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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Abnormal Slow Phonon Dynamics Toward Prolonging Excited States Dynamics Enabled by Crystalline‐Assembling Donor–Acceptor Molecules

Phonon dynamics are a critical factor to control the optical properties of excited states in light-emitting materials. Here, we report an extremely slow relaxation of photoexcited lattice vibrations enabled by assembling the donor-acceptor (D–A) molecules [2-(9,9-dimethylacridin-10(9H)-yl)-9,9-dimethyl-9H-thioxanthene 10,10-dioxide], namely AC molecules, into dipolar crystal. By using photoexcitation-modulated Raman spectroscopy, we find that the crystalline-lattice vibrations monitored by Raman-scattering laser beam of 785 nm demonstrate an un-usual slow relaxation in the time scale of seconds after ceasing photoexcitation beam of 343 nm in such dipolar crystal. This presents extremely slow phonon dynamics enabled by crystalline-assembling the D–A molecules into a dipolar crystal. Simultaneously, the photoluminescence (PL) exhibits a prolonged behavior, lasting 10 ms after ceasing photoexcitation in dipolar AC crystal. This phenomenon provides an experimental hypothesis that the slow phonon dynamics function as an important mechanism to unusually prolong excited states dynamics upon crystalline-assembling the D–A molecules into dipolar crystal. Here, this hypothesis can be verified by directly suppressing the phonon dynamics through freezing D–A molecular liquid into dipolar crystalline solid at 77 K to largely prolong the PL to 1 s- after removing photoexcitation. Clearly, crystalline-assembling D–A molecules provide the necessary conditions to enable slow phonon dynamics toward prolonging excited states dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Theoretical modeling of the interaction of phenylacetylene and styrene molecules with Pd{111}

The DFT-PBE method was used to calculate the structural and energy characteristics of all possible adsorption complexes of phenylacetylene (PA) and styrene (St) molecules with the Pd{111} surface. According to the calculations, the acetylene group of the PA molecule in the energetically preferred complexes is bound to three or four Pd atoms and the plane of the phenyl ring is parallel to the Pd surface. In the case of deficiency of fcc sites, the phenyl ring of the PA molecule is displaced from the Pd{111} surface. The number of Pd atoms required for the compact adsorption of two PA molecules is the same as that for the adsorption of one St molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Effect of Basicity and Structure on the Hydration of Protonated Molecules, Proton-Bound Dimer and Cluster Formation: An Ion Mobility-Time of Flight Mass Spectrometry and Theoretical Study

Protonation, hydration, and cluster formation of ammonia, formaldehyde, formic acid, acetone, butanone, 2-ocatanone, 2-nonanone, acetophenone, ethanol, pyridine, and its derivatives were studied by IMS-TOFMS technique equipped with a corona discharge ion source. It was found that tendency of the protonated molecules, MH{sup +}, to participate in hydration or cluster formation depends on the basicity of M. The molecules with higher basicity were hydrated less than those with lower basicity. The mass spectra of the low basic molecules such as formaldehyde exhibited larger clusters of M{sub n}H{sup +}(H{sub 2}O){sub n}, while for compounds with high basicity such as pyridine, only MH{sup +} and MH{sup +}M peaks were observed. The results of DFT calculations show that enthalpies of hydrations and cluster formation decrease as basicities of the molecules increases. Using comparison of mass spectra of formic acid, formaldehyde, and ethanol, effect of structure on the cluster formation was also investigated. Formation of symmetric (MH{sup +}M) and asymmetric proton-bound dimers (MH{sup +}N) was studied by ion mobility and mass spectrometry techniques. Both theoretical and experimental results show that asymmetric dimers are formed more easily between molecules (M and N) with comparable basicity. As the basicity difference between M and N increases, the enthalpy of MH{sup +}N formation decreases. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2013

Blinking effect and the use of quantum dots in single molecule spectroscopy

Highlights: Black-Right-Pointing-Pointer It is possible to eliminate the blinking effect of a water-soluble QD. Black-Right-Pointing-Pointer We provide a direct method to study protein function and dynamics at the single level. Black-Right-Pointing-Pointer QD, potent tool for single molecule studies of biochemical and biological processes. -- Abstract: Luminescent semiconductor nanocrystals (quantum dots, QD) have unique photo-physical properties: high photostability, brightness and narrow size-tunable fluorescence spectra. Due to their unique properties, QD-based single molecule studies have become increasingly more popular during the last years. However QDs show a strong blinking effect (random and intermittent light emission), which may limit their use in single molecule fluorescence studies. QD blinking has been widely studied and some hypotheses have been done to explain this effect. Here we summarise what is known about the blinking effect in QDs, how this phenomenon may affect single molecule studies and, on the other hand, how the 'on'/'off' states can be exploited in diverse experimental settings. In addition, we present results showing that site-directed binding of QD to cysteine residues of proteins reduces the blinking effect. This option opens a new possibility of using QDs to study protein-protein interactions and dynamics by single molecule fluorescence without modifying the chemical composition of the solution or the QD surface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Co(II)-doped MOF-5 nano/microcrystals: Solvatochromic behaviour, sensing solvent molecules and gas sorption property

Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were successfully obtained by solvothermal method. The products were characterized by powder X-ray diffraction (PXRD), energy dispersive spectrometry (EDS), field emission scanning electron microscopy (FESEM), thermogravimetric analysis (TGA), inductively coupled plasma optical emission spectrometer (ICP-OES), elemental analysis, UV–vis and infrared (IR) spectroscopy. The factors influencing the crystal morphology and size were investigated. The gas sorption measurements reveal that highly crystalline particles have large Langmuir surface area. It was found that the Co(II)-doped MOF-5 shows enhanced hydrostability and the sorption profiles of the Co(II)-doped MOF-5 nano/microcrystals are dependent on the morphology and size of the particles. Porous Co(II)-doped MOF-5 is stable upon the removal of guest molecules and exhibits different colour with accommodating different solvent molecule, which means that it can act as solvatochromic sensing materials for recognition of solvent molecules. - Graphical abstract: Co(II)-doped MOF-5 nano/microcrystals with different shapes and sizes were synthesized by a facile hydrothermal method, which not only enhance gas sorption properties and structural stability of MOFs towards moisture, but also act as new sensing materials for sensing small molecules. - Highlights: • Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were obtained. • Co(II)-doped MOF-5 nano/microcrystals enhance the structural stability towards moisture. • Co(II)-doped MOF-5 can act as new sensing material for sensing small molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Single-Molecule Tracking Measurements Reveal the Detailed Mechanisms of Molecular Diffusion in Solvent Mixtures under Nanoconfinement

Understanding mass transport mechanisms in nanopores is important for developing advanced materials for chemical separations, chemical sensing, and energy storage. This paper reports a novel imaging platform that is employed for the first time to investigate the detailed diffusion dynamics of single rhodamine B (RhB) dye molecules confined within solution-filled cylindrical anodic aluminum oxide (AAO) nanopores. The imaging platform relies on illumination of horizontally-oriented AAO nanopores in a highly inclined and laminated optical (HILO) light sheet microscopy geometry. The method was used to investigate the translational and orientational dynamics of single rhodamine B (RhB) molecules within horizontally-oriented 5- and 10-nm diameter AAO nanopores filled with water–ethanol mixtures. The established platform enabled the observation of one-dimensional motion along the pore axis involving occasional short- or long-term immobilization at the single-molecule level. Analysis of cumulative squared-displacement distributions revealed fast (5 – 30 µm²/s), intermediate (1 – 5 µm²/s), and slow (< 1 µm²/s) diffusion components. From the effects of mixture composition and pore size on the contributions of these three components, we inferred that the fast, intermediate, and slow components could be assigned to desorption-mediated hopping, crawling, and wiggling motions, respectively. The platform based on the horizontally-oriented AAO nanopores also permitted single-molecule emission polarization measurements that revealed the negligible steric confinement of individual diffusing RhB molecules within the AAO nanopores. The imaging platform based on AAO membranes and HILO microscopy provided a unique means to investigate how solvation-mediated surface interactions and nanoconfinement govern molecular transport in nanoporous environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Quantifying the Role of the Relative Humidity-Dependent Physical State of Organic Particulate Matter in the Uptake of Semivolatile Organic Molecules

The uptake of gas-phase dicarboxylic acids to organic particulate matter (PM) was investigated to probe the role of the PM physical state in exchange processes between gas-phase semivolatile organic molecules and organic PM. A homologous series of probe molecules, specifically isotopically labeled 13C-dicarboxylic acids, was used in conjunction with aerosol mass spectrometry to obtain a quantitative characterization of the uptake to organic PM for different relative humidities (RHs). The PM was produced by the dark ozonolysis of unlabeled α-pinene. The uptake of 13C-labeled oxalic, malonic, and α-ketoglutaric acids increased stepwise by 5 to 15 times with increases in RH from 15 to 80%. The enhanced uptake with increasing RH was explained primarily by the higher molecular diffusivity in the particle phase, as associated with changes in the physical state of the organic PM from a nonliquid state to a progressively less-viscous liquid state. At high RH, the partitioning of the probe molecules to the particle phase was more associated with physicochemical interactions with the organic PM than that with the co-absorbed liquid water. Additionally, uptake of the probe molecules also increased with a decrease in volatility along the homologous series. This study quantitatively shows the key roles of the particle physical state in governing the interactions of organic PM with semivolatile organic molecules.

42 ENGINEERING↗
DOE OSTI2022

Revisiting Competitive Adsorption of Small Molecules in the Metal–Organic Framework Ni-MOF-74

To precisely evaluate the potential of metal-organic frameworks (MOFs) for gas separation and purification applications, it is crucial to understand how various molecules competitively adsorb inside MOFs. In this paper, we combine in situ infrared spectroscopy with ab initio calculations to investigate the mechanisms associated with co-adsorption of a number of small molecules including CO, NO, and CO 2 inside the prototypical framework Ni-MOF-74. Surprisingly, we find that the displacement of CO bound inside Ni-MOF-74 (binding energy of 53 kJ/mol) is readily driven by CO 2 exposure, even though CO 2 has a noticeably weaker binding energy of only 41 kJ/mol; meanwhile, the significantly more strongly binding NO molecule (90 kJ/mol) is not able to easily displace bound CO inside Ni-MOF74. These results show that single-phase binding energies of a molecule inside the MOF cannot completely describe their interaction with the MOF in the presence of other guest molecules. Here, we unveil a number of crucial factors such as the kinetic barrier, partial pressure, secondary binding sites, and guest-host/lateral interactions that control the co-adsorption process and combined with the binding energy are better descriptors of the behavior and adsorption of gas mixtures inside MOFs.

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

3D-Scaffold: A Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds

The prerequisite of therapeutic drug design is to identify novel molecules with desired biophysical and biochemical properties. Deep generative models have demonstrated their ability to find such molecules by exploring a huge chemical space efficiently. An effective way to obtain molecules with desired target properties is the preservation of critical scaffolds in the generation process. To this end, we propose a domain aware generative framework called 3D-Scaffold that takes 3D coordinates of a desired scaffold as an input and generates 3D coordinates of novel therapeutic candidates as an output while always preserving the desired scaffolds in generated structures. We show that our framework generates predominantly valid, unique, novel, and experimentally synthesizable molecules that have drug-like properties similar to the molecules in the training set. Using domain specific datasets, we generate covalent and non-covalent antiviral inhibitors. Therefore, to measure the success of our framework in generating therapeutic candidates, generated structures were subjected to high throughput virtual screening via docking simulations, which shows favorable interaction against SARS-CoV-2 main protease and non-structural protein endoribonuclease (NSP15) targets. Most importantly, our model performs well with relatively small volumes of training data and generalizes to new scaffolds, making it applicable to other domain.

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

Two Cycling Centers in One Molecule: Communication by Through-Bond Interactions and Entanglement of the Unpaired Electrons

Many applications in quantum information science (QIS) rely on the ability to laser- cool molecules. The scope of applications can be expanded if laser-coolable molecules possess two or more cycling centers, i.e., moieties capable of scattering photons via multiple absorption-emission events. Here in this paper we employ equation-of-motion coupled-cluster method for double electron attachment (EOM-DEA-CCSD) to study the electronic structure of hypermetallic molecules with two alkaline earth metals connected by an acetylene linker. The electronic structure of the molecules is similar to that of two separated alkali metals; however, the interaction between the two electrons is weak and largely dominated by through-bond interactions. The communication between the two cycling centers is quantified by the extent of the entanglement of the two unpaired electrons associated with each center. This contribution highlights the rich electronic structure of hypermetallic molecules that may advance various applications in QIS and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Geometric structure, electronic structure, and spin transition of several Fe{sup II} spin-crossover molecules

We present a density functional study on the geometric structure, electronic structure, and spin transition of a series of Fe{sup II} spin-crossover (SCO) molecules, i.e., [Fe(abpt){sub 2}(NCS){sub 2}] (1), [Fe(abpt){sub 2}(NCSe){sub 2}] (2), and [Fe(dpbo)(HIm){sub 2}] (3) with dpbo diethyl(E,E)-2,2'-[1,2-phenylbis(iminomethylidyne)]bis[3-oxobutanoate](2-), N',O{sup 3},O{sup 3}', and abpt = 4-amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole in order to explore more about the way to control SCO behavior of transition metal complexes. Our calculated results show that the spin transition of these Fe{sup II} molecules is accompanied with charge transfer between the Fe atom and ligands. This causes change in the electrostatic energy ({Delta}U) as well as the total electronic energy of SCO molecules. Moreover, our calculated results demonstrate an important contribution of the interionic interactions to {Delta}U, and there is the relation between {Delta}U and the thermal hysteresis behavior of SCO molecules. These results should be helpful for developing new SCO molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2013

Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray

Diffracted X-ray tracking (DXT) enables the tilting and twisting motions of single protein molecules to be monitored with micro- to milliradian resolution using a highly brilliant X-ray source with a wide energy bandwidth. We have developed a technique to monitor single molecules using gold nanocrystals attached to individual protein molecules using the BL28B2 beamline at SPring-8. In this paper we present the installation of a single toroidal X-ray mirror at BL28B2 to focus X-rays in an energy range of 10–20 keV (△E/E = 82% for an X-ray with a wide energy bandwidth). With this beamline we tracked diffraction spots from gold nanocrystals over a wide angle range than that using quasi-monochromatic X-rays. Application of the wide angle DXT technique to biological systems enabled us to observe the on-site motions of single protein molecules that have been functionalized in vivo. We further extend the capability of DXT by observing the fractional tilting and twisting motions of inner proteins under various conditions. As a proof of this methodology and to determine instrumental performance the intramolecular motions of a human serum albumin complex with 2-anthracenecarboxylic acid was investigated using the BL28B2 beamline. The random tilting and twisting intramolecular motions are shown to be directly linked to the movement of individual protein molecules in the buffer solution.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Theoretical investigation on single-molecule chiroptical spectroscopy

Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.

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

A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules

The promising field of mechanochemistry suffers from a general lack of understanding of the distribution and propagation of force in a stretched molecule, which limits its applicability up to the present day. In this article, we introduce the JEDI (Judgement of Energy DIstribution) analysis, which is the first quantum chemical method that provides a quantitative understanding of the distribution of mechanical stress energy among all degrees of freedom in a molecule. The method is carried out on the basis of static or dynamic calculations under the influence of an external force and makes use of a Hessian matrix in redundant internal coordinates (bond lengths, bond angles, and dihedral angles), so that all relevant degrees of freedom of a molecule are included and mechanochemical processes can be interpreted in a chemically intuitive way. The JEDI method is characterized by its modest computational effort, with the calculation of the Hessian being the rate-determining step, and delivers, except for the harmonic approximation, exact ab initio results. We apply the JEDI analysis to several example molecules in both static quantum chemical calculations and Born-Oppenheimer Molecular Dynamics simulations in which molecules are subject to an external force, thus studying not only the distribution and the propagation of strain in mechanically deformed systems, but also gaining valuable insights into the mechanochemically induced isomerization of trans-3,4-dimethylcyclobutene to trans,trans-2,4-hexadiene. The JEDI analysis can potentially be used in the discussion of sonochemical reactions, molecular motors, mechanophores, and photoswitches as well as in the development of molecular force probes.

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

Structural and optoelectronic properties of hybrid bulk-heterojunction materials based on conjugated small molecules and mesostructured TiO{sub 2}

Improved hybrid bulk-heterojunction materials was fabricated by spin-casting a benchmark conjugated small molecule, namely, 3,6-bis(5-(benzofuran-2-yl)thiophen-2-yl)-2,5-bis(2-ethylhexyl) pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione (DPP(TBFu){sub 2}), into mesostructured TiO{sub 2}. Due to both a reduced molecular size and less hydrophobic nature of the conjugated molecules (relative to conjugated polymers), homogeneous and improved infiltration into the mesoporous TiO{sub 2} are achieved without the need for pre-treatment of the TiO{sub 2}. Remarkably, this small molecule can realize loadings of up to 25% of the total pore volume—2.5× the typical loadings achieved for conjugated polymers. The small molecule loading was determined using dynamic secondary ion mass spectroscopy and absorption spectroscopy. Further characterization such as charge transfer and nanoscale conducting atomic force microscopy helps to demonstrate the promise and viability of small molecule donors for hybrid optoelectronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Magnetic moment enhancement and spin polarization switch of the manganese phthalocyanine molecule on an IrMn(100) surface

The geometric, electronic, and magnetic structures of a manganese phthalocyanine (MnPc) molecule on an antiferromagnetic IrMn(100) surface are studied by density functional theory calculations. Two kinds of orientation of the adsorbed MnPc molecule are predicted to coexist due to molecular self-assembly on the surface—a top-site geometry with the Mn–N bonds aligned along the 〈100〉 direction, and a hollow-site orientation in which the Mn–N bonds are parallel to the 〈110〉 direction. The MnPc molecule is antiferromagnetically coupled to the substrate at the top site with a slight reduction in the magnetic moment of the Mn atom of the MnPc molecule (Mn{sub mol}). In contrast, the magnetic moment of the Mn{sub mol} is enhanced to 4.28 μB at the hollow site, a value larger than that in the free MnPc molecule (3.51 μB). Molecular distortion induced by adsorption is revealed to be responsible for the enhancement of the magnetic moment. Furthermore, the spin polarization of the Mn{sub mol} atom at around the Fermi level is found to change from negative to positive through an elongation of the Mn–N bonds of the MnPc. We propose that a reversible switch of the low/high magnetic moment and negative/positive spin polarization might be realized through some mechanical engineering methods.

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

Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry

Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when attached to Au(111). Two unpaired electrons in the d{sub z}{sup 2} and the degenerate dπ orbitals are screened stepwise, resulting in spin and spin+orbital Kondo effects, respectively. We investigated the impact on the Kondo effects of the coordination of CO and NO molecules to the Fe{sup 2+} ion as chemical stimuli by using scanning tunneling microscopy (STM) and density functional theory calculations. The impacts of the two diatomic molecules are different from each other as a result of the different electronic configurations. The coordination of CO converts the spin state from triplet to singlet, and then the Kondo effects completely disappear. In contrast, an unpaired electron survives in the molecular orbital composed of Fe d{sub z}{sup 2} and NO 5σ and 2π* orbitals for the coordination of NO, causing a sharp Kondo resonance. The isotropic magnetic response of the peak indicates the origin is the spin Kondo effect. The diatomic molecules attached to the Fe{sup 2+} ion were easily detached by applying a pulsed voltage at the STM junction. These results demonstrate that the single molecule chemistry enables us to switch and control the spin and the many-body quantum states reversibly.

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

Bombardment of gas molecules on single graphene layer at high temperature

Graphite is widely used as a material for rocket-nozzle inserts due to its excellent thermo-physical properties as well as low density. During the operation of rockets, the surface of the graphite nozzle is subjected to very high heat fluxes and the undesirable erosion of the surface occurs due to the bombardment of gas molecules with high kinetic energy, which causes a significant reduction of nozzle performance. However, the understanding and quantification of such bombardment is not satisfactory due to its complexity: The bond breaking-forming happens simultaneously for the carbon atoms of graphene, some gas molecules penetrate through the surface, some of them are reflected from the surface, etc. In the present study, we perform extensive molecular dynamics (MD) simulations to examine the bombardment phenomena in high temperature environment (several thousand Kelvin). Advanced from the previous studies that have focused on the bombardment by light molecules (e.g., H{sub 2}), we will concentrate on the impact by realistic molecules (e.g., CO{sub 2} and H{sub 2}O). LAMMPS is employed for the MD simulations with NVE ensemble and AIREBO potential for graphene. The molecular understanding of the interaction between graphene and highly energetic gas molecules will enable us to design an efficient thermo-mechanical protection system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗