Study of caffeine-DNA interaction in aqueous solution by parallel Monte Carlo simulation

Monte Carlo simulation of caffeine aqueous solutions containing a superhelical B-DNA fragment is performed using parallel computing. The binding sites of caffeine molecules with DNA were identified as well as the most probable structures of the resultant complexes. The degrees of caffeine molecule association in aqueous solutions with different concentrations were estimated and the main configuration types of molecular aggregates were revealed.     

Monte Carlo simulation of phase separation kinetics in a concentrated polymer solution

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Hydration of Fe+: A Monte Carlo simulation of water clusters and of a dilute aqueous solution

Monte Carlo statistical thermodynamic computer simulations are reported for several clusters Fe⁺ (H₂O)_n at different temperatures and for a dilute aqueous solution of Fe⁺ at 298 K. The energy of each configuration has been calculated in the pairwise additivity approximation using the MCY potential for the water–water interaction and an ab initio analytical potential built by us for the Fe⁺–H₂O interaction. Energy and structural analysis of the generated configurations lead to the prediction of a coordination number of six for the first hydration shell of the Fe⁺ ion, both in clusters and in dilute solution. Finally, the variation in the distance to the Fe⁺ ion of the energy and orientation of water molecules in the solution are discussed.     

Monte carlo simulation of ethane in dilute aqueous solution

A Monte Carlo simulation of a dilute aqueous solution of ethane both fixed and flexible conformation runs shows that energetically and entropically the eclipsed conformation of ethane is preferred to the staggered conformation in solution which is a reversal in the gas phase.     

A Monte Carlo simulation of Fe2+ aqueous solvation

A Monte Carlo simulation of Fe²⁺ aqueous solvation, at 298 K, including 100 water molecules, has been done using periodic boundary conditions under the minimum image conversion. The energy has been calculated in the pair-potential approach, employing the MCY potential for the H₂OH₂O interaction and an ab initio analytical potential generated by us for the Fe²⁺H₂O interaction. The examination of interaction energies and of the radial distribution functions clearly show that the first hydration shell is formed by eight water molecules. By classifying the generated configurations into different significant structures of the solvent, it has been found that the eight water molecules of the first hydration shell are situated in a lightly distorted D_4d structure which maximizes the water—solute stabilization and minimizes the water—water repulsion. Finally, the validity of our theoretical predictions is discussed.     

Nanoscale colloids in a freely adsorbing polymer solution: a Monte Carlo simulation study

A key issue in nanoscale materials and chemical processing is the need for thermodynamic and kinetic models covering colloid-polymer systems over the mesoscopic length scale (approximately 1-100 nm). We have applied Monte Carlo simulations to attractive nanoscale colloid-polymer mixtures toward developing a molecular basis for models of these complex systems. The expanded ensemble Monte Carlo simulation method is applied to calculate colloid chemical potentials (micro(c)) and polymer adsorption (gamma) in the presence of freely adsorbing Lennard-Jones (LJ) homopolymers (surface modifiers). gamma and micro(c) are studied as a function of nanoparticle diameter (sigma(c)), modifier chain length (n) and concentration, and colloid-polymer attractive strength over 0.3 < Rg/sigma(c) < 6 (Rg is the polymer radius of gyration). In the attractive regime, nanocolloid chemical potential decreases and adsorbed amount increases as sigma(c), or n is increased. The scaling of gamma with n from the simulations agrees with the theory of Aubouy and Raphael (Macromolecules 1998, 31, 4357) in the extreme limits of Rg/sigma(c). When Rg/sigma(c) is large, the "colloid" approaches a molecular size and interacts only locally with a few polymer segments and gamma approximately n. When Rg/sigma(c) is small, the system approaches the conventional colloid-polymer size regime where multiple chains interact with a single particle, and gamma approximately sigma(c)2, independent of n. In contrast, adsorption in the mesoscopic range of Rg/sigma(c) investigated here is represented well by a power law gamma approximately n(p), with 0 < p < 1 depending on concentration and LJ attractive strength. Likewise, the chemical potential from our results is fitted well with micro(c) approximately n(q)sigma(c)3, where the cubic term results from the sigma(c) dependence of particle surface area (approximately sigma(c)2) and LJ attractive magnitude (approximately sigma(c)). The q-exponent for micro(c) (micro(c) approximately n(q)) varies with composition and LJ attractive strength but is always very close to the power exponent for gamma (gamma approximately n(p)). This result leads to the conclusion that in attractive systems, polymer adsorption (and thus polymer-colloid attraction) dominates the micro(c) dependence on n, providing a molecular interpretation of the effect of adsorbed organic layers on nanoparticle stability and self-assembly.     

Hybrid Monte Carlo simulations of vertical electronic transitions in acetone in aqueous solution

A simulation of the absorption and the fluorescence of acetone in aqueous solution is reported. The model has an explicit solvent representation with an effective ab initio treatment of the solute. The model attempts to balance quantum chemistry, intermolecular interactions and statistical thermodynamics. It includes a non-electrostatic perturbation on the solute which models the solute–solvent exchange repulsion and the restriction put on the electronic structure of the solute by the antisymmetry to the solvent. The solvent shift to the absorption transition is found to be between 0.16 and 0.21 eV; the shift to the fluorescence transition is found to be between 0.02 and 0.05 eV. The simulation supports the conclusion that the first peak in the fluorescence spectrum of acetone is from a single molecule in equilibrium with the solvent, not from an excimer.     

Short and straightforward synthesis of 1,7-dimethyl-1,4,7,10-tetraazacyclododecane

A novel, cost-effective, and efficient process for the synthesis of 1,7-dimethyl-1,4,7,10-tetraazacyclododecane 1 has been developed. The two-step process involved the selective conversion of commercially available cyclen to N1,N7-diethylcarbamate cyclen 3 that afforded the title compound in high yield after the reduction step.     

Synthesis and crystal structure of a Ni(II)complex with 1,7-diaminoethyl-4,10-dimethyl-1,4,7,10-tetraazacyclododecane

The crystal structure of a. Ni(II) complex with 1,7-diaminoethyl-4,10-dimethyl-1,4,7,10-tetraazacyclododecane has been determined by X-ray diffraction method. Crystal data for NiC14H38Br2N6O: monoclinic, space group P21/n, a=0.8848(3), b=1.4656(3), c=1.5828(3) nm, β=90.47(3)°, V=2.0525 nm3, Z=4. The two pendant primary amino groups are located in cis positions in the complex, "their nitrogen atoms and the four nitrogen donors of the foled tetraaza-macrocycle coordinate Ni(II) ion, forming a distorted octahedral geometry.     

Synthesis and acid-base and complex-forming properties of 1,4,7,10-tetrakis(dihydroxyphosphorylmethyl)-1,4,7,10-tetraazacyclododecane

Conclusions A new complexone, 1,4,7,10-tetrakis(dihydroxyphosphorylmethyl)-1,4,7,10-tetraazacyclododecane, has been synthesized and its acid-base and complex-forming properties have been studied. It shows a very high complexing capability and marked selectivity for cations of large ionic radius (Cd²⁺, Hg²⁺, Pb²⁺, La³⁺).Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 844–849, April, 1984.     

Monte Carlo simulation of DNA electrophoresis

This paper describes an attempt to study the electrophoresis mobility of a DNA molecule in a gel by means of a Monte Carlo simulation. We find that the electrophoresis mobility mu can be well described by the empirical equation mu v kappa 1/N + kappa 2E2 with N being the number of monomers of the model chain and E being the applied field. For small E the data can merge into the linear response result mu = kappa 1/N. The paper also discusses necessary extensions of the present approach.     

Monte Carlo simulation of osmotic equilibria

We present a Metropolis Monte Carlo simulation algorithm for the Tpπ-ensemble, where T is the temperature, p is the overall external pressure, and π is the osmotic pressure across the membrane. The algorithm, which can be applied to small molecules or sorption of small molecules in polymer networks, is tested for the case of Lennard-Jones interactions.     

Monte Carlo simulation of polymer welding

Monte Carlo Modelling of random polymer chains, course grained onto a cubic F lattice, provides the ability to monitor the long range relaxation processes and the dynamic parameters of chains up to 400 units long. The model, described and verified by Haire et al. (Haire KR, Carver TJ, Windle AH. A Monte Carlo model for dense polymer systems and its interlocking with molecular dynamics simulation. Computational and Theoretical Polymer Science 2000; in press), is here applied to the study of molecular parameters in the vicinity of different types of surface and also to the process of polymer welding, whereby adhesion between two adjacent surfaces is achieved by the interpenetration of chains which are across the surface.The model demonstrates that a surface distorts the conformation of chains adjacent to it to give an oblate molecular envelope, that the concentration of vacant sites and chain ends increases near to the surface and that the density of points representing the centres of mass of the chains increases in the sub-surface regions. These results confirm earlier predictions and provide additional confidence in the model.Modelling of the welding process leads to the parameter intrinsic weld time, t_w, which is the time from initial perfect contact of the surfaces to the achievement of a weld within which the chain conformation is indistinguishable from the bulk. After the initial period in which the mating surfaces roughen, the welding proceeds according to the t^1/4 law predicted by reptation theory. The time to a given level of interdiffusion across the boundary is proportional to the chain length l, a comparatively weak dependence, while t_w is proportional to l³, a strong dependence. This is the same dependence on length as for the relaxation time of the chain end-to-end vectors. In fact, the agreement between the relaxation time, measured on the model of the bulk, and t_w is surprisingly close, at least for the monodisperse polymers investigated here.     

Monte Carlo simulation of polymer adsorption

We developed and employed the incremental gauge cell method to calculate the chemical potential (and thus free energies) of long, flexible homopolymer chains of Lennard-Jones beads with harmonic bonds. The free energy of these chains was calculated with respect to three external conditions: in the zero-density bulk limit, confined in a spherical pore with hard walls, and confined in a spherical pore with attractive pores, the latter case being an analog of adsorption. Using the incremental gauge cell method, we calculated the incremental chemical potential of free polymer chains before and after the globual-random coil transitions. We also found that chains confined in attractive pores exhibit behaviors typical of low temperature physisorption isotherms, such as layering followed by capillary condensation.     

Interaction between small colloidal particles and polymer chains in a semidilute solution: Monte Carlo simulation

 Interaction between flexible-chain polymers and small (nanometric) colloidal particles is studied by Monte Carlo simulation using two-dimensional and three-dimensional lattice models. Spatial distribution of colloidal particles and conformational characteristics of chains in a semidilute solution are considered as a function of the segment adsorption energy, ɛ. When adsorption is sufficiently strong, it induces effective attraction of polymer segments, which results in contraction of macromolecular coils. The strongly adsorbing polymer chains affect the equilibrium spatial distribution of the colloidal particles. The average size of colloidal aggregates <m> exhibits a nontrivial behavior: with ɛ increasing, the value of <m> first decreases and then begins to grow. The adsorption polycomplex formed at strong adsorption exhibits a mesoscopic scale of structural heterogeneity. The results of computer simulations are in a good agreement with predictions of the analytic theory [P.G. Khalatur, L.V. Zherenkova and A.R. Khokhlov (1997) J Phys II (France) 7:543] based on the integral RISM equation technique. Received: 4 August 1997 Accepted: 16 April 1998