Molecular dynamics simulation of cellobiose in water

The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Temperature dependence of the reactions of HO2 with NO and NO2

Mixtures of N₂O, H₂, O₂, and trace amounts of NO and NO₂ were photolyzed at 213.9 nm, at 245°–328°K, and at about 1 atm total pressure (mostly H₂). HO₂ radicals are produced from the photolysis and they react as follows: Reaction (1b) is unimportant under all of our reaction conditions. Reaction (1a) was studied in competition with reaction (3) from which it was found that k_1a/k₃^1/2 = 6.4 × 10^?6 exp { z?(1400 ± 500)/RT} cm^3/2/sec^1/2. If k₃ is taken to be 3.3 × 10^?12 cm³/sec independent of temperature, k_1a = 1.2 × 10^?11 exp {?(1400 ± 500)/RT} cm³/sec. Reaction (2a) is negligible compared to reaction (2b) under all of our reaction conditions. The ratio k_2b/k₁ = 0.61 ± 0.15 at 245°K. Using the Arrhenius expression for k_1a given above leads to k_2b = 4.2 × 10^?13 cm³/sec, which is assumed to be independent of temperature. The intermediate HO₂NO₂ is unstable and induces the dark oxidation of NO through reaction (?2b), which was found to have a rate coefficient k_?2b = 6 × 10¹⁷ exp {?26,000/RT} sec^?1 based on the value of k_1a given above. The intermediate can also decompose via Reaction (10b) is at least partially heterogeneous.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

Kinetics of the reaction HO2 + NO2(+M) = HO2NO2 using molecular modulation spectrometry

Rate constants for the reaction HO₂ + NO₂(+ M) = HO₂NO₂(+ M) have been obtained from direct observations of the HO₂ radical using the technique of molecular modulation ultraviolet spectrometry. HO₂ was generated by periodic photolysis of Cl₂ in the presence of excess H₂ and O₂, and k₁ was determined from the measured concentrations and lifetime of HO₂ with NO₂ present. k₁ increased with pressure in the range of 40–600 Torr, and a simple energy transfer model gave the following limiting second- and third-order rate constants at 283 K: k₁^∞ = 1.5 ± 0.5 × 10^?12 cm³/molec·sec and k₁^III = 2.5 ± 0.5 × 10^?31 cm⁶/molec·sec. The ultraviolet absorption spectrum of peroxynitric acid was also recorded in the range of 195–265 nm; it showed a broad feature with a maximum at 200 nm, σ_max = 4.4 × 10^?18 cm².     

Molecular dynamics simulation of the association of nonpolar spheres in water

We apply molecular dynamics (MD) simulations to the study of the association of nonpolar spheres of effective radii between 1.6 and 6.1 A dissolved in water. The constrained MD method is used to calculate the potential of mean force (PMF) of the interaction between spheres. The depth of the potential of mean force increases with increasing radius of the nonpolar sphere. Our results suggest that the PMF is largely governed by size or entropic effects, and that energetic effects associated with the breaking or distortion of hydrogen bonds are of minor importance.     

Molecular dynamics simulation of the renin inhibitor H142 in water

Summary H142 is a synthetic decapeptide designed to inhibit renin, an enzyme acting in the regulation of blood pressure. The inhibiting effect of H142 is caused by a reduction of a-Leu-Val-peptide bond (i. e. C(=O)-NHCH₂-NH). The conformational and dynamical properties of H142 and its unreduced counterpart (H142n) was modelled by means of molecular dynamics simulations. Water was either included explicitly in the simulations or as a dielectric continuum. When water molecules surround the peptides, they remain in a more or less extended conformation through the simulation. If water is replaced by a dielectric continuum, the peptides undergo a conformational change from an extended to a folded state. It is not clear whether this difference is a consequence of a too short simulation time for the water simulations, a force-field artifact promoting extended conformations, or if the extended conformation represents the true conformational state of the peptide. A number of dynamic properties were evaluated as well, such as overall rotation, translational diffusion, side-chain dynamics and hydrogen bonding.     

Molecular dynamics simulation of the PEO sulfonic acid anion in water

Atomistic molecular modeling has been used to study the sulfonic acid anion of poly(ethylene oxide) (PEO sulfonic acid anion) in vacuum and a polymer electrolyte system consisting of the PEO sulfonic acid anion in water. The vibrational spectra of the molecules were simulated by the local mode method and found to be in good agreement with the experimental IR and Raman spectra. The structure of PEO sulfonic acid anion was studied in vacuum and water and compared to the structure of an isolated PEO sulfonic acid in vacuum. The simulated value for the root mean square end-to-end distance for the PEO sulfonic acid anion was 22 Å in vacuum and 12 Å in water. The root mean square radius of gyration of the PEO sulfonic acid anion was 8.4 Å in vacuum and 5.6 Å in water. The PEO sulfonic acid anion was randomly coiled in water and in an extended shape in vacuum.     

Molecular dynamics simulation of pressure-driven water flow in silicon-carbide nanotubes

Many properties of silicon carbide (SiC) nanotubes, such as their high mechanical strength and resistance to corrosive environments, are superior to those of their carboneous counterparts, namely, carbon nanotubes (CNTs) and, therefore, SiC nanotubes can be a viable alternative to CNTs in a variety of applications. We employ molecular dynamics simulations to examine flow of water in SiC nanotubes and to study the differences and similarities with the same phenomenon in the CNTs. The simulations indicate that SiC nanotubes always provide larger flow enhancements than those reported for the CNTs. Moreover, a given flow enhancement in SiC nanotubes requires an applied pressure gradient that is at least an order of magnitude smaller than the corresponding value in a CNT of the same size.     

Molecular dynamics simulation of a water/metal interface

First results of a molecular dynamics study of a water/metal interface, lasting 3.3 ps at an average temperature of 294 K, are reported. The basic periodic box contains 216 water molecules and a crystal slab of 550 platinum atoms with (100) surface planes. A combination of a Lennard-Jones potential between centers of mass and a Coulomb potential arising from dielectric interactions of the water charge distribution with the metal is employed for the water-wall interaction, the ST2 model for the water-water, and a nearest-neighbour harmonic potential for the platinum-platinum interactions. Considerable adsorption at the interface together with a drastic change of the water structure is observed.     

Molecular dynamics simulation of liquid water between two walls

A molecular dynamics simulation, lasting ≈25 ps, has been performed with 150 ST2 water molecules between two quasi-hard repulsive walls, at a temperature of 302 K. A number of static and dynamic properties have been computed as a function of the distance from the walls, showing that water near the walls is in general more “ordered” than in the bulk, and that this bulk water behaves like ordinarv liquid ST2 water.     

Infrared detection of HO2 and HO3 radicals in water ice

Infrared spectroscopy has been used to detect HO(2) and HO(3) radicals in H(2)O + O(2) ice mixtures irradiated with 0.8 MeV protons. In these experiments, HO(2) was formed by the addition of an H atom to O(2) and HO(3) was formed by a similar addition of H to O(3). The band positions observed for HO(2) and HO(3) in H(2)O-ice are 1142 and 1259 cm(-1), respectively, and these assignments were confirmed with (18)O(2). HO(2) and HO(3) were also observed in irradiated H(2)O + O(3) ice mixtures, as well as in irradiated H(2)O(2) ice. The astronomical relevance of these laboratory measurements is discussed.     

Molecular dynamics simulation of the coalescence of nanometer-sized water droplets in n-heptane

Molecular dynamics simulations using a modified Drieding 2.21 force field were carried out to study the coalescence behavior of nanometer-sized water droplets in vacuum and in n-heptane. The coalescence mechanisms of the water droplets in the above-noted environments are fairly similar in a sense that the water droplets form a bridge linking the droplets before they merge. However, in the latter situation, due to the presence of n-heptane molecules in between the water droplets, the coalescence was observed to be slowed down considerably, especially in the first 10 ps of the process. However, once the bridge is formed, the water droplets, in both situations, spend about the same amount of time to form a single droplet. The maximum distance between the droplets above which coalescence does not occur was found to be 10 A. In terms of the dynamics, the diffusion coefficient of n-heptane in the emulsion system was very close to its value in the pure liquid form. This may be because n-heptane is the continuous phase. Nonetheless, the dynamic behavior of water in n-heptane is different from that of pure water during and after the coalescence. In particular, the self-diffusion coefficient of water molecules in n-heptane is about 20% higher than the experimental value of pure water. Due to the lack of strong attraction forces between water and n-heptane molecules, the n-heptane molecules were observed to orient themselves perpendicularly to the water/n-heptane interfaces so that the contacting area is minimized.     

Molecular dynamics simulation of diffusion and sorption of water in conducting polyaniline

Energy minimization and molecular dynamics simulations are used to develop, for the first time, atomistic models of HCl- and HBr-doped conducting polyanilines, in order to study diffusion and adsorption of water vapor in the polymers. Various morphological properties of the polymers are computed, including their pair correlation functions that are found to be in good agreement with the experimental data, and their accessible free volumes. Also computed are the sorption isotherms and effective self-diffusivity of water vapor in the polymers. The computed sorption isotherms are in quantitative agreement with the experimental data, while the diffusivities are within an order of magnitude of the data. The reasons for the differences between the computed and measured diffusivities are discussed.     

Molecular dynamics simulation of water in a contact with an iron pyrite FeS2 surface

A strong adsorption of the water molecules to the pyrite surface is shown by a molecular dynamic simulation of the water-iron pyrite FeS2 interface. Water molecules closest to the pyrite surface are bound by an electrostatic interaction to the iron atoms in grooves running parallel to one of the crystal axes. The grooves are about two atoms wide and are directed along 010 for the (001) surface. The position of the water-surface potential minimum and the energy of adsorption were determined by optimization for a single water molecule at the interface. At room temperature and normal density there are altogether three distinguishable layers of water above the surface. One is associated with the groove: one with H bonding to the sulphur atoms comprising the ridges separating the grooves, and the third with the soft wall boundary between the absorbed water layers and bulk region of water. Simulations were also used to explore the effect of a temperature range significant for geophysical studies.     

Conductance of Cs+ ion in water: Molecular dynamics simulation

The continuum theory of Hubbard-Onsager predicts for the friction coefficients the following behavior: >0 and /P<0. In contrast to Hubbard-Onsager theory, experimental observations on Cs⁺ ion in water show that at low temperatures <0 and /P>0. To explain the observed behavior of Nakahara et al. proposed the passage through cavities (PTC) mechanism. We performed a molecular dynamics computer simulation to determine if the PTC mechanism is responsible for the observed behavior of . No passage through cavities was observed. Molecular dynamics computer simulations were performed on Cs⁺ ion in water at temperature of 268 K and densities of 1.00 and 1.083 g-cm^–3. Our results indicate that the observed behavior of for Cs⁺ ion is related to the difference in the reorientation times of water molecules in the solvation shell and in the bulk.     

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Formation of nitric acid in the gas-phase HO2 + NO reaction: effects of temperature and water vapor

A high-pressure turbulent flow reactor coupled with a chemical ionization mass spectrometer was used to investigate the minor channel (1b) producing nitric acid, HNO3, in the HO2 + NO reaction for which only one channel (1a) is known so far: HO2 + NO --> OH + NO2 (1a), HO2 + NO --> HNO3 (1b). The reaction has been investigated in the temperature range 223-298 K at a pressure of 200 Torr of N2 carrier gas. The influence of water vapor has been studied at 298 K. The branching ratio, k1b/k1a, was found to increase from (0.18(+0.04/-0.06))% at 298 K to (0.87(+0.05/-0.08))% at 223 K, corresponding to k1b = (1.6 +/- 0.5) x 10(-14) and (10.4 +/- 1.7) x 10(-14) cm3 molecule(-1) s(-1), respectively at 298 and 223 K. The data could be fitted by the Arrhenius expression k1b = 6.4 x 10(-17) exp((1644 +/- 76)/T) cm3 molecule(-1) s(-1) at T = 223-298 K. The yield of HNO3 was found to increase in the presence of water vapor (by 90% at about 3 Torr of H2O). Implications of the obtained results for atmospheric radicals chemistry and chemical amplifiers used to measure peroxy radicals are discussed. The results show in particular that reaction 1b can be a significant loss process for the HO(x) (OH, HO2) radicals in the upper troposphere.