Hydrogen bonds and their relative strengths in proteins are of importance for understanding protein structure and protein motions. The correct strength of such hydrogen bonds is experimentally known to vary greatly from Ϸ5-6 kcal͞mol for the isolated bond to Ϸ0.5-1.5 kcal͞mol for proteins in solution. To estimate these bond strengths, here we suggest a direct novel kinetic procedure. This analyzes the timing of the trajectories of a properly averaged dynamic ensemble. Here we study the observed rupture of these hydrogen bonds in a molecular dynamics calculation as an alternative to using thermodynamics. This calculation is performed for the isolated system and contrasted with results for water. We find that the activation energy for the rupture of the hydrogen bond in a ␤-sheet under isolated conditions is 4.76 kcal͞mol, and the activation energy is 1.58 kcal͞mol for the same ␤-sheet in water. These results are in excellent agreement with observations and suggest that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.T he strength of the hydrogen bond in the linking of protein structures particular in a water environment is of essential importance to predict the activity of proteins such as enzyme action, protein folding, binding of proteins, and many other processes (1, 2). Although much has been written on protein dynamics in water (3), a detailed energy calculation including the correct water environment has been difficult to put into a computational framework. The energetics of hydrogen bonds within proteins is known to undergo large changes in water. The effect of water is also process dependent, so it is different here from protein signal transport (4). Such environmental changes in a hydrogen bond strength are important to the understanding of protein interactions, including drug design (5, 6). The drugreceptor hydrogen bond is operative in many applications (7).Hydrogen bonds are one of the major structural determinants, controlling active configurations by connecting protein structure in a fluxional equilibrium. The making and breaking of hydrogen bonds profoundly affects the rates and dynamic equilibria, which are responsible for much of the biological activity of proteins. This behavior is strongly medium dependent, so the action of these hydrogen bonds in isolated systems is quite different from the action in a water environment. The complex environment presented to the hydrogen bond by water is not easy to incorporate in calculations, but it is of major relevance, and results obtained need to be checked against experiments. A huge and complex phase space contributes to the effects of entropy on the hydrogen bond, particularly in water, and thus influences the free energy of these bonds. The general task of assessing the entropic contributions to the dynamic strength of these bonds is a matter of extensive research (8) and is difficult to quantify. Furthermore, it must be recognized that various relevant bonding environments will...

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A new type of bonding, termed anti-hydrogen bond, is identified in the benzene dimer and other carbon proton donor complexes from correlated ab initio computations. Gradient optimization of the benzene dimer at the MP2/6-31G* and MP2/6-31G** levels shows a shortening of the C-H bond of the proton donor and a blue-shift of the corresponding C-H stretching frequency. The harmonic C-H stretching vibrational frequency shift agrees well with that evaluated for various anharmonic approaches. The blue-shift of the C-H stretching frequency was also found in the case of benzene complexes with other carbon proton donors, CH 4 and CHCl 3 . The anti-H-bonds are expected to be very significant for the structure and dynamics of biomolecules.

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Point-wise evaluated coupled-cluster single double triple [CCSD(T)] stabilization energies are used to parameterize the nonempirical model (NEMO) empirical intermolecular potential of the benzene dimer in the ground electronic state. The potential is used for theoretical interpretation of the dimer structure and the dynamics of its intermolecular motions. Only one energy minimum, corresponding to the T-shaped structure, is found. A parallel displaced structure is the first-order transition structure separating the molecular symmetrically equivalent T-shaped structures. Due to a relatively high transition barrier (∼170 cm−1), the interconversion tunneling is unimportant in the energy region spanned by the available rotational spectra and is thus neglected (accordingly, the molecular symmetry group which is used for interpretation of the available experimental spectra is related to the T-shaped structure with two feasible internal rotations and nonequivalent monomers). The dimer undergoes a nearly free internal rotation along the axis connecting the benzene centers of mass in the T-shaped equilibrium geometry and a hindered internal rotation (the barrier being ∼46 cm−1) along the axis that is perpendicular to the “nearly free” internal rotation axis. The tunneling splittings observed in the rotational spectrum are likely due to this hindered rotation. An analysis assuming the latter rotation as an independent motion and using purely vibrational tunneling splittings (obtained by extrapolating to zero values of the rotational quantum numbers) indicates that the genuine value of the hindered rotation barrier is nearly twice higher than its ab initio value. Similarly, the difference ΔR=0.25 Å between the ab initio (equilibrium) and experimental (ground state) values for the distance of the mass centers of the benzene monomers is strong evidence that our theoretical potential is much shallower than the genuine one. The Raman bands observed at the 3–10 cm−1 region seem to involve states associated with the nearly free rotation and the “energy minimum path” bending motion. Unambiguous assigning of the weaker Raman features is infeasible, partly due to limitations in the accuracy of the theoretical potential, and partly due to the lack of knowledge of the polarizability tensor of the dimer and temperature at which the spectra were taken.

Isotopically mixed jets of benzene produced the various possible isotopic benzene dimers in a supersonic jet. Mass coincidence in time-of-flight multiphoton mass spectra separated the spectra due to the various dimers produced into distinguishable spectra even in the presence of overlap. From the many different isotopic spectral shifts a detailed model of interaction between the two halves of the dimer can be established revealing detailed new information on this interaction. In particular a splitting in the 0–0 transition is reported for the first time indicating an exciton interaction in the dimer of isotropic identical benzene molecules in the gas phase.

The energetics and structure of the benzene trimer and tetramer are investigated with the nonempirical model (NEMO) potential calibrated to high precision by comparison with CCSD(T) benzene dimer energies. From the obtained potential energy surface, possible configurations could be determined and the experimental observed structures could be identified. This potential also reproduces the binding energies and allows for the determination of all intermolecular modes. It could be shown that this potential is therefore well suited and important to predict the structure and thermodynamic data for larger clusters, which cannot be accurately computed by ab initio quantum chemical methods.