Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free-energy results in an efficient way. The formalism of the OS method is based on ensuring sampling of important overlapping phase space during perturbation calculations. This technique samples both forward and reverse free energy perturbation (FEP) to improve the free-energy calculation. It considers the asymmetry of the FEP calculation and features an ability to optimize both the precision and the accuracy of the measurement without affecting the simulation process itself. The OS method is tested at two optimization levels: no optimization (simple OS), and full optimization (equivalent to Bennett's method), and compared to conventional FEP techniques, including the widely used direct FEP averaging method, on three alchemical mutation systems: (a) an anion transformation in water solution, (b) mutation between methanol and ethane, and (c) alchemical change of an adenosine molecule. It is consistently shown that the reliability of free-energy estimates can be greatly improved using the OS techniques at both optimization levels, while the performance of Bennett's method is particularly striking. In addition, the efficiency of a calculation can be significantly improved because the method is able to (a) converge to the right answer quickly, and (b) work for large perturbations. The basic two-stage OS method can be extended to admit additional stages, if needed. We suggest that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations.     

Ketone enolization by lithium hexamethyldisilazide: structural and rate studies of the accelerating effects of trialkylamines

Mechanistic studies of the enolization of 2-methylcyclohexanone mediated by lithium hexamethyldisilazide (LiHMDS; TMS2NLi) in toluene and toluene/amine mixtures are described. NMR spectroscopic studies of LiHMDS/ketone mixtures in toluene reveal the ketone-complexed cyclic dimer (TMS2NLi)2(ketone). Rate studies using in situ IR spectroscopy show the enolization proceeds via a dimer-based transition structure, [(TMS2NLi)2(ketone)]++. NMR spectroscopic studies of LiHMDS/ketone mixtures in the presence of relatively unhindered trialkylamines such as Me2NEt reveal the quantitative formation of cyclic dimers of general structure (TMS2NLi)2(R3N)(ketone). Rate studies trace a >200-fold rate acceleration to a dimer-based transition structure, [(TMS2NLi)2(R3N)(ketone)]++. Amines of intermediate steric demand, such as Et3N, are characterized by recalcitrant solvation, saturation kinetics, and exceptional (>3000-fold) accelerations traced to the aforementioned dimer-based pathway. Amines of high steric demand, such as i-Pr2NEt, do not observably solvate (TMS2NLi)2(ketone) but mediate enolization via [(TMS2NLi)2(R3N)(ketone)]++ with muted accelerations. The most highly hindered amines, such as i-Bu3N, do not influence the LiHMDS structure or the enolization rate. Overall, surprisingly complex dependencies of the enolization rates on the structures and concentrations of the amines derive from unexpectedly simple steric effects. The consequences of aggregation, mixed aggregation, and substrate-base precomplexation are discussed.     

High-frequency and -field electron paramagnetic resonance of high-spin manganese(III) in tetrapyrrole complexes

High-field and -frequency electron paramagnetic resonance (HFEPR) spectroscopy has been used to study three complexes of high spin Manganese(III), 3d4, S = 2. The complexes studied were tetraphenylporphyrinatomanganese(III) chloride (MnTPPCI), phthalocyanatomanganese(III) chloride (MnPcCl), and (8,12-diethyl-2,3,7,13,17,18-hexamethylcorrolato)manganese(III) (MnCor). We demonstrate the ability to obtain both field-oriented (single-crystal like) spectra and true powder pattern HFEPR spectra of solid samples. The latter are obtained by immobilizing the powder, either in an n-eicosane mull or KBr pellet. We can also obtain frozen solution HFEPR spectra with good signal-to-noise, and yielding the expected true powder pattern. Frozen solution spectra are described for MnTPPCl in 2:3 (v/v) toluene/CH2Cl2 solution and for MnCor in neat pyridine (py) solution. All of the HFEPR spectra have been fully analyzed using spectral simulation software and a complete set of spin Hamiltonian parameters has been determined for each complex in each medium. Both porphyrinic complexes (MnTPPCl and MnPcCl) are rigorously axial systems, with similar axial zero-field splitting (zfs): D approximately -2.3 cm(-1), and g values quite close to 2.00. In contrast, the corrole complex, MnCor, exhibits slightly larger magnitude, rhombic zfs: D approximtely -2.6 cm(-1), absolute value(E) approximately 0.015 cm(-1), also with g values quite close to 2.00. These results are discussed in terms of the molecular structures of these complexes and their electronic structure. We propose that there is a significant mixing of the triplet (S = 1) excited state with the quintet (S= 2) ground state in Mn(III) complexes with porphyrinic ligands, which is even more pronounced for corroles.     

Preparation of benzyne complexes of group 10 metals by intramolecular suzuki coupling of ortho-metalated phenylboronic esters: molecular structure of the first benzyne-palladium(0) complex

A series of nickel(II) and palladium(II) aryl complexes substituted in the ortho position of the aromatic ring by a (pinacolato)boronic ester group, [MBr[o-C(6)H(4)B(pin)]L(2)] (M = Ni, L(2) = 2PPh(3) (2a), 2PCy(3) (2b), 2PEt(3) (2c), dcpe (2d), dppe (2e), and dppb (2f); M = Pd, L(2) = 2PPh(3) (3a), 2PCy(3) (3b), and dcpe (3d)), has been prepared. Many of these complexes react readily with KO(t)Bu to form the corresponding benzyne complexes [M(eta(2)-C(6)H(4))L(2)] (M = Ni, L(2) = 2PPh(3) (4a), 2PCy(3) (4b), 2PEt(3) (4c), dcpe (4d); M = Pd, L(2) = 2PCy(3) (5b)). This reaction can be regarded as an intramolecular version of a Suzuki cross-coupling reaction, the driving force for which may be the steric interaction between the boronic ester group and the phosphine ligands present in the precursors 2 and 3. Complex 3d also reacts with KO(t)Bu, but in this case disproportionation of the initially formed eta(2)-C(6)H(4) complex (5d) leads to a 1:1 mixture of a novel dinuclear palladium(I) complex, [(dcpe)Pd(mu(2)-C(6)H(4))Pd(dcpe)] (6), and a 2,2'-biphenyldiyl complex, [Pd(2,2'-C(6)H(4)C(6)H(4))(dcpe)] (7d). Complexes 2a, 3b, 3d, 4b, 5b, 6, and 7d have been structurally characterized by X-ray diffraction; complex 5b is the first example of an isolated benzyne-palladium(0) species.     

Highly stereoselective addition of stannylcuprates to alkynones

The addition of stannylcuprate reagents such as (Bu3Sn)(PhS)CuLi to alkynones has been found to proceed in high yield and with excellent stereoselectivity for the Z isomer of the product (>95%). The behavior of the stannylcuprates is thus very different from that of their "carbocuprate" counterparts such as Me2CuLi or Me2Cu(CN)Li2 which are nonstereoselective. Furthermore, in contrast to the reactions of (R3Sn)(PhS)CuLi with the corresponding alkynoates, the presence of a proton source in the reaction medium has no effect on the stereoselectivity of the reaction of alkynones.     

Reduction of octacyanomolybdate(V) by thioglycolic acid in aqueous media

In aqueous media at 25 degrees C [Mo(CN)(8)](3-) is reduced by thioglycolic acid (HSCH(2)COOH, TGA), and the reaction is strongly accelerated by the presence of trace amounts of copper ions. Dipicolinic acid (dipic) is an effective inhibitor of the copper catalysis. Both with and without dipic the reaction has the stoichiometry 2[Mo(CN)(8)](3-) + 2TGA --> 2[Mo(CN)(8)](4-) + RSSR, where RSSR is the disulfide derived from formal oxidative dimerization of TGA. In the presence of dipic, PBN (N-tert-butyl-alpha-phenyl-nitrone), and with a large excess of TGA the rate law for consumption of [Mo(CN)(8)](3-) is first order in both [TGA] and [Mo(CN)(8)(3-)]. The complex pH dependence is consistent with (-)SCH(2)CO(2)(-) being highly reactive (k = 1.8 x 10(4) M(-1) s(-1)), the monoanion being less reactive, and HSCH(2)CO(2)H being unreactive. A mechanism is proposed in which the dianion undergoes electron transfer to [Mo(CN)(8)](3-), thus generating the thiyl radical. Analysis of the electron-transfer rate constant in terms of Marcus theory yields an effective self-exchange rate constant for the thiolate/thiyl redox couple that is in reasonable agreement with the value derived previously from the reaction of TGA with [IrCl(6)](2-). When copper catalysis is inhibited, the two reactions differ substantially in that the yield of (-)O(3)SCH(2)CO(2)(-) is significant for [IrCl(6)](2-) but undetectable for [Mo(CN)(8)](3-).     

Investigation of bovine ubiquitin conformers separated by high-field asymmetric waveform ion mobility spectrometry: Cross section measurements using energy-loss experiments with a triple quadrupole mass spectrometer

High-field asymmetric waveform ion mobility spectrometry (FAIMS) was used to separate gas-phase conformers of bovine ubiquitin produced by electrospray ionization. These conformers were sampled by a triple quadrupole mass spectrometer where energy-loss experiments, following the work of Douglas and co-workers, were used to determine their cross sections. The measured cross sections for some conformers were readily altered by the voltages applied to the interface ion optics, therefore very gentle mass spectrometer interface conditions were required to preserve gas-phase conformers separated by FAIMS. Cross sections for 19 conformers (charge states +5 through +13) were measured. Two conformers for the +12 charge state, which were readily separated in FAIMS, were found to have similar cross sections. Based on a method to calibrate the collision gas thickness, the cross sections measured using the FAIMS/energy-loss method were compared with literature values determined using drift tube ion mobility spectrometry. The comparison illustrated that the conformers of bovine ubiquitin that were identified using drift tube ion mobility spectrometry were also observed using the FAIMS device.     

The synthesis and characterisation of 4,1,2-MC2B10 metallacarboranes

Reduction of the tethered carborane 1,2-(CH2)3-1,2-closo-C2B10H10 followed by treatment with CoCl2/NaCp, [(p-cymene)RuCl2]2(p-cymene=C6H4MeiPr-1,4), (PMe2Ph)2PtCl2 or (dppe)NiCl2(dppe=Ph2PCH2CH2PPh2) affords reasonable yields of the new 13-vertex metallacarboranes 1,2-(CH2)3-4-Cp-4,1,2-closo-CoC2B10H10 (1), 1,2-(CH2)3-4-(p-cymene)-4,1,2-closo-RuC2B10H10 (2), 1,2-(CH2)3-4,4-(PMe2Ph)2-4,1,2-closo-PtC2B10H10 (3) and 1,2-(CH2)3-4,4-(dppe)-4,1,2-closo-NiC2B10H10 (4), respectively. All compounds were characterised spectroscopically and crystallographically. The cobalt and ruthenium species 1 and 2 have Cs symmetry in both solution and the solid state, having henicosahedral cage structures featuring a trapezoidal C1C2B9B5 face. The platinum and nickel compounds 3 and 4 have asymmetric docosahedral cage structures in the crystal (the more so for 4 than for 3) although both appear, by 11B and 31P NMR spectroscopy, to have Cs symmetry in solution. Low-temperature experiments on the more soluble platinacarborane could not freeze out the diamond-trapezium-diamond fluctional process that we assume is operating in solution, and we therefore conclude that this process has a relatively low activation barrier, probably <35 kJ mol-1.     

Thermal isomerization of cis,anti,cis-tricyclo[6.3.0.0(2,7)]undec-3-ene to endo-tricyclo[5.2.2.0(2,6)]undec-8-ene

[reaction: see text] The gas-phase thermal isomerization of cis,anti,cis-tricyclo[6.3.0.0(2,7)]undec-3-ene (1) to endo-tricyclo[5.2.2.0(2,6)]undec-8-ene (2) at 315 degrees C occurs cleanly through a symmetry-forbidden [1,3] suprafacial,retention (sr) pathway.     

An examination of the validity of nonequilibrium molecular-dynamics simulation algorithms for arbitrary steady-state flows

Nonlinear-response theory of nonequilibrium molecular-dynamics simulation algorithms is considered under the imposition of an arbitrary steady-state flow field. It is demonstrated that the SLLOD and DOLLS algorithms cannot be used for general flows, although the SLLOD algorithm is rigorous for planar Couette flow. Following the same procedure used to establish SLLOD as the valid algorithm for planar Couette flow [D. J. Evans and E. P. Morriss, Phys. Rev. A 30, 1528 (1984)], it is demonstrated that the p-SLLOD algorithm is valid for arbitrary flows and produces the correct nonlinear response of the viscous pressure tensor.