Planarity of N,N-Dimethylacetamide, (CH3)2NC(O)CH3

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

A comparison of the molecular and crystal structures of the dimethylacetamide complexes from zinc chloride, bromide, and iodide

The dimethylacetamide complexes ZnCl2(dma)2 and ZnI2(dma)2 crystallise according to the respective space groups P212121 and P21/c. The molecules of the two compounds are conformationally different through differing ligand rotations about the Zn-O bonds. These are such as to enable a molecular packing in which there is a balance of the predominant CH3--X attractions and CH3--CH3 repulsions. The bromide is P¯1 triclinic, now with two conformationally different molecules in the asymmetric unit, but its molecular packing is similar to that of the iodide, again to balance the same attractions and repulsions. Approach distances to the amide carbon atoms are discussed.

Solvation Properties of N-Substituted Cis and Trans Amides Are Not Identical: Significant Enthalpy and Entropy Changes Are Revealed by the Use of Variable Temperature 1H NMR in Aqueous and Chloroform Solutions and ab Initio Calculations

The cis/trans conformational equilibrium of N-methyl formamide (NMF) and the sterically hindered tert-butylformamide (TBF) was investigated by the use of variable temperature gradient 1H NMR in aqueous solution and in the low dielectric constant and solvation ability solvent CDCl3 and various levels of first principles calculations. The trans isomer of NMF in aqueous solution is enthalpically favored relative to the cis (deltaH(o) = -5.79 +/- 0.18 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = -0.23 +/- 0.17 kJ mol(-1)) playing a minor role. The experimental value of the enthalpy difference strongly decreases (deltaH(o) = -1.72 +/- 0.06 kJ mol(-1)), and the contribution of entropy at 298 K (298 x deltaS(o) = -1.87 +/- 0.06 kJ mol(-1)) increases in the case of the sterically hindered tert-butylformamide. The trans isomer of NMF in CDCl3 solution is enthalpically favored relative to the cis (deltaH(o) = -3.71 +/- 0.17 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = 1.02 +/- 0.19 kJ mol(-1)) playing a minor role. In the sterically hindered tert-butylformamide, the trans isomer is enthalpically disfavored (deltaH(o) = 1.60 +/- 0.09 kJ mol(-1)) but is entropically favored (298 x deltaS(o) = 1.71 +/- 0.10 kJ mol(-1)). The results are compared with literature data of model peptides. It is concluded that, in amide bonds at 298 K and in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side chains, the free energy difference of the cis/trans isomers and both the enthalpy and entropy contributions are strongly dependent on the N-alkyl substitution and the solvent. The significant decreasing enthalpic benefit of the trans isomer in CDCl3 compared to that in H2O, in the case of NMF and TBF, is partially offset by an adverse entropy contribution. This is in agreement with the general phenomenon of enthalpy versus entropy compensation. B3LY/6-311++G** and MP2/6-311++G** quantum chemical calculations confirm the stability orders of isomers and the deltaG decrease in going from water to CHCl3 as solvent. However, the absolute calculated values, especially for TBF, deviate significantly from the experimental values. Consideration of the solvent effects via the PCM approach on NMF x H2O and TBF x H2O supermolecules improves the agreement with the experimental results for TBF isomers, but not for NMF.

What we can learn about fast chemical processes from slow diffraction experiments

The potential energy surface is an important determinant of a chemical reaction. Three ways of deducing non-trivial properties of such surfaces from the results of crystal structure analyses are discussed and illustrated with examples. (1) The mapping approach brings together structures of the same molecular fragment from different environments to outline reaction coordinates and vibrations. (2) Correlations between molecular structures and activation energies for a given reaction type reveal general and quantitative relations between seemingly independent entities such as ground state structure, force constants, reaction path length, activation energy and catalysis. (3) The evolution of atomic mean square amplitudes (displacement parameters) with temperature uncovers frequencies and atomic displacement patterns of large-amplitude vibrations in molecular crystals. Examples include the vibrations of molecular zeolite building blocks, the crankshaft motion of stilbenes, the dynamic coupling between pyramidal deformation of the amide NH2 group and hydrogen bonding, the bowl inversion of corannulenes and nucleophilic addition/elimination reactions.

Effect of fluorination: gas-phase structures of N,N-dimethylvinylamine and perfluoro-N,N-dimethylvinylamine

The gas-phase structures of N,N-dimethylvinylamine, (CH(3))(2)NC(H)=CH(2) (1), and perfluoro-N,N-dimethylvinylamine, (CF(3))(2)NC(F)=CF(2) (2), were determined by gas electron diffraction and quantum chemical methods (B3LYP and MP2 with 6-31G basis sets). The configuration around nitrogen is slightly pyramidal in both compounds, with the sum of the nitrogen bond angles 351.2(12) degrees and 354.8(6) degrees in 1 and 2, respectively. In the parent compound 1, the (CH(3))(2)N group lies nearly in the plane of the vinyl group, and the nitrogen lone pair (lp) is almost perpendicular to this plane (Phi(C=C-N-lp) = 98(6) degrees). In the perfluorinated species 2, however, the (CF(3))(2)N group is oriented perpendicular to the vinyl plane, and the lone pair is parallel to the C=C bond (Phi(C=C-N-lp) = 2(5) degrees). A natural bond orbital analysis provides a qualitative explanation for this conformational change upon fluorination. The sterically unfavorable in-plane orientation of the dimethylamino group in 1 is stabilized by conjugation between the nitrogen lone pair and the C=C pi-bond. The anomeric effect between the lone pair and the C(alpha)-F sigma-bond in addition to steric effects favors the perpendicular orientation of the (CF(3))(2)N group in 2. Both quantum chemical methods reproduce the experimental structures satisfactorily.

Alpha-ketoamides and alpha-ketocarbonyls: conformational analysis and development of all-atom OPLS force field

The molecular structures and barriers for the internal rotation around the OC-CO single bond in four alpha-ketoamides and eight alpha-ketocarbonyls have been determined from the MP3/aug-cc-pVDZ and MP2/aug-cc-pVDZ calculations. Alpha-ketocarbonyls with non-bulky substituents adopt planar conformations with two carbonyl oxygens in s-trans arrangement. The s-cis conformation is significantly less stable due to the electrostatic repulsion between the two carbonyl groups. Primary and secondary alpha-ketoamides are planar when the substituent at the carbonyl carbon is hydrogen or methyl group but tertiary alpha-ketoamides adopt a conformation where the OC-CO unit is significantly bent. Based on current ab initio structural data, a set of OPLS-AA force field parameters has been derived. These parameters can be used for the modeling of a variety of alpha-ketoamide or alpha-ketocarbonyl containing drugs such as novel protease inhibitors or neuroregenerative polyketides.