Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

Evidence that the β‐Peptide 14‐Helix is Stabilized by β3‐Residues with Side‐Chain Branching Adjacent to the β‐Carbon Atom

Oligomers of β‐substituted β‐amino acids (‘β³‐peptides') are known to adopt a helical secondary structure defined by 14‐membered ring hydrogen bonds ('14‐helix'). Here, we describe a deca‐β³‐peptide, 1 , that does not adopt the 14‐helical conformation and that may prefer an alternative secondary structure. β³‐Peptide 1 is composed exclusively of residues with side chains that are not branched adjacent to the β‐C‐atom (β³‐hLeu, β³‐hLys, and β³‐hTyr). In contrast, an analogous β‐peptide, 2 , containing β³‐hVal residues in place of the β³‐hLeu residues of 1 , adopts a 14‐helical conformation in MeOH, according to CD data. These results illustrate the importance of side‐chain branching in determining the conformational preferences of β³‐peptides.     

Reactions of RSe− (R = Me,Ph) Groups in [RSeFe(CO)4I and [RSeCr(CO)5−]

The anionic [MeSeFe(CO)₄] and [MeSeCr(CO)₅] complexes were synthesized by reaction of [PPN][HFe(CO)₄] and [PPN][HCr(CO)₅] with MeSeSeMe respectively via nucleophilic cleavage of the Se-Se bond. The ease of cleavage of the Se-Se bond follows the nucleophilic strength of metal-hydride complexes. Methylation of [RSeCr(CO)₅^?] by the soft alkylating agent MeI resulted in the formation of neutral (MeSeMe)Cr(CO)₅ in THF at 0°C. In contrast, the [ICr(CO)₅^?] was isolated at ambient temperature. Reaction of [MeSeFe(CO)₄^?] or [MeSeCr(CO)₅^?] with HBF₄ yielded (CO)₃Fc(μ-SeMe)₂Fe(CO)₃ dimer and anionic [(CO )₅Cr (μ-SeMe)Cr(CO)₅^?] respectively, and no neutral (HSeMe)Fe(CO)₄ and (HSeMe)Cr(CO)₅ were detected spectrally (IR) even at low temperature. Reaction of NOBF₄ or [Ph₃C][BF₄] and [MeSeCr(CO)₅^?] resulted in the neutral monodentate (MeSeSeMe)Cr(CO)₅ complex. Addition of 1 equiv CpFe(CO)₂I to 2 equiv [MeSeCr(CO)₅^?] gave CpFe(CO)₂(SeMe) and the anionic [(CO)₅Cr(μ-SeMe)Cr(CO)₅^?] in THF at ambient temperature.     

Pulsed field gel electrophoresis: studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system

We have studied the migration of DNA in pulsed field agarose gels under a variety of electrophoresis conditions. We have made use of an instrument which can generate electric fields of any orientation, magnitude, or duration to compare different separation techniques for DNA molecules of from 1 to several thousand kilobase pairs. We discuss the capabilities of the system and present results of gel runs in which electrophoresis conditions were changed individually or in combination. The mobility of DNA in pulsed field gels is shown to reflect a number of interdependent physical parameters.     

Oxidation-Induced Structural Alterations and Its Effect on Chaperone Function of Rat Lens α-Crystallin

An ascorbate-FeCl₃-EDTA-H₂O₂ system was used to oxidize rat lens α-crystallins. Under this oxidative insult, the chaperone activity of α-crystallin toward γ-crystallin was shown to decrease significantly, which is quite different from the result reported by Wang and Spector. (Invest. Ophthalmol. Vis. Sci. 1995 , 36, 311-321.) Fluorescence spectroscopy and circular dichroism were employed to characterize the structural changes of oxidized α-crystallin. It was found that fluorescence intensity of l-anilinonaphthalene-8-sul-phonate (ANS) bound to oxidized α-crystallin increased comparing to that bound to normal α-crystallin, suggesting oxidation causes the exposure of more hydrophobic regions. Further, α-crystallin's fluorescence intensity in response to tryptophan residues showed a pseudo first order decline. Amino acid analysis of normal versus oxidized α-crystallin confirmed actual decline in tryptophan levels, showing about 80% of tryptophan being modified after 10-hour oxidation. Circular dichroism showed both changes in the secondary and tertiary structures of oxidized α-crystallin, characterized by a large loss of aromatic-type amino acid interactions and a large loss of β-sheet structure. In conclusion, modified tryptophan, secondary and tertiary structural changes of α-crystallin correlate best with the reduction of chaperone function, the curves all showing a linear slope for 10 hours, then plateauing. These results indicate that the decrease of α-crystallin chaperone activity is attributed to the structural changes.     

Static ultrasonic oscillations induced degradation and its effect on the linear rheological behavior of novel propylene based plastomer melts

The ultrasonic degradation of novel propylene based plastomer (DP) melts with different melt viscosities was conducted in a “static” ultrasonic device where the samples were taken from various distances from the tip of an ultrasonic probe. The effects of ultrasonic time, oscillation temperature, ultrasonic intensity and the distance from the ultrasonic probe tip on the degradation behavior of DP melts as well as the ultrasonic degradation effect on the linear rheological behavior of DP melts were studied. The results show that the increase of initial melt viscosity of DP (higher molecular weight) has greater impact on the ultrasonic degradation of DP melt. The molecular weight and intrinsic viscosity of DP decrease with the increase of ultrasonic oscillation time and they approach to a limiting value. The molecular weight distribution of DP increases after ultrasonic degradation. Decreasing oscillation temperature and distance from probe tip and increasing ultrasonic intensity lead to an increase in the degradation of DP melt. The linear rheological behavior measurements of the samples obtained near the ultrasonic probe tip show that ultrasonic oscillations decrease the complex viscosity, zero shear viscosity, viscoelastic moduli, cross modulus, relaxation time and the slope of log G′ − log G″ for DP melts.     

Determination of phenolic compounds using high-performance liquid chromatography with Ce-Tween 20 chemiluminescence detection

A novel method for the simultaneous determination of phenolic compounds such as salicylic acid, resorcinol, phloroglucinol, p-hydroxybenzoic acid, 2,4-dihydroxybenzoic acid, and m-nitrophenol by high-performance liquid chromatography (HPLC) coupled with chemiluminescence (CL) detection was developed. The procedure was based on the chemiluminescent enhancement by phenolic compounds of the cerium(IV)-Tween 20 system in a sulfuric acid medium. The separation was carried out with an isocratic elution or with a gradient elution using a mixture of methanol and 1.5% acetic acid. For six phenolic compounds, the detection limits (3σ) were in the range 1.40-5.02 ng/ml and the relative standard deviations (n=11) for the determination of 0.1 μg/ml compounds were in the range 1.9-2.9%. The CL reaction was well compatible with the mobile phase of HPLC, no baseline drift often occurred in HPLC-CL detection was observed with a gradient elution. The method has been successfully applied to the determination of salicylic acid and resorcinol in Dermatitis Clear Tincture and p-hydroxybenzoic acid in apple juices.     

Complexation of silver and co-recovered metals with novel aza-crown ether macrocycles by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) is used to evaluate the metal binding selectivities of an array of novel caged macrocycles for silver, gold, copper, nickel, zinc, iron, lead, manganese and alkali metal ions. It is found that five of the new compounds display silver selectivity, and their relative affinities for various metals depend on the type, number, and arrangement of heteroatoms (N, O), the cavity size, and the presence of aromatic substituents. Alkali metal cation binding studies are used to evaluate the size-selectivities of the cavities of the macrocycles. Electronic structure calculation by B3LYP density function theory methods were used to model the metal complexes. The presence of nitrogen atoms in the macrocyclic ring is essential for silver selectivity over other transition metals and alkali metal ions, and the presence of aromatic groups also enhances silver avidity. Macrocycle 3, a triaza-18-crown-6 analog modified with two phenyl groups and a cage group, is capable of selective extraction of Ag+ from aqueous solutions in the presence of other transition metal ions and the most common alkali and alkaline earth metal ions.     

Asynchronous multicanonical basin hopping method and its application to cobalt nanoclusters

The multicanonical basin hopping (MUBH) method, which uses a multicanonical weight in the basin hopping (BH) Monte Carlo method, was found to be very efficient for global optimization of large-scale systems such as Lennard-Jones clusters containing more than 150 atoms. We have implemented an asynchronous parallel version of the MUBH method using the message passing interface (MPI) to take advantage of the full usage of multiprocessors in either a homogeneous or heterogeneous computational environment. Based on the intrinsic properties of the Monte Carlo method, this MPI implementation used the task parallelism to minimize interthread data communication. For a Co nanocluster consisting of N atoms, we have applied the asynchronous multicanonical basin hopping (AMUBH) method (for 181 < N < or = 200), together with BH (for 2 < or = N < 150) and MUBH (for 150 < or = N < or = 180), to search for the molecular configuration of the global energy minimum. AMUBH becomes the only practical computational scheme for locating the energy minimum within realistic computational time for a relatively large cluster.     

Polarographic Behaviour and Determination of Kinetic Parameters of Lead-Pamoate Complex in Dimethyl Sulfoxide

The polarography of lead ion in dimethyl sulfoxide (DMSO) was investigated in the DMSO concentration range 0–80 vol.%. The complex species identified were Pb₂(DMSO)⁴⁺₃, Pb(DMSO)²⁺₃ and Pb(DMSO)²⁺₆ in [DMSO]<10 vol.%, 10< [DMSO]<43 vol.% and [DMSO]>43 vol.%, respectively. In the presence of pamoic acid, the reduction of lead ion in DMSO was two-electron reversible diffusion-controlled at pH≤6.0, but it became irreversible at pH>6.0. The complex species identified was Pb(D_m)₂(P_m)₃(OH)^6? at pH>6.0. The rate constants of electro-reduction and electro-oxidation, activation energies were determined. The hydrolysis constants of lead ion in dimethyl sulfoxide concentration 40–70 vol.% at pH 4.5–6.0 were found to be of the order of 10^?6. The stability constants of the Pb(DMSO)²⁺₃ and Pb(DMSO)²⁺₀ were also determined to be of the orders of 10¹ and 10⁵, respectively.