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DOE OSTI2016

A Pareto Algorithm for Efficient De Novo Design of Multi-functional Molecules

Here, we have introduced a Pareto sorting algorithm into Synopsis, a de novo design program that generates synthesizable molecules with desirable properties. We give a detailed description of the algorithm and illustrate its working in 2 different de novo design settings: the design of putative dual and selective FGFR and VEGFR inhibitors, and the successful design of organic structure determining agents (OSDAs) for the synthesis of zeolites. We show that the introduction of Pareto sorting not only enables the simultaneous optimization of multiple properties but also greatly improves the performance of the algorithm to generate molecules with hard-to-meet constraints. This in turn allows us to suggest approaches to address the problem of false positive hits in de novo structure based drug design by introducing structural and physicochemical constraints in the designed molecules, and by forcing essential interactions between these molecules and their target receptor.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Traction-separation response of bilayer graphene interfaces: The role of an intercalated single atomic layer of water molecules and hydroxyl groups

Molecular dynamics simulations of the normal and shear traction-separation response of dry and wet bilayer graphene interfaces were performed. The influence of a single, atomic layer of water molecules sandwiched between graphene layers and hydroxyl functionalization on one or both layers were investigated. Hydroxyl groups provided a shielding effect during normal separation while favoring stick-slip friction under sliding conditions. The single, atomic layer of water molecules confined between hydrophilic and asymmetric hydrophobic/hydrophilic surfaces was found to ease sliding friction. The mechanisms arose from the balance between the attractive and repulsive graphene/water interactions through bridges of single water molecules between the two surfaces and the structure of the water monolayer under confinement for which an out-of-plane water/water hydrogen bond network could not be developed. The single, atomic layer of water molecules reduced the sliding friction the most when both surfaces were hydrophilic and lowered the sliding friction of the asymmetric hydrophobic/hydrophilic interfaces to that when both surfaces were hydrophobic. An optimal hydroxyl surface coverage of less than 10% may exist for efficient water lubrication, with diminishing effect with increasing number of hydroxyl groups. Finally, the findings offer a design strategy for assembling bilayer graphene interfaces with tailored friction and sliding contact properties.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Structural changes of linear DNA molecules induced by cisplatin

Interaction between long DNA molecules and activated cisplatin is believed to be crucial to anticancer activity. However, the exact structural changes of long DNA molecules induced by cisplatin are still not very clear. In this study, structural changes of long linear double-stranded DNA (dsDNA) and short single-stranded DNA (ssDNA) induced by activated cisplatin have been investigated by atomic force microscopy (AFM). The results indicated that long DNA molecules gradually formed network structures, beads-on-string structures and their large aggregates. Electrostatic and coordination interactions were considered as the main driving forces producing these novel structures. An interesting finding in this study is the beads-on-string structures. Moreover, it is worth noting that the beads-on-string structures were linked into the networks, which can be ascribed to the strong DNA–DNA interactions. This study expands our knowledge of the interactions between DNA molecules and cisplatin. - Highlights: • We investigate structural changes of dsDNA and ssDNA induced by cisplatin. • AFM results indicated long dsDNA formed network, beads-on-string and aggregates. • ssDNA can form very similar structures as those of long linear dsDNA. • A possible formation process of theses novel structure is proposed.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

BODIPY based A-D-A molecules: Effect of CF3 group substitution at meso phenyl group

Two pairs of A-D-A molecules have been created with fluorene and benzodithiophene as the central donor subunits and terminal BODIPY units, functionalized with either a 4-methylphenyl or 4-trifluoromethylphenyl group at the meso position. The effect of the para substituent of the meso phenyl group on the photophysical properties of these molecules is studied through steady state absorption and fluorescence spectroscopy as well as femtosecond transient absorption and time resolved fluorescence spectroscopy techniques. Applicability of these molecules as donors in solution processed solar cell active layers was investigated through time resolved microwave conductivity measurements on blends with PC60BM acceptor, which shows a varying yield of charge transfer with choice of substituent. Transient absorption spectroscopy is then employed to investigate the role of the 4-trifluoromethylphenyl group in altering the efficiency of charge transfer from these A-D-A molecules to PC60BM. The results show a consistent picture of picosecond charge transfer and a component of a few hundred ps geminate recombination that results in a small yield of long-lived free charges optimized for the methylphenyl derivatives.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Machine learning for the redox potential prediction of molecules in organic redox flow battery

Here, organic redox flow batteries (ORFB) are recognized as an innovative technology for the large-scale storage of renewable energy. The redox potential of organic redox-active molecules plays a vital role in their performance. Advanced screening techniques like high-throughput experiment and machine learning (ML) have significantly enhanced organic material performance and transformed the field of ORFB. However, the scarcity of experimental data poses a considerable challenge for ML model development in this domain. In our study, we developed lightweight graph-based Gaussian process regression (GPR) models with GPU-accelerated marginalized graph kernel and hybrid kernel to predict the redox potentials of organic redox-active molecules for ORFBs, specifically focusing on small datasets. To evaluate model accuracy, we created a new experimental database of organic redox-active molecules by the data from hundreds of published papers and assembled previous computational datasets. We also considered some key parameters, such as pH conditions and solvent type, to assess their impact on redox potential prediction. Our GPR model predicted redox potentials with high accuracy across all datasets using minimal training data. The study provides powerful tools for molecule screening and design and delivers valuable guidance on designing training datasets for costly experiments.

25 ENERGY STORAGE↗

DOE OSTI2022

Line coupling and line mixing effects on calculated widths of symmetric-top molecules with the k-degeneracy: A theoretical study of N 2 -, O 2 -, and air-broadened lines of CH 3 I

Calculations of the N 2 -, O 2 -, and air-broadened widths, together with their temperature dependence exponents have been made for transitions of CH 3 I in the ν 5 and ν 6 bands. The calculations are based on a semi-classical line shape formalism developed by the current authors through modifying and refining the Robert-Bonamy formalism. In recent years, we have applied this formalism for linear molecules, symmetric-top molecules with inversion symmetry, and asymmetric-top molecules. For symmetric-top molecules with the k degeneracy such as CH 3 I, the formalism has a new feature. In this case, one should consider each of the CH 3 I transitions labeled by k i or f ≠ 0 as a doublet. Then, one needs to consider the effects of the line mixing process between these two components. Furthermore, comparisons of our theoretical predictions with some data available demonstrate a very reasonable agreement. Finally, we propose new experiments at higher perturber pressures that would enable one to check the theoretically calculated relaxation matrices and to extend the analysis to the inter-doublet mixing effects.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2013

Two proton-conductive hybrids based on 2,2 Prime -biimidazole molecules and Keggin-type heteropolyacids

Two proton-conductive organic/inorganic complexes were constructed by Keggin-type heteropolyacids and 2,2 Prime -biimidazole molecules. Single-crystal X-ray diffraction analyses revealed that two complexes crystallized in the triclinic space group Pi, exhibited very close unit cell parameters, and presented similar three-dimensional (3D) hydrogen-bonded networks constructed by H{sub 2}biim, [PM{sub 12}O{sub 40}]{sup 3-} (M=W for 1 and Mo for 2) and solvent molecules. The results of thermogravimetric analyses (TG) suggest that two supramolecular complexes have similar thermal stability based on the same 3D packing. Two complexes at 100 Degree-Sign C under 98% relative humidity showed a good proton conductivity of about 10{sup -4} S cm{sup -1}. A possible mechanism of the proton conduction was proposed according to the experimental results. - Graphical Abstract: Two molecular hybrids constructed by Keggin-type heteropolyacids and 2,2 Prime -biimidazole molecules showed good proton conductivities of 10{sup -4} S cm{sup -1} in the temperature range of 85-100 Degree-Sign C under 98% relative humidity. Highlights: Black-Right-Pointing-Pointer H{sub 2}biim shows the ability to form hydrogen bonds via the N-H groups in the context of crystal engineering. Black-Right-Pointing-Pointer Heteropolyacids have suitable characteristics to be used excellent proton conductors. Black-Right-Pointing-Pointer Two new supramolecular complexes based-on Keggin-type heteropolyacids and H{sub 2}biim molecules were constructed. Black-Right-Pointing-Pointer The structure was determined by using single-crystal X-ray diffraction data. Black-Right-Pointing-Pointer Both complexes showed good proton conductivities of 10{sup -4} S cm{sup -1} in the temperature range of 85-100 Degree-Sign C.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Two proton-conductive hybrids based on 2-(3-pyridyl)benzimidazole molecules and Keggin-type heteropolyacids

Two proton-conductive organic/inorganic complexes were constructed by Keggin-type heteropolyacids and 2-(3-pyridyl)benzimidazole molecules. Single-crystal X-ray diffraction analyses revealed that two complexes crystallized in the monoclinic space group P2{sub 1}/c, exhibited different unit cell parameters, and presented different hydrogen-bonded networks constructed by 2-(3-pyridyl)benzimidazole molecules, [PMo{sub 12}O{sub 40}]{sup 3−} anions and solvent molecules. The results of thermogravimetric analyses suggest that two supramolecular complexes have different thermal stability based on the different hydrogen-bonded networks. Two complexes at 100 °C under 35–98% relative humidity showed a good proton conductivity of about 10{sup −3} S cm{sup −1}. The proton conductivities of two complexes under 98% relative humidity both increase on a logarithmic scale with temperature range from 25 to 100 °C. At 100 °C, both complexes showed poor proton conductivities of 10{sup −8}–10{sup −9} S cm{sup −1} under acetonitrile or methanol vapor. - Graphical abstract: Two molecular hybrids constructed by Keggin-type heteropolyacids and 2-(3-pyridyl)benzimidazole molecules showed good proton conductivities of 10{sup −3} S cm{sup −1} at 100 °C under 35–98% relative humidity. Display Omitted - Highlights: • 2-(3-Pyridyl)benzimidazole could form hydrogen bonds via the N–H groups. • Heteropolyacids have suitable characteristics to be used excellent proton conductors. • Two proton-conductive hybrids based on Keggin HPAs and 3-PyBim were constructed. • The structures were determined by using single-crystal X-ray diffraction data. • They showed good proton conductivities of 10{sup −3} S cm{sup −1} at 100 °C under 35–98% RH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Impact of dipolar molecules on the reliability of organic photovoltaic cells

Blending two non-fullerene acceptors (NFAs) to form bulk heterojunctions (BHJs) in ternary organic photovoltaics (OPVs) has been shown to lead to an end-capping exchange reaction that results in the generation of several new dipolar species whose impact on OPV operational stability remains uncertain. Here, we investigate the reliability of a ternary OPV system intentionally blended with dipolar NFA molecules. We reveal that an intrinsic contribution to OPV degradation is the reorganization and reorientation of the dipolar molecules during operation, which leads to an increased dielectric constant (ε r ) of the BHJ. Consequently, the electric field across the BHJ with dipolar molecules decreases compared with that of a non-dipolar BHJ under the same applied voltage, leading to a larger reduction in charge collection efficiency over time. This result has implications on the stability of a range of organic electronic devices containing dipolar molecules.

14 SOLAR ENERGY↗

DOE OSTI2025

Dirhodium(II,II) Complexes as Panchromatic Single-Molecule Photocatalysts for Hydrogen Evolution

The growing global energy demand and climate change have prompted a shift from carbon-based fuels to sustainable energy sources. Hydrogen production by harnessing solar energy and using abundant proton sources represents an attractive approach to addressing this crisis. Single-molecule single-chromophore photocatalysts, capable of both absorbing the incident photon and catalyzing the chemical transformation, are able to circumvent energy losses present in multicomponent systems that require a photosensitizer and a catalyst, often employing additional redox relay molecules. Here, the series of complexes derived from cis-[Rh 2 (μ-DPhF) 2 (μ-bncn) 2 ] 2+ (1; DPhF = N,N′-diphenylformamidinate, bncn = benzo[c]cinnoline) discussed in this Account presents robust and air-stable single-molecule photocatalysts with panchromatic absorption from the ultraviolet spectral region to the near-infrared (NIR), with high turnover frequencies of ∼20 to 30 h –1 under red light irradiation. For comparison, other single-molecule hydrogen-evolving photocatalysts reported to date exhibit low photocatalytic efficiency, are not operable in the visible or NIR regions, and are unstable under an ambient atmosphere.

Absorption↗

DOE OSTI2016

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metal oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Laser Ablation Molecular Isotopic Spectrometry for Molecules Formation Chemistry in Femtosecond-Laser Ablated Plasmas

Recently, laser ablated molecular isotopic spectrometry (LAMIS) has expanded its capability to explore molecules formation mechanism in laser-induced plasma in addition to isotope analysis. LAMIS is a powerful tool for tracking the origination of atoms that is involved in formation of investigated molecules by labeling atoms with their isotopic substitution. The evolutionary formation pathways of organic molecules, especially of C 2 dimers and CN radicals, were frequently reported. However, very little is known about the formation pathways for metallic radicals and heterodimers in laser ablated plasma. This research focuses on elucidating the formation pathways of AlO radicals in femtosecond laser ablated plasma from 18 O-labeled Al 2 O 3 pellet. Plasmas expanding with strong forward bias in the direction normal to the sample surface were generated in the wake of a weakly ionized channel created by a femtosecond laser. The formation mechanism of AlO and influence of air were investigated with multiple plasma diagnostic methods such as monochromatic fast gating imaging, spatiotemporal resolved optical emission spectroscopy, and LAMIS. An advanced LAMIS fitting procedure was used to deduce the spatiotemporal distributions of Al 18 O and Al 16 O number densities and also their ratios. We found that the Al 16 O/Al 18 O number density ratio is higher for plasma portion closer to the sample surface, which suggests that chemical reactions between the plasma plume and ambient air are more intense at the tail of the plasma. The results also reveals that direct association of free Al and O atoms is the main mechanism for the formation of AlO at the early stage of the plasma. Finally, to the contrast, chemical reactions between plasma materials and ambient oxygen molecules and the isotope exchange effect are the dominant mechanisms of the formation of AlO and evolution of Al 16 O/Al 18 O number density ratio at the late stage of the plasma.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Out-of-Oblivion Cage Molecules and Their Porous Crystalline Phases

An automated molecular porosity detection approach was developed and applied to PubChem, a repository of ca. 94 million molecules, to discover intrinsically porous cage molecules, which, although previously considered by chemists, have remained in oblivion to the porous solids community as neither their crystal structures nor solid-state porosity have been previously reported. The effort led to identification of six such cage molecules reported over the span of the last two decades. The following crystal structure prediction effort suggested that these molecules can form stable low-energy porous crystalline phases. One of the identified lowest energy phases exhibits zeolite-range porosity with pore diameters of ca. 8 Å and internal surface area of 1070 m 2 /g.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Mechanistic Study of Nucleation Enhancement in Atomic Layer Deposition by Pretreatment with Small Organometallic Molecules

Thermal atomic layer deposition (ALD) of metals on metal oxide surfaces typically suffers from nucleation delays that result in poor-quality films. The poor nucleation may be caused by a lack of suitable chemisorption sites on the oxide surface, which are needed for metal nucleation to occur. In this work, we demonstrate that prefunctionalizing the surface with a single monolayer of small organometallic molecules from the vapor phase can lead to a significant increase in surface coverage of the metal deposited by ALD. This process is demonstrated for Pt ALD from (methylcyclopentadienyl)trimethylplatinum (MeCpPtMe 3 ) and O 2 , with nucleation enhanced almost 3-fold at 100 ALD cycles after the pretreatment. We hypothesize that the high coverage of the organometallic molecule provides an alternative chemisorption mechanism for the platinum precursor and thus leads to an increase in its uptake. The proposed chemisorption mechanism is robust across several organometallic molecule pretreatments and could potentially be exploited for other organometallic-based metal ALD processes. This chemisorption mechanism was probed using in situ quadrupole mass spectrometry (QMS). The growth of the platinum deposits was investigated in depth through scanning electron microscopy (SEM) and grazing incidence small-angle X-ray scattering (GISAXS). These studies show that the pretreatment also results in the improved wettability of Pt nanoparticles (NPs). The improved wettability is likely to affect the Pt diffusion properties, further contributing to the enhancement observed on the treated substrates. In addition, GISAXS and SEM studies indicate the growth of larger, denser, and more highly ordered Pt NPs at early cycle numbers, which subsequently coalesce into continuous and pinhole-free films. Surface pretreatment by organometallic molecules therefore introduces a potential route to achieve improved nucleation and growth of ultrathin films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Distributive Nd-to-Yb Energy Transfer within Pure [YbNdYb] Heterometallic Molecules

Facile access to site-selective hetero-lanthanide molecules will open new avenues in the search of novel photophysical phenomena based on Ln-to-Ln' energy transfer (ET). This challenge demands strategies to segregate efficiently different Ln metal ions among different positions in a molecule. We report here the one-step synthesis and structure of a pure [YbNdYb] (1) coordination complex featuring short Yb···Nd distances, ideal to investigate a potential distributive (i.e., from one donor to two acceptors) intramolecular ET from one Nd 3+ ion to two Yb 3+ centers within a well-characterized molecule. The difference in ionic radius is the mechanism allowing to allocate selectively both types of metal ion within the molecular structure, exploited with the simultaneous use of two β-diketone-type ligands. To assist the photophysical investigation of this heterometallic species, the analogues [YbLaYb] (2) and [LuNdLu] (3) have also been prepared. Sensitization of Yb 3+ and Nd 3+ in the last two complexes, respectively, was observed, with remarkably long decay times, facilitating the determination of the Nd-to-Yb ET within the [YbNdYb] composite. This ET was demonstrated by comparing the emission of iso-absorbant solutions of 1, 2, and 3 and through lifetime determinations in solution and solid state. The comparatively high efficiency of this process corroborates the facilitating effect of having two acceptors for the nonradiative decay of Nd 3+ created within the [YbNdYb] molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Nature of Hyperfine Interactions in TbPc 2 Single-Molecule Magnets: Multiconfigurational Ab Initio Study

Lanthanide-based single-ion magnetic molecules can have large magnetic hyperfine interactions as well as large magnetic anisotropy. Recent experimental studies reported tunability of these properties by changes of chemical environments or by application of external stimuli for device applications. In order to provide insight onto the origin and mechanism of such tunability, here we investigate the magnetic hyperfine and nuclear quadrupole interactions for a 159 Tb nucleus in TbPc 2 (Pc = phthalocyanine) single-molecule magnets using multiconfigurational ab initio methods including spin–orbit interaction. Since the electronic ground and first-excited (quasi)doublets are well separated in energy, the microscopic Hamiltonian can be mapped onto an effective Hamiltonian with an electronic pseudospin S = 1/2. From the ab initio calculated parameters, we find that the magnetic hyperfine coupling is dominated by the interaction of the Tb nuclear spin with electronic orbital angular momentum. The asymmetric 4f-like electronic charge distribution leads to a strong nuclear quadrupole interaction with significant transverse terms for the molecule with low symmetry. The ab initio calculated electronic–nuclear spectrum including the magnetic hyperfine and quadrupole interactions is in excellent agreement with the experiment. We further find that the transverse quadrupole interactions significantly influence the avoided level crossings in magnetization dynamics and that the molecular distortions affect mostly the Fermi contact terms as well as the transverse quadrupole interactions. Synopsis Hyperfine interactions for 159 Tb nucleus in TbPc 2 single-molecule magnets are investigated from first-principles using multiconfigurational calculations. Strong nuclear quadrupole and magnetic hyperfine coupling are found, with the latter being dominated by the paramagnetic spin-orbital mechanism. Furthermore, we construct an ab initio pseudospin Hamiltonian and obtain the electronic-nuclear spectrum that is in excellent agreement with experiment. The Zeeman diagram is calculated, and the magnetization dynamics is discussed. The effects of molecular distortions are researched.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Theoretical Investigations on the Plasmon-Mediated Dissociation of Small Molecules in the Presence of Silver Atomic Wires

Plasmonic nanoparticles can promote bond activation in adsorbed molecules under relatively benign conditions via excitation of the nanoparticle’s plasmon resonance. As the plasmon resonance often falls within the visible light region, plasmonic nanomaterials are a promising class of catalysts. However, the exact mechanisms through which plasmonic nanoparticles activate the bonds of nearby molecules are still unclear. Herein, we evaluate Ag 8 –X 2 (X = N, H) model systems via real-time time-dependent density functional theory (RT-TDDFT), linear response time-dependent density functional theory (LR-TDDFT), and Ehrenfest dynamics in order to better understand the bond activation processes of N 2 and H 2 facilitated by the presence of the atomic silver wire under excitation at the plasmon resonance energies. We find that dissociation is possible for both small molecules at high electric field strength. Activation of each adsorbate is symmetry- and electric field-dependent, and H 2 activates at lower electric field strengths than N 2 . Furthermore, this work serves as a step toward understanding the complex time-dependent electron and electron–nuclear dynamics between plasmonic nanowires and adsorbed small molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A Comparison of Electronic Structure Methods for Predicting the Hydrogenation Energies of Candidate Molecules for Hydrogen Storage

The development of novel energy materials and fuels is required to expand current available energy sources. Aiming to reach this goal, there is growing interest in using molecular hydrogen as an energy carrier due to its abundance and high energy density. Liquid organic hydrogen carriers (LOHCs) are a promising route to the large-scale storage and transport of hydrogen for use in the energy economy. The search for thermodynamically viable LOHC molecules for real world use has led to a set of constraints on the dehydrogenation enthalpy and the minimum gravimetric hydrogen capacity. These constraints allow one to formulate the search for an ideal LOHC candidate molecule as an optimization problem well suited to the strengths of machine learning and artificial intelligence computational approaches. A critical barrier to a large-scale, high-throughput screening of LOHC candidate molecules is the lack of reliable training data. Computational electronic structure methods including density functional theory, coupled cluster approximations, and diffusion Monte Carlo can be used to provide training data where experimental data are either unreliable or do not exist. In this work, we use these methods to calculate the dehydrogenation energies and enthalpies of candidate LOHC molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗