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Hydrogen-bonding patterns in pyrimethaminium pyridine-3-sulfonate.

ABSTRACT: IN THE ASYMMETRIC UNIT OF THE TITLE SALT [SYSTEMATIC NAME: 2,4-diamino-5-(4-chloro-phen-yl)-6-ethyl-pyrimidin-1-ium pyri-dine-3-sulfonate], C(12)H(14)N(4)Cl(+)·C(5)H(4)NSO(3) (-), there are two independent pyrimethaminium cations and two 3-pyridine sulfonate anions. Each sulfonate group inter-acts with the corresponding protonated pyrimidine ring through two N-H?O hydrogen bonds, forming a cyclic hydrogen-bonded bimolecular R(2) (2)(8) motif. Even though the primary mode of association is the same, the next higher level of supra-molecular architectures are different due to different hydrogen-bonded networks. In one of the independent molecules in the asymmetric unit, the pyrimethamine cation is paired centrosymmetrically through N-H?N hydrogen bonds, generating an R(2) (2)(8) ring motif. In the other molecule, the pyrimethamine cation does not form any base pairs; instead it forms hydrogen bonds with the 3-pyridine sulfonate anion. The structure is further stabilized by C-H?O, C-H?N and ?-? stacking [centroid-centroid distance = 3.9465?(13)?Å] inter-actions.

SUBMITTER: Nirmalram JS

PROVIDER: S-EPMC3007288 | biostudies-other | 2010

REPOSITORIES: biostudies-other

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Hydrogen-bonding patterns in pyrimethaminium pyridine-3-sulfonate.

Nirmalram Jeyaraman Selvaraj JS Thomas Muthiah Packianathan P

Acta crystallographica. Section E, Structure reports online 20100724 Pt 8

IN THE ASYMMETRIC UNIT OF THE TITLE SALT [SYSTEMATIC NAME: 2,4-diamino-5-(4-chloro-phen-yl)-6-ethyl-pyrimidin-1-ium pyri-dine-3-sulfonate], C(12)H(14)N(4)Cl(+)·C(5)H(4)NSO(3) (-), there are two independent pyrimethaminium cations and two 3-pyridine sulfonate anions. Each sulfonate group inter-acts with the corresponding protonated pyrimidine ring through two N-H⋯O hydrogen bonds, forming a cyclic hydrogen-bonded bimolecular R(2) (2)(8) motif. Even though the primary mode of association is the sa ...[more]

PMID: 21588411

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Project description:BackgroundTrimethoprim [2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidine] is an antifolate drug. It selectively inhibits the bacterial dihydrofolate reductase (DHFR) enzyme.ResultsIn the crystal structures of trimethoprim (TMP)-hydrogen phthalate (1) and trimethoprim-hydrogen adipate (2), one of the N atoms of the pyrimidine ring is protonated and it interacts with the deprotonated carboxylate oxygens through a pair of nearly parallel N-H...O hydrogen bonds to form a fork-like interaction. In the compound 1, the pyrimidine moieties of the TMP cations are centrosymmetrically paired through a pair of N-H...N hydrogen bonds involving 4-amino group and the N (N3) atom of the pyrimidine rings to form a 8-membered hydrogen bonded ring [R2(2)(8)]. The 4-amino group of one TMP moiety and 2-amino group of another TMP moiety (both moieties are members of a base pair) are bridged by the carbonyl oxygen of the phthalate moiety through N-H...O hydrogen bonds forming 8-membered hydrogen-bonded ring [R2(2)(8)]. The characteristic hydrogen-bonded rings observed in the structure aggregate into a supramolecular ladder consisting of a pair of chains, each of which is built up of alternate TMP and hydrogen phthalate ions. In the compound 2, two TMP cations and two hydrogen adipate anions are arranged about an inversion center so that the complementary DDAA (D = donor, A = acceptor) arrays of quadruple hydrogen-bonding patterns are formed. The head-to-tail arrangement of the hydrogen adipate ions leads to a hydrogen-bonded supramolecular chain. From crystal engineering point of view, it is interesting to note that the compound 1 has a hydrogen-bonded network remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly the compound 2, resembles its homolog trimethoprim hydrogen glutarate.ConclusionIn the crystal structure of trimethoprim hydrogen phthalate, the hydrogen-bonded network is remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly in the crystal structure of trimethoprim hydrogen adipate the hydrogen bonded network resembles its homolog trimethoprim hydrogen glutarate.

Project description:Elastic network models (ENMs) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function. However, despite a shared purpose of these approaches, the topological nature of rigidity analysis, and thereby the absence of motion modes, has impeded a direct comparison. Here, we present an alternative, kinematic approach to rigidity analysis, which circumvents these drawbacks. We introduce a novel protein hydrogen bond network spectral decomposition, which provides an orthonormal basis for collective motions modulated by noncovalent interactions, analogous to the eigenspectrum of normal modes. The zero modes decompose proteins into rigid clusters identical to those from topological rigidity, while nonzero modes rank protein motions by their hydrogen bond collective energy penalty. Our kinematic flexibility analysis bridges topological rigidity theory and ENM, enabling a detailed analysis of motion modes obtained from both approaches. Analysis of a large, structurally diverse data set revealed that collectivity of protein motions, reported by the Shannon entropy, is significantly reduced for rigidity theory compared to normal mode approaches. Strikingly, kinematic flexibility analysis suggests that the hydrogen bonding network encodes a protein-fold specific, spatial hierarchy of motions, which goes nearly undetected in ENM. This hierarchy reveals distinct motion regimes that rationalize experimental and simulated protein stiffness variations. Kinematic motion modes highly correlate with reported crystallographic B factors and molecular dynamics simulations of adenylate kinase. A formal expression for changes in free energy derived from the spectral decomposition indicates that motions across nearly 40% of modes obey enthalpy-entropy compensation. Taken together, our results suggest that hydrogen bond networks have evolved to modulate protein structure and dynamics, which can be efficiently probed by kinematic flexibility analysis.

Dataset Information

Hydrogen-bonding patterns in pyrimethaminium pyridine-3-sulfonate.

Publications

Hydrogen-bonding patterns in pyrimethaminium pyridine-3-sulfonate.

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