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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Evidence for Ultralow-Energy Vibrations in Large Organic Molecules

The quantum efficiency or the rate of conversion of incident photon to free electron in photosynthesis is known to be extremely high. It has been speculated that the origin of this efficiency are molecular vibrations leading to a very fast separation of electrons and holes within the involved molecules. However, molecular vibrations are commonly in the range above 100 meV, which is too high for excitations in an ambient environment. Here, we analyze experimental spectra of single organic molecules on metal surfaces at ~4 K, which often exhibit a pronounced dip. We show that measurements on iron(II) [tetra-(pentafluorophenyl)]porphyrin resolve this single dip at 4 K into a series of step-shaped inelastic excitations at 0.4 K. Via extensive spectral maps under applied magnetic fields and corresponding theoretical analysis we find that the dip is due to ultralow-energy vibrations of the molecular frame, typically in the range below 20 meV. This discovery indicates that ultralow energy vibrations in organic molecules are much more common than currently thought and may be all-pervasive for molecules above a certain size.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Recent Advances in Probing Electron Delocalization in Conjugated Molecules by Attached Infrared Reporter Groups for Energy Conversion and Storage

This review article reports an overview of the recent developments in the field of electron delocalization study in organic conjugated molecules by utilizing the vibration frequencies exhibited by the attached functional groups such as nitrile (–C≡N), alkyne (–C≡C–), or carbonyl (–C=O). A brief introduction to electron delocalization, methods for study, and their importance is given first, followed by the application of infrared spectroscopy in organic molecules. Details of molecules with various infrared reporter groups have been explained in respective subsections based on the functional groups. All the reported organic molecules have been structured and presented with the electron delocalization properties studied using an infrared reporter group. Finally, an outlook on this recently promising, exciting, and interesting field of probing electron delocalization using infrared reporter groups is provided.

25 ENERGY STORAGE↗
DOE OSTI2022

Triacetic Acid Lactone and 4-Hydroxycoumarin as Bioprivileged Molecules for the Development of Performance-Advantaged Organic Corrosion Inhibitors

Biomass conversion, especially the development of bioprivileged molecules utilizing integration of biological and chemical processes, has shown potential to produce novel chemicals with enhanced properties. Here, organic corrosion inhibitors based on triacetic acid lactone and 4-hydroxycoumarin have been synthesized in good yield and tested for corrosion inhibition on mild steel in both sulfuric acid and hydrochloric acid. Sixteen novel corrosion inhibitors derived from triacetic acid lactone and 4-hydroxycoumarin were efficiently synthesized and twelve of them showed high corrosion inhibition efficiency as confirmed by electrochemical impedance spectroscopy (giving values greater than 78%) and polarization analysis. While triacetic acid lactone-based compounds showed good corrosion inhibition performance, the 4-hydroxycoumarin-based compounds showed further improvement in corrosion inhibition performance. Scanning electron microscopy (SEM) analysis of the mild steel coupon in the presence of selected inhibitors showed that corrosion was significantly diminished, with complementary X-ray photoelectron spectroscopy (XPS) analysis suggesting the inhibitor molecules strongly adsorbed on the steel surface. Quantum chemical calculations showed poor correlation between calculated parameters and the performance of these molecules. This large set of corrosion inhibitors containing a dozen promising corrosion inhibitors is useful for future rational design of corrosion inhibitors. In conclusion, the results demonstrate a new direction for the development of bioprivileged molecules.

09 BIOMASS FUELS↗
DOE OSTI2011

Small Molecule Inhibition of the TNF Family Cytokine CD40 Ligand Through a Subunit Fracture Mechanism

BIO8898 is one of several synthetic organic molecules that have recently been reported to inhibit receptor binding and function of the constitutively trimeric tumor necrosis factor (TNF) family cytokine CD40 ligand (CD40L, aka CD154). Small molecule inhibitors of protein-protein interfaces are relatively rare, and their discovery is often very challenging. Therefore, to understand how BIO8898 achieves this feat, we characterized its mechanism of action using biochemical assays and X-ray crystallography. BIO8898 inhibited soluble CD40L binding to CD40-Ig with a potency of IC{sub 50} = 25 {mu}M and inhibited CD40L-dependent apoptosis in a cellular assay. A co-crystal structure of BIO8898 with CD40L revealed that one inhibitor molecule binds per protein trimer. Surprisingly, the compound binds not at the surface of the protein but by intercalating deeply between two subunits of the homotrimeric cytokine, disrupting a constitutive protein-protein interface and breaking the protein's 3-fold symmetry. The compound forms several hydrogen bonds with the protein, within an otherwise hydrophobic binding pocket. In addition to the translational splitting of the trimer, binding of BIO8898 was accompanied by additional local and longer-range conformational perturbations of the protein, both in the core and in a surface loop. Binding of BIO8898 is reversible, and the resulting complex is stable and does not lead to detectable dissociation of the protein trimer. Our results suggest that a set of core aromatic residues that are conserved across a subset of TNF family cytokines might represent a generic hot-spot for the induced-fit binding of trimer-disrupting small molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Single-Molecule Fluorescence Microscopy Reveals Energy Transfer Active versus Inactive Nanocrystal/Dye Conjugate Pairs

Defect-mediated energy transfer (EnT) is a radiative process that occurs between donor defect states in the forbidden bandgap of semiconductor nanocrystals (NCs) and dye molecules bound to their surfaces. The EnT efficiency depends on the number of dye molecules attached to each NC, the donor–acceptor distance, and the dipole orientation factor between the donor and acceptor, all of which vary across all individual NCs in a sample. While ensemble-level fluorescence spectroscopy measurements have provided average values for donor–acceptor distances, dye-to-NC ratios, and EnT rate constants, questions remain about the impact of donor/acceptor heterogeneity on observed EnT efficiencies. Notably, ensemble-level measurements cannot distinguish between bare NCs and EnT-active versus inactive NC/dye pairs in the same sample batch, limiting the ability to design systems with 100% EnT efficiency. To address this, we studied defect-mediated EnT between AlexaFluor 555 dye acceptors chemically bound to ZnO NC donors at the level of single molecules and single NCs. Interestingly, 20% of bound NC/dye pairs are EnT-inactive, likely contributing to residual defect photoluminescence (PL) observed in ensemble-level measurements and reducing overall EnT efficiency. Single particle-level ZnO defect PL and acceptor fluorescence trajectories exhibited distinct microfluctuations, which are absent in bare ZnO NCs. We hypothesized that our observations can be explained with a competitive dye fluorescence quenching pathway, possibly due to charge transfer between the excited state dye and the ZnO NC. Numerical simulations of single-molecule PL traces for this scenario produced microfluctuations consistent with the experimental results. These findings highlight the impact of sample heterogeneity on EnT processes and provide insights for designing light-harvesting systems with optimized EnT efficiency.

25 ENERGY STORAGE↗
DOE OSTI2021

Single-Molecule Charge Transport through Positively Charged Electrostatic Anchors

The charge transport in single-molecule junctions depends critically on the chemical identity of the anchor groups that are used to connect the molecular wires to the electrodes. In this research, we report a new anchoring strategy — called the electrostatic anchor here — formed through the efficient Coulombic interaction between the gold electrodes and the positively charged pyridinium terminal groups. Our results show that these pyridinium groups serve as efficient electrostatic anchors forming robust gold–molecule–gold junctions. Here, we have also observed binary switching in dicationic viologen molecular junctions, demonstrating an electron injection-induced redox switching in single-molecule junctions. We attribute the difference in low- and high conductance states to a dicationic ground state and a radical cationic metastable state, respectively. Overall, this anchoring strategy and redox switching mechanism could constitute the basis for a new class of redox-activated single-molecule switches.

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

Visualizing the Three-Dimensional Arrangement of Hydrogen Atoms in Organic Molecules by Coulomb Explosion Imaging

Structure-sensitive methods based on femtosecond light or electron pulses are now making it possible to measure how molecular structures change during light-induced processes. Despite significant progress, high-fidelity imaging of nuclear positions remains a challenge even for relatively small molecular systems and, notably, regarding the positions of hydrogen atoms. As demonstrated in recent work, X-ray-induced Coulomb explosion imaging (CEI) may overcome this obstacle, as its sensitivity does not depend on the mass of the imaged atoms. The photoinduced ring opening of the heterocyclic molecule 2(5 H )-thiophenone has attracted recent interest. Here, in this work, we show that CEI offers a powerful route to imaging the peripheral H atoms in this molecule and thus, more generally, to tracking detailed nuclear motions (e.g., isomerizations) in organic molecules on ultrafast time scales. Specifically, we record momentum-space Coulomb explosion images that report on the three-dimensional positioning of all nuclei within the molecule, for instance, distinguishing H atoms in C–H bonds that lie within or are directed out of the plane defined by the heavy atoms. The prospect of imaging peripheral H atoms to probe photochemical dynamics is explored by coupling ab initio molecular dynamics with classical Coulomb explosion simulations, thereby differentiating potential photoproduct isomers, including those whose structures primarily differ in the position of the hydrogens.

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

Ab Initio Polariton Spectra of ZnTPP Molecules Collectively Coupled Inside an Optical Cavity

Exciton-polaritons are quasi-particles formed by the quantum mechanical hybridization of electronic and photonic excitations. Despite extensive investigations, a fundamental understanding of molecular polariton spectra and the polariton delocalization from an ab initio theoretical perspective remains elusive. We simulate experimentally measured linear transmission spectroscopy of many Zinc(II) tetraphenylporphyrin (ZnTPP) molecules collectively coupled to a cavity from first principles. Our theoretical approach incorporates many low-lying electronic excitations in ZnTPP molecules, as well as collective light-matter couplings between ZnTPP and the quantized radiation modes, both of which are shown to be the key to accurately recovering the experimental spectra. We further analyzed to what extent the polariton and dark states are delocalized over many molecules, for the first time, using fully ab initio descriptions of the molecules. We finally investigate the line width as a function of detuning, providing new theoretical insights into the experimentally observed motional narrowing behavior. Our work presents first-ofits- kind theoretical studies on molecular polariton spectra, offering a new perspective on molecular polariton formation in realistic ab initio molecular systems whose rich, many-state nature provides spectral features enabled by the high density of electronic states beyond simple quantum optics models.

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

Stability of push–pull small molecule donors for organic photovoltaics: spectroscopic degradation of acceptor endcaps on benzo[1,2- b :4,5- b ′]dithiophene cores

High efficiency organic photovoltaic devices have relied on the development of new donor and acceptor materials to optimize opto-electronic properties, promote free carrier generation, and suppress recombination losses. With single junction efficiencies exceeding 15%, materials development must now target long-term stability. This work focuses on the photobleaching dynamics and degradation chemistries of a class of small molecule donors inspired by benzodithiophene terthiophene cores (BDT-3T) with rhodanine endcaps, which have demonstrated 9% efficiency in single junction devices and >11% in ternary cells. Density functional theory was used to design three additional molecules with similar synthetic pathways and opto-electronic properties by simply changing the electron accepting endcap to benzothiazoleacetonitrile, pyrazolone, or barbituric acid functional groups. This new class of semiconductors with equivalent redox properties enables systematic investigation into photobleaching dynamics under white light illumination in air. Degradation chemistries are assessed via unique spectroscopic signatures for the BDT-3T cores and the endcaps using photoelectron spectroscopies. We show that the pyrazolone undergoes significant degradation due to ring opening, resulting in complete bleaching of the chromophore. The barbituric and rhodanine endcap molecules have moderate stability, while the benzothiazoleacetonitrile group produces the most stable chromophore despite undergoing some oxidative degradation. Collectively, our results suggest the following: (i) degradation is not just dependent on redox properties; (ii) core group stability is not independent of the endcap choice; and (iii) future design of high efficiency materials must consider both photo and chemical stability of the molecule as a whole, not just individual donor or acceptor building blocks.

14 SOLAR ENERGY↗
DOE OSTI2013

Investigating the molecule-substrate interaction of prototypic tetrapyrrole compounds: Adsorption and self-metalation of porphine on Cu(111)

We report on the adsorption and self-metalation of a prototypic tetrapyrrole compound, the free-base porphine (2H-P), on the Cu(111) surface. Our multitechnique study combines scanning tunneling microscopy (STM) results with near-edge X-ray absorption fine-structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS) data whose interpretation is supported by density functional theory calculations. In the first layer in contact with the copper substrate the molecules adsorb coplanar with the surface as shown by angle-resolved NEXAFS measurements. The quenching of the first resonance in the magic angle spectra of both carbon and nitrogen regions indicates a substantial electron transfer from the substrate to the LUMO of the molecule. The stepwise annealing of a bilayer of 2H-P molecules sequentially transforms the XP and NEXAFS signatures of the nitrogen regions into those indicative of the coordinated nitrogen species of the metalated copper porphine (Cu-P), i.e., we observe a temperature-induced self-metalation of the system. Pre- and post-metalation species are clearly discriminable by STM, corroborating the spectroscopic results. Similar to the free-base porphine, the Cu-P adsorbs flat in the first layer without distortion of the macrocycle. Additionally, the electron transfer from the copper surface to the molecule is preserved upon metalation. This behavior contrasts the self-metalation of tetraphenylporphyrin (2H-TPP) on Cu(111), where both the molecular conformation and the interaction with the substrate are strongly affected by the metalation process.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Adsorption and dissociation of oxygen molecules on Si(111)-(7×7) surface

The adsorption and dissociation of O{sub 2} molecules on Si(111)-(7×7) surface have been studied by first-principles calculations. Our results show that all the O{sub 2} molecular species adsorbed on Si(111)-(7×7) surface are unstable and dissociate into atomic species with a small energy barrier about 0.1 eV. The single O{sub 2} molecule adsorption tends to form an ins×2 or a new metastable ins×2* structure on the Si adatom sites and the further coming O{sub 2} molecules adsorb on those structures to produce an ad-ins×3 structure. The ad-ins×3 structure is indeed highly stable and kinetically limited for diving into the subsurface layer to form the ins×3-tri structure by a large barrier of 1.3 eV. Unlike the previous views, we find that all the ad-ins, ins×2, and ad-ins×3 structures show bright images, while the ins×2*, ins×3, and ins×3-tri structures show dark images. The proposed oxidation pathways and simulated scanning tunneling microscope images account well for the experimental results and resolve the long-standing confusion and issue about the adsorption and reaction of O{sub 2} molecules on Si(111) surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Manipulating transport through a single-molecule junction

Molecular Electronics deals with the realization of elementary electronic devices that rely on a single molecule. For electronic applications, the most important property of a single molecule is its conductance. Here we show how the conductance of a single octanethiol molecule can be measured and manipulated by varying the contact's interspace. This mechanical gating of the single molecule junction leads to a variation of the conductance that can be understood in terms of a tunable image charge effect. The image charge effect increases with a decrease of the contact's interspace due to a reduction of the effective potential barrier height of 1.5 meV/pm.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Complexation of n SO{sub 2} molecules (n = 1, 2, 3) with formaldehyde and thioformaldehyde

Ab initio and density functional theory calculations are used to examine complexes formed between H{sub 2}CO and H{sub 2}CS with 1, 2, and 3 molecules of SO{sub 2}. The nature of the interactions is probed by a variety of means, including electrostatic potentials, natural bond orbital, atoms in molecules, energy decomposition, and electron density redistribution maps. The dimers are relatively strongly bound, with interaction energies exceeding 5 kcal/mol. The structures are cyclic, containing both a O/S⋯S chalcogen bond and a CH⋯O H-bond. Addition of a second SO{sub 2} molecule leads to a variety of heterotrimer structures, most of which resemble the original dimer, where the second SO{sub 2} molecule engages in a chalcogen bond with the first SO{sub 2}, and a C⋯O attraction with the H{sub 2}CX. Some cooperativity is apparent in the trimers and tetramers, with an attractive three-body interaction energy and shortened intermolecular distances.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Electron ionization of open/closed chain isocarbonic molecules relevant in plasma processing: Theoretical cross sections

In this paper, we report theoretical electron impact ionization cross sections from threshold to 2000 eV for isocarbonic open chain molecules C{sub 4}H{sub 6}, C{sub 4}H{sub 8}, C{sub 4}F{sub 6} including their isomers, and closed chain molecules c-C{sub 4}H{sub 8} and c-C{sub 4}F{sub 8}. Theoretical formalism employed presently, viz., Complex Scattering Potential-ionization contribution method has been used successfully for a variety of polyatomic molecules. The present ionization calculations are very important since results available for the studied targets are either scarce or none. Our work affords comparison of C{sub 4} containing hydrocarbon versus fluorocarbon molecules. Comparisons of the present ionization cross sections are made wherever possible, and new ionization data are also presented.

2-METHYLPROPENE↗
DOE OSTI2014

Tunneling electron induced chemisorption of copper phthalocyanine molecules on the Cu(111) surface

The adsorption of up to one monolayer (ML) of copper phthalocyanine (CuPc) molecules on a room temperature Cu(111) surface has been studied using scanning tunneling microscopy (STM). Below 1 ML the molecules are in a fluid state and are highly mobile on the surface. At 1 ML coverage the molecules coalesce into a highly ordered 2D crystal phase. At sub-ML coverages, chemisorption of individual CuPc molecules can be induced through exposure to tunneling electrons at a tunneling bias voltage exceeding a threshold value. This tunneling electron induced effect has been exploited to perform molecular STM lithography.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Aromatic molecules as spintronic devices

In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

The adsorption properties of CO molecules on single-layer graphene nanoribbons

The adsorption properties of CO molecules on graphene nanoribbons (GRNs) are studied through the molecular dynamics (MD) method. The AIREBO and LJ potentials are used to describe the C-C bonds in GNR and the interactions between the carbon atoms in GNR and CO molecules, respectively. The influences of the environmental pressure and charge density on the adsorption properties of CO molecules on GRNs are taken into account in this study. The effects of charges carried by GNRs on the adsorption properties are investigated in two aspects: atom distribution and energy evolution. Its observation from the results shows that the Coulomb force plays a more important role in the adsorption phenomenon than the van der Waals force, and the higher the charge density is, the larger the amount of the adsorbed CO molecules becomes. Low charge densities (<3.291 C/m{sup 2}) do little for the system, that is to say, the GNRs present similar properties to the ones with no charges. However, relatively high charge densities (>4.937 C/m{sup 2}) have an obvious effect on the whole system. The results also indicate that the environmental pressure has great influence on the adsorption properties of COs on GRN, and the higher the pressure is, the greater the adsorption energy becomes.

36 MATERIALS SCIENCE↗
DOE OSTI2014

A photo-driven dual-frequency addressable optical device of banana-shaped molecules

We propose a photonic switch employing a blend of host banana-shaped liquid crystalline molecules and guest photoisomerizable calamitic molecules. The material exhibits a change in the sign of the dielectric anisotropy switching from positive to negative, at a certain crossover frequency of the probing field. The consequent change in electric torque can be used to alter the orientation of the molecules between surface-determined and field-driven optical states resulting in a large change in the optical transmission characteristics. Here, we demonstrate the realization of this feature by an unpolarized UV beam, the first of its kind for banana-shaped molecules. The underlying principle of photoisomerization eliminates the need for a second driving frequency. The device also acts as a reversible conductance switch with an order of magnitude increase of conductivity brought about by light. Possible usage of this for optically driven display devices and image storage applications is suggested.

36 MATERIALS SCIENCE↗