Aatto Laaksonen

M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures

A general purpose, scalable parallel molecular dynamics package for simulations of arbitrary mixtures of flexible or rigid molecules is presented. It allows use of most types of conventional molecular-mechanical force fields and contains a variety of auxiliary terms for inter- and intramolecular interactions, including an harmonic bond-stretchings. It can handle both isotropic or ordered systems. Besides an NVE MD ensemble, the simulations can also be carried out in either NVT or NPT ensembles, by employing the Nose–Hoover thermostats and barostats, respectively. If required, the NPT ensemble can be generated by maintaining anisotropic pressures. The simulation cell can be either cubic, rectangular, hexagonal or a truncated octahedron, with corresponding periodic boundary conditions and minimum images. In all cases, the optimized Ewald method can be used to treat the Coulombic interactions. Double time-step or constrained dynamics schemes are included. An external electric field can be applied across the simulation cell. The whole program is highly modular and is written in standard Fortran 77. It can be compiled to run efficiently both on parallel and sequential computers. The inherent complexity of the studied system does not affect the scalability of the program. The scaling is good with the size of the system and with the number of processors. The portability of the program is good, it runs regularly on several common single- and multiprocessor platforms, both scalar and vector architectures included.

Sorbents for CO2 capture from flue gas—aspects from materials and theoretical chemistry

Predictions of future climate change have triggered a search for ways to reduce the release of greenhouse gases into the atmosphere. Carbon capture and storage (CCS) assists this goal by reducing carbon dioxide emissions, and CO(2) adsorbents in particular can reduce the costs of CO(2) capture. Here, we review the nanoscale sorbent materials that have been developed and the theoretical basis for their function in CO(2) separation, particularly from N(2)-rich flue gases.

Hydration of Li+ ion. An ab initio molecular dynamics simulation

Ab initio Car–Parrinello molecular dynamics simulations of a Li+ ion in water have been carried out using the density-functional theory with Becke–Lee–Yang–Parr (BLYP) functional and ultrasoft Vanderbildt pseudopotentials. Both structural and dynamical properties of Li+ have been studied in detail and compared with available neutron scattering and spectroscopic data. Excellent agreement is obtained with the existing experimental data for the structure of the first hydration shell around the Li+ ion. Spectral features of bound water are compared to those of bulk water. Reasonable agreement is obtained with IR and Raman experiments. The ab initio simulation results have also been used to derive a Li+–water interaction potential. The best fit of the data gave a simple single-exponential potential function, which reproduces very well the liquid structure from the original ab initio simulations. This potential model, together with the simple point charge (SPC) water model, was applied to calculate the hydratio...

On the Competition between Water, Sodium Ions, and Spermine in Binding to DNA: A Molecular Dynamics Computer Simulation Study

The interaction of DNA with the polyamine spermine(4+) (Spm(4+)), sodium ions, and water molecules has been studied using molecular dynamics computer simulations in a system modeling a DNA crystal. The simulation model consisted of three B-DNA decamers in a periodic hexagonal cell, containing 1200 water molecules, 8 Spm(4+), 32 Na(+), and 4 Cl(-) ions. The present paper gives a more detailed account of a recently published report of this system and compares results on this mixed Spm(4+)/Na(+)-cation system with an molecular dynamics simulation carried out for the same DNA decamer under similar conditions with only sodium counterions (Korolev et al., J. Mol. Biol. 308:907). The presence of Spm(4+) makes significant influence on the DNA hydration and on the interaction of the sodium ions with DNA. Spermine pushes water molecules out of the minor groove, whereas Na(+) attracts and organizes water around DNA. The major binding site of the Spm(4+) amino groups and the Na(+) ions is the phosphate group of DNA. The flexible polyamine spermine displays a high presence in the minor groove but does not form long-lived and structurally defined complexes. Sodium ions compete with Spm(4+) for binding to the DNA bases in the minor groove. Sodium ions also have several strong binding sites in the major groove. The ability of water molecules, Spm(4+), and Na(+) to modulate the local structure of the DNA double helix is discussed.

NaKA sorbents with high CO2-over-N2 selectivity and high capacity to adsorb CO2

The uptake of carbon dioxide and nitrogen gas by zeolite NaKA was studied. A very high ideal CO(2)-over-N(2) selectivity and a high CO(2) capacity were observed at an optimal K(+) content of 17 at.%. NaKA is a very promising adsorbent for CO(2) separation from water-free flue gases.

Molecular dynamics simulation of a nematic liquid crystal

The article describes molecular dynamics simulations of 4‐n‐pentyl‐4’‐cyanobiphenyl (5CB) in the nematic phase at 300 K using two interaction models. The first model comprises united atoms, while in the second, shorter simulation, the hydrogen atoms are explicitly included. Liquid crystalline order parameters were calculated using various definitions of molecular frames and were found to be in reasonable agreement with experiments. Distributions of dihedral angles and relative populations of various conformations in the alkyl chain have been determined. Translational and rotational diffusion processes were investigated using time correlation functions, and were compared with experimental results. Local order parameters, relevant for deuterium nuclear magnetic resonance (NMR) spectra, were determined for the segments in the alkyl chain. Proton NMR line shapes were calculated from the trajectory using an approximate method for determination of the dipole–dipole Hamiltonian matrix. These line shapes were fou...

Finite perturbation–configuration interaction calculations of nuclear spin–spin coupling constants. I. The first row hydrides and the hydrogen molecule

The finite perturbation scheme for calculations of nuclear spin–spin couplings based on the numerical computation of the second derivative of the total energy is described and compared to the earlier approach which uses the first derivative of the spin density matrix. The method is applied, at the Hartree–Fock and configuration interaction level of approximation, to calculations of the Fermi contact contribution to proton–proton and proton–first‐row‐atom coupling constants in H2, HF, H2O, NH3, and CH4. The analysis and the numerical calculations prove that for the many‐electron systems the finite perturbation method is superior to the conventional second order perturbation theory approach if the same type of CI expansion is used. For the hydrogen molecule the two methods have to give identical results. The finite perturbation calculations for the first row hydrides show the following: (i) Upon going from the Hartree–Fock to the CI level the contact contributions are reduced by about 50% for the proton–pro...

The electronic properties of water molecules in water clusters and liquid water

Abstract A novel, self-consistent approach, applicable both for ground and excited electronic states, is introduced to calculate molecular properties in clusters and liquids. Using the method, carried out here at the second-order Moller–Plesset perturbation theory (MP2) level, we obtain an average dipole moment of 2.65 D for water in liquid. Significant changes in quadrupole moment and polarizability, due to surrounding molecules, are also found along the water plane in the direction perpendicular to the axis bisecting the H–O–H bond angle.

Systematic coarse-graining of molecular models by the Newton inversion method

Systematic construction of coarse-grained molecular models from detailed atomistic simulations, and even from ab initio simulations is discussed. Atomistic simulations are first performed to extract structural information about the system, which is then used to determine effective potentials for a coarse-grained model of the same system. The statistical-mechanical equations expressing the canonical properties in terms of potential parameters can be inverted and solved numerically according to the iterative Newton scheme. In our previous applications, known as the Inverse Monte Carlo, radial distribution functions were inverted to reconstruct pair potential, while in a more general approach the targets can be other canonical averages. We have considered several examples of coarse-graining; for the united atom water model we suggest an easy way to overcome the known problem of high pressure. Further, we have developed coarse-grained models for L- and D-prolines, dissolved here in an organic solvent (dimethylsulfoxide), keeping their enantiomeric properties from the corresponding all-atom proline model. Finally, we have revisited the previously developed coarse-grained lipid model based on an updated all-atomic force field. We use this model in large-scale meso-scale simulations demonstrating spontaneous formation of different structures, such as vesicles, micelles, and multi-lamellar structures, depending on thermodynamical conditions.

Surface tension of water droplets: A molecular dynamics study of model and size dependencies

The applicability of two frequently used interaction potentials for water, the five-site ST2 model and the four-site TIP4P model, is investigated in computer simulations of water droplets of varying cluster size from N=64 to N=512. The orientation of the water molecules in the surface region is investigated for the both models. Surface properties, such as work of cluster formation, local density profiles, kinetic and total energy profiles, and pressure profiles as a function of the droplet size, obtained using the two models are compared. Moreover, the surface potential and the electric potential profiles are calculated. Surface tension is calculated and its dependence on the cluster size is investigated. It is found that surface properties are very sensitive to the used potential models. For example, the water molecules are found to lie differently in the inner region of the surface layer, the ST2 molecules being predominantly perpendicular to the surface, while the TIP4P molecules lie mainly parallel to...