Formamide dimer

Florian, J., Johnson, B. G., 1995, Structure, Energetics, and Force Fields of the Cychc Formamide Dimer MP2, Hartree-Fock, and Density Functional Study , J. Phys. Chem., 99, 5899. 

Figure 5.19 The optimized structure of the linear formamide dimer and leading n0->-cTNH+ interactions with distinct c-type n0(a) and in-plane p-type no1 lone pairs.

Further synergistic enhancement of amide resonance and H-bonding occurs when both monomers can participate in two complementary H-bonds, once as a Lewis base and once as a Lewis acid. Such concerted (cooperative) pairs of H-bonds occur in the cyclic formamide dimer, as illustrated in Fig. 5.20. In this case the strength of each H-bond is further enhanced (to 6.61 kcalmol-1, about 4.7 times that of the prototype (5.31c)), the bond orders ben and bco are further shifted (to 1.384 and 1.655, respectively), and the bond lengths undergo further shifts in the... 

Limbach et 1 performed DFT calculations on. I(N, 11) and 2hJ(N,N) couplings in the anion [C = N-L-N = C] (L = H, D) and in the cyclic bonded formamide dimer (HCNHNH2)2 to study how such couplings depend on the geometry of the hydrogen bond. To describe such a relationship they employed the valence bond order model and compared the NHN and FHF- hydrogen bonded systems. 

Florian J, Johnson B (1995) Structure, energetics, and force fields of the cyclic formamide dimer MP2, Hartree-Fock, and density functional study, J Phys Chem, 99 5899-5908... 

Figure 21-15. Attachment of an excess tt electron to a cyclic hydrogen-bonded cluster facilitates inter-molecular proton transfer (a) formic acid dimer, (b) formamide dimer, and (c) formic acid-formamide (Figure 1 of ref. [51]. Reused with permission. Copyright 2005, American Institute of Physics)...

Figure 2.21 Formamide dimer, illustrating the definition of two intermolecular angles.

Table 2.44 Optimized geometries (A and degs) of formamide dimer and interaction energy (kcal/mol) ° parameters defined in Fig. 2.21.

Figure 2.24 Geometries of the formamide dimer, computed at the SCF/DZP level . Bond lengths refer to distances between nonhydrogen atoms.

Intermolecular frequencies, calculated with various basis sets, are listed in Table 3.80. The authors point out that the normal modes are far from pure and that their nomenclature is very approximate. For example, the H-bond stretch contains a strong element of donor libration. Their designation of strain refers to simultaneous in-phase rotations of the two molecules, while they use the term bend to indicate out-of-phase rotations. The imaginary frequencies of the torsional modes are evidence that the true equilibrium geometry of the formamide dimer is nonplanar. The mode appears at about 120 cm , a little smaller than that for H2CO---HOH where a water molecule donates a proton to the carbonyl oxy-... 

Table 3.80 Frequencies (in cm ) of intermolecular vibrational modes of the formamide dimer. Data calculated at SCF level...

Table 3.81 Computed intramolecular force constants (mdyn/A) of the cyclic formamide dimer ...

Table 3.82 Comparison of force constant for intermolecular stretch of the cyclic formamide dimer with the computed binding energy, without BSSE correction. Data ° are at SCF level unless otherwise indicated.

Recently, considerable effort has been devoted to obtaining quantum mechanical intermolecular potentials suitable for fluid simulations. For some examples see 75 for (HF)2 76 for (N2)2 77-80 for (CO)2 81 for the benzene dimer 82 for the SiH4 dimer 83 for water-argon and water-methane potentials 84 for the formamide dimer and N,N-dimethylformamide 85 for lithium iodide in dimethylsulfoxide and 86 for Ni2+ in aqueous solution. Rather than discuss each of these studies, here we will focus on a few important developments that we anticipate could alter the capacity or approach to development... 

The work on the formic acid dimer focused on the double-well potential for a highly symmetric system. An attempt to locate a double-well potential for a less symmetric system was made by Zielinski and Poirier (1984). They studied the formamide dimer and isolated a possible structure for the transition state for a double-proton transfer along the reaction path to the formimidic acid dimer (a dimer of the enol form of formamide) using the 3-21G basis set. The proposed transition state is only slightly less stable than the formimidic acid dimer. In other words, a very asymmetric double-well potential was found with a very shallow well on the formimidic acid dimer side of the reaction. It will be interesting to see the shape of the function for a double-proton transfer between formamide and amidine, which would more closely mimic the double-proton transfer that may be possible for the A-T pair. 

The cooperative effects in secondary protein structures, helix and sheet have been reported [53]. The linear chain of formamide which resembles peptides has large cooperativity in H-bond, which is 2.5 times that of formamide dimer. For the parallel and antiparallel sheet in secondary protein structures, there was no cooperativity in the parallel direction, while significant cooperativity exists in perpendicular direction. In methanol solvent system, the cooperative effects were reduced, indicating that the cooperativity is due to the polarization effect. 

Sponer, J. and Hobza, P. (2000) Interaction energies of hydrogen-bonded formamide dimer, formamidine dimer, and selected DNA base pairs obtained with large basis sets of atomic orbitals, J. Phys. Chem. A 104, 4592-4597. 

To provide more insight into the nature of heteronuclear intermolecular RAHBs, ab initio calculations at the MP2/6-311++G(Quantum Theory Atoms in Molecules ) calculations were performed for the formamide dimer (Fig. 13) and its simple fluoro derivatives... 

The other dimers in Fig. 29.7 show asymmetry. If the proton transfer potential is asymmetric, there will be no synchronous transfer and at most accidental level splittings. In the formamide dimer [44] the two hydrogen bonds are the same but the donor and acceptor groups are different. The available calculations indicate that the structure of the equilibrium configuration is intermediate between the equilibrium configurations of dimeric formic acid and dimeric formamidine, as... 

The coupling constants in a linear formamide dimer, treated as a model of hydrogen bonds in peptides, have been calculated by means of the finite field DFT method by Bagno. In the same work, the couplings between selected residues of ubiquitin are calculated, with aU aminoacids except the ones of interest removed or replaced (adjacent ones) by -COCH3 groups. 

Figure 4.3 Comparision of EDA frozen energies in kcal/mol along an angle for water dimer [upper] and formamide dimer [lower] with DEDA [blue curves] and MO-EDA [red curves] The MO-EDA employs the Heitler-London [HL] antisymmetrization of two fragments wave functions to represent the frozen density state. Reprinted with permission from Lu, Z., Zhou, N., Wu, Q. and Zhang, Y. Directional dependence of hydrogen bonds A density-based energy decomposition analysis and its implications on force field development./Chem Theory Comput 7, 4038-4049 [2011]. Copyright [2011] American Chemical Society.

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