Polymorphism,Intermolecular Interactions,and Spectroscopic Properties in Crystal Structures of Sulfonamides

The antibiotics family of sulfonamides has been used worldwide intensively in human therapeutics and farm livestock during decades. Intermolecular interactions of these sulfamides are important to understand their bioactivity and biodegradation. These interactions are also responsible for their supramolecular structures. The intermolecular interactions in the crystal polymorphs of the sulfonamides, sulfamethoxypyridazine, and sulfamethoxydiazine, as models of sulfonamides, have been studied by using quantum mechanical calculations. Different conformations in the sulphonamide molecules have been detected in the crystal polymorphs. Several intermolecular patterns have been studied to understand the molecular packing behavior in these antibiotics. Strong intermolecular hydrogen bonds and π-π interactions are the main driving forces for crystal packing in these sulfonamides. Different stability between polymorphs can explain the experimental behavior of these crystal forms. The calculated infrared spectroscopy frequencies explain the main intermolecular interactions in these crystals.     

Head-to-tail sequences and other patterns of peptide aggregation in the solid state

Encouraged by the results of our earlier study on the occurrence and the geometrical features of head-to-tail sequences involving amino acids, which have been suggested to be of probable relevance to prebiotic polymerisation, the available crystal structures of unprotected peptides have been analysed with a view to investigating head-to-tail sequences and other patterns of peptide aggregation in the solid state. The number of available dipeptide structures is large enough to permit meaningful conclusions. The dipeptide molecules in the crystal structures can be broadly classified as extended or folded depending upon their conformations. The basic elements of dipeptide aggregation are different types of head-to-tail sequences and sequences involving hydrogen bonds with the peptide nitrogen atom as the donor, generated by periodic translations and 2₁ screw axes. Using these basic elements and the known geometrical preferences of hydrogen bonds, it is possible to construct several plausible idealized patterns, mostly two-dimensional, of dipeptide aggregation for extended as well as folded molecules. The patterns observed in crystal structures are in substantial agreement with these idealized patterns. Infinite hydrogen-bonded sequences of the type observed in dipeptide structures remain the basic elements of aggregation in the structures of higher peptides also. The present analysis shows that peptide aggregation in the solid state is controlled primarily by interactions involving main chain atoms. Also, despite the increased molecular flexibility of peptides in comparison with amino acids and the presence of additional hydrogen bonding groups in them, head-to-tail sequences remain the most important intrinsic feature not only of amino acid aggregation but of peptide aggregation as well.     

Thermodynamic and structural aspects of novel 1,2,4-thiadiazoles in solid and biological mediums

Novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments, and comparative analysis of packing architecture and hydrogen bond networks was carried out. Thermodynamic aspects of sublimation processes of the compounds under study were analyzed using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. The melting points correlate with sublimation Gibbs energies. Moreover, an increase of donor-acceptor interactions in crystal structures leads to growth of Gibbs energy values. Relationships between the melting points and the fragmental contributions to the packing energies were established: R(1)-R(4) fragmental interactions are responsible for the fusion processes of this class of compounds. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n-hexane and n-octanol were studied within a wide range of temperature intervals, and their thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. It was found that the melting points correlate with sublimation Gibbs energies. Distribution processes of compounds in buffer/n-octanol and buffer/n-hexane systems (describing different types of membranes) were investigated. Transfer processes of the studied molecules from the buffer to n-octanol/n-hexane phases were analyzed by the diagram method with evaluation of the enthalpic and entropic terms. This approach allowed us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. The trend between the ability to inhibit Glu-Ca uptake and the distribution coefficients in buffer/hexane system was observed.     

X‐ray studies on crystalline complexes involving amino acids and peptides. XXXVI. Crystal structures of hydrated glycyl‐l‐histidine andl‐histidyl‐l‐alanine complexes with oxalic acid

Abstract: The crystal structures of the complexes of oxalic acid with glycyl‐l ‐histidine and l ‐histidyl‐l ‐alanine were determined. The three crystallographically independent peptide molecules in the complexes have closed conformations. The terminal carboxyl group of the dipeptide and the oxalate ion in the Gly–His complex exhibit unusual ionization states and are connected by a symmetric O‐ ‐ ‐O hydrogen bond. The peptide aggregation in the complex is almost identical to that in the corresponding semisuccinate complex and is similar to one of the predicted aggregation patterns for Ala–Ala, demonstrating that dipeptide aggregation is controlled primarily by main‐chain interactions and is substantially unaffected by disturbing influences such as those arising from polar side chains, ions and water molecules. The peptide molecules in the highly pseudosymmetric crystals of the His–Ala complex, however, exhibit a hitherto unobserved aggregation pattern. Thus, in spite of the repeated occurrence of a few patterns, the possibility of the existence of new patterns needs to be taken into account.     

Guanidyl-carboxylate interactions: crystal structures of arginine dipeptides*

The crystal structures of the hydrated dipeptides l -arginyl-l -aspartic acid and l -arginyl-l -glutamic acid have been determined from three-dimensional X-ray diffraction data. Each peptide crystallizes as a double-zwitterion with both the main and side-chain carboxyl groups ionized and the amino and guanidyl termini protonated. The peptide backbone conformation in both peptides is remarkably similar. Both peptides adopt a trans conformation for the peptide linkage with the guanidyl and acidic side-chains extended on opposite sides of the peptide backbone. The arginyl side-chain conformations differ between peptides; the conformation observed for arginyl aspartic acid is unique. Extensive intermolecular hydrogen bonding networks are observed in both structures; however, in neither structure is there evidence of intramolecular hydrogen bonding. The intermolecular guanidyl-carboxylate interactions are detailed. These interactions include a modified Type A interaction which models the possible bridging of adjacent peptide carbonyl oxygens in an α-helix by the guanidinium moiety.     

Effects of Hydrogen Bond Acceptor Ability of Solvents on Molecular Self-Assembly of Sulfadiazine Solvates

The solvate formation of sulfadiazine (SDZ) was systematically studied in the 4 selected solvents with the aids of experiment and simulation methods. The intermolecular interactions between solute and solvent molecules in different solid states were analyzed and compared through their single crystal structures, and the solution behavior of SDZ was discussed using molecular dynamics simulations. The results indicated that SDZ was easy to form solvates with the solvents having strong hydrogen bond acceptor ability, which determined the formation of hydrogen bonding synthon. Furthermore, the SDZ molecules conformation and packing were compared in various crystal structures. In addition, the desolvation processes of SDZ solvates were studied to investigate the role of solvent in different solvate structures.     

Interplay between molecular conformation and intermolecular interactions in conformational polymorphism: a molecular perspective from electronic calculations of tolfenamic acid

Tolfenamic acid exhibits conformational polymorphism. The molecules in its two commonly occurred crystal structures form similar hydrogen-bonded dimers but differ in conformation. The conformational variance was analyzed by electronic calculation methods with the aim to unravel intrinsic connection between the conformational flexibility and intermolecular interactions in the polymorphs. The study was conducted mainly by conceptual density functional theory (DFT) and natural bond orbital (NBO) analysis. It is found that the conformational polymorphism is resulted from the energy competition between intramolecular π-conjugation and intermolecular hydrogen bonding. By adapting conformation that departs from being the most energetically stable, tolfenamic acid molecules can strengthen the intermolecular hydrogen-bonding interactions in the crystals. The study illustrates how the molecule's electronic properties are influenced by conformational variation and, inherently, how the intermolecular interactions become regulated. Moreover, understanding molecular interaction and crystal packing necessitates electronic structure calculation and analysis, which can be further facilitated by utilizing DFT and NBO concepts.     

Molecular Complexes of Alprazolam with Carboxylic Acids,Boric Acid,Boronic Acids,and Phenols. Evaluation of Supramolecular Heterosynthons Mediated by a Triazole Ring

A series of molecular complexes, both co-crystals and salts, of a triazole drug—alprazolam—with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O–H?N hydrogen bonds with the triazole ring. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3743–3753, 2010     

Conformational flexibility and hydrogen-bonding patterns of the neotame molecule in its various solid forms

The conformational flexibility and the molecular packing patterns of the neotame molecule in its various crystal forms, including neotame monohydrate, methanol solvate, ethanol solvate, benzene solvate, and anhydrate polymorph G, are analyzed in this work. The Cerius2 molecular modeling program with the Dreiding 2.21 force field was employed to calculate the most stable conformations of neotame molecules in the gaseous state and to analyze the conformations of the neotame molecule in its various crystal forms. Using graph set analysis, the hydrogen bond patterns of these crystal forms were compared. The neotame molecule takes different conformations in its crystal forms and in the free gaseous state. Cerius2 found 10 conformers with lower conformational energies than those in the actual crystal structures, which represent an energetic compromise. The relatively large differences between the energies of the conformers indicate the necessity for rewriting or customizing the force field for neotame. The hydrogen bonding patterns of the neotame methanol and ethanol solvates are identical, but different from those of the other three forms, which also differ from each other. The neotame molecule in its various crystal forms takes different conformations that differ from those in the gaseous state because of the influence of crystal packing. The intramolecular ring, S5, is present in all the crystal forms. The following hydrogen bonding patterns occur in some of the crystal forms: diad, D; intramolecular rings, S(6) and S(7); chains, C(5) and C(6); and an intermolecular ring, R2(2)(12).     

A SURVEY OF ATOM PACKING IN GLOBULAR PROTEINS

This survey of the atom packing in the high resolution X-ray crystal structures of 21 proteins indicates that the atom density around a given central atom is determined primarily by its covalently bonded neighbors and proximity to the surface of the protein. Long-range hydrophobic, hydrogen bonding, and electrostatic interactions are strictly of secondary importance. Both radial and angular atom densities were calculated about various central atoms of several residue types, averaged over all occurrences of the chosen residue type in all 21 proteins. Polar interactions, such as hydrogen bonding, involve on the average shorter distances than hydrophobic interactions do, and are more directional. Spatial segregation of polar and non-polar atoms is never complete in long-range interactions since the types of atoms are linked together covalently.     

Dehydration behavior and structural characterization of the GW275919X monohydrate

GW275919X, a central muscle relaxant for the treatment of lower back pain, exists in a monohydrate. Knowledge of the solid state dehydration behavior and the crystal structure is essential for determining its relative physical stability. Thermal analysis and hot-stage powder X-ray diffraction were used to study the solid state phase transformation during the dehydration process. Crystal structure was determined by single crystal X-ray analysis. Molecular modeling with Cerius(2) software was used to visualize the hydrate crystal structure and to construct the molecular packing and hydrogen bond diagram. Morphology prediction was performed using the BFDH calculation. Crystallographic data: monoclinic, space group, P21/c, a (Angstrom)=14.3734, b (Angstrom)=5.0336, c (Angstrom)=15.4633 and beta=105.11 degrees. Water molecules in the hydrate crystal of GW275919X are involved in the hydrogen bonds and these hydrogen bonds contribute to the coherence of the crystal structure. The longest dimension of the predicted morphology is in the b-direction, which would correspond to the needle axis of the experimental crystals.     

Hydrophobic effect and hydrogen bonds account for the improved activity of a complement inhibitor, compstatin

Tryptophans at positions 4 and 7 of compstatin, a peptide complement inhibitor, are crucial for its interaction with C3. However, the nature of their involvement has not been studied to date. Here we investigate the molecular forces involved in the C3-compstatin interactions, mediated by aromatic residues, by incorporating in these two positions various tryptophan analogues (5-methyltryptophan, 5-fluorotryptophan, 1-methyltryptophan, and 2-naphthylalanine) and assessing the resulting peptides for activity by enzyme-linked immunosorbent assay (ELISA) and binding by isothermal titration calorimetry (ITC). Of all the compstatin analogues, peptides containing 1-methyltryptophan at position 4 exhibited the highest binding affinity (Kd = 15 nM) and activity (IC50 = 0.205 microM), followed by a peptide containing 5-fluorotryptophan at position 7. Our observations suggest that hydrophobic interactions involving residues at position 4 and the hydrogen bond initiated by the indole nitrogen are primarily responsible and crucial for the increase in activity. These findings have important implications for the design of clinically useful complement inhibitors.     

Stabilized helical peptides: overview of the technologies and its impact on drug discovery

Introduction: Protein-protein interactions are predominant in the workings of all cells. Until now, there have been a few successes in targeting protein-protein interactions with small molecules. Peptides may overcome some of the challenges of small molecules in disrupting protein-protein interactions. However, peptides present a new set of challenges in drug discovery. Thus, the study of the stabilization of helical peptides has been extensive.

Areas covered: Several technological approaches to helical peptide stabilization have been studied. In this review, stapled peptides, foldamers, and hydrogen bond surrogates are discussed. Issues regarding design principles are also discussed. Furthermore, this review introduces select computational techniques used to aid peptide design and discusses clinical trials of peptides in a more advanced stage of development.

Expert opinion: Stabilized helical peptides hold great promise in a wide array of diseases. However, the field is still relatively new and new design principles are emerging. The possibilities of peptide modification are quite extensive and expanding, so the design of stabilized peptides requires great attention to detail in order to avoid a large number of failed lead peptides. The start of clinical trials with stapled peptides is a promising sign for the future.     

Vancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding

Bacterial resistance to vancomycin has been attributed to the loss of an intermolecular hydrogen bond between vancomycin and its peptidoglycan target when cell wall biosynthesis proceeds via depsipeptide intermediates rather than the usual polypeptide intermediates. To investigate the relative importance of this hydrogen bond to vancomycin binding, we have determined crystal structures at 1.0 A resolution for the vancomycin complexes with three ligands that mimic peptides and depsipeptides found in vancomycin-sensitive and vancomycin-resistant bacteria: N-acetylglycine, D-lactic acid, and 2-acetoxy-D-propanoic acid. These, in conjunction with structures that have been reported previously, indicate higher-affinity ligands elicit a structural change in the drug not seen with these low-affinity ligands. They also enable us to define a minimal set of drug-ligand interactions necessary to confer higher-affinity binding on a ligand. Most importantly, these structures point to factors in addition to the loss of an intermolecular hydrogen bond that must be invoked to explain the weaker affinity of vancomycin for depsipeptide ligands. These factors are important considerations for the design of vancomycin analogues to overcome vancomycin resistance.     

HYDROGEN BONDS IN CRYSTAL STRUCTURES OF AMINO ACIDS,PEPTIDES AND RELATED MOLECULES

The results of a survey of 439 hydrogen bonds in 95 recently determined crystal structures of amino acids, peptides and related molecules suggest that the following generalizations hold true for linear (angle X–H—Y > 150°) hydrogen bonds. (1) The charge on the acceptor group does not influence the length of a hydrogen bond. (2) For a given acceptor group, the hydrogen bond lengths increase in the order imidazolium N–H < ammonium N–H < guanidinium N–H; this order holds true for oxygen anion acceptor groups. Cl^- ions and the uncharged oxygen of water molecules. (3) The uncharged imidazole N–H group forms shorter hydrogen than the amide N–H group. (4) The carboxyl O–H groups form shorter hydrogen bonds than other hydroxyl groups. (5) The hydrogen bonds involving a halogen ion are longer than hydrogen bonds with other acceptors when corrected for their longer vander Waals radii. The observed differences between the lengths of hydrogen bonds formed by different donor and acceptor groups in amino acids and peptides, imply differences in the energetics of their formation.     

Occurrence and geometrical features of head-to-tail sequences involving amino acids in crystal structures

A careful study of the crystal structures of commonly occurring amino acids, and their racemates and complexes reveals that each hydrogen bond connecting the α-amino and the α-carboxylate groups and its symmetry equivalents generally give rise to an infinite head-to-tail sequence in which the two groups are periodically brought into close proximity. Such sequences, which have earlier been suggested to be of probable relevance to prebiotic polymerisation, appear to be an almost universal feature of amino acid aggregation in the solid state. These sequences belong to two main categories in terms of the geometrical arrangement of amino acid molecules in them. The sequences in the first category consist of straight chains of molecules related mostly by the shortest cell translation in the crystals. The sequences of the second category form hydrogen bonded two fold helices centred around crystallographic 2₁ screw axes. The sequences can be further sub-divided into different types on the basis of the geometrical features of the hydrogen bonds involved in them. A few sequences involving both l and d isomers have also been observed in the crystal structures of some dl -amino acids. The shortest cell translation in most crystals under consideration has a value in the neighbourhood of 5.3 Å and corresponds to the periodicity of a straight head-to-tail sequence or, less frequently, that of a helical sequence or both. The crystal structures of amino acids and their complexes can be classified in terms of the occurrence and the geometrical disposition of different types of head-to-tail sequences in them.     

X-ray studies on crystalline complexes involving amino acids and peptides

The hexahydrate of a 1:1 complex between L-histidyl-L-serine and glycyl-L-glutamic acid crystallizes in space group P1 with a = 4.706(1), b= 8.578(2), c= 16.521(3) ÅA; α= 85.9(1), β= 89.7(1)°, n?= 77.4(1). The crystal structure, solved by direct methods, has been refined to an R value of 0.046 for 2150 observed reflections. The two peptide molecules in the structure have somewhat extended conformations. The unlike molecules aggregate into separate alternating layers. Each layer is stabilized by hydrogen bonded head-to-tail sequences as well as sequences of hydrogen bonds involving peptide groups. The arrangement of molecules in each layer is similar to one of the plausible idealized arrangements of L-alanyl-L-alanine worked out from simple geometrical considerations. Adjacent layers in the structure are held together by interactions involving side chains as well as water molecules. The water structure observed in the complex provides a good model, at atomic resolution, for that in protein crystals. An interesting feature of the crystal structure is the existence of two water channels in the interfaces between adjacent peptide layers.     

Aromatic interactions in tryptophan‐containing peptides: crystal structures of model tryptophan peptides and phenylalanine analogs*

Abstract: The crystal structures of the peptides, Boc‐Leu‐Trp‐Val‐OMe ( 1) , Ac‐Leu‐Trp‐Val‐OMe ( 2a and 2b), Boc‐Leu‐Phe‐Val‐OMe ( 3 ), Ac‐Leu‐Phe‐Val‐OMe ( 4 ), and Boc‐Ala‐Aib‐Leu‐Trp‐Val‐OMe ( 5 ) have been determined by X‐ray diffraction in order to explore the nature of interactions between aromatic rings, specifically the indole side chain of Trp residues. Peptide 1 adopts a type I β‐turn conformation stabilized by an intramolecular 4→1 hydrogen bond. Molecules of 1 pack into helical columns stabilized by two intermolecular hydrogen bonds, Leu(1)NH…O(2)Trp(2) and IndoleNH…O(1)Leu(1). The superhelical columns further pack into the tetragonal space group P4₃ by means of a continuous network of indole–indole interactions. Peptide 2 crystallizes in two polymorphic forms, P2₁ ( 2a ) and P2₁2₁2₁ ( 2b ). In both forms, the peptide backbone is extended, with antiparallel β‐sheet association being observed in crystals. Extended strand conformations and antiparallel β‐sheet formation are also observed in the Phe‐containing analogs, Boc‐Leu‐Phe‐Val‐OMe ( 3 ) and Ac‐Leu‐Phe‐Val‐OMe ( 4 ). Peptide 5 forms a short stretch of 3₁₀‐helix. Analysis of aromatic–aromatic and aromatic–amide interactions in the structures of peptides, 1 , 2a , 2b are reported along with the examples of 14 Trp‐containing peptides from the Cambridge Crystallographic Database. The results suggest that there is no dramatic preference for a preferred orientation of two proximal indole rings. In Trp‐containing peptides specific orientations of the indole ring, with respect to the preceding and succeeding peptide units, appear to be preferred in β‐turns and extended structures.     

Ibuprofen crystals with optimized properties

The common analgesic drug ibuprofen shows bad dissolution and tableting behavior due to its hydrophobic structure. Additionally its high cohaesivity results in low flowability. Because of the bad compaction behavior ibuprofen has to be granulated usually before tableting. Another problem in manufacturing is the high tendency for sticking to the punches. A crystal form with optimized properties of ibuprofen was prepared and characterized in this study. Crystallization was carried out using the solvent change technique in the presence of different water-soluble additives. These additives were only present during the crystallization process and removed after precipitation by a washing process. A nearly pure ibuprofen powder was received, as GC-analysis showed. Plate-shaped crystals with increased powder dissolution, increased flowability and good tableting behavior were obtained. All crystals were determined as isomorphic by DSC and X-ray analysis. Thus the improvement of the substance characteristics of ibuprofen is reached by changes in the outer appearance of the crystals and in surface modifications. Due to the fact that ibuprofen molecules can form hydrogen bonds, additives that can interact with these hydrogen bonds during the crystallization process can modify the properties of the resulting crystals.     

Synthesis,Pharmacology, Crystal Properties,and Quantitative Solvation Studies from a Drug Transport Perspective for Three New 1,2,4-thiadiazoles

A novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments and comparative analysis of molecular conformational states, packing architecture, and hydrogen bonds networks were carried out. Thermodynamic aspects of sublimation processes of studied compounds were determined using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n-hexane and n-octanol were studied within the wide range of temperature intervals and thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. Distribution processes of compounds in buffer/n-octanol and buffer/n-hexane systems (describing different types of membranes) were investigated. Analysis of transfer processes of studied molecules from the buffer to n-octanol/n-hexane phases was carried out by the diagram method with evaluation of the enthalpic and entropic terms. This approach allows us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3754-3768, 2010