X-ray scattering and density-functional theory calculations to study the presence of hydrogen-bonded clusters in liquid N-methylacetamide

Force fields optimized against experimental data for large compound families using CombiFF: Validation considering non-target properties and polyfunctional compounds

The CombiFF scheme is a workflow for the automated calibration of force-field parameters against condensed-phase experimental data considering simultaneously entire classes of organic molecules. The main steps of this scheme are: (i) selection of a molecule family; (ii) enumeration of all isomers; (iii) query for experimental data; (iv) automatic construction of the molecular topologies; (v) iterative refinement of the force-field parameters considering the entire family. In two recent articles, CombiFF was applied to the design of GROMOS-compatible united-atom force fields for the saturated acyclic haloalkanes and for saturated acyclic compounds involving eight common chemical functional groups of oxygen and nitrogen. This calibration and the subsequent initial validation involved two limitations: (i) the experimental data considered was restricted to values for the pure-liquid density ρ_liq and the vaporization enthalpy ΔH_vap of the compounds; (ii) beyond monofunctional compounds, the training set only involved homo-polyhaloalkanes (possibly mixing halogen types) in the first study, and homo-polyfunctional compounds of the considered oxygen or nitrogen functional groups (no mixing of different group types) in the second one. The goal of this article is to further test the accuracy of CombiFF-generated force fields by extending the validation to: (i) nine additional properties that were not used as optimization targets (pure-liquid thermodynamic, dielectric and transport properties, as well as solvation properties); (ii) hetero-polyfunctional molecules that were not included in the calibration and initial validation sets. The results for the nine additional properties show good agreement with experiment, except for the shear viscosity and the dielectric permittivity. There, larger discrepancies are observed, likely due to the united-atom representation adopted for the aliphatic groups and to the implicit treatment of electronic polarization effects. The results for the hetero-polyfunctional molecules also show reasonable agreement with experiment in terms of the monitored properties.

Correcting the record: the dimers and trimers of trans-N-methylacetamide

Raman jet spectroscopy reveals three N-methylacetamide molecules organizing into a ring structure, previously overlooked in computations.

An innovative synergistic grid approach to the computational study of protein aggregation mechanisms

Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.

Understanding the dielectric properties of liquid amides from a polarizable force field

The role played by electronic polarization in the dielectric properties of liquid N-methyl acetamide (NMA) is examined using molecular dynamics simulations with a polarizable force field based on classical Drude oscillators. The model presented is the first force field shown to reproduce the anomalously large dielectric constant of liquid NMA. Details of the molecular polarizability are found to be important. For instance, all elements of the polarizability tensor, rather then just the trace, impact on the condensed phase properties. Two factors related to electronic polarizability are found to contribute to this large dielectric constant. First is the significant enhancement of the mean amide molecular dipole magnitude, which is 50% larger in the liquid than in the gas phase. Second is the consequent strong hydrogen bonding between molecular neighbors that enhances the orientational alignment of the molecular dipoles. Polarizable models of amide compounds that have two (acetamide) and zero (N,N-dimethyl acetamide) polar hydrogen-bond donor atoms are also investigated. Experimentally, the neat liquid dielectric constants at 373 K are 100 for NMA, 66 for acetamide and 26 for N,N-dimethyl acetamide. The polarizable models replicate this trend, predicting a dielectric constant of 92+/-5 for NMA, 66+/-3 for acetamide and 23+/-1 for N,N-dimethyl acetamide.

The Ultrafast Dynamics of Hydrogen-Bonded Liquids: Molecular Structure-Dependent Occurrence of Normal Arrhenius or Fractional Stokes−Einstein−Debye Rotational Diffusive Relaxation

The ultrafast rotational-diffusive dynamics of the peptide linkage model compounds N-methylacetamide (NMA), acetamide (Ac), and N,N-dimethylacetamide (DMA) have been studied as a function of temperature using optically heterodyne-detected optical Kerr effect (OHD-OKE) spectroscopy. Both NMA and Ac exhibit a non-Arrhenius temperature dependence of the rotational diffusive relaxation time. By contrast, the non-hydrogen-bonding DMA exhibits normal hydrodynamic behavior. The unusual dynamics of NMA and Ac are attributed to the decoupling of single-molecule rotational diffusive relaxation from the shear viscosity via a transition between stick and slip boundary conditions, which arises from local heterogeneity in the liquid due to the formation of hydrogen-bonded chains or clusters. This provides new insight into the structure and dynamics of an important peptide model compound and the first instance of such a phenomenon in a room-temperature liquid. The OHD-OKE responses of carboxylic acids acetic acid (AcOH) and dichloroacetic acid (DCA) are also reported. These, along with the terahertz Raman spectra, show no evidence of the effects observed in amide systems, but display trends consistent with the presence of an equilibrium between the linear and cyclic dimer structures at all temperatures and moderate-to-high mole fractions in aqueous solution. This equilibrium manifests itself as hydrodynamic behavior in the liquid phase.

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes

A polarizable intermolecular potential function (PIPF) employing the Thole interacting dipole (TID) polarization model has been developed for liquid alkanes and amides. In connection with the internal bonding terms of the CHARMM22 force field, the present PIPF-CHARMM potential provides an adequate description of structural and thermodynamic properties for liquid alkanes and for liquid amides through molecular dynamics simulations. The computed heats of vaporization and liquid density are within 1.4% of experimental values. Polarization effects play a major role in liquid amides, which are reflected by an increase of 1.5 to 1.8 D in molecular dipole moment for primary and secondary amides. Furthermore, the computed polarization energies contribute to the total intermolecular interaction energy by 6 to 24%. The ability of the PIPF-CHARMM force field to treat protein backbone structures is tested by examining the potential energy surface of the amide bond rotation in N-methylacetamide and the Ramachandran surface for alanine dipeptide. The agreement with ab initio MP2 results and with the original CHARMM22 force field is encouraging, suggesting the PIPF-CHARMM potential can be used as a starting point to construct a complete polarizable force field for proteins.

Local Order in Fully Deuterated Liquid N-Methylacetamide (C3D7NO) As Studied by Neutron Diffraction and Density-Functional Theory Calculations

A structural investigation of fully deuterated liquid N-methylacetmide (NMAd7) is performed at 308 K and atmospheric pressure by using neutron diffraction together with density-functional theory (DFT). The analysis of experimental data yields the total structure factor SM(Q), the molecular form factor F1(Q), and the distinct pair correlation function gL(r). The DFT calculations are performed to study the relative stability of the two possible isomers (trans and cis) and to examine some possible clusters recently published that may describe the intermolecular arrangement in the liquid state. Neutron measurements can be interpreted in terms of trans linear trimer (T1) and cis cyclic trimer (T2) where the total number of hydrogen bonds is respectively equal to two and three. The theoretical structure factors obtained on the basis of intermolecular arrangements agree fairly well with the experimental one beyond Q = 2 A-1. All through the study, a comparison is made with complementary X-ray results.