrate controlled contact of an STM tip to the “available” Cl group and lift-up of the molecule while it is anchored to the surface via an O atom. The asymmetric bonding motifs of the molecule to the electrodes allow for reversible control of the junction.

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

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. Here, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by construction captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. This approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Block copolymer templated self-assembly of disk-shaped molecules

Stacking of disk-shaped organic molecules is a promising strategy to develop electronic and photovoltaic devices. Here, we investigate the capability of a soft block copolymer matrix that microphase separates into a cylindrical phase to direct the self-assembly of disk-shaped molecules by means of molecular simulations. We show that two disk molecules confined in the cylinder domain experience a depletion force, induced by the polymer chains, which results in the formation of stacks of disks. This entropic interaction and the soft confinement provided by the matrix are both responsible for the structures that can be self-assembled, which include slanted or columnar stacks. In addition, we evidence the transmission of stresses between the different minority domains of the microphase, which results in the establishment of a long-ranged interaction between disk molecules embedded in different domains; this interaction is of the order of the microphase periodicity and may be exploited to direct assembly of disks at larger scales.

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

Electronic structure of mononuclear Cu-based molecule from density-functional theory with self-interaction correction

In this paper, we investigate the electronic structure of a planar mononuclear Cu-based molecule [Cu(C 6 H 4 S 2 ) 2 ] z in two oxidation states ( z = –2, –1) using density-functional theory (DFT) with Fermi–Löwdin orbital (FLO) self-interaction correction (SIC). The dianionic Cu-based molecule was proposed to be a promising qubit candidate. Self-interaction error within approximate DFT functionals renders severe delocalization of electron and spin densities arising from 3 d orbitals. The FLO-SIC method relies on optimization of Fermi–Löwdin orbital descriptors (FODs) with which localized occupied orbitals are constructed to create SIC potentials. Starting with many initial sets of FODs, we employ a frozen-density loop algorithm within the FLO-SIC method to study the Cu-based molecule. We find that the electronic structure of the molecule remains unchanged despite somewhat different final FOD configurations. In the dianionic state (spin S = 1/2), FLO-SIC spin density originates from the Cu d and S p orbitals with an approximate ratio of 2:1, in quantitative agreement with multireference calculations, while in the case of SIC-free DFT, the orbital ratio is reversed. Overall, FLO-SIC lowers the energies of the occupied orbitals and, in particular, the 3 d orbitals unhybridized with the ligands significantly, which substantially increases the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) compared to SIC-free DFT results. The FLO-SIC HOMO–LUMO gap of the dianionic state is larger than that of the monoanionic state, which is consistent with experiment. Our results suggest a positive outlook of the FLO-SIC method in the description of magnetic exchange coupling within 3 d -element-based systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An optimally tuned range-separated hybrid starting point for ab initio GW plus Bethe–Salpeter equation calculations of molecules

The ab initio GW plus Bethe–Salpeter equation (GW-BSE, where G is the one particle Green's function and W is the screened Coulomb interaction) approach has emerged as a leading method for predicting excitations in both solids and molecules with a predictive power contingent upon several factors. Among these factors are the (1) generalized Kohn–Sham eigensystem used to construct the GW self-energy and to solve the BSE and (2) the efficacy and suitability of the Tamm–Dancoff approximation. Here, we present a detailed benchmark study of low-lying singlet excitations from a generalized Kohn–Sham (gKS) starting point based on an optimally tuned range-separated hybrid (OTRSH) functional. We show that the use of this gKS starting point with one-shot G0W0 and G0W0-BSE leads to the lowest mean absolute errors (MAEs) and mean signed errors (MSEs), with respect to high-accuracy reference values, demonstrated in the literature thus far for the ionization potentials of the GW100 benchmark set and for low-lying neutral excitations of Thiel’s set molecules in the gas phase, without the need for self-consistency. The MSEs and MAEs of one-shot G0W0-BSE@OTRSH excitation energies are comparable to or lower than those obtained with other functional starting points after self-consistency. Additionally, we compare these results with linear-response time-dependent density functional theory (TDDFT) calculations and find GW-BSE to be superior to TDDFT when calculations are based on the same exchange-correlation functional. This work demonstrates tuned range-separated hybrids used in combination with GW and GW-BSE can greatly suppress starting point dependence for molecules, leading to accuracy similar to that for higher-order wavefunction-based theories for molecules without the need for costlier iterations to self-consistency.

McKeon, Caroline A. (ORCID:0000000217373503)↗
DOE OSTI2023

Mass-selected ion–molecule cluster beam apparatus for ultrafast photofragmentation studies

We describe an apparatus for investigating the excited-state dissociation dynamics of mass-selected ion–molecule clusters by mass-resolving and detecting photofragment-ions and neutrals, in coincidence, using an ultrafast laser operating at high repetition rates. The apparatus comprises a source that generates ion–molecule clusters, a time-of-flight spectrometer, and a mass filter that selects the desired anions, and a linear-plus-quadratic reflectron mass spectrometer that discriminates the fragment anions after the femtosecond laser excites the clusters. The fragment neutrals and anions are then captured by two channeltron detectors. The apparatus performance is tested by measuring the photofragments: I – , CF 3 I – , and neutrals from photoexcitation of the ion–molecule cluster CF 3 I·I – using femtosecond UV laser pulses with a wavelength of 266 nm. Here, the experimental results are compared with our ground state and excited state electronic structure calculations as well as the existing results and calculations, with particular attention to the generation mechanism of the anion fragments and dissociation channels of the ion–molecule cluster CF 3 I·I – in the charge-transfer excited state.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Disentangling the confounding spectroscopy of C 1 molecules: Without symmetry as a guide, everything is allowed

The spectra of C 1 molecules are confounding in that each of the fundamental vibrational modes transform as the same irreducible representation (A) and hence each band consists of a seemingly random distribution of a-, b-, and c-type transitions. This is in contrast to higher symmetry molecules for which band types are readily deduced by simple symmetry rules. Herein, we present a method to simulate the convoluted rotational contours in the gas-phase spectra of C 1 molecules by combining existing ab initio calculations with Colin Western’s PGOPHER rotational contour program. Specifically, ab initio calculations in the NWC HEM suite of programs were employed to predict the components of the dipole moment derivatives along the principal axes of the moments of inertia. This information was then input into PGOPHER to model the fundamental band contours as a sum of a-, b-, and c-type transitions. This method was applied to simulate the rotational contour spectra of a series of representative C 1 molecules which were then compared against both ab initio stick spectra and experimentally measured broadband IR spectra from the Pacific Northwest National Laboratory infrared gas-phase database. In addition to providing further insight beyond what is revealed in a typical stick spectrum, the simulated contours showed good agreement with the measured spectra.

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

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

ZnO quantum dot–molecule conjugates: Chemical interactions, charge dynamics, and spin polarization

Conjugates between molecules and quantum dots (QDs) have been explored for a range of potential applications from photocatalysis and photovoltaics to quantum information science technologies. A particularly ubiquitous material in many of these applications are ZnO QDs since they can accept and transport electrons and can also act as hosts for unique spin states. Conjugates between molecular light absorbers and ZnO QDs have been explored for decades as components in dye-sensitized solar cells. Recently, these materials have also attracted interest for their ability to produce spin-polarized states upon photoexcitation. The current paper employs a series of light absorbing perylene molecules with different ZnO QD sizes to explore key features of these QD–molecule conjugates: (1) chemical interactions, (2) charge dynamics, and (3) spin polarization. The chemical interactions between the molecules and QDs are determined with binding equilibria and reveal dramatic impact of ligand size. The charge transfer dynamics from photoexcited perylenes to ZnO QDs were found to depend exponentially on the linker length. Finally, time-resolved electron paramagnetic resonance experiments reveal that these conjugates generate spin-polarized states in the form of radical pairs and triplets. These spin states hold promise as potential qubits and also offer an avenue to efficiently sensitize molecular triplets.

Hernandez, Frida S. [Amherst College, MA (United S↗
DOE OSTI2020

Strong mutual increase in the efficiency of isotope-selective laser IR dissociation of molecules under nonequilibrium thermodynamic conditions of the compression shock under irradiation in a bimolecular mixture

We have revealed a strong (by a factor of 2 to 5) mutual increase in the yield of IR molecular dissociation (by the example of CF{sub 2}HCl and CF{sub 3}Br) and a significant (by a factor of 1.5 to 3) lowering of dissociation thresholds in the nonequilibrium thermodynamic conditions of compression shock in the irradiation of the molecules by resonance IR laser radiation in the bimolecular mixture in comparison with their individual irradiation. This opens up the possibility to perform efficient isotope-selective IR dissociation of molecules at lower excitation energy densities (Φ ⩽ 1.5 – 2.0 J cm{sup −2}) and thereby to improve the dissociation selectivity. This was demonstrated by the example of chlorine- and bromine-isotope selective dissociation of the specified molecules, which are characterised by quite small (less than 0.25 cm{sup −1}) isotope shifts in the IR vibrational absorption spectra excited by laser radiation. The enrichment coefficients K {sub enr}({sup 35}Cl / {sup 37}Cl) = 0.90 ± 0.05 in the residual CF{sub 2}HCl gas and K {sub enr}({sup 79}Br / {sup 81}Br) in the resultant Br{sub 2} product are obtained when the CF{sub 2}HCl : CF{sub 3}Br = 1 : 1 molecular mixture and CF{sub 3}Br molecules, respectively, are irradiated by the 9R(30) CO{sub 2} laser line (frequency, 1084.635 cm{sup −1}) at an energy density Φ ≈ 1.3 J cm{sup −2}. (laser isotope separation)

36 MATERIALS SCIENCE↗
DOE OSTI2018

A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin

The influenza virus hemagglutinin (HA) glycoprotein mediates receptor binding and membrane fusion during viral entry in host cells. Blocking these key steps in viral infection has applications for development of novel antiinfluenza therapeutics as well as vaccines. However, the lack of structural information on how small molecules can gain a foothold in the small, shallow receptor-binding site (RBS) has hindered drug design against this important target on the viral pathogen. Here, we report on the serendipitous crystallization-based discovery of a small-molecule N -cyclohexyltaurine, commonly known as the buffering agent CHES, that is able to bind to both group-1 and group-2 HAs of influenza A viruses. X-ray structural characterization of group-1 H5N1 A/Vietnam/1203/2004 (H5/Viet) and group-2 H3N2 A/Hong Kong/1/1968 (H3/HK68) HAs at 2.0-Å and 2.57-Å resolution, respectively, revealed that N -cyclohexyltaurine binds to the heart of the conserved HA RBS. N -cyclohexyltaurine mimics the binding mode of the natural receptor sialic acid and RBS-targeting bnAbs through formation of similar hydrogen bonds and CH-π interactions with the HA. In H3/HK68, N -cyclohexyltaurine also binds to a conserved pocket in the stem region, thereby exhibiting a dual-binding mode in group-2 HAs. We conclude these long-awaited structural insights into RBS recognition by a noncarbohydrate-based small molecule enhance our knowledge of how to target this important functional site and can serve as a template to guide the development of novel broad-spectrum small-molecule therapeutics against influenza virus.

60 APPLIED LIFE SCIENCES↗