Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.     

Thermodynamic Properties and Relative Stability of Polyhydroxylated Dibenzo-p dioxins Calculated by Density Functional Theory

In this work, partial thermodynamic properties of polyhydroxylated dibenzo-p-dioxins (PHODDs) are calculated by density functional theory (DFT) with the Gaussian 03 program at the B3LYP/6-311G** level. By comparing the total energy Eθ values, it is found that two types of hydrogen bonds exist in PHODDs, one between a hydroxyl and the parent compound (dibenzop-dioxin) with bond energy of approximate 15.7 kJ/mol and the other between two ortho hydroxyl groups with higher bond energy of about 18.3 kJ/mol. Hydrogen bonds have an effect on the conformation stability. On the basis of evaluating the strength of these two types of hydrogen bonds, 75 most stable congeners are ascertained. The relations of calculated thermodynamic parameters (total energy Eθ, zero-point vibrational energy ZPE, correction value of thermal energy Ethθ, heat capacity at constant volume CVθ) with the number and position of hydroxyl substitution (NPHOS) are also discussed. The results show that the NPHOS models can be used to predict the thermodynamic properties for PHODD congeners. In addition, the values of molar heat capacities at constant pressure (Cp,m) from 200 to 1000 K for PHODD congeners are calculated, and the temperature dependence relation of Cp,m is obtained with the least-squares method.     

Prediction of microscopic protonation constants of polybasic molecules via computational methods: A complete microequilibrium analysis of spermine

For the first time, a simple methodology is reported for theoretical calculation of microscopic protonation constants of polybasic molecules in solution. Density functional theory study was used for complete microequilibrium analysis of spermine, H₂N(CH₂)₃NH(CH₂)₄NH(CH₂)₃NH₂, a linear tetraamine with 16 known microspecies. A general thermodynamic cycle is proposed to calculate protonation microconstants of polybasic molecules using calculated micro‐ΔG values in aqueous solution. The microscopic protonation constants were determined with considering both the most abundant and most stable conformers for all microspecies. The results show that the microscopic protonation constants derived from the most abundant conformers (i.e., linear conformers in which the intramolecular hydrogen bonding does not exist) are in good agreement with the corresponding available experimental data. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Kinetic and thermodynamic control of g-quadruplex folding

A matter of speed: When allowed to fold in a K(+) /poly(ethylene glycol) solution, the guanine?(G)-rich strand of vertebrate telomere DNA forms a parallel/antiparallel G-quadruplex, which is a (3+1) hybrid, within microseconds before slowly transforming into the parallel one within hours. Thus, the conformation that a G-quadruplex initially adopts under physiological conditions may not be the one it adopts at the equilibrium state.     

DFT study of hydrogen storage in Pd-decorated C60 fullerene

Hydrogen storage reactions on Pd-doped C₆₀ fullerene are investigated by using the state-of-the-art density functional theory calculations. The Pd atom prefers to bind at the bridge site between two hexagonal rings, and can bind up to four hydrogen molecules with average adsorption energies of 0.61, 0.45, 0.32, and 0.21 eV per hydrogen molecule. With no metal clustering, the system gravimetric capacities are expected to be as large as 5.8 wt%. While the desorption activation barriers of the complexes nH₂ + Pd–C₆₀ with n = 1 are outside the department of energy (DOE) domain (?0.2 to ?0.6 eV), the desorption activation barriers of the complexes nH₂ + Pd–C₆₀ with n = 2–4 are inside this domain. While the interaction of 1H₂ with Pd + C₆₀ is irreversible at 459 K, the interaction of 2H₂ with Pd + C₆₀ is reversible at 529 K. The hydrogen storage of the irreversible 1H₂ + Pd–C₆₀ and reversible 2H₂ + Pd–C₆₀ interactions are characterised in terms of densities of states, infrared, Raman, and proton magnetic resonance spectra, electrophilicity, and statistical thermodynamic stability.     

Thermodynamics of substituted coumarin VII: Potentiometric and spectrophotometric studies of 1-acetyl-2-(coumarin-iminecarboxamide-3-yl) hydrazine transition metal complexes

The dissociation constant of l-acetyl-2-(coumariniminecarboxamide-3-yl) hydrazine (ACCH) has been determined potentiometrically in 0.1 M KC1 and 40% (v/v) ethanol-water mixture. The stepwise stability constants of the formed complexes of Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺ and UO₂ ²⁺ with ACCH have been determined. The stability constants were found to UO₂ ²⁺ > Cu²⁺> Zn²⁺ > Ni²⁺ < CO²⁺ < Mn²⁺. The effect of temperature on the dissociation of ACCH and the stability of its formed complexes were studied. The corresponding thermodynamic functions were also determined and discussed. The spectral data of ACCH were investigated in pure organic solvents as well as in Britton Robinson buffer solutions of varying pH values. The dissociation constant pK^H ₁ of ACCH and the overall stability constants logβ of their complexes were determined in 20% (v/v) ethanol-water mixture at 298K.     

Small-Angle and Wide-Angle X-Ray Scattering Study of Slow Relaxation Following Phase Transitions of New Bolaamphiphiles Based on N-(12-Betainylamino-Dodecane)-octyl β-D-Glucofuranosiduronamide Chloride

In the present study, we investigated the polymorphism and its time-dependence of a new series of bolaamphiphile molecules based on N-(12-Betainylamino-dodecane)-octyl β-D-Glucofuranosiduronamide Chloride. To obtain six members of this series, the length of the main bridging chain and the lateral chain were varied in order to modify the hydrophilic–lipophilic balance. Another chemical modification was to introduce a diacetylenic unit in the middle of the bridging chain to study the influence of the π–π stacking on the supramolecular organization of these molecules. Dry bolaamphiphiles self-organize in supramolecular structures such as lamellar crystalline structure, L_c; lamellar gel structure, L_β′; lamellar fluid structure, L_α; and lamellar isotropic structure, L. Thermal hysteresis of these structures, following phase transitions, are investigated by small-angle and wide-angle X-ray scattering. Once the thermal cycle is accomplished, the system remains in the kinetically stabilized undercooled high-temperature phase at the temperature of 20°C. Subsequently, the time-dependence of the relaxation to the thermodynamically stable phase is followed, and very slow relaxation for a period on the order of hours or days is observed. The study of the polymorphism and the stability of various phases of this new series of bolaamphiphiles—which are issued from natural primary resources (sugar beet and wheat) and thus interesting for potential application in pharmaceutical, cosmetics, or food industry—was undertaken in this work.     

弱相互作用费米气体的热力学性质

根据赝势法导出无外势时弱相互作用费米气体的化学势、内能和定容热容的解析表达式.在此基础上，采用局域密度近似研究谐振势中弱相互作用费米气体的热力学性质，探讨粒子间相互作用对系统性质的影响. 关键词： 费米气体 相互作用 赝势法 局域密度近似 热力学性质     

燃气轮机考虑经济性和环保因素的热力分析

主要符号表人，从，C，H年运行小时数对热效率风，i二1，2价格方程的系数Hu燃料低位发热量雷压比c燃料含碳百分比d贴现率，温比CO投资额J单位质量C02罚款Cj年均燃料费M比例系数下标Cth年均运行维修费N电站容量0基准值COE发电成本。运行年限C发电成本E考虑变工况的系数P单位功率价格…最佳值G空气流量马单位能量燃料价格，热效率G，燃料流量产年投资费用率1概述在进行动力机械的循环热力分析时，结合经济因素与环保因素来定量进行，是实际生产的要求，也是热力循环分析的一次创新。本文将以燃气轮机发电机组为例，对此进行首次试探，…