1,721,002 research outputs found
Parameterization and validation of intramolecular force fields derived from DFT calculations
No full textThe energy and its first and second geometrical derivatives obtained by DFT calculations for a number of conformations of a single molecule are used to parametrize intramolecular force fields, suitable for computer simulations. A systematic procedure is proposed to adequately treat either fully atomistic or more simplified force fields, as within the united atom approach or other coarse grained models. The proposed method is tested and validated by performing molecular dynamics simulations on several different molecules, comparing the results with literature force fields and relevant experimental data. Particular emphasis is given to the united atom approach for flexible molecules characterized by "soft" torsional potentials which are known to retain a high degree of chemical specificity
Torsional barriers and correlations between dihedrals in p-polyphenyls
No full textThe torsional energy curves for biphenyl, p-terphenyl, and p-quaterphenyl are calculated using the B3LYP density functional with a triple-zeta polarized basis set. In agreement with recent accurate literature data, barriers of similar height are found at 0degrees and 90degrees for biphenyl. For the higher members, the torsional energy curves show an increasing tendency to lower the barrier of the coplanar conformations. The correlation effects between different dihedrals are reasonably small and discussed extensively. In addition, torsional potential functions at different levels of accuracy, suitable for computer simulations, are proposed for all the members of the series up to p-quinquephenyl
Subdiffusive dynamics of a liquid crystal in the isotropic phase
No full textThe isotropic phase dynamics of a system of 4-n-hexyl-4'-cyano-biphenyl (6CB) molecules has been studied by molecular dynamics computer simulations. We have explored the range of 275-330 K keeping the system isotropic, although supercooled under its nematic transition temperature. The weak rototranslational coupling allowed us to separately evaluate translational (TDOF) and orientational degrees of freedom (ODOF). Evidences of subdiffusive dynamics, more apparent at the lowest temperatures, are found in translational and orientational dynamics. Mean square displacement as well as self-intermediate center of mass and rotational scattering functions show a plateau, also visible in the orientational correlation function. According to the mode coupling theory (MCT), this plateau is the signature of the beta-relaxation regime. Three-time intermediate scattering functions reveal that the plateau is related to a homogeneous dynamics, more extended in time for the orientational degrees of freedom (up to 1 ns). The time-temperature superposition principle and the factorization property predicted by the idealized version of MCT hold, again for both kinds of dynamics. The temperature dependence of diffusion coefficient and orientational relaxation time is well described by a power law. Critical temperatures T(c) are 244 +/- 6 and 258 +/- 6 K, respectively, the latter is some 10 K below the corresponding experimental values. The different values of T(c) we obtained indicate that ODOF freezes earlier than TDOF. This appears due to the strongly anisotropic environment that surrounds a 6CB molecule, even in the isotropic phase. The lifetime of these "cages," estimated by time dependent conditional probability functions, is strongly temperature dependent, ranging from some hundreds of picoseconds at 320 K to a few nanoseconds at 275 K
Force-field modeling through quantum mechanical calculations: molecular dynamics simulations of a nematogenic molecule in its condensed phases
No full textInteraction energy of the 4-n-pentyloxy-4'-cyanobiphenyl (5OCB) dimer is Computed at MP2 level, for many geometrical arrangements using the Fragmentation Reconstruction Method (FRM). DFT calculations are performed for a number of geometries of the monomer. The resulting database is used to parameterize an atomistic intra- and inter-molecular force-field suitable for classical bulk simulations. Several structural and dynamical properties in 5OCB isotropic and liquid crystalline phases are computed from molecular dynamics simulation mainly in the NPT ensemble. Lengthy runs (more than 70 us) and large sample sizes (up to 806 molecules) were used to determine the nematic to isotropic transition temperature up to a precision of few K. Good agreement was found in most of the investigated properties, thus validating the accuracy of the proposed model potential. only derived by quantum mechanical calculations
Solvent-Induced Stereochemical Behavior of a Bile Acid-Based Biphenyl Phosphite: A Computational Study
No full textThe origin of the stereochemical behavior experimentally found in a bile acid-derived biphenyl phosphite is studied by means of quantum mechanical methods. The molecular mechanisms driving the screw sense of the dihedral angle between the two phenyl rings of the biphenyl phosphite unit are investigated with density functional theory calculations. Energy, geometry, and circular dichroism spectra have been computed and compared between the two resulting diastereoisomers. We evaluated the solvent effect on the torsional energy profile by discussing the results obtained for the isolated molecule with those found with polarizable continuum model (PCM) calculations performed in different solvents. The results we obtain with the PCM model do not reproduce the solvent effect on the stereochemical equilibrium of this phosphite
Geometry optimization of large and flexible van der Waals dimers: a Fragmentation-Reconstruction Approach
No full textA novel approach for exploring the energy minima of the potential energy surface of large and flexible van der Waals dimers is proposed and tested The total dimer energy is divided into intra- and intermolecular contributions, which can be computed at different levels of theory The intermolecular energy, which is the time-consuming part of the calculation, is computed by means of the fragmentation reconstruction method (FRM), making possible the calculation of the interaction energy of large molecules The method is validated by performing geometry optimizations through a quasi-Newton technique on two benchmark medium-sized systems, where the comparison with a direct ab initio calculation is still computationally feasible In both cases, good agreement is achieved between geometries and energies of the resulting energy minima
Atomistic computer simulation and experimental study on the dynamics of the n-cyanobiphenyls mesogenic series
No full textSeveral dynamic properties of the 4-n-alkyl-4'-cyanobiphenyls series (nCB) with n = 5, 6, 7, 8 have been studied by atomistic molecular dynamics (MD) simulations in the NVE ensemble adopting an ab initio derived force field (J. Phys. Chem. B 2007, 111, 2130). For each homologue, at least two state points, in the nematic and in the isotropic phase, as determined from lengthy equilibration runs performed in the previous work, have been considered. More than 10 ns have been produced at each state point, allowing us to calculate single-molecule properties as the translational and rotational diffusion coefficients along the series. An oscillating behavior of the diffusion coefficients, similar to the observed odd-even effect in static properties, has been predicted by MD. A good agreement with the results of purposely carried out (1)H NMR measurements is achieved, provided the MD values are increased by a factor that accounts for density overestimation. Spinning and tumbling rotational motions, monitored by calculating the rotational diffusion coefficients for all homologues in both phases, agree well with experimental data, at least for 5CB where NMR measures are reported. Collective properties, such as the isotropic shear viscosity and the rotational viscosity coefficient, have been computed for all homologues, and the MD values agree well with the experimental data reported in the literature. Finally, the origin of the odd-even effect, found for all the computed dynamic properties, is addressed
An automated approach for the parameterization of accurate intermolecular force-fields. Pyridine as a case study
No full textAn automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts
Simulating DNA Hybridization on an Amine-Functionalized Silicon Substrate
No full textThe ability of DNA biosensors to capture oligonucleotide molecules in solution is of great importance in genetics, medical diagnostics, and drug discovery. The DNA hybridization event in which the probe, which is usually a single-stranded DNA segment covalently immobilized on a functionalized surface via a crosslinker molecule, recognizes the complementary target and forms a stable duplex structure is the basis of highly specific biorecognizing devices. The rate of hybridization depends on the solvent, length of the strands, complexity of the system, and other factors and could be considerably altered by the type of attachment and by the density of the probe on the substrates. Recent experimental investigations have shown that some probes can hybridize directly from bulk solutions. In this computational study, we provide a model for the behavior of these systems choosing cross-linker, probe, and target on the basis of experimental data. MD simulations of the single-stranded DNA fragment 5'-d(TGGC)-3' attached to an allylamine-functionalized Si(111) surface through an oxanine cross-linker in aqueous solution containing the complementary sequence, i.e. 5'-d(CGCCA)-3', are presented. A possible probe target capture mechanism obtained using explicit solvent and state-of-the-art classical molecular dynamics simulation protocols is described. The hybridization process of the tethered DNA single strand, the intermediate structures appeared during the formation of the double helix, their internal dynamics and their behavior with respect to the substrate are characterized in detail
An Integrated Protocol for the Accurate Calculation of Magnetic Interactions in Organic Magnets
No full textA new, fast, and efficient computational protocol for the accurate calculation of singlet triplet magnetic splittings in organic diradicals is tested and validated. This procedure essentially consists of three steps: the adoption of modified virtual orbitals (MVO) and a mixed variational-perturbational approach (CSPA) are now combined with a third method that exploits the reduction of the configurational space dimensions achieved by fragmentation/localization criteria. This innovative approach is successfully tested on four different substituted m-phenylene bis(tert-butyl) nitroxides, which show paramagnetic behavior, by computing singlet triplet energy gaps and comparing them with their experimental counterparts
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