Dynamics of energy transfer in peptide-surface collisions

Classical trajectory simulations are performed to study energy transfer in collisions of protonated triglycine (Gly)(3) and pentaglycine (Gly)(5) ions with n-hexyl thiolate self-assembled monolayer (SAM) and diamond [111] surfaces, for a collision energy E(i) in the range of 10-110 eV and a collision angle of 45 degrees. Energy transfer to the peptide ions' internal degrees of freedom is more efficient for collision with the diamond surface; i.e., 20% transfer to peptide vibration/rotation at E(i) = 30 eV. For collision with diamond, the majority of E(i) remains in peptide translation, while the majority of the energy transfer is to surface vibrations for collision with the softer SAM surface. The energy-transfer efficiencies are very similar for (Gly)(3) and (Gly)(5). Constraining various modes of (Gly)(3) shows that the peptide torsional modes absorb approximately 80% of the energy transfer to the peptide's internal modes. The energy-transfer efficiencies depend on E(i). These simulations are compared with recent experiments of peptide SID and simulations of energy transfer in Cr(CO)(6)(+) collisions with the SAM and diamond surfaces.     

Temperature-induced gelation in dilute nanofluids

We report a temperature-induced gelation in dilute nanofluids containing surfactant capped iron oxide and alumina particles of average diameter ~10 nm. We observe a dramatic enhancement in the elastic modulus, viscous modulus, and viscosity, by 3-6 orders of magnitude for a volume fraction (φ) less than 0.035, above a critical shear rate ( ?γ(c)) and temperature (T(c)). The T(c) follows a weak power law scaling with φ as T(c) ~ φ(β), where the scaling exponent β is found to be -0.24. The observed gel-like transition at elevated temperature is attributed to strong van der Waals attractions on the kT energy scale due to poor solvent conditions, which is reminiscent of the phase behavior reported in polymer-coated colloids.     

Effects of counterion valency on the damping of phonons propagating along the axial direction of liquid-crystalline DNA

The phonon propagation and damping along the axial direction of films of aligned 40 wt % calf-thymus DNA rods are studied by inelastic x-ray scattering (IXS). The IXS spectra are analyzed with the generalized three effective eigenmode theory, from which we extract the dynamic structure factor S(Q,E) as a function of transferred energy E=variant Planck's over 2piomega, and the magnitude of the transferred wave vector Q. S(Q,E) of a DNA sample typically consists of three peaks, one central Rayleigh scattering peak, and two symmetric Stokes and anti-Stokes Brillouin side peaks. By analyzing the Brillouin peaks, the phonon excitation energy and damping can be extracted at different Q values from about 4 to 30 nm(-1). A high-frequency sound speed is obtained from the initial slope of the linear portion of the dispersion relation below Q=4 nm(-1). The high-frequency sound speed obtained in this Q range is 3100 ms, which is about twice faster than the ultrasound speed of 1800 ms, measured by Brillouin light scattering at Q approximately 0.01 nm(-1) at the similar hydration level. Our observations provide further evidence of the strong coupling between the internal dynamics of a DNA molecule and the dynamics of the solvent. The effect on damping and propagation of phonons along the axial direction of DNA rods due to divalent and trivalent counterions has been studied. It is found that the added multivalent counterions introduce stronger phonon damping. The phonons at the range between approximately 12.5 and approximately 22.5 nm(-1) are overdamped by the added counterions according to our model analyses. The intermediate scattering function is extracted and it shows a clear two-step relaxation with the fast relaxation time ranging from 0.1 to 4 ps.     

The state of the guanosine nucleotide allosterically affects the interfaces of tubulin in protofilament

The dynamics of microtubules is essential for many microtubule-dependent cellular functions such as the mitosis. It has been recognized for a long time that GTP hydrolysis in αβ-tubulin polymers plays a critical role in this dynamics. However, the effects of the changes in the nature of the guanosine nucleotide at the E-site in β-tubulin on microtubule structure and stability are still not well understood. In the present work, we performed all-atom molecular dynamics simulations of a αβα-tubulin heterotrimer harboring a guanosine nucleotide in three different states at the E-site: GTP, GDP-Pi and GDP. We found that changes in the nucleotide state is associated with significant conformational variations at the α-tubulin N- and β-tubulin M-loops which impact the interactions between tubulin protofilaments. The results also show that GTP hydrolysis reduces αβ-tubulin interdimer contacts in favor of intradimer interface. From an atomistic point view, we propose a role for α-tubulin glutamate residue 254 in catalytic magnesium coordination and identified a water molecule in the nucleotide binding pocket which is most probably required for nucleotide hydrolysis. Finally, the results are discussed with reference to the role of taxol in microtubule stability and the recent tubulin-sT2R crystal structures.     

混合稀土对ZA27合金阻尼性能的影响

研究了ＺＡ２７合金的稀土变质机制及阻尼性能,利用悬臂梁测试了阻尼能力。结果表明,合金中加入Ａｌ－１０％ＲＥ中间合金可以细化组织和提高阻尼能力,稀土添加量为０．３％时有最佳的变质效果和最佳高的阻尼能力。     

The "neutral" hydrolysis of simple carboxylic esters in water and the rate enhancements produced by acetylcholinesterase and other carboxylic acid esterases

Experiments at elevated temperatures permit the determination of rate constant and thermodynamic activation parameters for the neutral hydrolysis of the neurotransmitter acetylcholine in water. At 25 °C, the extrapolated rate constant for the uncatalyzed (or neutral) hydrolysis of acetylcholine is 3.9 × 10(-7) s(-1) at 25 °C (ΔH(?) = 20.0 kcal/mol; TΔS(?) = -6.1 kcal/mol). Acetylcholine is more susceptible to neutral and base-catalyzed hydrolysis than ethyl acetate but less susceptible to acid-catalyzed hydrolysis. For acetylcholinesterase from the electric eel, the catalytic proficiency [(k(cat)/K(m))/k(neutral)] is 2 × 10(16) M(-1), comparable in magnitude with the catalytic proficiencies of aminohydrolases that act on peptides and nucleosides.     

Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters

The mechanism of the hydrolysis reaction of the unprotonated methyl triphosphate (MTP) ester in water clusters has been modeled. The effective fragment potential based quantum mechanical-molecular mechanical (QM/MM) approach has been applied in the simulations. It is shown that the minimum energy reaction path is consistent with an assumption of a two-step dissociative-type process similar to the case of the guanosine triphosphate (GTP) hydrolysis in the Ras-GAP protein complex (Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Cachau, R. E.; Burt, S. K. Proteins: Struct., Funct., Bioinf. 2005, 60, 495). At the first stage, a unified action of environmental molecular groups and the catalytic water molecule leads to a substantial spatial separation of the gamma-phosphate group from the rest of the molecule. At the second stage, inorganic phosphate H2PO4- is formed from water and the metaphosphate anion PO3- through the chain of proton transfers along hydrogen bonds. The estimated activation barriers for MTP in aqueous solution at both stages (20 and 14 kcal/mol) are substantially higher than the corresponding barriers for the GTP hydrolysis in the protein.     

Infrared spectroscopic ellipsometry of n-alkylthiol (C5-C18) self-assembled monolayers on gold

The infrared spectroscopic ellipsometry (IRSE) of n-alkylthiol (CH3(CH2)xSH, x = 4, 6, 7, 8, 10, 13, 15, and 17, self-assembled monolayers (SAMs), with 5-18 carbon atoms (C5-C18), grown on gold-coated Si(100) substrates) was investigated at room temperature. The C-H stretching vibrations could be resolved even for pentathiol, the shortest chain studied. The symmetric and asymmetric stretching vibrations of the CH2 groups are located at about 2850 and 2920 cm(-1), and those of CH3 are at about 2877 and 2962 cm(-1), respectively; they show a slight shift with the number of CH2 units. In addition, Fermi resonance of the symmetric CH3 stretching vibration at 2940 cm(-1) appears with decreasing chain length due to weak coupling with the asymmetric CH2 stretching vibration. The "odd-even effect" of the n-alkylthiol SAMs with varying CH2 units could be distinguished by the two interactive IRSE parameters. The relative ellipsometric spectra for the four longest chains could be reproduced quite well by using a Lorentz multioscillator model with a three-phase optical model (air/SAMs/gold). On the basis of the theoretical calculations, the vibrational strength of these oscillators is very weak, its magnitude being 10(-4)-10(-5). The full width at half-maximum (fwhm) of the peaks varies from 7 to 33 cm(-1). Moreover, the intensity of the C-H vibrations increases with the number of methylene units, due to strong lateral interactions and ordering effects occurring for longer chains.     

Magnesium ion catalyzed P-N bond hydrolysis in imidazolide-activated nucleotides. Relevance to template-directed synthesis of polynucleotides

Magnesium, an ion necessary in enzymatic as well as in nonenzymatic template-directed polynucleotide-synthesizing reactions, has been found to catalyze the hydroxide ion attack on the P-N bond of selected 5'-monophosphate imidazolide derivatives of nucleotides, such as guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG), guanosine 5'-monophosphate imidazolide (ImpG), and adenosine 5-monophosphate 2-methylimidazolide (2-MeImpA). Calcium ion behaves similarly, but quantitatively the effects are smaller. Pseudo-first-order rate constants of 2-MeImpG and ImpG hydrolysis as a function of Mg2+ concentration have been obtained in the range 6 < or = pH < or = 10 at 37 degrees C. Mg2+ catalysis is particularly effective around pH 10 where a 0.02 M concentration leads to 15-fold acceleration and a 0.2 M concentration to a 115-fold acceleration of the rate. At other pH values Mg2+ catalysis is less dramatic, mainly because the noncatalyzed reaction is faster. Mg2+ catalysis is attributed to the reaction of the zwitterionic form of the substrate (SH+/-, imidazolide moiety protonated) with OH- rather than reaction of the anionic form (S-, imidazolide moiety deprotonated) with water. This conclusion is based on a study of the N-methylated substrates N-MeImpG and 1,2-diMeImpg, respectively, which were generated in situ by the equilibrium reaction of ImpG with N-methylimidazole and 2-MeImpG with 1,2-dimethylimidazole, respectively. In contrast, the absence of Mg2+ the reaction of S- with water competes with the reaction of SH+/- with OH-. The present study bears on the mechanism of the Mg2(+)-catalyzed template-directed synthesis of oligo-and polynucleotides derived from 2-MeImpG and on the competition between oligonucleotide synthesis and hydrolysis of 2-MeImpG.     

Ballistic Impact Behaviour of Glass/Epoxy Composite Laminates Embedded with Shape Memory Alloy (SMA) Wires

This paper aims to estimate the enhancement in the energy absorption characteristics of the glass fiber reinforced composites (GFRP) by embedding prestrained pseudo-elastic shape memory alloy (SMA) that was used as a secondary reinforcement. The pseudo-elastic SMA (PE-SMA) embedded were in the form of wires and have an equiatomic composition (i.e., 50%–50%) of nickel (Ni) and titanium (Ti). These specimens are fabricated using a vacuum-assisted resin infusion process. The estimation is done for the GFRP and SMA/GFRP specimens at four different impact velocities (65, 75, 85, and 103 m/s) using a gas-gun impact set-up. At all different impact velocities, the failure modes change as we switch from GFRP to SMA/GFRP specimen. In the SMA/GFRP specimen, the failure mode changed from delamination in the primary region to SMA-pull out and SMA deformation. This leads to an increase in the ballistic limit. It is observed that energy absorbed by SMA/GFRP specimens is higher than the GFRP specimens subjected to the same levels of impact energy. To understand the damping capabilities of SMA embedment, vibration signals are captured, and the damping ratio is calculated. SMA dampens the vibrations imparted by the projectile to the specimen. The damping ratio of the SMA/GFRP specimens is higher than the GFRP specimens. The damping effect is more prominent below the ballistic limit when the projectile got rebounded (65 m/s).     

Triazole‐Tailored Guanosine Dinucleosides as Biomimetic Ion Channels to Modulate Transmembrane Potential

A “click” ion channel platform has been established by employing a clickable guanosine azide or alkyne with covalent spacers. The resulting guanosine derivatives modulated the traffic of ions across the phospholipid bilayer, exhibiting a variation in conductance spanning three orders of magnitude (pS to nS). Förster resonance energy transfer studies of the dansyl fluorophore with the membrane binding fluorophore Nile red revealed that the dansyl fluorophore is deeply embedded in the phospholipid bilayer. Complementary cytosine can inhibit the conductance of the supramolecular guanosine channels in the phospholipid bilayers.     

Intramolecular charge transfer assisted by conformational changes in the excited state of fluorene-dibenzothiophene-S,S-dioxide co-oligomers

The strong solvatochromism observed for two fluorene-dibenzothiophene-S,S-dioxide oligomers in polar solvents has been investigated using steady-state and time-resolved fluorescence techniques. A low-energy absorption band, attributed to a charge-transfer (CT) state, is identified by its red shift with increasing solvent polarity. In nonpolar solvents, the emission of these conjugated luminescent oligomers shows narrow and well-resolved features, suggesting that the emission comes from a local excited state (LE), by analogy to their conjugated fluorene-based polymer counterparts. However, in polar solvents, only a featureless broad emission is observed at longer wavelengths (CT emission). A linear correlation between the energy maximum of the fluorescence emission and the solvent orientation polarizability factor Deltaf (Lippert-Mataga equation) is observed through a large range of solvents. In ethanol, below 230 K, the emission spectra of both oligomers show dual fluorescence (LE-like and CT) with the observation of a red-edge excitation effect. The stabilization of the CT emissive state by solvent polarity is accompanied/followed by structural changes to adapt the molecular structure to the new electronic density distribution. In ethanol, above 220 K, the solvent reorganization occurs on a faster time scale (less than 10 ps at 290 K), and the structural relaxation of the molecule (CT(unrelaxed) --> CT(Relaxed)) can be followed independently. The magnitude of the forward rate constant, k(1)(20 degrees C) approximately 20 x 10(9) s(-1), and the reaction energy barrier, E(a) approximately 3.9 kcal mol(-1), close to the energy barrier for viscous flow in ethanol (3.54 kcal mol(-1)), show that large-amplitude molecular motions are present in the stabilization of the CT state.     

Fundamental reaction mechanism for cocaine hydrolysis in human butyrylcholinesterase

Butyrylcholinesterase (BChE)-cocaine binding and the fundamental pathway for BChE-catalyzed hydrolysis of cocaine have been studied by molecular modeling, molecular dynamics (MD) simulations, and ab initio calculations. Modeling and simulations indicate that the structures of the prereactive BChE/substrate complexes for (-)-cocaine and (+)-cocaine are all similar to that of the corresponding prereactive BChE/butyrylcholine (BCh) complex. The overall binding of BChE with (-)-cocaine and (+)-cocaine is also similar to that proposed with butyrylthiocholine and succinyldithiocholine, i.e., (-)- or (+)-cocaine first slides down the substrate-binding gorge to bind to Trp-82 and stands vertically in the gorge between Asp-70 and Trp-82 (nonprereactive complex) and then rotates to a position in the catalytic site within a favorable distance for nucleophilic attack and hydrolysis by Ser-198 (prereactive complex). In the prereactive complex, cocaine lies horizontally at the bottom of the gorge. The fundamental catalytic hydrolysis pathway, consisting of acylation and deacylation stages similar to those for ester hydrolysis by other serine hydrolases, was proposed on the basis of the simulated prereactive complex and confirmed theoretically by ab initio reaction coordinate calculations. Both the acylation and deacylation follow a double-proton-transfer mechanism. The calculated energetic results show that within the chemical reaction process the highest energy barrier and Gibbs free energy barrier are all associated with the first step of deacylation. The calculated ratio of the rate constant (k(cat)) for the catalytic hydrolysis to that (k(0)) for the spontaneous hydrolysis is approximately 9.0 x 10(7). The estimated k(cat)/k(0) value of approximately 9.0 x 10(7) is in excellent agreement with the experimentally derived k(cat)/k(0) value of approximately 7.2 x 10(7) for (+)-cocaine, whereas it is approximately 2000 times larger than the experimentally derived k(cat)/k(0) value of approximately 4.4 x 10(4) for (-)-cocaine. All of the results suggest that the rate-determining step of the BChE-catalyzed hydrolysis of (+)-cocaine is the first step of deacylation, whereas for (-)-cocaine the change from the nonprereactive complex to the prereactive complex is rate-determining and has a Gibbs free energy barrier higher than that for the first step of deacylation by approximately 4 kcal/mol. A further analysis of the structural changes from the nonprereactive complex to the prereactive complex reveals specific amino acid residues hindering the structural changes, providing initial clues for the rational design of BChE mutants with improved catalytic activity for (-)-cocaine.     

Kinetics of hydrolysis of 8-(arylamino)-2'-deoxyguanosines

The 8-(arylamino)-2'-deoxyguanosines, or C-8 adducts, are the major adducts formed by reaction of N-arylnitrenium ions derived from carcinogenic and mutagenic amines with 2'-deoxyguanosine (d-G) and guanosine residues of DNA. The hydrolysis kinetics of three C-8 adducts 1a-c were determined by UV and HPLC methods at 20 degrees C under acidic, neutral, and mildly alkaline conditions. At pH < 2 the dominant hydrolysis process is spontaneous cleavage of the C-N bond of the doubly protonated substrate, 1H(2)(+2) (Scheme 2). The C-8 adducts are 2- to 5-fold more reactive than d-G under these conditions. At 3 < pH < 6 the hydrolysis kinetics are dominated by cleavage of the C-N bond of the monoprotonated nucleoside 1H(+). Under these conditions the hydrolysis kinetics are accelerated by 40- to 1300-fold over that of d-G. The rate increase appears to be caused by a combination of steric acceleration of C-N bond cleavage and a decrease in the ionization constant of 1H(+), K(a1), due to the electron-donating properties of the arylamino C-8 substituent. Under neutral pH conditions a slow (k(obs) approximately 10(-8) s(-1) to 5 x 10(-7) s(-1)) spontaneous cleavage of the C-N bond of the neutral nucleoside, 1, occurs that has not been previously reported for simple purine nucleosides. Finally, under mildly alkaline conditions a process consistent with spontaneous decomposition of the anion 1(-) or OH(-)-induced decomposition of 1 is observed. The latter process has been observed for other purine nucleosides, including the closely related 1d, and involves nucleophilic attack of OH(-) on C-8 to cleave the imidazole ring of the purine.     

Hydrolysis of uranium(VI) at variable temperatures (10-85 degrees C)

The hydrolysis of uranium(VI) in tetraethylammonium perchlorate (0.10 mol dm(-3) at 25 degrees C) was studied at variable temperatures (10-85 degrees C). The hydrolysis constants (*beta(n,m)) and enthalpy of hydrolysis (Delta H(n,m)) for the reaction mUO(2)(2+) + nH(2)O = (UO(2))(m)(OH)(n)((2m-n))+) + nH(+) were determined by titration potentiometry and calorimetry. The hydrolysis constants, *beta(1,1), *beta(2,2), and *beta(5,3), increased by 2-5 orders of magnitude as the temperature was increased from 10 to 85 degrees C. The enthalpies of hydrolysis, Delta H(2,2) and Delta H(5,3), also varied: Delta H(2,2) became more endothermic while Delta H(5,3) became less endothermic as the temperature was increased. The heat capacities of hydrolysis, Delta C(p(2,2)) and Delta C(p(5,3)), were calculated to be (152 +/- 43) J K(-1) mol(-1) and -(229 +/- 34) J K(-1) mol(-1), respectively. UV/Vis absorption spectra supported the trend that hydrolysis of U(VI) was enhanced at elevated temperatures. Time-resolved laser-induced fluorescence spectroscopy provided additional information on the hydrolyzed species at different temperatures. Approximation approaches to predict the effect of temperature were tested with the data from this study.     

Catalytic proficiency: the extreme case of S-O cleaving sulfatases

As benchmarks for judging the catalytic power of sulfate monoesterases, we sought to determine the rates of spontaneous hydrolysis of unactivated alkyl sulfate monoesters by S-O bond cleavage. Neopentyl sulfate proved to be unsuitable for this purpose, since it was found to undergo hydrolysis by a C-O bond cleaving mechanism with rearrangement of its carbon skeleton. Instead, we examined the temperature dependence of the spontaneous hydrolyses of aryl sulfate monoesters, which proceed by S-O cleavage. Extrapolation of a Bronsted plot [log(k(25)(N)) = (-1.81 ± 0.09) pK(a)(LG) + (3.6 ± 0.7)] based on the rate constants at 25 °C for hydrolysis of a series of sulfate monoesters to a pK(a)(LG) value of 16.1, typical of an aliphatic alcohol, yields k(25)(N) = 3 × 10(-26) s(-1). Comparison of that value with established k(cat) values of bacterial sulfatases indicates that these enzymes produce rate enhancements (k(cat)/k(uncat)) of up to 2 × 10(26)-fold for the hydrolysis of sulfate monoesters. These rate enhancements surpass by several orders of magnitude the ~10(21)-fold rate enhancements that are generated by phosphohydrolases, the most powerful biological catalysts previously known. The hydrolytic rates of phosphate and sulfate monoesters are compared directly, and the misleading impression that the two classes of ester are of similar reactivity is dispelled.     

Effect of GTP and GDP nucleotides on vinblastine binding affinity to tubulin: a DFT study

Vinblastine (VLB) is an anticancer agent that inhibits microtubule assembly by binding with tubulin. Density functional theory (DFT) calculations are used to examine low-energy minima of the energy surface of vinblastine-tubulin complex. Thermodynamic data of the binding site of vinblastine to tubulin are extracted with the hybrid DFT (B3LYP (Becke, three-parameter, Lee–Yang–Parr)) method, and then the influence of several solvents, such as water, methanol and ethanol, and different temperatures are discussed on infrared parameters by self-consistent reaction field (SCRF = dipole) method. The effect of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) nucleotides on vinblastine binding affinity to tubulin was realised in water solvent by comparing the changes of ?G (Gibbs free energy) of VLB-tubulin and VLB-tubulin bonded to GTP or GDP. The result showed that GDP and GTP increase significantly the binding affinity and the role of GDP is more important than that of GTP.     

Atomic force microscopy in viscous ionic liquids

Extracting quantitative information from amplitude-modulation atomic force microscopy (AM-AFM) in viscous ionic liquids is difficult because existing theory requires knowledge of the cantilever natural frequency, which cannot be measured in the absence of a resonance peak. We present a new model that describes cantilever dynamics in an overdamped medium (Q < 0.5) and derive the theory necessary to extract the stiffness and damping in highly viscous liquids. The proposed methodology is used to measure the solvation layers of an ionic liquid at a gold electrode.     

A quadruply hydrogen bonded heterocomplex displaying high-fidelity recognition

An exceptionally strong quadruply hydrogen-bonded complex is formed between 2,7-diamido-1,8-naphthyridine 3 (DAN) and the butylurea of guanosine 6 (UG) in chloroform. The UG unit can be prepared in four steps from guanosine on a 10 g scale in excellent yields without chromatographic purification. The association constant (Kassoc approximately 5 x 10(7) M(-1)) for the UG.DAN complex determined by fluorescence energy transfer from the naphthyridine unit of 3 to coumarin 343 covalently linked UG (18) is among the highest reported for a neutral DNA base-pair analogue. The weak self-association of DAN (Kdimer < 10 M(-1)) and UG (Kdimer ca. 200-300 M(-1)) means that the UG.DAN complex forms with unparalleled fidelity.