Crystallographic and theoretical investigation of interactions of water molecule with aryl ring (original) (raw)
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Journal of Chemical Theory and Computation, 2010
The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H · · · π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/ aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.
Proceedings of The National Academy of Sciences, 2002
A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program TOPXD and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP͞6 -31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l ؍ 4) is found to be within 2-3 kJ͞mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.
Nature of the water/aromatic parallel alignment interactions
Journal of Computational Chemistry, 2014
The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its OAH bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to DE CCSD(T)(limit) 5 22.45 kcal mol 21 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CHÁÁÁO water/benzene interactions, but weaker than OHÁÁÁp interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type p ! r*(OAH) between the monomers also exists. V
Journal of Chemical Information and Modeling
G iven current interest in short noncovalent interactions (NCIs), we were naturally attracted by a recent publication by Helena W. Qi and Heather J. Kulik (Q&K) from the Massachusetts Institute of Technology on this topic. 1 We regret to inform you that we found serious shortcomings in the methodology and the conclusions of this paper. Briefly, the authors analyzed the Protein Data Bank (PDB) with the aim to characterize unexpectedly short non-covalent distances in crystal structures of proteins. For that, they curated ≈11 000 high-quality protein crystal structures comprising a subset of >900 ultrahigh-resolution structures (≤1.2 Å) leading them to characterize an ensemble of over 75 000 close contacts defined by a nonbonded distance between two heavy atoms that is no more than 85% of the sum of their van der Waals (vdW) radii.
Determination of effective pair interactions from the structure factor
Physical Review E, 2004
In this work we present an efficient procedure to evaluate effective pair potentials, compatible with "experimental" structure factors, using a Monte Carlo simulation scheme. The procedure does not require the use of inverse Fourier transforms and is robust and rapidly convergent. As a test case the structure factor of liquid Selenium obtained from a Tight-Binding Molecular Dynamics simulation is inverted to obtain an effective pair potential and, as a by-product, the pair distribution function. The inversion procedure yields a pair structure in perfect agreement with the original molecular dynamics calculations and the analysis of the triplet structure and the dynamics also illustrates the limitations of the use of pair potentials in the description of liquids with strongly directional bonding, such as the covalent liquid Selenium.
The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol À1 RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol À1 .
4_delange_et_al_2017_Struct_Chem.pdf
We have discovered, using developed by us recently FALDI and FAMSEC computational techniques, fundamentally distinct mechanisms of intramolecular red-and blue-shifted H-bond formation that occurred in different conformers of the same molecule (amino-acid β-alanine) involving the same heteroatoms (O-H⋅⋅⋅N and N-H⋅⋅⋅O). Quantitative topological, geometric and energetic data of both H-bonds obtained with well-known QTAIM and IQA methodologies agree with what is known regarding H-bonding in general. However, the FALDI charge and decomposition scheme for calculating in real space 3D conformational deformation densities provided clear evidence that the process of electron density redistribution taking place on the formation of the stronger red-shifted H-bond is fundamentally distinct from the weaker blue-shifted H-bond. Contributions made by atoms of the X-H⋅⋅⋅Y-Z fragment (IUPAC notation) as well as distinct atoms on the H-bond formation were fully explored. The FAMSEC energy decomposition approach showed that the atoms involved in formation of the red-shifted H-bond interact in a fundamentally different fashion, both locally and with the remainder of the molecule, as compared with those of the blue-shifted H-bond. Excellent correlations of trends obtained with QTAIM, IQA, FAMSEC and FALDI techniques were obtained. Commentary regarding IUPAC recommended definition of an H-bond and validity of observed AILs (or bond paths) of the two H-bond kinds is also discussed.
Molecular Physics, 2010
The performance of density fitting, local correlation methods (DF-LMP2 and DF-LCCSD) in studies of non-covalent interactions is tested against literature data for a standard set of 22 intermolecular complexes. Partitioning of interaction energy in the local correlation approach, based on the classes of occupied and virtual orbital involved in the interaction, clearly distinguishes the three types of interaction present in the set of complexes, in agreement with previous classifications. Geometry optimisation is found to be straightforward with DF-LMP2 without the need for counterpoise correction, resulting in geometries very close to previous, counterpoisecorrected structures. Spin-component scaling of gradients to correct for the known shortcomings of conventional MP2 has only a small effect on geometries in most cases, but significantly alters the distance between aromatic rings in stacked complexes. Harmonic frequency calculation is made possible by efficient use of parallel computing resources, and confirms all structures to be true minima, unlike previous estimates using density functional theory. Corrections for the change in zero-point vibrational energy are determined from this data, and typically constitute between 10 and 50% of the overall binding energy of the complex.
Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 1993
The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.