Donor-stabilized cations and imine transfer from N-silylphosphoranimines

A series of donor-stabilized N-silylphosphoranimine salts [DMAP.PCl2=NSiMe3]+X- (DMAP = 4-(dimethylamino)pyridine) were prepared by the reaction of Cl3P=NSiMe3 with DMAP in the presence of silver salts AgX (X = OSO2CF3, BF4, and SbF6). Repeating the reaction in the absence of AgX gave the chloride salt [DMAP.PCl2=NSiMe3]Cl which has been shown to be in equilibrium with free DMAP and Cl3P=NSiMe3. Attempts to stabilize a N-silylphosphoranimine cation with phosphine donors led to unexpected imine transfer chemistry. For example, Cl3P=NSiMe3 reacts with phosphines, R3P (R = nBu and Ph), to produce the metathesis products PCl3 and R3P=NSiMe3 which subsequently react together to afford the N-phosphinophosphoranimines R3P=N-PCl2 and ClSiMe3 as a byproduct.     

Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.     

Level decay and orientational kinetics of the rhodamine B monomer and dimer

The population kinetics and the rotational diffusion of the rhodamine B monomer and dimer were measured by using picosecond pulses from a mode-locked Nd : YAG laser to induce and time resolve the concentration-dependent transient absorption saturation of various aqueous solutions of this organic dye.     

Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Bruck nets,codes, and characters of loops

Numerous computational examples suggest that if _{k-1 k} are (k- 1)- and k-nets of order n, then rank _{p k} - rank _{p k-1} n - k + 1 for any prime p dividing n at most once. We conjecture that this inequality always holds. Using characters of loops, we verify the conjecture in case k = 3, proving in fact that if p ^e n, then rank _{p 3} 3n - 2 - e, where equality holds if and only if the loop G coordinatizing ₃ has a normal subloop K such that G/K is an elementary abelian group of order p ^e . Furthermore if n is squarefree, then rank _p = 3n - 3 for every prime p ¦ n, if and only if ₃ is cyclic (i.e., ₃ is coordinated by a cyclic group of order n).The validity of our conjectured lower bound would imply that any projective plane of squarefree order, or of order n 2 mod 4, is in fact desarguesian of prime order.     

Rare numbers

Suppose thatX ₁,X ₂,... is a sequence of iid random variables taking values inZ ⁺. Consider the random sequenceA(X)(X ₁,X ₂,...). LetY _n be the number of integers which appear exactly once in the firstn terms ofA(X). We investigate the limit behavior ofn ^–(1–) Y _n for [0, 1].     

Gap-Free Set Partitions

A set partition is called “gap-free” if its block sizes form an interval. In other words, there is at least one block of each size between the smallest and largest block sizes. Let B(n) and G(n), respectively, denote the number of partitions and the number of gap-free partitions of the set [n]. We prove that      

Reactions of (di)manganese carbonyl ions with 1,4,7-trimethyl-1,4,7-triazacyclononane (Me3TACN) in the gas phase

The gas-phase reactions of a series of (di)manganese carbonyl positive ions with 1,4,7-trimethyl-1,4,7-triazacyclononane (Me(3)TACN) have been examined with the aid of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. The monomanganese carbonyl ions, [Mn(CO)(n)](+) (n = 2-5), react predominantly by ligand exchange and to a minor extent by electron transfer with the formation of the radical cation of Me(3)TACN. For the [Mn(CO)(n)](+) (n = 2-4) ions, the ligand exchange results in the exclusive formation of a [Mn(Me(3)TACN)](+) complex, whereas small amounts of [Mn(CO)(Me(3)TACN)](+) ions are also generated in the reactions of the [Mn(CO)(5)](+) ion. The [Mn(2)(CO)(n)](+) ions (n = 2, 4 and 5) react also by competing electron transfer and ligand exchange. The reaction of the [Mn(2)(CO)(2)](+) and [Mn(2)(CO)(4)](+) ions is associated with cleavage of the Mn--Mn bond as evidenced by the pronounced formation of [Mn(Me(3)TACN)](+) ions. For [Mn(2)(CO)(5)](+), the ligand exchange leads mainly to the formation of [Mn(2)(CO)(n)(Me(3)TACN)](+) (n = 1-3) ions. These primary product ions react subsequently by the incorporation of a second Me(3)TACN molecule to afford [Mn(2)(CO)(Me(3)TACN)(2)](+) and [Mn(2)(CO)(2)(Me(3)TACN)(2)](+) ions. Both of these latter species incorporate an oxygen molecule with formation of ions with the assigned composition of [Mn(2)(O(2))(CO)(Me(3)TACN)(2)](+) and [Mn(2)(O(2))(CO)(2)(Me(3)TACN)(2)](+).     

The role of angular momentum in collision-induced vibration-rotation relaxation in polyatomics

Vibrational relaxation of the 6(1) level of S(1)((1)B(2u)) benzene is analyzed using the angular momentum model of inelastic processes. Momentum-(rotational) angular momentum diagrams illustrate energetic and angular momentum constraints on the disposal of released energy and the effect of collision partner on resultant benzene rotational excitation. A kinematic "equivalent rotor" model is introduced that allows quantitative prediction of rotational distributions from inelastic collisions in polyatomic molecules. The method was tested by predicting K-state distributions in glyoxal-Ne as well as J-state distributions in rotationally inelastic acetylene-He collisions before being used to predict J and K distributions from vibrational relaxation of 6(1) benzene by H(2), D(2), and CH(4). Diagrammatic methods and calculations illustrate changes resulting from simultaneous collision partner excitation, a particularly effective mechanism in p-H(2) where some 70% of the available 6(1)-->0(0) energy may be disposed into 0-->2 rotation. These results support the explanation for branching ratios in 6(1)-->0(0) relaxation given by Waclawik and Lawrance and the absence of this pathway for monatomic partners. Collision-induced vibrational relaxation in molecules represents competition between the magnitude of the energy gap of a potential transition and the ability of the colliding species to generate the angular momentum (rotational and orbital) needed for the transition to proceed. Transition probability falls rapidly as DeltaJ increases and for a given molecule-collision partner pair will provide a limit to the gap that may be bridged. Energy constraints increase as collision partner mass increases, an effect that is amplified when J(i)>0. Large energy gaps are most effectively bridged using light collision partners. For efficient vibrational relaxation in polyatomics an additional requirement is that the molecular motion of the mode must be capable of generating molecular rotation on contact with the collision partner in order to meet the angular momentum requirements. We postulate that this may account for some of the striking propensities that characterize polyatomic energy transfer.     

Evidence for specific solvation of two halocarbene amides

Laser flash photolysis (LFP, 308 nm) of endo-10-halo-10'-N,N-dimethylcarboxamidetricyclo[4.3.1.0]-deca-2,4-diene (1Cl and 1F) releases indan and halocarbene amide (2Cl and 2F). Although the carbenes are not UV-vis active, they react rapidly with pyridine to form ylides (4Cl, 4F), which are readily detected in LFP experiments (lambda(max) = 450 nm). Dioxane decreases the observed rate of carbene reaction with pyridine in CF(2)ClCFCl(2). Small amounts of THF decrease the observed rate of reaction of carbene 2F with pyridine but increase the rate of reaction of carbene 2Cl with pyridine. LFP (266 nm) of dienes 1Cl and 1F in CF(2)ClCFCl(2) with IR detection produces carbenes 2Cl and 2F with carbonyl vibrations at 1635 and 1650 cm(-1), respectively. In dioxane or THF solvent, LFP produces the corresponding ether ylides (5Cl, 5F) by capture of carbenes 2Cl and 2F. The ylides have broad carbonyl vibrations between 1560 and 1610 cm(-1). The addition of a small amount of dioxane in CFCl(2)CF(2)Cl extends the lifetime of the carbene. This observation, together with the ether-induced retardation of the rates of carbene capture by tetramethylethylene and pyridine, is evidence for solvation of the carbene by dioxane.