DIADORIM: a Monte Carlo Program for liquid simulations including quantum mechanics and molecular mechanics (QM/MM) facilities: applications to liquid ethanol

Abstract

Um programa computacional para a simulação de líquidos e soluções utilizando o Método de Monte Carlo com algoritmo de Metropolis (MMC) é apresentado. Neste programa a energia total de interação é dividida em clássica e quântica, QM/MM: a contribuição clássica é obtida utilizando campo de força e a contribuição quântica é calculada utilizando métodos de química quântica. As seguintes facilidades foram implementadas: (i) o programa MOPAC 6 foi incorporado como uma sub-rotina do programa principal; (ii) alternativamente, um banco de dados de energias previamente obtidas pode ser utilizado; (iii) Simulações nos ensembles isotérmico e isobárico, NpT, e canônico, NVT, podem ser realizadas; (iv) a trajetória obtida ao longo do processo de MMC pode ser armazenada em disco rígido, utilizando o formato xtc, para análise e visualização utilizando outros programas. O programa foi utilizado para calcular propriedades estruturais e termodinâmicas do líquido etanol no ensemble NpT a 1,0 atm e 298 K. Distâncias e ângulos de ligação das moléculas de etanol foram mantidos constantes, mas amostragem do ângulo diedral definido pelos átomos H-O-C-C foi efetuada. Para calcular a energia interna em função deste ângulo foram utilizados os métodos AM1, PM3 e MNDO implementados no programa MOPAC 6. Cálculos também foram efetuados utilizando energias obtidas com HF/6-31g*, MP2/6-31g* e B3LYP/6-31g*. Diferenças significativas foram observadas na distribuição dos ângulos diedrais na fase líquida. Entretanto, distribuições de energia para as interações de pares são muito semelhantes, o mesmo acontecendo com as distribuições radiais de pares. Resultados obtidos para a densidade e calor de vaporização do líquido estão em ótimo acordo com dados experimentais. This paper presents a Metropolis Monte Carlo (MMC) computer program developed to simulate liquids and solutions including QM/MM facilities: the energy from intermolecular interactions is calculated with classical force field functions and the internal molecular energies are calculated using Quantum Chemistry methods. The following facilities were implemented: (i) the semiempirical MOPAC 6 quantum chemistry package was included as a subroutine of the main MMC simulation program; (ii) alternatively, an interface with an external data bank was developed to allow the use of energies previously obtained; (iii) calculation in NpT and NVT ensembles are available; (iv) the trajectory generated along the MMC sampling can be saved using standard xtc file format allowing trajectory visualization and data analysis using external programs. The program was used to calculate thermodynamical and structural properties of liquids ethanol (ET) in the NpT ensemble at 1.0 atm and 298 K. Bond angles and bond distances of ethanol molecules were kept constant but torsions along the dihedral angle defined by the H-O-C-C atoms were sampled in the simulation. QM/MM calculations were performed using the MOPAC AM1, PM3 and MNDO Hamiltonians to calculate the internal molecular energy. Calculations using internal energi...

A hybrid neutron diffraction and computer simulation study on the solvation of N-methylformamide in dimethylsulfoxide

“…5 is shown the pair energy distribution from the simulation box for the intermolecular interaction between the NMF and the DMSO molecules, obtained using a protocol previously reported. 58 As is standard in H-bonded liquids, 24 it is noted a first distribution of pairs, at very negative energy, attributed to the H-bonded pairs followed for a most likely set of pairs with energies in the range of about 0.0 and −2.0 kcal/mol. Nevertheless, different from other H-bonded liquids including pure water, 24 ethanol, 58 and the NMF itself, 34 the pair energy distribution of the NMF-DMSO mixture presents a shoulder around −5.5 kcal/mol, suggesting the presence of a particular kind of stable dimers in the mixture.…”

“…As the results indicate, these H-bonded molecules are less stable than the OD H-bonded ones, as it should be expected, considering the characteristics of the two different electronegative atoms concerned. For better elucidating the detail of the liquid structure, the dipole-dipole correlation between the NMF and DMSO in the mixture was calculated using the same routine as above 58 and the cos θ (where θ is the angle between the vector of the molecular dipole moments of the two molecules under consideration) was plotted as a function of the distance between the molecules. The result is seen in Fig.…”

“…For detailing the pair distribution energy and the dipole moment correlation, the simulation box has been scanned using a Monte Carlo protocol reported in Ref. 58.…”

A Monte Carlo revisiting of N-methylformamide and acetone

“…The simulations were carried out in the NPT ensemble at 298 K and 1 atm, with Metropolis importance sampling and periodic boundary conditions 63 on systems consisting of a cubic box containing 400 molecules. In calculating the total configurational energy using equation 1, a full intermolecular interaction was considered whenever the rij site-to-site distance was inside a cutoff radius of 11 Å. Lennard-Jones potential contributions due to interactions beyond the cutoff radius were calculated using the formalism presented elsewhere.…”

“…19 Thus, taking into account that from the point of view of the g(r) plots the model is able to reproduce the structure of the liquid, one may use the liquid simulations to further explore the intermolecular interactions. As a starting point, the pair energy distribution along the simulation pathway for the intermolecular correlations was calculated, and the results are shown in Figure 2.At first glance, the pairwise energy is significantly more negative than for other organic polar liquids, as for instance ethanol, 63 and the bimodal shape of the curve is characteristic of liquids with H-bonding between the molecules, as previously noticed 19,67 (the comparison with the curve obtained for acetone, shown later, will better illustrate this point). Thus, there are preponderantly two kinds of molecular correlation, molecules that are hydrogen-bonded to each other and molecules that are correlated through another kind of interaction.…”