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At least 793 records · Page 44

IMPROVING THE ACCURACY OF COMPOSITE METHODS: A G4MP2 METHOD WITH G4-LIKE ACCURACY AND IMPLICATIONS FOR MACHINE LEARNING

G4MP2 theory has proven to be a reliable and accurate quantum chemical composite method for the calculation of molecular energies using an approximation based on second-order perturbation theory to lower computational costs compared to G4 theory. However, it has been found to have significantly increased errors when applied to larger organic molecules with 10 or more nonhydrogen atoms. We report here on an investigation of the cause of the failure of G4MP2 theory for such larger molecules. One source of error is found to be the "higher-level correction (HLC)", which is meant to correct for deficiencies in correlation contributions to the calculated energies. This is because the HLC assumes that the contribution is independent of the element and the type of bonding involved, both of which become more important with larger molecules. We address this problem by adding an atom-specific correction, dependent on atom type but not bond type, to the higher-level correction. We find that a G4MP2 method that incorporates this modification of the higher-level correction, referred to as G4MP2A, becomes as accurate as G4 theory (for computing enthalpies of formation) for a test set of molecules with less than 10 nonhydrogen atoms as well as a set with 10-14 such atoms, the set of molecules considered here, with a much lower computational cost. The G4MP2A method is also found to significantly improve ionization potentials and electron affinities. Finally, we implemented the G4MP2A energies in a machine learning method to predict molecular energies.

Dandu, Naveen↗

Theoretical modeling of the infrared fluorescence from interstellar polycyclic aromatic hydrocarbons

We have modeled the family of interstellar IR emission bands at 3.3, 6.2, 7.7, 8.6, 11.3, and 12.7 microns by calculating the fluorescence from a size distribution of interstellar polycyclic aromatic hydrocarbons (PAHs) embedded in the radiation field of a hot star. It is found that the various emission bands are dominated by distinctly different PAHs, from molecules with much less than about 80 C atoms for the 3.3 micron feature, to molecules with 10 exp 2-10 exp 5 C atoms for the emission in the IRAS 12 and 25 micron bands. We quantitatively describe the influence on the emergent spectrum of various PAH properties such as the molecular structure, the amount of dehydrogenation, the intrinsic strength of the IR active modes, and the size distribution. Comparing our model results to the emission spectrum from the Orion Bar region, we conclude that interstellar PAHs are likely fully, or almost fully, hydrogenated. Moreover, it is found that the intrinsic strengths of the 6.2 and 7.7 micron C-C stretching modes, and the 8.6 micron C-H in-plane bending mode are 2-6 times larger than measured for neutral PAHs in the laboratory.

Schutte, W. A.↗

Emission Control from Transition Metal Dichalcogenide Monolayers by Aggregation-Induced Molecular Rotors

Organic–inorganic (O–I) heterostructures, consisting of atomically thin inorganic semiconductors and organic molecules, present synergistic and enhanced optoelectronic properties with a high tunability. Here, we develop a class of air-stable vertical O–I heterostructures comprising a monolayer of transition-metal dichalcogenides (TMDs), including WS 2 , WSe 2 , and MoSe 2 , on top of tetraphenylethylene (TPE) core-based aggregation-induced emission (AIE) molecular rotors. The created O–I heterostructures yields a photoluminescence (PL) enhancement of up to ~950%, ~500%, and ~330% in the top monolayer WS 2 , MoSe 2 , and WSe 2 as compared to PL in their pristine monolayers, respectively. The strong PL enhancement is mainly attributed to the efficient photogenerated carrier process in the AIE luminogens (courtesy of their restricted intermolecular motions in the solid state) and the charge-transfer process in the created type I O–I heterostructures. Moreover, we observe an improvement in photovoltaic properties of the TMDs in the heterostructures including the quasi-Fermi level splitting, minority carrier lifetime, and light absorption. Overall, this work presents an inspiring example of combining stable, highly luminescent AIE-based molecules, with rich photochemistry and versatile applications, with atomically thin inorganic semiconductors for multifunctional and efficient optoelectronic devices.

14 SOLAR ENERGY↗

D-Band EPR and ENDOR Spectroscopy of 15 N-Labeled Photosystem I

For billions of years, nature has optimized the photosynthetic machinery that converts light energy into chemical energy. Key primary reactions of photosynthesis occur in large membrane protein-cofactor complexes. The light-induced sequential electron transfer reactions occur through a chain of donor/acceptor cofactors embedded in the protein matrix resulting in a long-lived transmembrane charge-separated state. EPR is the method of choice to study electron transfer and the interaction of protein environment with redox-active cofactors. However, the spectra of organic cofactor radicals typically are not fully resolved and severely overlap at conventional X-band EPR. Even at Q-band EPR, this overlap is present and often a serious problem. As a result, there is a large variation of the reported EPR data and limited understanding of electronic structures of several redox-active cofactors. These serious problems can often be overcome by the excellent spectral resolution provided by high-frequency EPR (HF EPR). In this work, we study the electronic structure of the primary electron donor P 700 and the secondary electron acceptor A 1 of Photosystem I (PSI) using 130 GHz (D-band) EPR and Electron-Nuclear-Double-Resonance (ENDOR) spectroscopy. PSI was isotopically labeled with 15 N (I = $\frac{1/2}$) to avoid quadrupolar interactions in the most abundant nitrogen isotope 14 N (I = 1) and simplify the ENDOR spectra. ENDOR spectroscopy is central for determining the hyperfine coupling of nitrogen atoms of the two chlorophyll molecules comprising oxidized P 700 and the involvement of protein nitrogen atoms with reduced A 1 . While HF ENDOR of A 1 - allows identification of two nitrogen atoms, HF ENDOR of P 700 + still does not permit unique assignment of the recorded hyperfine couplings.

15N↗

Insights from 20 years of the Molecule of the Month

For 20 years, Molecule of the Month articles have highlighted the functional stories of 3D structures found in the Protein Data Bank (PDB). The PDB is the primary archive of atomic structures of biological molecules, currently providing open access to more than 150,000 structures studied by researchers around the world. The wealth of knowledge embodied in this resource is remarkable, with structures that allow exploration of nearly any biomolecular topic, including the basic science of genetic mechanisms, mechanisms of photosynthesis and bioenergetics, and central biomedical topics like cancer therapy and the fight against infectious disease. The central motivation behind the Molecule of the Month is to provide a user-friendly introduction to this rich body of data, charting a path for users to get started with finding and exploring the many available structures. The Molecule of the Month and related materials are updated regularly at the education portal PDB-101 (http://pdb101.rcsb.org/), offering an ongoing resource for molecular biology educators and students around the world.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of nitrogen molecular breakup on divertor conditions in JET L-mode plasmas using SOLPS-ITER

SOLPS-ITER simulations of nitrogen-seeded, low-confinement mode plasmas in the Joint European Torus (JET) predict that the electron temperature in the low-field side (LFS) divertor leg is reduced locally by up to an order of magnitude when nitrogen is assumed to recycle as molecules (N 2 ) instead of atoms using a fixed nitrogen injection rate. The LFS divertor temperature reduction under the assumption of molecular recycling occurs due to a three-step mechanism: (1) the plasma penetration of nitrogen atoms is increased due to the strong triple bond of the N 2 molecule and the kinetic energy release in the dissociation event, both mechanisms contributing equally, (2) the abundance of (particularly multiply-charged) nitrogen ions in the divertor is increased and (3) the electron temperature is reduced due to the increase in radiation (by up to a factor of 4) from nitrogen ions. Setting the volume-integrated nitrogen radiated power to a constant value (0.6 MW) instead of the nitrogen injection rate, SOLPS-ITER predicts under the molecular nitrogen recycling assumption that the peak line-integrated N II, N III and N IV intensities in the LFS divertor are approximately within 15%, 35% and 5%, respectively, of the reference atomic nitrogen recycling case. The predicted peak N II, N III and N IV intensities under either assumption are within 30%, 65% and 5%, respectively, of measurements using the vertically viewing mirror-link divertor spectrometer (Meigs et al., 2010) in nitrogen-seeded JET L-mode plasmas (Lomanowski et al., 2019). ERO2.0 simulations using a constant nitrogen seeding rate on static background plasma solutions from EDGE2D-EIRENE (previously presented in Mäenpää et al., (2022), revised here to include fast reflections) predict that N II to N IV line emission is increased by 20% to 30% when nitrogen is assumed to recycle as molecules, demonstrating the importance of considering the effect of molecular dissociation reactions on the divertor plasma in a self-consistent manner.

Divertor↗

Rare Gases Inserted into Biological Building Blocks: A Theoretical Study of Glycine - Rg Compounds (Rg-Xe, Kr, Ar)

Compounds formed by insertion of rare-gas atoms (Xe, Kr, and Ar) into glycine molecule are investigated using accurate ab initio computational methods. Identification of such insertion compounds may open new frontiers in the field of rare-gas chemistry, such as possible existence of biological molecules that include chemically bound rare gas atoms. The most stable glycine-Rg configuration is found to correspond to insertion of Rg atoms into the 0-H bond of glycine. These NH2CH2COORgH compounds are metastable , but separated by sizable potential barriers from the Rg + glycine dissociation products. Preliminary calculations show that NH2CH2COOXeH compound is energetically stable with respect to another (3-body) dissociation channel (NH2CH2COO + Rg + H), while the corresponding Ar species is not stable in this respect. The compound with the inserted Kr is a borderline case, with the 3-body dissociation products being close in energy to the NH2CH2COOKrH minimum.

Chaban, Galina M.↗

Accelerating Biomimetic Solar - Energy Harvesting: Mapping the Interaction Landscape of Plasmonic-Excitonic Hybrid Nanosystems (Final Report)

In general, excitonic and plasmonic nanoscale materials in close proximity show high potential for significant breakthroughs in energy related materials research. The interactions between these two kinds of materials result in coupled optical transitions (plexcitons), distinct from those of both the individual exciton and plasmon as well as from those of the sum of their constituents (synergistic effects). By linking together materials-research and physical-research approaches, this project contributes to a concerted approach on nanomaterials energy research. The project’s overall goal is to accelerate the development of well-defined plexcitonic model systems consisting of carefully engineered plasmonic and excitonic nanomaterial— essential for both gaining a fundamental understanding of plexcitonic nanomaterials and the development of novel design principles for biomimetic solar energy harvesting. During the 3-year project period and the terminal renewal with limited support for a 12-month period, we successfully synthesized and characterized (1) a robust excitonic nanomaterial and (2) a library of plasmonic nanoparticles as well as developed (3) a microfluidic platform for homogenous nanosynthesis as summarized below: (1) Robust Excitonic Nanomaterial. Supramolecular assemblies are Nature’s most successful material system for solar energy harvesting. However, photovoltaic devices based on artificial supramolecular assemblies continue to be stymied by disappointing efficiencies and poor stability. The conceptual failure may lie in current solar cell architectures, which rely on solidifying supramolecular assemblies as an ensemble into a solid matrix, neglecting the intrinsic fragility of the assemblies’ internal structure, thus disrupting or even destroying their delicate optoelectronic properties, that is, delicate Frenkel excitonic properties. Supramolecular assemblies may finally serve as usable light harvesting material systems for solar energy conversion technologies, only if they meet the following criteria: (a) Stability, that is, the fragile structure including its delicate Frenkel excitonic character needs to be stable, (b) Robustness, that is, resistant against elevated and fluctuating temperatures, and (c) Viability for device integration, that is, capable of being immobilized onto solid substrates. Here, by developing a nanocomposite via a tunable, cage-like scaffold design, we successfully provided stable supramolecular nanocomposites, that inhabit robust Frenkel excitons despite harming environmental conditions such as extreme heat stress. (2) Library of Plasmonic Nanoparticles. Naturally, current models describing plasmonic hybrid quantum states—plasmonic hybridizations—parallel those developed for molecular orbitals, equating individual plasmonic nanostructures with “atoms” and the plasmonic nanoassemblies with “molecules.” In analogy to organic synthesis, a suitably robust fabrication method would allow for “atom-like” manipulation of “molecule-like” plasmonic nanoassemblies; of high value for next-generation energy nanotechnologies. Despite this frequent comparison, current plasmonic nanoassembly fabrication methods favor top-down templating over wet-chemical synthesis, however, achieving precise control over nanostructure’s geometry and surface characteristics remain an art and a scientific challenge. The conceptual failure may lie in the current wet-chemical synthesis paradigm, as it relies on the accessibility of a multi-dimensional synthesis parameter space through limited, rather one-dimensional synthesis procedures by employing step-by-step approaches. Solution-based nanoarchitectonics for rational design of precisely built plasmonic nanoassemblies via solution-based fabrication may finally be possible only if multi-dimensional syntheses approaches are available that allow for comprehensive control over the plasmonic nanomaterials’ (a) Structural Properties and (b) Surface Properties. Here, by developing an innovative multidimensional 1,3-propanediol based polyol synthesis, we successfully provided control over the plasmonic building-block’s geometry (size and shape) together with its surface characteristics. Our results present a critical step toward the vision of a “periodic table-like” system for plasmonic materials based on straightforward wet-chemical syntheses for energy nanotechnologies. Developing deliberate modifications on this synthesis, we generated a library of plasmonic nanostructures covering the vast parameter space—opening the door for fundamental investigation of plexcitonic model systems. (3) Microfluidic Platform for Homogenous Nanosynthesis. Control over structural properties of plexcitonic nanocomposites remains a challenge due to current limitations in nanosynthesis techniques. Slight variations in nanostructure’s geometry impact their optoelectronic properties, demanding precise synthesis beyond the capabilities of solution-based (batch) synthesis processes. In contrast, the small, confined liquid volumes used in microfluidics—a reaction technique where the manipulation of fluids takes place in channels with dimensions of tens of micrometers—allows for homogenous synthesis conditions, providing excellent control of the reaction and, as a result, of the materials’ geopmetry and composition. However, thus far, the majority of plexcitonic systems has been developed via batch synthesis. Here, by successfully developing a two-channel microreactor, our microfluidic-supported synthesis approach combines the advantages of both microfluidics and batch platforms, allowing for precise spatio-temporal control over all synthesis parameters opening the possibility for homogenous nanosythnesis of well-defined plexcitonic model systems.

14 SOLAR ENERGY↗

Potential energy surfaces for high-energy N + O 2 collisions

Potential energy surfaces for high-energy collisions between an oxygen molecule and a nitrogen atom are useful for modeling chemical dynamics in shock waves. In the present work, we present doublet, quartet, and sextet potential energy surfaces that are suitable for studying collisions of O 2 ( 3 Σ$^{–}_{g}$) with N( 4 S) in the electronically adiabatic approximation. Two sets of surfaces are developed, one using neural networks (NNs) with permutationally invariant polynomials (PIPs) and one with the least-squares many-body (MB) method, where a two-body part is an accurate diatomic potential and the three-body part is expressed with connected PIPs in mixed-exponential-Gaussian bond order variables (MEGs). We find, using the same dataset for both fits, that the fitting performance of the PIP-NN method is significantly better than that of the MB-PIP-MEG method, even though the MB-PIP-MEG fit uses a higher-order PIP than those used in previous MB-PIP-MEG fits of related systems (such as N 4 and N 2 O 2 ). However, the evaluation of the PIP-NN fit in trajectory calculations requires about 5 times more computer time than is required for the MB-PIP-MEG fit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2 × 2 × 2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquidlike motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intraprotein) and between different protein molecules (interprotein). The interprotein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intraprotein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally, the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall, our findings increase our understanding of the connection between molecular motions and diffraction data and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Manipulating Core Excitations in Molecules by X-Ray Cavities

Core excitations on different atoms are highly localized and therefore decoupled. By placing molecules in an x-ray cavity the core transitions become coupled via the exchange of cavity photons and form delocalized hybrid light-matter excitations known as core polaritons. Here, we demonstrate these effects for the two inequivalent carbon atoms in 1,1-difluoroethylene. Polariton signatures in the x-ray absorption, two-photon absorption, and multidimensional four-wave mixing signals are predicted.

74 ATOMIC AND MOLECULAR PHYSICS↗

Effect of rotational and vibrational excitation on interaction of diatomic molecules

A general and computationally efficient approach evaluating the central-force potentials for interaction of rotationally and vibrationally excited molecules and molecular ions is presented. Examples of numerical calculations are given for interactions of diatomic systems (H2, N2 and O2) in ground electronic states. The approach can be applied in straightforward way to interaction of atoms and atomic ions with diatomic molecules in arbitrary rotational-vibrational states.

Kunc, Joseph A.↗

Central-force potentials for interaction of rotationally and vibrationally excited molecules

A general and computationally efficient approach evaluating the central-force potentials for interaction of rotationally and vibrationally excited molecules and molecular ions is presented. Examples of numerical calculations are given for interactions of diatomic systems (H2, N2 and O2) in ground electronic states. The approach can be applied in a straightforward way to interactions of atoms and atomic ions with diatomic molecules in arbitrary rotational-vibrational states.

Kunc, Joseph A.↗

Photo-excitation of long-lived transient intermediates in ultracold reactions

In many chemical reactions, the transformation from reactants to products is mediated by transient intermediate complexes. For gas-phase reactions involving molecules with a few atoms, these complexes typically live on the order of 10 ps or less before dissociating, and are therefore rarely influenced by external processes. Here, we demonstrate that the transient intermediate complex K 2 Rb 2 *, formed from collisions between ultracold KRb molecules, undergoes rapid photo-excitation in the presence of a continuous-wave laser source at 1,064 nm, a wavelength commonly used to confine ultracold molecules. These excitations are facilitated by the exceptionally long lifetime of the complex under ultracold conditions. Indeed, by monitoring the change in the complex population after the sudden removal of the excitation light, we directly measure the lifetime of the complex to be 360 ± 30 ns, in agreement with our calculations based on the Rice–Ramsperger–Kassel–Marcus (RRKM) statistical theory. Furthermore, our results shed light on the origin of the two-body loss widely observed in ultracold molecule experiments. Additionally, the long complex lifetime, coupled with the observed photo-excitation pathway, opens up the possibility to spectroscopically probe the structure of the complex with high resolution, thus elucidating the reaction dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron-Molecule Col1isions: Quantitative Approaches, and the Legacy of Aaron Temkin

This article, on electron-molecule collisions, is dedicated to the legacy of my good friend and sometime collaborator, Aaron Temkin on his retirement from the NASA-Goddard Space Flight Center after many years of work at the highest intellectual level in the theoretical treatment of electron-atom and electron-molecule scattering. Aaron's contributions to the manner in which we think about electron-molecule collisions is clear to all of us who have worked in this field. I doubt that the great progress that has occurred in the computational treatment of such complex collision problems could have happened without these contributions. For a brief historical account, see the discussion of Temkin's contribution to electron-molecule scattering in the first article of this volume by Dr. A. K. Bhatia. In this article, I will concentrate on the application of the so called, non-adiabatic R-matrix theory, to vibrational excitation and dissociative attachment, although I will also present some results applying the Linear Algebraic and Kohn-Variational methods to vibrational excitation. As a starting point for almost all computationally effective approaches to electron-molecule collisions, is the fixed nuclei approximation. That is, one recognizes, just as one does with molecular bound states, that there is a separation of electronic(fast) and nuclear(s1ow) degrees of freedom. This separation makes it possible to "freeze" the nuclei in space, calculate the collision parameters for the frozen molecule and then, somehow to add back the vibrations and rotations. The manner in which this is done, depends on the details of the collision problem. It is the work of Aaron and a number of other researchers that has provided the guidance necessary to resolve these issues.

Schneider, B.I.↗

Hyperfine interactions for small systems including transition-metal elements using self-interaction corrected density-functional theory

The interactions between the electronic magnetic moment and the nuclear spin moment, i.e., magnetic hyperfine (HF) interactions, play an important role in understanding electronic properties of magnetic systems and in realizing platforms for quantum information science applications. We investigate the HF interactions for atomic systems and small molecules, including Ti or Mn, by using Fermi–Löwdin orbital (FLO) based self-interaction corrected (SIC) density-functional theory. We calculate the Fermi contact (FC) and spin-dipole terms for the systems within the local density approximation (LDA) in the FLO-SIC method and compare them with the corresponding values without SIC within the LDA and generalized-gradient approximation (GGA), as well as experimental data. For the moderately heavy atomic systems (atomic number Z ≤ 25), we find that the mean absolute error of the FLO-SIC FC term is about 27 MHz (percentage error is 6.4%), while that of the LDA and GGA results is almost double that. Therefore, in this case, the FLO-SIC results are in better agreement with the experimental data. For the non-transition-metal molecules, the FLO-SIC FC term has the mean absolute error of 68 MHz, which is comparable to both the LDA and GGA results without SIC. For the seven transition-metal-based molecules, the FLO-SIC mean absolute error is 59 MHz, whereas the corresponding LDA and GGA errors are 101 and 82 MHz, respectively. Therefore, for the transition-metal-based molecules, the FLO-SIC FC term agrees better with experiment than the LDA and GGA results. We observe that the FC term from the FLO-SIC calculation is not necessarily larger than that from the LDA or GGA for all the considered systems due to the core spin polarization, in contrast to the expectation that SIC would increase the spin density near atomic nuclei, leading to larger FC terms.

Chemistry↗

Photo-thermo-dissociation. I - A general mechanism for destroying molecules

Photothermodissociation (PTD) of an isolated molecule is the name of the process when a photon is absorbed by an electronic transition, the energy is transferred to the vibrations (hot molecule) and then an atom or a fragment is ejected. A statistical physics treatment is presented that goes beyond the thermal approximation and fully takes into account the isolation of the system. A model is given that permits an explicit calculation of the ejection rates of hydrogen and carbon fragments from aromatic molecules as a function of their size and internal energy. Then, the lifetime of species against PTD in different astronomical radiation fields will result when a precise dynamical evolution of their internal energy can be established.

Leger, A.↗

X‐ray characterization of three possible edible oleogelators: Experiment and theory

Abstract Three oleogelator molecules (Triacontane (TC), Stearic acid (SA), and Behenyl Lignocerate (BL)) were studied individually, in pairs, or all together to make an oleogel using triolein as the oil. WAXS, SAXS and USAXS were used to elucidate the solid structures from angstroms to a few micrometers. A two‐dimensional mapping of atomic positions for each molecule was carried out to understand the crystalline multilayer structures formed. We assumed that the molecules were rigidly extended and that they underwent no significant (hindered) rotations so that the free energy is determined by the Lennard‐Jones interactions of closely packed multilayers. TC molecules were predicted to form a tilt angle of , yielding a SAXS line at Å ─1 , in acceptable agreement with the measured . For SA crystals (predicted) yielding a SAXS line at compared to (observed). No mixed crystals were observed for any pair of molecules or when all three were used. USAXS data showed that SA forms large nanocrystals compared to TC and BL. All three combinations of molecular pairs showed basic scatterers smaller or similar to those of individual molecules. The theory presented here, together with the experimental results, showed why no mixed crystals are formed from two or all three molecules. Data from the USAXS region suggested that, when using all three molecules, a more compact fractal structure was obtained, compared with those if one or two of the molecules were used.

Chemistry↗