Home About us Contact
Intermolecular Interaction Energies (intermolecular + interaction_energy)
Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004
Application to the ATP-binding site of a binuclear bacterial enzyme.
Abstract We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog,enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 160,168, 2004 [source]
Progress in the Understanding of Drug,Receptor Interactions, Part,2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C30H30N6O3S)CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2007
Raffaella Soave Dr.
Abstract A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug,receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17,K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of S,,,O and S,,,N intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NH,,,N hydrogen bond with an energy of about 50,kJ,mol,1. Key pharmacophoric features responsible for attractive electrostatic interactions include CH,,,X hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions. [source]
Semilocalized approach to investigation of chemical reactivityINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2003
V. GineityteArticle first published online: 21 JUL 200
Abstract Application of the power series for the one-electron density matrix Gineityte, V., J Mol Struct Theochem 1995, 343, 183 to the case of two interacting molecules is shown to yield a semilocalized approach to investigate chemical reactivity, which is characterized by the following distinctive features: (1) Electron density (ED) redistributions embracing orbitals of the reaction centers of both molecules and of their neighboring fragments are studied instead of the total intermolecular interaction energy; (2) the ED redistributions are expressed directly in the basis of fragmental orbitals (FOs) without passing to the basis of delocalized molecular orbitals (MOs) of initial molecules; (3) terms describing the ED redistributions due to an intermolecular contact arise as additive corrections to the purely monomolecular terms and thereby may be analyzed independently; (4) local ED redistributions only between orbitals of the reaction centers of both molecules are described by lower-order ter s of the power series, whereas those embracing both the reaction centers and their neighborhoods are represented by higher-order terms. As opposed to the standard perturbative methods based on invoking the delocalized (canonical) MOs of isolated molecules, the results of the approach suggested are in-line with the well-known intuition-based concepts of the classic chemistry concerning reactivity, namely, with the assumption about different roles of the reaction center and of its neighborhood in a chemical process, with the expectation about extinction of the indirect influence of a certain fragment (substituent) when its distance from the reaction center grows, etc. Such a parallelism yields quantum chemical analogs for the classic concepts and thereby gives an additional insight into their nature. The scope of validity of these concepts also is discussed. Applicability of the approach suggested to specific chemical problems is illustrated by a brief consideration of the SN2 and AdE2 reactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 302,316, 2003 [source]
Conformational disorder in 4-(5,5,-dibromo-2,-chloro-4,4,-bipyridyl-2-yl)benzaldehyde: role of ,,, and halogen interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010
The crystal packing of the title compound, C17H9Br2ClN2O, is governed by strong ,,, stacking, where molecules are tightly bound within infinite (100) planes; these planes interact mainly through non-optimal ,,, stacking where arene rings are noticeably displaced from perfect overlap, and also through halogen,halogen interactions. The aldehyde group shows conformational disorder, with a significant population difference between the two conformers; this difference is rationalized by the energetic analysis of the crystal packing using the PIXEL method, which also allows a decomposition of intermolecular interaction energy into Coulombic, polarization, dispersion and repulsion contributions. Using such an analysis, it is found that the main reason for this unequal population of the two conformers in the crystal is two hydrogen bonds that are present only for the major conformer. [source]