Single Molecule Rectification Induced by the Asymmetry of a Single Frontier Orbital
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bio-inspired↗
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Results for “molecule”
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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Understanding Small-Molecule Interactions in Metal-Organic Frameworks: Coupling Experiment with Theory
Metal-organic frameworks (MOFs) have gained much attention as next generation porous media for various applications, especially gas separations/storage and catalysis. New MOFs are regularly reported; however, to develop better materials in a timely manner for specific applications, the interactions between guest molecules and the internal surface of the framework must first be understood. In this review, we present a combined experimental and theoretical approach that proves essential for the elucidation of small-molecule interactions in a model MOF system known as M 2 (dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Cu, or Zn), a material whose adsorption properties can be readily tuned via chemical substitution. Here, we additionally show that the study of extensive families like this one can provide a platform to test the efficacy and accuracy of developing computational methodologies in slightly varying chemical environments, a task that is necessary for their evolution into viable, robust tools for screening large numbers of materials.
36 MATERIALS SCIENCE↗
Nanodomains and Their Temperature Dependence in a Phosphonium-Based Ionic Liquid: A Single-Molecule Tracking Study
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Opare-Addo, Jemima↗
Can Kohn–Sham density functional theory predict accurate charge distributions for both single-reference and multi-reference molecules?
Dipole moments are the first moment of electron density and are fundamental quantities that are often available from experiments. An exchange–correlation functional that leads to an accurate representation of the charge distribution of a molecule should accurately predict the dipole moments of the molecule. It is well known that Kohn–Sham density functional theory (DFT) is more accurate for the energetics of single-reference systems than for the energetics of multi-reference ones, but there has been less study of charge distributions. Here, in this work, we benchmark 48 density functionals chosen with various combinations of ingredients, against accurate experimental data for dipole moments of 78 molecules, in particular 55 single-reference molecules and 23 multi-reference ones. We chose both organic and inorganic molecules, and within the category of inorganic molecules there are both main-group and transition-metal-containing molecules, with some of them being multi-reference. As one would expect, the multi-reference molecules are not as well described by single-reference DFT, and the functionals tested in this work do show larger mean unsigned errors (MUEs) for the 23 multi-reference molecules than the single-reference ones. Five of the 78 molecules have relatively large experimental error bars and were therefore not included in calculating the overall MUEs. For the 73 molecules not excluded, we find that three of the hybrid functionals, B97-1, PBE0, and TPSSh (each with less than or equal to 25% Hartree–Fock (HF) exchange), the range-separated hybrid functional, HSE06 (with HF exchange decreasing from 25% to 0 as interelectronic distance increases), and the hybrid functional, PW6B95 (with 28% HF exchange) are the best performing functionals with each yielding an MUE of 0.18 D. Perhaps the most significant finding of this study is that there exists great similarity among the success rate of various functionals in predicting dipole moments. In particular, of 39 functionals designed as general-purpose functionals and that do not have a global value of 100% HF exchange, the average MUE is 0.23 D, with a standard deviation of only 0.04 D. Among gradient approximations, which are especially interesting because of their speed and portability, the best overall performance is by PBE, HCTH/407, OLYP, OreLYP, and GAM, each with MUE of 0.22 D.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Interference in electron–molecule elastic scattering
General formulas describing the multiple scattering of electron by polyatomic molecules have been derived within the framework of the model of non-overlapping atomic potentials. These formulas are applied to different carbon molecules, both for fixed-in-space and randomly oriented molecules. Here, the molecular continuum wave function is represented as a plane wave plus a linear combination of the Green’s functions for free motion and the derivatives of these functions. Far from the target the electron spherical waves interfere as in the case of the Young’s double slits experiment. This interference manifests itself as diffraction oscillations in the differential and total cross sections for elastic electron scattering. The amplitude of electron scattering by a molecule is defined by the phase shifts for each of the atoms forming the target and its geometry. The numerical calculation of the scattering amplitude in closed form (rather than in the form of S-matrix expansion) is reduced to solving a system of algebraic equations. The number of atoms in a molecule and the atomic phase shifts for the orbital angular momenta included in the calculation define the number of equations.
74 ATOMIC AND MOLECULAR PHYSICS↗
Shape-persistent ladder molecules exhibit nanogap-independent conductance in single-molecule junctions
Molecular electronic devices require precise control over the flow of current in single molecules. However, the electron transport properties of single molecules critically depend on dynamic molecular conformations in nanoscale junctions. Here, in this work, we report a unique strategy for controlling molecular conductance using shape-persistent molecules. Chemically diverse, charged ladder molecules, synthesized via a one-pot multicomponent ladderization strategy, show a molecular conductance (d[log( G/G 0 )]/d x ≈ -0.1 nm -1 ) that is nearly independent of junction displacement, in stark contrast to the nanogap-dependent conductance (d[log( G/G 0 )]/d x ≈ -7 nm -1 ) observed for non-ladder analogues. Ladder molecules show an unusually narrow distribution of molecular conductance during dynamic junction displacement, which is attributed to the shape-persistent backbone and restricted rotation of terminal anchor groups. These principles are further extended to a butterfly-like molecule, thereby demonstrating the strategy's generality for achieving gap-independent conductance. Overall, our work provides important avenues for controlling molecular conductance using shape-persistent molecules. Achieving robust and controllable conductance in single-molecule junctions is challenging due to the dynamic nature of molecular conformations that fluctuate over operational timescales. A strategy using shape-persistent molecules has now been developed that demonstrates nearly junction-displacement-independent conductance, providing a stable solution for single-molecule electronic properties.
molecular electronics↗
Impact of D1-V185 on the Water Molecules That Facilitate O 2 Formation by the Catalytic Mn 4 CaO 5 Cluster in Photosystem II
The oxidations of the O 2 -evolving Mn 4 CaO 5 cluster in Photosystem II are coupled to the release of protons to the thylakoid lumen via one or more proton egress pathways. These pathways are comprised of extensive networks of hydrogen-bonded water molecules and amino acid side chains. The hydrophobic residue, D1-V185, is adjacent to numerous water molecules in one of these pathways. The D1-V185N mutation dramatically slows O–O bond formation. This impairment has been attributed to a disruption of the hydrogen-bonded water molecules that are crucial for proton egress or whose rearrangement is required for catalysis. In this study, Fourier transform infrared spectroscopy was employed to characterize the impact of the D1-V185N mutation on the carboxylate groups and water molecules that form a network of hydrogen bonds in this putative proton egress pathway. By analyzing carboxylate stretching modes, carbonyl stretching modes of hydrogen-bonded carboxylic acids, O–H stretching modes of hydrogen-bonded water molecules, and D–O–D bending modes, we obtain evidence that the D1-V185N mutation perturbs the extensive network of hydrogen bonds that extends from Y Z to D1-D61 to a greater extent than any mutation yet examined but does not alter the water molecules that interact directly with D1-D61. The mutation also alters the environments of the carboxylate groups whose pK a values change in response to the S 1 to S 2 and S 2 to S 3 transitions. Lastly, the mutation alters the environment of the water molecule whose bending mode vanishes during the S 2 to S 3 transition, consistent with assigning the Ca 2+ -bound W3 as the water molecule that deprotonates and joins oxo bridge O5 during the S 2 to S 3 transition, possibly as the second substrate water molecule for O 2 formation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Photo-assisted intersystem crossing: The predominant triplet formation mechanism in some isolated polycyclic aromatic molecules excited with pulsed lasers
Naphthalene, anthracene, and phenanthrene are shown to have very long-lived triplet lifetimes when the isolated molecules are excited with nanosecond pulsed lasers resonant with the lowest singlet state. For naphthalene, triplet state populations are created only during the laser pulse, excluding the possibility of normal intersystem crossing at the one photon level, and all molecules have triplet lifetimes greater than hundreds of microseconds, similar to the behavior previously reported for phenylacetylene. Although containing 7–12 thousand cm{sup −1} of vibrational energy, the triplet molecules have ionization thresholds appropriate to vibrationless T{sub 1} states. The laser power dependences (slopes of log-log power plots) of the excited singlet and triplet populations are about 0.7 for naphthalene and about 0.5 for anthracene. Kinetic modeling of the power dependences successfully reproduces the experimental results and suggests that the triplet formation mechanism involves an enhanced spin orbit coupling caused by sigma character in states at the 2-photon level. Symmetry adapted cluster-configuration interaction calculations produced excited state absorption spectra to provide guidance for estimating kinetic rates and the sigma character present in higher electronic states. It is concluded that higher excited state populations are significant when larger molecules are excited with pulsed lasers and need to be taken into account whenever discussing the molecular photodynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples
Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.
Colby, Sean M.↗
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples
Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.
Colby, Sean M↗
Interfacial engineering of phthalocyanine molecules on graphitic and metal substrates
Metal porphyrin and phthalocyanine have found variety of applications in catalysis, electronic and spintronic devices and photovoltaic cells, many of which rely on accurate position of the molecules and alignment of their electronic levels with respect to the substrate. The substrate and local environment affect significantly the electronic properties of these macrocyclic molecules. Computational simulations provide valuable insights for engineering the molecule–metal, molecule–molecule and molecule–ligand interfaces. In this review, we focus on adsorption of metal phthalocyanine, particularly iron phthalocyanine, on graphite, epitaxial graphene, and metal substrates. Furthermore, these systems show varied interfacial binding strength and chameleon-like molecular electronic structures. Spin of the molecules can be controlled by small ligands, and the ground state can be tuned between S = 1, S = 1/2 and S = 0. Inclusion of van der Waals interaction in the first-principles calculations is shown to be essential for accurate description of the interfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Laser Spectroscopic and Theoretical Studies of the Structures and Encapsulation Motifs of Functional Molecules
Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) "hosts" interacting with N2, acetylene, water, and ammonia "guest" molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes
electronic structure calculations↗
Non-adiabatic dynamics of molecules in optical cavities
Strong coupling of molecules to the vacuum field of micro cavities can modify the potential energy surfaces thereby opening new photophysical and photochemical reaction pathways. While the influence of laser fields is usually described in terms of classical field, coupling to the vacuum state of a cavity has to be described in terms of dressed photon-matter states (polaritons) which require quantized fields. We present a derivation of the non-adiabatic couplings for single molecules in the strong coupling regime suitable for the calculation of the dressed state dynamics. The formalism allows to use quantities readily accessible from quantum chemistry codes like the adiabatic potential energy surfaces and dipole moments to carry out wave packet simulations in the dressed basis. The implications for photochemistry are demonstrated for a set of model systems representing typical situations found in molecules.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Perturbation of bacteriochlorophyll molecules in Fenna–Matthews–Olson protein complexes through mutagenesis of cysteine residues
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solar (fuels), photosynthesis (natural and artific↗
Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase
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Padayatti, Pius S.↗
Comparative stereodynamics in molecule-atom and molecule-molecule rotational energy transfer: NO(A{sup 2}Σ{sup +}) + He and D{sub 2}
We present a crossed molecular beam scattering study, using velocity-map ion-imaging detection, of state-to-state rotational energy transfer for NO(A{sup 2}Σ{sup +}) in collisions with the kinematically identical colliders He and D{sub 2}. We report differential cross sections and angle-resolved rotational angular momentum polarization moments for transfer of NO(A, v = 0, N = 0, j = 0.5) to NO(A, v = 0, N′ = 3, 5-12) in collisions with He and D{sub 2} at respective average collision energies of 670 cm{sup −1} and 663 cm{sup −1}. Quantum scattering calculations on a literature ab initio potential energy surface for NO(A)-He [J. Kłos et al., J. Chem. Phys. 129, 244303 (2008)] yield near-quantitative agreement with the experimental differential scattering cross sections and good agreement with the rotational polarization moments. This confirms that the Kłos et al. potential is accurate within the experimental collisional energy range. Comparison of the experimental results for NO(A) + D{sub 2} and He collisions provides information on the hitherto unknown NO(A)-D{sub 2} potential energy surface. The similarities in the measured scattering dynamics of NO(A) imply that the general form of the NO(A)-D{sub 2} potential must be similar to that calculated for NO(A)-He. A consistent trend for the rotational rainbow maximum in the differential cross sections for NO(A) + D{sub 2} to peak at more forward angles than those for NO(A) + He is consistent with the NO(A)-D{sub 2} potential being more anisotropic with respect to NO(A) orientation. No evidence is found in the experimental measurements for coincident rotational excitation of the D{sub 2}, consistent with the potential having low anisotropy with respect to D{sub 2}. The NO(A) + He polarization moments deviate systematically from the predictions of a hard-shell, kinematic-apse scattering model, with larger deviations as N′ increases, which we attribute to the shallow gradient of the anisotropic repulsive NO(A)-He potential energy surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Building and testing correlations for the estimation of one‐electron reduction potentials of a diverse set of organic molecules
We describe and evaluate a method for computationally predicting reduction potentials of a diverse group of organic molecules by linearly correlating calculated lowest unoccupied molecular orbital energies with ground state reduction potentials measured in acetonitrile. The approach is shown to provide a unique combination of extreme computational simplicity and excellent accuracy across a diverse range of organic structures and a wide window of reduction potentials. A disparate set of molecules (74 compounds belonging to six distinct structural families, comprised of molecules containing C, H, N, O, F, Cl, and Br, with functional groups including esters, ketones, halides, nitriles, quinones, alkenes, arenes, heteroarenes, and pyridinium and higher benzologs, all containing conjugated pi systems, spanning a 3.5‐V range of reduction potentials) was used to build the correlations. This methodology was found to be computationally inexpensive compared with other approaches and to permit the useful prediction of reduction potentials of additional molecules of diverse structural types not included in the families used to determine the correlation parameters. The effects of varying the basis set used in the B3LYP electronic structure calculations and including solvent (compared with calculations in gas phase) were also examined. It was found that the inclusion of a continuum solvent model in the calculations was required for accurate results, particularly when including cationic species in the correlations (although when only neutral molecules were examined, reasonable results could even be obtained in vacuo ). Several of the best correlations were used to predict the reduction potentials of seven much larger and structurally diverse chromophores that were not included in the correlation data set. Strong correlations ( r 2 values > 0.99) with very good predictive abilities (root mean square deviation < 60 mV) were found. This extremely simple and computationally efficient entirely closed‐shell methodology is proven robust and useful for the design of new molecules capable of participating in redox processes, including electron transfer reactions. Copyright © 2015 John Wiley & Sons, Ltd.
Méndez‐Hernández, Dalvin D.↗
Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule–Surface Disulfide Bridges
Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. Here, we present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid–S–S–Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.
36 MATERIALS SCIENCE↗