Unravelling the effect of the E545K mutation on PI3Kα kinase

PI3Kα controls several cellular processes and its aberrant signalling is implicated in tumorigenesis. One of its hotspot mutations, E545K, increases PI3Kα lipid kinase activity, but its mode of action is only partially understood. Here, we perform biased and unbiased molecular dynamics simulations of PI3Kα and uncover, for the first time, the free energy landscape of the E545K PI3Kα mutant. We reveal the mechanism by which E545K leads to PI3Kα activation in atomic-level detail, which is considerably more complex than previously thought.

The mechanism by which the cancer-causing E545K mutation may lead to PI3Kα activation is described in atomic-level detail.     

Electronic states and radiative transitions in LiAr

Ab initio MRD-CI calculations have been carried out on the ground and the eight lowest excited electronic states of LiAr, correlating with excited Li atom states up to 3d ²D. The ground (X²∑⁺ (2s)) and 2 ²Σ⁺ (2p) electronic states are repulsive while the higher excited states show shallow Rydberg minima. Rates of radiative bound-bound and bound-free transitions have been also calculated.     

17O NMR studies of electronic and steric interactions of substituted quinoxaline-2(1H),3(4H)-diones

¹⁷O nmr studies, at natural abundance, of substituted quinoxaline-2(1H),3(4H)-diones demonstrate that the ¹⁷O chemical shift data can provide new insights into steric and electronic interactions due to long range substituent effects on the aromatic ring. The role of considerable “keto” character and torsion angle deformation of the diamide group in solution is emphasized.     

Solvation properties of N-substituted cis and trans amides are not identical: significant enthalpy and entropy changes are revealed by the use of variable temperature 1H NMR in aqueous and chloroform solutions and ab initio calculations

The cis/trans conformational equilibrium of N-methyl formamide (NMF) and the sterically hindered tert-butylformamide (TBF) was investigated by the use of variable temperature gradient 1H NMR in aqueous solution and in the low dielectric constant and solvation ability solvent CDCl3 and various levels of first principles calculations. The trans isomer of NMF in aqueous solution is enthalpically favored relative to the cis (deltaH(o) = -5.79 +/- 0.18 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = -0.23 +/- 0.17 kJ mol(-1)) playing a minor role. The experimental value of the enthalpy difference strongly decreases (deltaH(o) = -1.72 +/- 0.06 kJ mol(-1)), and the contribution of entropy at 298 K (298 x deltaS(o) = -1.87 +/- 0.06 kJ mol(-1)) increases in the case of the sterically hindered tert-butylformamide. The trans isomer of NMF in CDCl3 solution is enthalpically favored relative to the cis (deltaH(o) = -3.71 +/- 0.17 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = 1.02 +/- 0.19 kJ mol(-1)) playing a minor role. In the sterically hindered tert-butylformamide, the trans isomer is enthalpically disfavored (deltaH(o) = 1.60 +/- 0.09 kJ mol(-1)) but is entropically favored (298 x deltaS(o) = 1.71 +/- 0.10 kJ mol(-1)). The results are compared with literature data of model peptides. It is concluded that, in amide bonds at 298 K and in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side chains, the free energy difference of the cis/trans isomers and both the enthalpy and entropy contributions are strongly dependent on the N-alkyl substitution and the solvent. The significant decreasing enthalpic benefit of the trans isomer in CDCl3 compared to that in H2O, in the case of NMF and TBF, is partially offset by an adverse entropy contribution. This is in agreement with the general phenomenon of enthalpy versus entropy compensation. B3LY/6-311++G** and MP2/6-311++G** quantum chemical calculations confirm the stability orders of isomers and the deltaG decrease in going from water to CHCl3 as solvent. However, the absolute calculated values, especially for TBF, deviate significantly from the experimental values. Consideration of the solvent effects via the PCM approach on NMF x H2O and TBF x H2O supermolecules improves the agreement with the experimental results for TBF isomers, but not for NMF.     

Tandem rearrangement involving a β-hydroxysulfoxide and cyclization processes toward the 1-benzenesulfonyl-5-benzenethio-1,2,2a,3,4,5-hexahydrobenz[c,d]indole oxygenated at the 4-position

Treatment of compound 4 with trifluoroacetic anhydride under reflux in chlorobenzene underwent a tandem rearrangement to produce compound 5 . When the acetylated derivative of 4 , was treated with trifluoroacetic anhydride in the presence of Lewis acids produced two cis cyclized conformers 7a and 7b , presumably through the intermediate B .     

Synthese und Kristallstruktur von Cadmium‐Dodekahydro‐closo‐Dodekaborat‐Hexahydrat,Cd(H2O)6[B12H12]

Synthesis and Crystal Structure of Cadmium Dodecahydro closo‐Dodecaborate Hexahydrate, Cd(H₂O)₆[B₁₂H₁₂] Through neutralization of the aqueous free acid (H₃O)₂[B₁₂H₁₂] with cadmium carbonate (CdCO₃) and after isothermic evaporation of the resulting solution, colourless lath‐shaped single crystals of Cd(H₂O)₆[B₁₂H₁₂] are obtained. Cadmium dodecahydro closo‐dodecaborate hexahydrate crystallizes at room temperature in the monoclinic system (space group: C2/m) with the lattice constants a = 1413.42(9), b = 1439.57(9), c = 749.21(5) pm and β = 97.232(4)° (Z = 4). The crystal structure of Cd(H₂O)₆[B₁₂H₁₂] can be regarded as a monoclinic distortion variant of the CsCl‐type structure. Two crystallographically different [Cd(H₂O)₆]²⁺ octahedra (d(Cd–O) = 227–230 pm) are present which only differ in their relative orientation. The intramolecular bond lengths for the quasi‐icosahedral [B₁₂H₁₂]^2? cluster anions range in the intervals usually found for dodecahydro closo‐dodecaborates (d(B–B) = 177–179 pm, d(B–H) = 103–116 pm). The hydrogen atoms of the [B₁₂H₁₂]^2? clusters have no direct coordinative influence on the Cd²⁺ cations. Due to the fact that no “zeolitic” crystal water molecules are present, a stabilization of the lattice takes place mainly via the B–H^δ?···^+δH–O hydrogen bonds.     

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations

We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference.     

Theory of the two step enantiomeric purification of 1,3 dimethylallene

An application of a recently proposed [P. Kral et al., Phys. Rev. Lett. 90, 033001 (2003)] two step optical control scenario to the purification of a racemic mixture of 1,3 dimethylallene is presented. Both steps combine adiabatic and diabatic passage phenomena. In the first step, three laser pulses of mutually perpendicular linear polarizations, applied in a "cyclic adiabatic passage" scheme, are shown to be able to distinguish between the L and D enantiomers due to their difference in matter-radiation phase. In the second step, which immediately follows the first, a sequence of pulses is used to convert one enantiomer to its mirror-imaged form. This scenario, which only negligibly populates the first excited electronic state, proves extremely useful for systems such as dimethylallene, which can suffer losses from dissociation and internal conversion upon electronic excitation. We computationally observe conversion of a racemic mixture of dimethylallene to a sample containing approximately 95% of the enantiomer of choice.     

A multireference coupled-cluster potential energy surface of diazomethane, CH(2)N(2)

The intrinsically multireference dissociation of the C-N bond in ground-state diazomethane (CH(2)N(2)) at different angles has been studied with the multireference Brillouin-Wigner coupled-cluster singles and doubles (MRBWCCSD) method. The morphology of the calculated potential energy surface (PES) in C(s)() symmetry is similar to a multireference perturbational (CASPT3) PES. The MRBWCCSD/cc-pVTZ H(2)C-N(2) dissociation energy with respect to the asymptotic CH(2)(?(1)A(1)) + N(2)(X(1)Sigma(g)(+)) products is D(e) = 35.9 kcal/mol, or a zero-point corrected D(0) = 21.4 kcal/mol with respect to the ground-state CH(2)(X(3)B(1)) + N(2)(X(1)Sigma(g)(+)) fragments.     

The preparation of 1-benzoyl-6,7-dimethoxy-5-keto-1,2,2a,3,4,5-hexahydrobenz[cd]indole

The synthesis of 1 - benzoyl - 6,7 - dimethoxy - 5 - keto - 1,2,2a,3,4,5 - hexahydrobenz[cd]indole (10) is described. Reduction of the pyrrole ring of 3 - (5',6' - dimethoxy - 3' - indolyl)propanoic acid (6) with borane pyridine complex and a proton source, followed by N-benzoylation furnished the corresponding indoline derivative 3 - (1' -benzoyl - 5', 6' - dimethoxy - 3' - indolinyl)propanoic acid (7). This acid was cyclized with PPA to the target tricyclic ketone (10).