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Polymers having pendant polycyclic aromatic hydrocarbon (PAH) groups covalently bound to the polymer backbone via thioester bonds are provided. The PAH groups are covalently bound to the backbone of the polymer by a molecular linker that includes a thioester bond. Also provided are dispersions of polymer-coated carbon nanotubes and carbon nanotube films formed from the dispersions.
The use of pressure to obtain new materials that can be recovered under ambient conditions is a central problem in high-pressure physics. Despite decades of research, this goal has only been achieved in the laboratory for a few notable examples, such as diamond and cubic boron nitride. An area of significant interest is the transformation under compression of light-element molecular compounds to extended covalent-bonded (polymeric) solids. Among them, CO 2 has been extensively studied because of its status as a prototypical simple molecular system with a rich phase diagram and due to its fundamental role in Earth’s physics and chemistry. One of its polymeric crystalline phases, accessible at extreme pressures and temperatures, has been recently quenched to ambient pressure, but below room temperature. Here we report ab initio calculations predicting that isothermal compression of a carbon monoxide and oxygen mixture (CO+O 2 ), rather than the compound CO 2 , lowers the onset of C-polymerization at room temperature from ~ 118 GPa to ~ 7 GPa (complete by ~ 23 GPa). Moreover, it leads to the formation of an intrinsically different polymer with enhanced metastability. We predict that this dense phase is an energetic material which can potentially be recovered to ambient pressure and temperature.
Dynamical electron correlation has a major impact on the computed values of molecular properties and the energetics of molecular processes. This study focused on the effect of dynamical electron correlation on the spectroscopic constants ($R$ e , $ω$ e , $D$ e ), and potential energy curves, Δ$E$($R$), of the covalently bound AH and AF molecules, A = B–F. The changes in the spectroscopic constants (Δ$R$ e , Δ$ω$ e , Δ$D$ e ) caused by dynamical correlation are erratic and, at times, even surprising. These changes can be understood based on the dependence of the dynamical electron correlation energies of the AH and AF molecules as a function of the bond distance, i.e., Δ$E$ DEC ($R$). At large $R$, the magnitude of Δ$E$ DEC ($R$) increases nearly exponentially with decreasing $R$, but this increase slows as $R$ continues to decrease and, in many cases, even reverses at very short $R$. The changes in Δ$E$ DEC ($R$) in the region around $R$ e were as unexpected as they were surprising, e.g., distinct minima and maxima were found in the curves of Δ$E$ DEC ($R$) for the most polar molecules. The variations in Δ$E$ DEC ($R$) for $R$ ≲ $R$ e are directly correlated with major changes in the electronic structure of the molecules as revealed by a detailed analysis of the spin-coupled generalized valence bond wave function. In conclusion, the results reported here indicate that we have much to learn about the nature of dynamical electron correlation and its effect on chemical bonds and molecular properties and processes.
Perturbations to water, both by ions and confining media, have been the focus of numerous experimental and theoretical studies. Yet, several open questions remain, including the extent to which such perturbations modify the structural and dielectric properties of the liquid. Here, we present a first-principles molecular dynamics study of alkali cations in water (Li + , Na + , and K + ) as well as of water and LiCl and KCl solutions under confinement within carbon nanotubes (CNTs) of small diameter (1.1-1.5 nm). Our simulations support the view that the water structure is only modified locally in the presence of cations. We found that molecular polarizabilities are fingerprints of hydrogen bonding modifications, which occur at most up to the second solvation shell for all cations in bulk water. Under confinement, we found that the overall value of the molecular polarizability of water molecules near the surface is determined by the balance of two effects, which are quantitatively different in CNTs of different radii: the presence of broken hydrogen bonds at the surface leads to a decrease in the polarizabilities of water molecules, while the interaction with the CNT enhances polarizabilities. Interestingly, the reduction in dipole moments of interfacial water molecules under confinement is instead driven only by changes in the water structure and not by interfacial interactions. As expected, confinement effects on water molecular polarizabilities and dipole moments are more pronounced in the case of the 1.1 nm CNT.
Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.
A trivalent plutonium–pyrazinyl–tetrazolate complex Na 2 [Pu(Hdtp)(dtp) 2 (H 2 O) 4 ]·9H 2 O (Pu_dtp, H 2 dtp = 2,3-di-1H-tetrazol-5-ylpyrazine) was synthesized through metathesis reaction of plutonium bromide and Na 2 (dtp)·2H 2 O in water. This structure is particularly notable among complexes formed by trivalent f-elements and the dtp 2− ligand in aqueous media. In contrast to other trivalent f-elements, including all Ln 3+ (with the exception of Pm 3+ ) and Cm 3+ , preferentially coordinated with eight water molecules rather than the nitrogen donors of the dtp 2− ligand, Pu 3+ exhibits a distinct affinity for nitrogen coordination. This observation provides strong evidence that the 5f electrons in Pu 3+ are more delocalized than other studied trivalent f-elements. In Pu_dtp, three distinct Pu(III)–N bonds are present: one Pu(III)–N5 from pyrazinyl, one Pu(III)–N4 from the least electronegative nitrogen in the tetrazolate, and three Pu(III)–N1/N2/N3 from the most electronegative nitrogens in the tetrazolate. Experimental Pu(III)–N bond lengths, Wiberg bond indices (WBI), natural localized molecular orbitals (NLMO), quantum theory of atoms in molecules (QTAIM), and energy decomposition analysis (EDA), reveal a covalency trend: Pu(III)–N from the most electronegative nitrogen in tetrazolate > Pu(III)–N from the least electronegative nitrogen in tetrazolate > Pu(III)–N from pyrazinyl. This trend arises from the increased negative charge on the most electronegative nitrogen atoms in the tetrazolate ring, enhancing electrostatic Pu–N1/N2/N3 interactions. These stronger electrostatic interactions lead to shorter bond lengths, thereby enhancing orbital overlap and greater covalency, compared to the less electronegative nitrogen in tetrazolate (Pu–N4) and the neutral pyrazinyl nitrogen (Pu–N5).
Microscopic segregation and molecular heterogeneities in complex liquids are the result of the interplay between different intermolecular forces, all of which contribute to the energy landscape of the system. A consequence of the intricate energy landscape is the nontrivial effect on the solvation dynamics. Here, the impact of molecular heterogeneities on the solvation dynamics is studied using infrared spectroscopies and molecular dynamics simulations. In particular, this study focuses on the dynamical effect of nanoscopic heterogeneities present in deep eutectic solvents (DESs) composed of lauric acid (LA) and N-methylacetamide (NMA). To this end, a molecular probe containing a carbon triple bond is used as an infrared reporter. The results show that the vibrational probe is likely to be located in the NMA polar domains. Furthermore, the probe solvation dynamics derived from the 2DIR spectra presents a slowdown of its timescale with increasing LA concentration in the DES. Kubo modeling of the probe solvation dynamics shows a correlation between the amplitude of its long time component and the presence of molecular heterogeneities in the sample. Semiclassical modeling of the vibrational line shape of the triple bond stretch demonstrates that the heterogeneities affect the whole solvation dynamics of the system through the amplitudes of the frequency fluctuations. Molecular dynamics simulations confirm the experimental results and their interpretation by showing a slowdown of the solvation dynamics when the LA heterogeneities are present. Overall, the study presents a molecular framework to explain the effect of confinement created by nanoscopic LA heterogeneities on the solvation dynamics of the system.
Abstract We report an investigation of the friction mechanisms of MoS 2 thin films under changing environments and contact conditions using a variety of computational and experimental techniques. Molecular dynamics simulations were used to study the effects of water and molecular oxygen on friction and bonding of MoS 2 lamellae during initial sliding. Characterization via photoelectron emission microscopy (PEEM) and Kelvin probe force microscopy (KPFM) were used to determine work function changes in shear modified material within the top few nanometers of MoS 2 wear scars. The work function was shown to change with contact conditions and environment, and shown by density functional theory (DFT) calculations and literature reports to be correlated with lamellae size and thickness of the basally oriented surface layer. Results from nanoscale simulations and macroscale experiments suggest that the evolution of the friction behavior of MoS 2 is linked primarily to the formation or inhibition of a basally oriented, molecularly thin surface film with long-range order.
Weakening and cleaving N-H bonds is crucial for improving molecular ammonia oxidation catalysts. In this work, we report the synthesis and hydrogen atom abstraction chemistry of bis(ammonia) Cr porphyrin complexes Cr(TPP)(NH 3 ) 2 and Cr(TMP)(NH 3 ) 2 (TPP = 5,10,15,20-tetraphenyl-meso-porphyrin and TMP = 5,10,15,20-tetramesityl-meso-porphyrin) using bulky aryloxyl radicals. The triple hydrogen atom abstraction reaction results in the formation of Cr V (por)(≡N), with the nitride deriving from ammonia, as indicated by UV-Vis and FT-IR spectroscopy, and a single crystal structural determination of Cr(TPP)(≡N). Subsequent oxidation of this chromium(V)-nitrido complex results in the formation of Cr III (por), with scission of the Cr≡N bond. A computational analysis illustrates the progression from Cr II to Cr V and evaluates the energetics of abstracting hydrogen atoms from Cr II -NH 3 to generate Cr V ≡N. The formation and isolation of Cr V (por)(≡N) illustrates the stability of these species and the need to chemically activate the nitride moiety for atom transfer or N-N coupling reactivity.
Comets are believed to retain some interstellar materials, stored in fairly pristine conditions since-their formation. The composition and properties of cometary dust grains should reflect those of grains in the outer part of the protosolar nebula which, at least in part, were inherited from the presolar molecular cloud. However, infrared emission features in comets differ from their interstellar counterparts. These differences imply processing of interstellar material on its way to incorporation in comets, but C and N appear to be retained. Overall dust evolution from the interstellar medium (ISM) to planetary materials is accompanied by an increase in proportion of complex organics and a decrease in pure carbon phases. The composition of cometary dust grains was measured in situ during fly-by missions to comet Halley in 1986. The mass spectra of about 5000 cometary dust grains with masses of 5 x 10(exp -17) - 5 x 10(exp -12) g provide data about the presence and relative abundances of the major elements H, C, N, O,Na, Mg, Al, Si, S, Cl, K, Ca, Ti, Cr, Fe, Ni. The bulk abundances of major rock-forming elements integrated over all spectra were found to be solar within a factor of 2, while the volatile elements H, C, N, O in dust are depleted in respect to their total cosmic abundances. The abundances of C and N in comet dust are much closer to interstellar than to meteoritic and are higher than those of dust in the diffuse ISM. In dense molecular clouds dust grains are covered by icy mantles, the average composition of which is estimated to be H:C:N:O = 96:14:1:34. Up to 40% of elemental C and O may be sequestered in mantles. If we use this upper limit to add H, C, N and O as icy mantle material to the abundances residing in dust in the diffuse ISM, then the resulting values for H. C, and N match cometary abundances. Thus, ice mantles undergoing chemical evolution on grains in the dense ISM appear to have been transformed into less volatile and more complex organic residues wherein the H, C and N are largely retained and ultimately accreted in cometary dust. The abundance of O is about the same for cometary dust, meteorites and interstellar dust. In all these samples, most of O in a solid phase is bonded to silicates. In dense molecular clouds, the abundance of O in dust+mantles is significantly higher then in cometary dust. This difference may reflect the greater lability of oxygenated species toward astrophysical processing. Laboratory studies show that O-bearing functional groups in organic compounds tend to be relatively easily removed by heating and/or UV and particle irradiation . In Halley's coma, O-containing organic grains, being unstable, were located closest to the nucleus. The decomposition of the organic grain component in the coma provided a significant extended source contribution to O-containing gaseous species such as CO and H2CO.
Abstract Methanol–water mixtures find use in many applications, particularly catalytic energy conversion processes. Their importance has motivated numerous computational studies, most of which employed molecular dynamics based on classical force fields. These enable simulations of large systems on long time scales but do not reliably describe reactive dynamics involving bond breaking and bond formation. In contrast, ab initio molecular dynamics (AIMD) based on density functional theory (DFT) is generally more reliable for such applications but has a high computational cost, which discourages systematic studies of alcohol-water mixtures. To remedy this, we trained a machine learning interatomic potential capable of probing the properties of aqueous methanol mixtures at the DFT level using the SCAN functional. Our results show that SCAN qualitatively reproduces multiple key experimental features arising from the amphiphilic nature of methanol, including density, diffusion coefficients, X-ray structure factors, and Kirkwood–Buff integrals. We also find that structural correlations between water molecules are somewhat overestimated, leading to a stronger preferential association than that predicted by experiments. However, increasing the temperature by 30 K mitigates this effect and also recovers the correct mobilities of both methanol and water. These results indicate that SCAN provides an accurate description of methanol–water mixtures, making it a reliable choice for investigating the reactive dynamics in such systems.
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.
Values of the bond dissociation energies, ionization potentials, and electron affinities that were taken from the literature are presented in tables for some monatomic, diatomic, and polyatomic molecules which are found in many high-temperature chemical reactions including combustion reactions. Much of the information came from literature published after 1950 which either reported experimental and theoretical energy values or gave a review of previous literature on the subject. In some cases values for the bond dissociation energies were calculated from recently published heats of formation.
The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were correlated to molecular structure and the results of torsional braid analysis (TBA). A large friction transition (0.23 to 0.03) was found to occur at 45 C + or - 5 C. It was postulated that this transition was initiated by some molecular relaxation, which gave the molecules a degree of freedom by which an external mechanical stress could rearrange the molecules into a structure, such as an extended chain, which is conducive to easy shear. Above 300 C the friction characteristics were found to be dependent on the thermal prehistory of the film.
The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an ‘inactive’ conformation with fast binding to mannose to an ‘active’ conformation with slow detachment from mannose. Because mechanical tensile force favors separation of the domains and, thus, FimH activation, it has been thought that the catch bonds can only be manifested in a fluidic shear-dependent mode of adhesion. Here, we used recombinant FimH variants with a weakened inter-domain interaction and show that a fast and sustained allosteric activation of FimH can also occur under static, non-shear conditions. Moreover, it appears that lectin domain conformational activation happens intrinsically at a constant rate, independently from its ability to interact with the pilin domain or mannose. However, the latter two factors control the rate of FimH deactivation. Thus, the allosteric catch bond mechanism can be a much broader phenomenon involved in both fast and strong cell-pathogen attachments under a broad range of hydrodynamic conditions. In conclusion, this concept that allostery can enable more effective receptor-ligand interactions is fundamentally different from the conventional wisdom that allostery provides a mechanism to turn binding off under specific conditions.
First-principles calculations and analysis of the thermodynamic, structural, and electronic properties of liquid SiO 2 characterize the bonded-to-atomic transition at 0.1–1.6 TPa and 10 4 –10 5 K (1–9 eV), the high-energy-density regime relevant to understanding planetary interiors. We find strong ionic bonds that become short-lived due to high kinetics during the transition, with sensitivity of the transition temperature to pressure, and our calculated Hugoniots agree with past experimental data. Furthermore, these results reconcile previous experimental and theoretical findings by clarifying the nature of the bond dissociation process in early Earth and “rocky” (oxide) constituents of large planets.
Thorium and its compounds have been widely investigated as important nuclear materials. Previous research focused on the potential use of thorium hydrides, such as ThH 2 , ThH 4 , and Th 4 H 15 , as nuclear fuels. Here, we report studies of the anion, ThH 5 , by anion photoelectron spectroscopy and computations. The resulting experimental and theoretical vertical detachment energies (VDE) for ThH 5 are 4.09 eV and 4.11 eV, respectively. These values and the agreement between theory and experiment facilitated the characterization of the structure of the ThH 5 anion and showed its neutral counterpart, ThH 5 to be a superhalogen. ThH 5 , which exhibits a C 4v structure with five Th–H single bonds, possesses the largest known H/M ratio among the actinide elements, M. Here, the adaptive natural density partitioning (AdNDP) method was used to further analyze the chemical bonding of ThH 5 – and to confirm the existence of five Th–H single bonds in the ThH 5 – molecular anion.