AM1 study of hydrogen bonded complexes of water

Water interactions with hydrophobic groups: assessment and recalibration of semiempirical molecular orbital methods

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

Self-consistent polarization neglect of diatomic differential overlap: application to water clusters

Semiempirical self-consistent field (SCF) methods based on the neglect of diatomic differential overlap (NDDO) formalism have the ability to treat the formation and breaking of chemical bonds but have been found to poorly describe hydrogen bonding and weak electrostatic complexes. In contrast, most empirical potentials are not able to describe bond breaking and formation but have the ability to add missing elements of hydrogen bonding by using classical electrostatic interactions. We present a new method which combines aspects of both NDDO-based SCF techniques and classical descriptions of polarization to describe the diffuse nature of the electronic wavefunction in a self-consistent manner. We develop the "self-consistent polarization neglect of diatomic differential overlap" (SCP-NDDO) theory with the additional description of molecular dispersion developed as a second-order perturbation theory expression. The current study seeks to model water-water interactions as a test case. To this end, we have parametrized the method to accurate ab initio complete basis set limit estimates of small water cluster binding energies of Xantheas and co-workers [J. Chem. Phys. 116, 1493 (2002); 120, 823 (2004)]. Overall agreement with the ab initio binding energies (n=2-6, and 8) is achieved with a rms error of 0.19 kcal/mol. We achieve noticeable improvements in the structure, vibrational frequencies, and energetic predictions of water clusters (n< or =21) relative to standard NDDO-based methods.

Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach

This work examines the ability of semiempirical methods to describe the structure of liquid water. Particularly, the standard AM1 and PM3 methods together with recently developed PM3-PIF and PM3-MAIS parametrizations have been considered. We perform molecular dynamics simulations for a system consisting of 64 or 216 water molecules in a periodic cubic box. The whole system is described quantum mechanically. Calculations with 64 molecules have been carried out using standard SCF techniques whereas calculations with 216 molecules have been done using the divide and conquer approach. This method has also been used in one simulation case with 64 molecules for test purposes. Within this scope, the molecular dynamics program ROAR have been coupled with a linear scaling semiempirical code (DivCon) implemented in a parallel MPI version. The predicted liquid water structure using either AM1 or PM3 is shown to be very poor due to well-known limitations of these methods describing hydrogen bonds. In contrast, PM3-PIF and PM3-MAIS calculations lead to results in reasonably good agreement with experimental data. The best results for the heat of vaporization are obtained with the PM3-PIF method. The average induced dipole moment of the water molecule in the liquid is underestimated by all semiempirical techniques, which seems to be related to the NDDO approximation and to the use of minimal basis sets. A brief discussion on charge-transfer effects in liquid water is also presented.

Models and molecular orbital semiempirical calculations in the study of the spectroscopic properties of bovine serum amine oxidase quinone cofactor

The electronic properties of 2,4,5-trihydroxyphenylalanine quinone (TPQ), the cofactor of bovine serum amine oxidase [Janes, S. M., Mu, D., Wemmer, D., Smith, A. J., Kaur, S., Maltby, D., Burlingame, A. L., & Klinman, J. P. (1990) Science 248, 981-987], and some adducts with hydrazines were investigated by means of low-molecular-weight models and semiempirical molecular orbital calculation methods. The enzyme visible band was assigned to the first pi-->pi* transition of the cofactor in p-quinonic form, with the C-4 hydroxyl ionized and hydrogen bonded either to a water molecule or to a basic protein residue. The spectra of the protein adducts with some substituted hydrazines were well accounted for by assuming the inhibitor bound to the C-5 carbonyl, usually in azo form. The adduct with the unsubstituted hydrazine was instead assigned an o-quinone hydrazone form, stabilized by an internal hydrogen bond between the amino group and the ortho carbonyl oxygen, a larger electron delocalization, and formation of a hydrogen bond at the C-6 ionized hydroxyl. On the basis of these assignments, the reaction of the protein with benzylhydrazine [Morpurgo, L., Agostinelli, E., Muccigrosso, J., Martini, F., Mondovi, B., & Avigliano, L. (1989) Biochem. J. 260, 19-25] was rewritten. All examined electronic transitions, though highly sensitive to cofactor ionization and hydrogen bonding, could be accounted for without introducing perturbations due to copper. This confirms that copper is not within bonding distance of the oxidized cofactor.

SCF-MO study of the polyhydration of N,N'-dimethylmalonamide

The effect of hydration on the conformation of the N,3 nylons has been studied using AM1 SCF-MO on the model molecule N,N'-dimethylmalonamide (NNMA). The polyhydration model has been used, so that only the water molecules directly bonded to solute molecule are considered. The study reveals that, although hydration induces dramatic changes in the torsional angles of the molecule, the new conformation still remains in the helical region of the Ramachandran map.