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At least 649 records · Page 36

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time-resolved imaging of bound and dissociating nuclear wave packets in strong-field ionized iodomethane

Here, we report the results of a time-resolved coincident ion momentum imaging experiment probing nuclear wave packet dynamics in the strong-field ionization and dissociation of iodomethane (CH 3 I), a prototypical polyatomic system for photochemistry and ultrafast laser science. By measuring yields, kinetic energies, and angular distributions of CH 3 + + I + and CH 3 + + I ++ ion pairs as a function of the delay between two 25 fs, 790 nm pump and probe pulses, we map both, bound and dissociating nuclear wave packets in intermediate cationic states, thereby tracking different ionization and dissociation pathways. In both channels, we find oscillatory features with a 130 fs periodicity resulting from vibrational motion (C–I symmetric stretch mode) in the first electronically excited state of CH 3 I + . This vibrational wave packet dephases within 1 ps, in good agreement with a simple wave packet propagation model. Our results indicate that the first excited cationic state plays a key role in the dissociative ionization of CH 3 I and that it represents an important intermediate in the sequential double and multiple ionization at moderate intensities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comment on “A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states” [J. Chem. Phys. 142 , 124312 (2015)]

In a recent article, Nguyen et al. report the discovery of a new decomposition pathway for small Criegee intermediates. Prior to this publication, the lowest known pathway for decomposition of Criegee intermediates involved ring closure to form a dioxirane followed by ring opening to make a methylenebisoxy biradical, which can then isomerize or decompose via a variety of pathways. The new pathway reported by Nguyen et al. involves the partial cleavage of the OO bond of the Criegee intermediate forming nascent H 2 CO and O( 1 D) fragments. The O( 1 D) fragment then orbits around the H 2 CO fragment in a manner reminiscent of roaming radical reactions and eventually inserts into one of the CH bonds of the H 2 CO fragment leading directly to formic acid. The authors report saddle point geometries for this pathway determined at a number of different levels of theory in which the distance between the oxygen atom and the formaldehyde varies from 2.0 Å to 3.5 Å depending on the level of theory. Density functional theory (DFT) calculations are found to give more compact, planar saddle point structures while coupled cluster, CCSD(T), and complete active space self consistent field, CASSCF, optimizations lead to looser saddle point structures in which the O atom orbits above the plane of the H 2 CO fragment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reactivity descriptors in acid catalysis: acid strength, proton affinity and host–guest interactions

Brønsted acids mediate chemical transformations via proton transfer to bound species and interactions between the conjugate anion and bound cationic intermediates and transition states that are also stabilized by van der Waals forces within voids of molecular dimensions in inorganic hosts. This Feature Article describes the relevant descriptors of reactivity in terms of the properties of acids and molecules that determine their ability to donate and accept protons and to reorganize their respective charges to optimize their interactions at bound states. The deprotonation energy (DPE) of the acids and the protonation energy (Eprot) of the gaseous analogs of bound intermediates and transition states reflect their respective properties as species present at non-interacting distances. These properties accurately describe the reactivity of acids of a given type, such as polyoxometalates (POM) with a given type of addenda atom but different central atoms and heterosilicates, for different families of reactions. They do not fully capture, however, differences among acid types (e.g., Mo and W POM, heterosilicates, mineral acids) for diverse types of chemical transformations (e.g., elimination, isomerization, dimerization, condensation). The incompleteness of such descriptors reflects their inability to describe how protonated molecular species and conjugate anions restructure their respective charges when present as a binding pair at interacting distances. Such interaction energies represent electrostatic forces that depend on charge distributions in the cations and anions and the ability to reorganize the distributions to maximize the interactions. In the case of deprotonation, the electrostatic and charge reorganization components of DPE for various acids solely reflect the ability of the conjugate anion to accept and distribute the negative charge, a characteristic unique of each type of solid acid and specifically of the composition of its extended conjugate anion framework. The energy required to accept and rearrange the positive charge in bound intermediates and transition states reflects, in turn, their respective ability to recover the ionic and covalent components of DPE, the energy required to detach proton from conjugate anions. The DPE components and the recovery fractions together lead to a modified DPE, which captures only the part of DPE that remains unrecovered by the ion-pair interactions at bound intermediates and transition states, as the unifying descriptor for broad families of acids and reactions. The electrostatic and charge reorganization energies involved in these general descriptors are placed in historical context by assessing their connections to the heuristics of hard–soft acid–base displacements. Further development of these concepts requires benchmarking and extension of electrostatic and reorganization components of energies for a more diverse set of reaction types and acid families and advancement of methods for more efficient calculations of electrostatic interactions. Reactivity descriptors must also account for dispersive interactions between host cavities and guest molecules, requiring a framework analogous to the one described here for ion-pair interactions; these dispersive interactions depend on the fit between their shapes and sizes as well as their ‘‘structural stiffness’’ that determines the ability to modify the shapes of molecules and voids to minimize free energy. Entropy considerations and estimates of their dependence on properties of catalysts and molecules are also required for accurately determining Gibbs free energies that ultimately determine reaction rates.

Deshlahra, Prashant↗

Entangled Biphoton Virtual-State Spectroscopy of the A(exp 2)Sigma(sup +)-X(exp 2)Pi System of OH

This Letter describes the first application of entanglement-induced virtual-state spectroscopy to a molecular system. Non-classical, non-monotonic behavior in a two-photon absorption cross section of the OH A-X system, induced by an entangled biphoton state is theoretically demonstrated. A Fourier transform analysis of the biphoton cross section permits access to the energy eigenvalues of intermediate rovibronic states with a fixed excitation photon energy. The dependence of the Fourier spectrum on the tuning range of the entanglement time (T(sub e)) and the relative path delay (tau(sub e)) is discussed. Our analysis reveals that the implementation of molecular virtual-state spectroscopy for the OH A-X system requires the tuning of tau(sub e) over a pico-second range with femto-second resolution.

Kojima, Jun↗

Entangled Biphoton Virtual-State Spectroscopy of the A(exp 2)Sigma(+) - X(exp 2)Pi System of OH

This Letter describes the first application of entanglement-induced virtual-state spectroscopy to a molecular system. Non-classical, non-monotonic behavior in a two-photon absorption cross section of the OH A-X system, induced by an entangled biphoton state is theoretically demonstrated. A Fourier transform analysis of the biphoton cross section permits access to the energy eigenvalues of intermediate rovibronic states with a fixed excitation photon energy. The dependence of the Fourier spectrum on the tuning range of the entanglement time T(sub e), and the relative path delay tau(sub e) is discussed. Our analysis reveals that the implementation of molecular virtual-state spectroscopy for the OH A-X system requires the tuning of tau(sub e) over a pico-second range with femto-second resolution.

Kojima, Jun↗

The Binding Process of a Nonspecific Enzyme with DNA

Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Fourier-transform spectroscopy and deperturbation analysis of the spin-orbit coupled A{sup 1}Σ{sup +} and b{sup 3}Π states of KRb

Fourier-transform A{sup 1}Σ{sup +} − b{sup 3}Π → X{sup 1}Σ{sup +} laser-induced fluorescence spectra were recorded for the natural mixture of {sup 39,41}K{sup 85,87}Rb isotopologues produced in a heatpipe oven. Overall 4200 rovibronic term values of the spin-orbit coupled A{sup 1}Σ{sup +} and b{sup 3}Π states were determined with an uncertainty of about 0.01 cm{sup −1} in the energy range [10 850, 14 200] cm{sup −1} covering rotational quantum numbers J′ ∈ [3, 280]. Direct deperturbation analysis of the A ∼ b complex performed within the framework of the A{sup 1}Σ{sup +} ∼ b{sup 3}Π{sub Ω=0,1,2} coupled-channel approach reproduced experimental data with a standard deviation of 0.004 cm{sup −1}. Initial parameters of the internuclear potentials and spin-orbit coupling functions along with the relevant transition dipole moments were obtained by performing the quasi-relativistic electronic structure calculations. The mass-invariant molecular parameters obtained from the fit were used to predict energy and radiative properties of the A ∼ b complex for low J levels of {sup 39}K{sup 85}Rb as well as for {sup 41}K{sup 87}Rb isotopologues, allowing us to identify the most reasonable candidates for the stimulated Raman transitions between the initial uppermost vibrational levels of the a{sup 3}Σ{sup +} and X{sup 1}Σ{sup +} states, the intermediate levels of the A ∼ b complex, and the lowest absolute ground X{sup 1}Σ{sup +}(v = 0, J = 0) state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How Hydrologic Connectivity Regulates Water Quality in River Corridors

Abstract Downstream flow in rivers is repeatedly delayed by hydrologic exchange with off‐channel storage zones where biogeochemical processing occurs. We present a dimensionless metric that quantifies river connectivity as the balance between downstream flow and the exchange of water with the bed, banks, and floodplains. The degree of connectivity directly influences downstream water quality — too little connectivity limits the amount of river water exchanged and leads to biogeochemically inactive water storage, while too much connectivity limits the contact time with sediments for reactions to proceed. Using a metric of reaction significance based on river connectivity, we provide evidence that intermediate levels of connectivity, rather than the highest or lowest levels, are the most efficient in removing nitrogen from Northeastern United States’ rivers. Intermediate connectivity balances the frequency, residence time, and contact volume with reactive sediments, which can maximize the reactive processing of dissolved contaminants and the protection of downstream water quality. Our simulations suggest denitrification dominantly occurs in riverbed hyporheic zones of streams and small rivers, whereas vertical turbulent mixing in contact with sediments dominates in mid‐size to large rivers. The metrics of connectivity and reaction significance presented here can facilitate scientifically based prioritizations of river management strategies to protect the values and functions of river corridors.

Harvey, Jud↗

Spin-Vibronic Effect in Photoinduced Electron Transfer

The spin-vibronic effect (SVE) accelerates quantum-mechanically forbidden electronic transitions, but experimental manifestations of this phenomenon remain limited. In this contribution, the role of SVE in photoinduced electron transfer (PET) dynamics is probed by coherent vibrational wavepacket (CVWP) motions in Pt­(II) dimer-naphthalene diimide donor–acceptor complexes. Metal–metal-to-ligand charge-transfer (MMLCT) excitation of the donor triggers ballistic PET, driving the molecule away from equilibrium. The SVE then directs the PET trajectory from the 1 MMLCT excited state to an intermediate ligand-centered triplet state, modulating the CVWP dynamics along the reaction coordinates. Herzberg–Teller type oscillations indicate that the Pt–Pt stretching vibration, arising from the formation of the excited triplet intermediate, serves as the reaction coordinate for charge separation. Finally, our experimental findings advance the understanding of the interplay between electronic, vibrational, and spin degrees of freedom in ultrafast photoactivated processes.

Kim, Pyosang [Argonne National Laboratory (ANL), A↗

Prediction of magnetic moment collapse in ZrFe{sub 2} under hydrostatic pressure

Electronic structure and magnetic properties of ZrFe{sub 2} in the cubic Laves phase are investigated by calculations based on density functional theory. The magnetic moment decreases with the increase of the hydrostatic pressure in an unusual way: Two-step magnetic collapse is predicted. The first one is a continuous change from 1.53 μ{sub B}/Fe to 0.63 μ{sub B}/Fe at about 3.6 GPa, and the other is from 0.25 μ{sub B}/Fe to the nonmagnetic state at about 15 GPa in a first order manner under the local spin density approximation of the exchange correlation potential. A metastable state with intermediate spin moment about 0.15 μ{sub B}/Fe may exist before that. We understand this process by the changes of density of states during it. The magnetic moment decreases under the pressure in the vicinity of the experimental lattice constant with dlnm/dp=−0.038 GPa{sup −1}. The spontaneous volume magnetostriction is 3.6%, which is huge enough to find potential applications in magnetostriction actuators and sensors. We suggest that the Invar effect of this compound may be understood when considering the magnetic moment variation according to the magnetostrictive model of Invar.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On the Nature of the Variability Power Decay towards Soft Spectral States in X-Ray Binaries. Case Study in Cyg X-1

A characteristic feature of the Fourier Power Density Spectrum (PDS) observed from black hole X-ray binaries in low/hard and intermediate spectral states is a broad band-limited noise, characterized by a constant below some frequency (a "break" frequency) and a power law above this frequency. It has been shown that the variability of this type can be produced by the inward diffusion of the local driving perturbations in a bounded configuration (accretion disk or corona). In the framework of this model, the perturbation diffusion time to is related to the phenomenological break frequency, while the PDS power-law slope above the "break" is determined by the viscosity distribution over the configuration. The perturbation diffusion scenario explains the decay of the power of X-ray variability observed in a number of compact sources (containing black hole and neutron star) during an evolution of theses sources from low/hard to high/soft states. We compare the model predictions with the subset of data from Cyg X-1 collected by the Rossi X-ray Time Explorer (RXTE). Our extensive analysis of the Cyg X-1 PDSs demonstrates that the observed integrated power P(sub x), decreases approximately as a square root of the characteristic frequency of the driving oscillations v(sub dr). The RXTE observations of Cyg X-1 allow us to infer P(sub dr), and t(sub o) as a function of v(sub dr). We also apply the basic parameters of observed PDSs, power-law index and low frequency quasiperiodic oscillations. to infer Reynolds (Re) number from the observations using the method developed in our previous paper. Our analysis shows that Re-number increases from values about 10 in low/hard state to that about 70 during the high/soft state. Subject headings: accretion, accretion disks-black hole physics-stars:individual (Cyg X-1) :radiation mechanisms: nonthermal-physical data and processes

Titarchuk, Lev↗

Evidence for a universal Fermi-liquid scattering rate throughout the phase diagram of the copper-oxide superconductors

Abstract The phase diagram of the cuprate superconductors continues to pose formidable scientific challenges. While these materials are typically viewed as doped Mott insulators, it is well known that they are Fermi liquids at high hole-dopant concentrations. It was recently demonstrated that at moderate doping, in the pseudogap (PG) region of the phase diagram, the charge carriers are also best described as a Fermi liquid. Nevertheless, the relationship between the two Fermi-liquid (FL) regions and the nature of the strange-metal (SM) state at intermediate doping have remained unsolved. Here we show for the case of the model cuprate superconductor HgBa 2 CuO 4+ δ that the normal-state transport scattering rate determined from the cotangent of the Hall angle remains quadratic in temperature across the PG temperature, upon entering the SM state, and that it is doping-independent below optimal doping. Analysis of prior transport results for other cuprates reveals that this behavior is universal throughout the entire phase diagram and points to a pervasive FL transport scattering rate. These observations can be reconciled with a variety of other experimental results for the cuprates upon considering the possibility that the PG phenomenon is associated with the gradual, non-uniform localization of one hole per planar CuO 2 unit.

Barišić, N.↗

Thermoelectric power as a probe of density of states in correlated actinide materials: The case of PuCoGa 5 superconductor

We present measurements of the thermoelectric power of the plutonium-based unconventional superconductor PuCoGa 5 . The data is interpreted within a phenomenological model for the quasiparticle density of states of intermediate valence systems and the results are compared with results obtained from photoemission spectroscopy. The results are consistent with intermediate valence nature of 5f-electrons, furthermore, we propose that measurements of the Seebeck coefficient can be used as a probe of density of states in this material, thereby providing a link between transport measurements and photoemission in strongly correlated materials. Here, we discuss these results and their implications for the electronic structure determination of other strongly correlated systems, especially nuclear materials.

36 MATERIALS SCIENCE↗

Correlation between antiferromagnetic and Mott states in spin orbit coupled Sr 2 Ir O 4 : A study of Sr 2 Ir 1 – x M x O 4 ( M = Fe or Co)

Sr 2 IrO 4 is an archetypal spin-orbit-coupled Mott insulator with an antiferromagnetic state below 240 K. Here we report results of our study on single crystals of Sr 2 Ir 1–x Fe x O 4 (0 ≤ x < 0.32) and Sr 2 Ir 1–x Co x O 4 (0 ≤ x < 0.22). Fe doping retains the antiferromagnetic state but simultaneously precipitates an emergent metallic state whereas Co doping causes a rapid collapse of both the antiferromagnetic and Mott states, giving rise to a confined metallic state featuring a pronounced linearity of the basal-plane resistivity up to 700 K. The results indicate tetravalent Fe 4+ (3d 4 ) ions in the intermediate spin state with S = 1 and Co 4+ (3d 5 ) ions in the high spin state with S = 5/2 substituting for Ir 4+ (5d 5 ) ions in Sr 2 IrO 4 , respectively. The effective magnetic moment closely tracks the Néel temperature as doping increases, suggesting that the spin state of the dopant predominately determines the magnetic properties in doped Sr 2 IrO 4 . Furthermore, all relevant properties including charge-carrier density (e.g., 10 28 /m 3 ), Sommerfeld coefficient (e.g., 19 mJ / mole K 2 ), and Wilson ratio (e.g., 2.6) consistently demonstrate an emergent metallic state that is both robust and highly correlated in the two systems, arising from the percolation of bound states and the weakening of structural distortions. Furthermore, this study strongly indicates that the antiferromagnetic and Mott states are correlated in an unconventional manner in Sr 2 IrO 4 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Solid-State Recrystallization Pathways of Sodium Aluminate Hydroxy Hydrates

Crystallization of Al-bearing solid phases from highly alkaline Na 2 O:Al 2 O 3 :H 2 O solutions commonly necessitates an Al 3+ coordination change from tetrahedral to octahedral, but intermediate coordination states are often difficult to isolate. Here, a similar Al 3+ coordination change process is examined during the solid-state recrystallization of sodium oxohydroxoaluminate hydrate (MSA) to nonasodium bis(hexahydroxy aluminate) trihydroxide hexahydrate (NSA) at ambient temperature. While the MSA structure contains solely polymerized tetrahedral Al 3+ , the NSA structure is a molecular aluminate salt solely based upon monomeric octahedral Al 3+ . Spontaneous recrystallization of MSA and excess sodium hydroxide hydrate into NSA over 3 days of reaction time was clearly evident in X-ray diffractograms and in Raman spectra. In situ 27 Al multiple quantum MAS NMR spectroscopy showed no evidence of intermediate aluminates, suggesting that intermediates, such as pentacoordinate Al 3+ , are short-lived and require more highly time resolved spectroscopies to detect. Such research is advancing upon detailed mechanistic understanding of Al 3+ coordination change mechanisms in these highly alkaline systems, with relevance to aluminum refining, corrosion sciences, and nuclear waste processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-pressure X-ray diffraction and X-ray emission studies on iron-bearing silicate perovskite under high pressures

Iron-bearing silicate perovskite is believed to be the most abundant mineral of the Earth's lower mantle. Recent studies have shown that Fe{sup 2+} exists predominantly in the intermediate-spin state with a total spin number of 1 in silicate perovskite in the lower part of the lower mantle. Here we have measured the spin states of iron and the pressure-volume relation in silicate perovskite [(Mg{sub 0.6},Fe{sub 0.4})SiO{sub 3}] at pressure conditions relevant to the lowermost mantle using in situ X-ray emission and X-ray diffraction in a diamond cell. Our results showed that the intermediate-spin Fe{sup 2+} is stable in the silicate perovskite up to {approx} 125 GPa but starts to transition to the low-spin state at approximately 135 GPa. Concurrent X-ray diffraction measurements showed a decrease of approximately 1% in the unit cell volume in the silicate perovskite [(Mg{sub 0.6},Fe{sub 0.4})SiO{sub 3}], which is attributed to the intermediate-spin to the low-spin transition. The transition pressure coincides with the pressure conditions of the lowermost mantle, raising the possibility of the existence of the silicate perovskite phase with the low-spin Fe{sup 2+} across the transition from the post-perovskite to the perovskite phases in the bottom of the D{double_prime} layer.

36 MATERIALS SCIENCE↗

Influence of a Strong Magnetic Field on Magnetic Order in Polycrystalline Layered Cobaltites EuBaCo{sub 2 –x}O{sub 5.5 – δ}

The magnetic properties of polycrystalline EuBaCo{sub 2 –x}O{sub 5.5 – δ} (x ≤ 0.1, δ ≤ 0.14) are studied in the temperature range 2 K < T < 300 K in magnetic fields H ≤ 90 kOe. A comparison is made of the dependencies of magnetization M on temperature T and magnetic field H for polycrystalline and single crystal EuBaCo{sub 1.90}O{sub 5.36}, in which only Cu(III) ions are present. It is shown that in the magnetically ordered temperature range of magnetic order, the samples are ferrimagnetic, in which antiferromagnetic interactions between the nearest Co{sup 3+} ions with the same spins compete with the ferromagnetic exchange. With a decrease in temperature, a strong magnetic field affects the magnetic order. At T = 2 K in fields H = 50–90 kOe, all samples exhibit the properties of mictomagnetism. There are a shift in the hysteresis loops M(H) and a large difference in the values of the magnetization of the sample cooled in a magnetic field M (FC) and without a field M (ZFC) due to unidirectional magnetic anisotropy. In this case, there is no saturation of magnetization. The field dependences of magnetization taken in the cooling and heating in unequal fields (CHUF) mode indicate a metastable magnetic state. Near T = 20–30 K, an orientational transition characteristic of micromagnets takes place and a complex ferrimagnetic structure is formed. The main reasons for the manifestation of mictomagnetism properties in layered cobaltites are the presence of magnetoactive Co{sup 3+} ions in the states with intermediate and high spins at low temperatures and structural defects that affect the exchange interaction between the nearest neighbors. Nonmagnetic Co{sup 3+} ions in the low-spin state can also act as defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗