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After deep venous thrombosis (DVT), many patients have impaired quality of life (QOL). We aimed to assess whether pharmacomechanical catheter-directed thrombolysis (PCDT) improves short-term or long-term QOL in patients with proximal DVT and whether QOL is related to extent of DVT.The Acute Venous Thrombosis: Thrombus Removal with Adjunctive Catheter-Directed Thrombolysis (ATTRACT) trial was an assessor-blinded randomized trial that compared PCDT with no PCDT in patients with DVT of the femoral, common femoral, or iliac veins. QOL was assessed at baseline and 1 month, 6 months, 12 months, 18 months, and 24 months using the Venous Insufficiency Epidemiological and Economic Study on Quality of Life/Symptoms (VEINES-QOL/Sym) disease-specific QOL measure and the 36-Item Short Form Health Survey (SF-36) physical component summary (PCS) and mental component summary general QOL measures. Change in QOL scores from baseline to assessment time were compared in the PCDT and no PCDT treatment groups overall and in the iliofemoral DVT and femoral-popliteal DVT subgroups.Of 692 ATTRACT patients, 691 were analyzed (mean age, 53 years; 62% male; 57% iliofemoral DVT). VEINES-QOL change scores were greater (ie, better) in PCDT vs no PCDT from baseline to 1 month (difference, 5.7; P = .0006) and from baseline to 6 months (5.1; P = .0029) but not for other intervals. SF-36 PCS change scores were greater in PCDT vs no PCDT from baseline to 1 month (difference, 2.4; P = .01) but not for other intervals. Among iliofemoral DVT patients, VEINES-QOL change scores from baseline to all assessments were greater in the PCDT vs no PCDT group; this was statistically significant in the intention-to-treat analysis at 1 month (difference, 10.0; P .0001) and 6 months (8.8; P .0001) and in the per-protocol analysis at 18 months (difference, 5.8; P = .0086) and 24 months (difference, 6.6; P = .0067). SF-36 PCS change scores were greater in PCDT vs no PCDT from baseline to 1 month (difference, 3.2; P = .0010) but not for other intervals. In contrast, in femoral-popliteal DVT patients, change scores from baseline to all assessments were similar in the PCDT and no PCDT groups.Among patients with proximal DVT, PCDT leads to greater improvement in disease-specific QOL than no PCDT at 1 month and 6 months but not later. In patients with iliofemoral DVT, PCDT led to greater improvement in disease-specific QOL during 24 months.

First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom-atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms of urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. The vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea.

SUMMARY The RNA polymerase II (RNAPII) carboxyl-terminal domain (CTD) heptapeptide repeats (Y1-S2-P3-T4-S5-P6-S7) undergo dynamic phosphorylation and dephosphorylation during the transcription cycle to recruit factors that regulate transcription, RNA processing and chromatin modification. We show here that RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains and interact preferentially via CTD interaction domains (CIDs) with CTD repeats phosphorylated at S2 and S7. Our high resolution crystal structures of the RPRD1A, RPRD1B and RPRD2 CIDs, alone and in complex with CTD phosphoisoforms, elucidate the molecular basis of CTD recognition. In an interesting example of cross-talk between different CTD modifications, our data also indicate that RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and, by interacting with CTD repeats where phospho-S2 and/or phospho-S7 bracket a phospho-S5 residue, serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2.

Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data., Advanced Monte Carlo sampling strategies in conjunction with Kohn−Sham density functional theory enable the prediction of reaction equilibria for nitrogen/oxygen mixtures without the need for predetermined reaction steps.

We have resolved the inconsistency in quantifying the surface potential at the liquid-vapor interface when using explicit ab initio electronic charge density and effective atomic partial charge models of liquid water. This is related, in part, to the fact that the resulting electric potentials from partial-charge models and ab initio charge distributions are quite different except for those regions of space between the molecules. We show that the electrostatic surface potential from a quantum mechanical charge distribution compares well to high-energy electron diffraction and electron holography measurements, as opposed to the comparison with electrochemical measurements. We suggest that certain regions of space be excluded when comparing computed surface potentials with electrochemical measurements. This work describes a novel interpretation of ab initio computed surface potentials through high-energy electron holography measurements as useful benchmarks toward a better understanding of electrochemistry.

Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavourable chemical conditions on the planet and the high heat from impact. In contrast, we find that impact-induced shock compression of cometary ices followed by expansion to ambient conditions can produce complexes that resemble the amino acid glycine. Our ab initio molecular dynamics simulations show that shock waves drive the synthesis of transient C-N bonded oligomers at extreme pressures and temperatures. On post impact quenching to lower pressures, the oligomers break apart to form a metastable glycine-containing complex. We show that impact from cometary ice could possibly yield amino acids by a synthetic route independent of the pre-existing atmospheric conditions and materials on the planet.

In recent years, theoretical as well as experimental studies have presented a novel view of the aqueous interface, wherein hard and/or multiply charged ions are excluded from the interface but large polarizable anions show interfacial enhancement relative to the bulk. The observed trend in the propensity of anions to adsorb at the air/water interface appears to follow an inverse order of the Hofmeister series for anions. This study focuses on experimental and theoretical examination of the partitioning behavior of perchlorate (ClO(4)(-)) and chloride (Cl(-)) ions at the air/water interface. We have used ambient pressure X-ray photoelectron spectroscopy to directly probe the interfacial concentrations of ClO(4)(-) and Cl(-) ions in sodium perchlorate and sodium chloride solutions, respectively. In the case of ClO(4)(-) ion, experimental observations are compared with molecular dynamics simulations utilizing both first principles based interaction potentials as well as polarizable classical force fields. Both the experimental and the theoretical results show enhancement of ClO(4)(-) ion at the interface, compared with the absence of such enhancement in the case of the Cl(-) ion. Our observations are in agreement with the expected trend in the interfacial propensity of anions based on the Hofmeister series.

Elongation by RNA polymerase II (RNAPII) is a finely regulated process in which many elongation factors contribute to gene regulation. Among these factors are the polymerase-associated factor (PAF) complex, which associates with RNAPII, and several cyclin-dependent kinases, including positive transcription elongation factor b (P-TEFb) in humans and BUR kinase (Bur1–Bur2) and C-terminal domain (CTD) kinase 1 (CTDK1) in Saccharomyces cerevisiae . An important target of P-TEFb and CTDK1, but not BUR kinase, is the CTD of the Rpb1 subunit of RNAPII. Although the essential BUR kinase phosphorylates Rad6, which is required for histone H2B ubiquitination on K123, Rad6 is not essential, leaving a critical substrate(s) of BUR kinase unidentified. Here we show that BUR kinase is important for the phosphorylation in vivo of Spt5, a subunit of the essential yeast RNAPII elongation factor Spt4/Spt5, whose human orthologue is DRB sensitivity-inducing factor. BUR kinase can also phosphorylate the C-terminal region (CTR) of Spt5 in vitro. Like BUR kinase, the Spt5 CTR is important for promoting elongation by RNAPII and recruiting the PAF complex to transcribed regions. Also like BUR kinase and the PAF complex, the Spt5 CTR is important for histone H2B K123 monoubiquitination and histone H3 K4 and K36 trimethylation during transcription elongation. Our results suggest that the Spt5 CTR, which contains 15 repeats of a hexapeptide whose consensus sequence is S[T/A]WGG[A/Q], is a substrate of BUR kinase and a platform for the association of proteins that promote both transcription elongation and histone modification in transcribed regions.

The surface potential of the vapor-liquid interface of pure water is relevant to electrochemistry, solvation thermodynamics of ions, and interfacial reactivity. The chemistry of an ion near the vapor-liquid interface is influenced by the surface potential. Indirect determinations of the surface potential have been experimentally attempted many times, yet there has been little agreement as to its magnitude and sign (-1.1 to +0.5 V). We present the first computation of the surface potential of water using ab initio molecular dynamics and find a surface potential of -18 mV with a maximum interfacial electric field of +8.9 x 10(7) V/m, which are consistent with structural data from experiment. A comparison is made between our results and those from experiments and previous molecular simulations. The associated electric field can alter interfacial reactivity and transport, while the surface potential can be used to determine the "chemical" contribution to the real and electrochemical potentials for ion transport through the vapor-liquid interface.

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of methanol utilizing both ab initio (based on density functional theory) and empirical (fixed charge) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times are characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for the interface of neat methanol. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the density functional theory interaction potential predicts a significant decrease in the molecular dipole moment and slight expansion in the oxygen-oxygen distance as the interface is approached. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE. For submission to Journal of Physical Chemistry B

We have studied the OHCl(-) complex in a six-water cluster and in bulk liquid water by means of Born−Oppenheimer molecular dynamics based on generalized gradient-corrected BLYP density functional theory. Self-interaction-corrected results, which predict a hydrogen-bonded OH···Cl(-) complex, are compared to the uncorrected results, which predict a hemibonded (HO-Cl)(-). A second-order Møller−Plesset potential energy landscape of the gas-phase complex in its ground-state was computed to determine which of the two configurations represents the true nature of the complex. Because no evidence of a local minimum was found in the vicinity of the geometry corresponding to (HO-Cl)(-), we conclude that the self-interaction-corrected results are more accurate and, therefore, that the complex is held together by a hydrogen-bond-like interaction in both an asymmetric solvation environment, as represented by the cluster, and a symmetric solvation environment, as represented by the bulk system. We postulate that the mechanism that governs the atmospheric oxidation of Cl(-)(aq) to Cl(2)(g) on the surface of marine aerosols is initiated by the formation of a H-bonded OH···Cl(-) complex. Furthermore, because no evidence of charge transfer from Cl(-) to OH was found, in either the liquid or the cluster environment, we propose that the second step of the oxidation of Cl(-) is the reaction of the complex with a second Cl(-), resulting in the formation of the species Cl(2)(-) and OH(-). Cl(2)(g) could then be formed via an electron-transfer reaction with an impinging OH molecule.

Despite decades of study, the mechanism by which orotidine-5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine monophosphate remains unresolved. A computational investigation of the direct decarboxylation mechanism has been performed using mixed quantum mechanical/molecular mechanical (QM/MM) dynamics simulations. The study was performed with the program CP2K that integrates classical dynamics and ab initio dynamics based on the Born-Oppenheimer approach. Two different QM regions were explored. The free energy barriers for direct decarboxylation of orotidine-5'-monophosphate (OMP) in solution and in the enzyme (using the larger QM region) were determined with the metadynamics method to be 40 and 33 kcal/mol, respectively. The calculated change in activation free energy (DeltaDeltaG++) on going from solution to the enzyme is therefore -7 kcal/mol, far less than the experimental change of -23 kcal/ mol (for k(cat.)/k(uncat.): Radzicka, A.; Wolfenden, R., Science 1995, 267, 90-92). These results do not support the direct decarboxylation mechanism that has been proposed for the enzyme. However, in the context of QM/MM calculations, it was found that the size of the QM region has a dramatic effect on the calculated reaction barrier.

The molecular dipole moments and local environments of water in its liquid phase were examined for a series of first-principles Gibbs ensemble Monte Carlo simulations along the vapour–liquid coexistence curve using the Becke–Lee–Yang–Parr (BLYP) and Perdew–Burke–Ernzerhof (PBE) exchange/correlation density functionals. Molecular dipole moments were computed using maximally localized Wannier functions with the Berry phase scheme, while the structure was analysed with respect to tetrahedral order parameter and hydrogen bonding. Increasing the temperature results in a decrease of both the average molecular dipole moment and the local structure, although the width of the dipole distribution remains fairly constant. A correlation is found between the extent of the local structure and the magnitude of the molecular dipole moment, but this correlation is limited to the first solvation shell.

Gibbs ensemble Monte Carlo simulations were run with an efficient mixed-basis electronic structure method to explore the phase equilibria of water from first principles using Kohn–Sham density functional theory. The Perdew–Burke–Ernzerhof exchange/correlation density functional gives a higher critical temperature (700 K) and boiling point (480 K) than experiment, although good agreement is found for the saturated liquid densities. A systematic increase in the size of the basis set for the Becke–Lee–Yang–Parr exchange/correlation density functional from a double-ζ to quadruple-ζ split valence leads to further deviations from experiment on the saturated liquid and vapor densities, while the intermediate basis set gives the best results for the heat of vaporization at T = 423 K. Analysis of the liquid structure for all simulations shows changes that can partially be explained by the different densities at a given temperature, and both density functionals show a similar temperature dependence of the liquid st...

Using first principles molecular dynamics simulations in the isobaric–isothermal ensemble (T = 300 K, p = 1 atm) with the Becke–Lee–Yang–Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.

Using first principles molecular dynamics simulation, we have studied a fluoride anion embedded in a periodically replicated water slab composed of 215 water molecules to mimic both bulk and interfacial solvation. In contrast to some recent experiments, our findings suggest that there are only small structural changes for fluoride and its first solvation shell in the bulk. Moreover, the presence of fluoride does not significantly alter the rotational dynamics of nearby water. In addition, we have computed the molecular dipole moments using Wannier centers. At the interface, the presence of fluoride increases the molecular dipole moments of nearby water molecules, whereas in the bulk, the dipole moments for water appear to be essentially invariant to the presence of fluoride in the vicinity. Previous studies of the air-water interface have showed interfacial water to have higher average HOMO energies and, thus, likely to be more prone to electrophilic attack. With the addition of fluoride, the most likely reactive site for electrophilic reactions shifts to the anion. This finding could explain the known large increase in reaction rates for heterogeneous process of interest in atmospheric science. The reactive properties of other anions near the air-water interface are of general interest in heterogeneous chemistry and can be elucidated using a similar type of analysis, as performed here for the fluoride anion.

Gibbs ensemble Monte Carlo simulations were carried out to investigate the properties of a frozen-electron-density (or Kim–Gordon, KG) model of water along the vapor–liquid coexistence curve. Because of its theoretical basis, such a KG model provides for seamless coupling to Kohn–Sham density functional theory in mixed quantum mechanics/molecular mechanics implementations. The Gibbs ensemble simulations indicate limited transferability of a KG model to other state points. Specifically, a KG model that was parameterized by Barker and Sprik to the properties of liquid water at 300 K, yields saturated vapor pressures and a critical temperature that are significantly under- and overestimated, respectively.

X-Ray photoemission spectroscopy operating under ambient pressure conditions is used to probe ion distributions throughout the interfacial region of a free-flowing aqueous liquid micro-jet of 6 M potassium fluoride. Varying the energy of the ejected photoelectrons by carrying out experiments as a function of X-ray wavelength measures the composition of the aqueous-vapor interfacial region at various depths. The F(-) to K(+) atomic ratio is equal to unity throughout the interfacial region to a depth of 2 nm. The experimental ion profiles are compared with the results of a classical molecular dynamics simulation of a 6 M aqueous KF solution employing polarizable potentials. The experimental results are in qualitative agreement with the simulations when integrated over an exponentially decaying probe depth characteristic of an APPES experiment. First principles molecular dynamics simulations have been used to calculate the potential of mean force for moving a fluoride anion across the air-water interface. The results show that the fluoride anion is repelled from the interface, consistent with the depletion of F(-) at the interface revealed by the APPES experiment and polarizable force field-based molecular dynamics simulation. Together, the APPES and MD simulation data provide a detailed description of the aqueous-vapor interface of alkali fluoride systems. This work offers the first direct observation of the ion distribution at an aqueous potassium fluoride solution interface. The current experimental results are compared to those previously obtained for saturated solutions of KBr and KI to underscore the strong difference in surface propensity between soft/large and hard/small halide ions in aqueous solution.

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

This research focuses on Taiwan's semiconductor equipment manufacturers, whose place in Taiwan's semiconductor value chain is dominated by foreign equipment suppliers. Master of Business Administration (Banking & Finance)

With the aim to understand the relatively high solubility of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an important energetic material with a high degree of inter- and intra-molecular hydrogen bonding, in fluoride anion containing ionic liquids (ILs), first principles molecular dynamics simulations in the isobaric-isothermal ensemble were carried out for a system using hydrous tetramethylammonium fluoride as the prototypical solvent. Simulations initiated from both molecular TATB and its Meisenheimer complex (i.e., a σ-complex of the fluoride and the electrophilic ring of TATB) yield a Zundel-type complex where a proton is shared between an amino group and an F(-) ion, whereas the Meisenheimer complex is found to be only transiently stable. An analysis of the electronic structure probing the Wannier function centers supports the finding of a proton-sharing complex with a three-center four-electron like bond. The Zundel-type complex also yields an electronic absorption spectrum consistent with the experimentally observed color change. This study provides evidence that the remarkable solubility of otherwise hard-to-dissolve molecular crystals in ILs can be aided by chemical modification of the solute.

We report herein first principles simulations of water under shock loading and the chemical reactivity under these hot, compressed conditions. Using a recently developed simulation technique for shock compression, we observe that water achieves chemical equilibrium in less than 2 ps for all shock conditions studied. We make comparison to the experimental results for the Hugoniot pressure and density final states. Our simulations show that decomposition occurs through the reversible reaction H(2)O--H(+) + OH(-), in agreement with experiment. Near the approximate intersection of the Hugoniot and the Neptune isentrope, we observe high concentrations of charged species that contribute electronic states near the band gap.