Structure and bonding in the formamide crystal: A complete fourth‐order many‐body perturbation theoretical study

The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals

Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.

Origin of the Director Tilt in the Lyotropic Smectic C* Analog Phase: Hydration Interactions and Solvent Variations

The origin and long-range correlation of the director tilt in the recently discovered Lα'* phase, which is the lyotropic analog of the thermotropic smectic C* (SmC*) liquid crystalline phase, are investigated. Polarized micro-Raman spectroscopy reveals that the director tilt in the Lα'* phase originates from a tilting of the aromatic 2-phenylpyrimidine cores of the surfactant molecules. Optical measurements of the tilt angle show that its magnitude decreases with increasing solvent concentration, suggesting that the long-range inter-lamellar correlation of the tilt directions is reduced at increasing thickness of the solvent layers. The phase diagrams with four different solvents (water, formamide, N-methylformamide, N,N-dimethylformamide) are investigated, showing that the Lα'* phase is only formed with those solvents that exhibit a dense network of hydrogen bonds. This observation suggests that these hydrogen bond networks play an essential role in the long-range correlation of the director tilt between adjacent surfactant layers. To verify this assumption, mixtures with deuterated solvents are investigated, showing that the tilt angle in the Lα'* phase is indeed reduced by this modification of the solvent's hydrogen bond network.

Kinetically controlled formation of formamide trimer from first principles

The formation of formamide trimers was simulated using Car-Parrinello molecular dynamics. A variety of different initial setups were compared to study the effects of spatial arrangement, concentration, and temperature on the trimer product distribution. A total of nine different trimer species were obtained by simulation. Although a triangular initial arrangement of the three monomers is found to favour a less energetically stable chain-like product at high concentration, the more compact global minimum structure is expected to be the most abundant species overall in experiment. This is because there is evidence of a low activation barrier for conversion of the chain-like trimer to the lowest-energy structure. For one, this process is observed upon increasing the length of the trajectories. Furthermore, a slight rise in temperature drastically reduces the number of chain-like trimers. With regard to the intermolecular forces driving the aggregation dynamics, dispersion corrections to the underlying density functional theory description have a strong effect on the product distribution, again favouring the global minimum species. Certain local minimum structures are significantly destabilised relative to the global minimum by dispersion correction while the relative energies of the majority of species are practically unchanged.

Enthalpies of hydration of N-methylacetamide by one, two, and three waters and the effect upon the C=O stretching frequency. An Ab initio DFT study

DFT calculations at the B3LYP/D95++(d,p) level of clusters of N-methylacetamide (NMA) with one, two, and three waters that were geometrically optimized on the counterpoise-corrected potential energy surfaces show that the gas-phase enthalpy of the interactions of NMA with three waters is -14.11 kcal/mol. Since the interactions between the three waters is 0.99 kcal/mol, the interaction enthalpy would become -15.10 if these interactions were subtracted. The internal geometry of the NMA molecule is sensitive to the degree of hydration, as are the H-bond lengths. Changes in the internal bond lengths with degree of hydration are approximately additive. The calculated C=O stretching frequencies correlate extremely well with the calculated C=O bond lengths, which suggests that the solvent effect upon this stretch could not be a purely electrostatic interaction. The calculated C=O stretch for NMA solvated by three waters in the gas phase agrees very well with that experimentally observed in aqueous solution.

Electron Density Redistribution Accounts for Half the Cooperativity of α Helix Formation

The energy of alpha helix formation is well known to be highly cooperative, but the origin and relative importance of the contributions to helical cooperativity have been unclear. Here we separate the energy of helix formation into short range and long range components by using two series of helical dimers of variable length. In one dimer series two monomeric helices interact by forming hydrogen bonds, while in the other they are coupled only through long range, primarily electrostatic interactions. Using Density Functional Theory, we find that approximately half of the cooperativity of helix formation is due to electrostatic interactions between residues, while the other half is due to nonadditive many-body effects brought about by redistribution of electron density with helix length.

Electron localization in negatively charged formamide clusters studied by photodetachment spectroscopy

Size-dependent features of the electron localization in negatively charged formamide clusters (FAn-, n = 5-21) have been studied by photodetachment spectroscopy. In the photoelectron spectra for all the sizes studied, two types of bands due to different isomers of anions were found. The low binding energy band peaking around 1 eV is assigned to the solvated electron state by relative photodetachment cross-section measurements in the near-infrared region. It is suggested that nascent electron trapping is dominated by formation of the solvated electron. The higher energy band originates from the covalent anion state generated after a significant relaxation process, which exhibits a rapid increase of electron binding energy as a function of the cluster size. A unique behavior showing a remarkable band intensity of the higher energy band was found only for n = 9.

Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies

Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.