INTRAMOLECULAR HYDROGEN BOND

The hydration free energy function was optimized and validated using the two data sets. One contains 639 FSD molecules that were divided into 439 and 200 to consti- tute the training and test sets, respectively, and the other consists of 77 reference molecules (training set) and 47 SAMPL4 molecules (test set). Prior to the optimization of atomic parameters, we defined a total of 52 and 36 atom types to represent a variety of chemical circumstances in FSD and SAMPL4 molecules, respectively. Some abnor- mal atom types were required for coping with FSD mol- ecules such as hexavalent sulfur (S.12) and pentavalent phosphorus (P.10) atoms. O–H type IHBs were found both in FSD and in SAMPL4 molecules while F–H and Cl–H forms were present in the former only. These IHBs were identified by the conformational searches for the presence of non-bond interactions between hydrogen and polar heavy atoms with the interatomic distance shorter than 2.5 Å.

This structure is similar to 2-(4-acetyl-3,5-dihydroxy-2-methylphenoxy)-4,6-dimethoxy-3-methylbenzoic acid (Chantrapromma et al., 2000). A displacement ellipsoid plot with the numbering scheme is shown in Fig. 1. The bond lengths and angles observed in the structure are normal and agree reasonably with the reported values (Elix et al., 1978; Allen et al., 1987; Chantrapromma et al., 1998, 2000). The benzene rings are nearly perpendicular to each other [dihedral angle 75.2 (1)°]. The two methoxy groups and the acetyl group are nearly coplanar with the benzene rings [C18—O6— C11—C10 172.8 (3)°, C17—O5—C9—C10 5.4 (4)° and C2—C3—C13—C14 - 0.2 (5)°]. There are two hydroxyl groups in a molecule involved in hydrogen bonding: one hydroxyl group, O4—H4A, involved as a donor in an intramolecular hydrogen bond with the O3 acetyl group acting as acceptor, the other, O2—H2A, involved in an intermolecular hydrogen bond with the O6 methoxy group of an adjacent molecule.

intramolecular contact distance between O7 and H10A is 2.165 (2) Å, indicating the formation of a weak intramolecular hydrogen bond. With this hydrogen bond, the six atoms O7, C6, C2, C3, N10 and H10A form a six-membered pseudo- ring. Since the hydrogen bond closing the ring is a weak one, the observed length of the single and double bonds in the pseudo-ring (Table 1) are close to the typical values (Glusker et al., 1994), which excludes the formation of a weak conjugated π-electron system inside this pseudo-ring.

Fig. 1 shows the molecular structure of (I) with the atom-numbering scheme. The β-alanine molecule exists in the cationic form with a positively charged amino group and an uncharged carboxylic acid group. The maleic acid molecule exists in the mono-ionized state. The semi-maleate ion is essentially planar as observed in the crystal structures of similar complexes. In the semi-meleate ion, the intramolecular hydrogen bond between atoms O3 and O5 is found to be

The molecular structure of the imidazonaphthyridine cation has an N—H N intramolecular hydrogen bond between atoms N7 and N5, forming an intramolecular S(7) ring (Bernstein et al., 1995). The positioning and orientation of the two pairs of cations and anions in the asymmetric unit lead to two different intermolecular N—H O hydrogen bonds between them. The protonated N atom N7A forms a strong hydrogen bond with O1A, whereas N7B forms a weak bond with O4B. In addition, the crystal structure is stabilized by C— H O and C—H F intra- and intermolecular hydrogen bonds. Interestingly, only the Br1B Br1B ii (symmetry code as in Table 2) short contact of 3.679 (1) A ˚ is observed between

Molecular packing for (I) viewed along the b axis. Dashed lines indicate a trifurcated O—H···O four centre hydrogen bond involving a O3E—H3E···O4E intramolecular hydrogen bond and a weak C—H···O interaction with that of picrate anion. Weak C—H···O interactions are responsible for the formation of cation-anion-cation trimers resulting in a 1D chain along [0 1 0]. H atoms not involved in hydrogen bonding have been removed for clarity.

hydrogen bond. An asymmetric intramolecular hydrogen bond is observed in the crystal structures of maleic acid (James & Williams, 1974), glycinium maleate and l-alaninium maleate; it is found to be symmetric in the crystal structures of complexes of maleic acid with dl- and l-arginine (Ravish- ankar et al., 1998) and l-histidine and l-lysine (Pratap et al., 2000) with an H atom shared between the respective O atoms. Fig. 2 shows the packing of the molecules of (I), viewed down the a axis. The semi-maleate ions do not have direct hydrogen-bonded interactions among themselves except for a weak CÐH O hydrogen bond which links them to form an in®nite one-dimensional chain down the a axis. There is a head-to-tail hydrogen bond among the centrosymmetrically- related amino acid molecules leading to the formation of a dimer. The non-polar side chains of the dl-valinium cations form alternating hydrophobic columns down the a axis. The crystal packing is characterized by OÐH O and NÐH O hydrogen bonds. However, considering the presence of many strong OÐH O and NÐH O bonds, it seems unlikely that weak hydrogen bonds of the type CÐH O play a role in determining the packing modes of the molecules. The aggre- gation pattern has some similarities with that observed in l- phenylalaninium maleate, but is distinctly different from glycinium maleate and l-alaninium maleate.

hydrogen bonds that exist between the perchlorate anion and the alaninium residue play an important role in stabilizing the structure. The amino-N atom is also involved in a chelated three-centered hydrogen bond with acceptor O atoms (O2 and O3) of the perchlorate anion. The amino-N atom is also found to be engaged in a three-centered hydrogen bond, with (i) the carboxyl atom O1A (intramolecular hydrogen bond) and atom O4 of the perchlorate anion and (ii) two O atoms of the perchlorate anions across a center of inversion, forming in®- nite chains. The presence of the three-centered hydrogen bond is due to an excess of acceptors over donors or proton de®- ciency (Jeffrey & Saenger, 1991).

difference can be drawn from the packing diagrams. As shown in Fig. 2, two molecules are connected by two N5— H···N3 hydrogen bonds, forming an elongated hexagon. The hydrogen bonding information is given in Table 2 and a packing diagram is shown in Fig. 3. In addition, the molecules in the crystal are held together by van der Waals forces by a number of intermolecular N—H···O interactions. A weak N—H···N intramolecular hydrogen bond stabilizes the cation conformation (Fig. 1).

mentioned above, there is no intramolecular hydrogen bond involving the carbonyl O atom, O1, of the coordinated (pyridin-2-ylmethyl)amide moiety, and the NH H atom of the protonated N6-pyridine ring [(pyridinium-2-ylmethyl)amide moiety], where the carbonyl O atom, O2, coordinates to the symmetry related Cu atom. In (I), the protonated pyridine ring is twisted in the opposite direction and hydrogen bonds to a water molecule of crystallization (O2W ii ). The non-coord-

The crystal structure of salicylaldehyde benzoylhydrazone features an intramolecular hydrogen bond between the donor OH group of the salicylaldehyde moiety and the acceptor ═N–NH— group of the benzhydrazidyl moiety (Lyubchova et al., 1995); the short hydrogen bond permits the amino nitrogen of the ═N–NH– unit to interact with the –C═O– unit of an adjacent molecule. Such a hydrogen-bonding scheme is also found in 5-chlorosalicylaldehyde benzoylhydrazone (Ali et al., 2005).

An ORTEP-3 (Farrugia, 1997) view of the molecule is shown in Fig. 1. The ÐN NÐ double-bond length is 1.247 (5) AÊ, which is longer than in the azo compound 2-hydroxy-5-([4-(2-pyridinylamino)sulfonyl]phenyl)azobenz- oic acid (van der Sluis & Spek, 1990) [1.223 (7) AÊ], which has no intramolecular hydrogen bond. The high s.u. values and high displacement parameters of some atoms in the molecule are likely caused by some disorder. Atom C18 of the methyl group shows positional disorder, with occupancy factors of 0.550 (5) and 0.450 (5). The phenyl rings show also orienta- tional disorder with the same occupancy factors (Fig. 1). The molecule exists as the keto±amine tautomer. Some special bond lengths are C10ÐO1 = 1.279 (5) AÊ and C11ÐC12 = 1.340 (6) AÊ. The corresponding bond lengths in N-(2-¯uoro-3- methoxy)salicylaldimine, which exists in the phenol±imine tautomeric form, are 1.347 (3) and 1.374 (3) AÊ, respectively (UÈnver et al., 2002). An H atom was located on N3 rather than on O1, thus con®rming a preference for the keto±amine tautomer in the solid state. There is a strong intramolecular N3ÐH1 O1 hydrogen bond, which is a common feature of o-hydroxysalicylidene systems (OdabasËogÆlu, Albayrak, BuÈyuÈkguÈngoÈr & Goesmann, 2003; OdabasËogÆlu, Albayrak, BuÈyuÈkguÈngoÈr & LoÈnnecke, 2003; Filarowski et al., 2003; Nazõr et al., 2000; Yõldõz et al., 1998).

(GoÈrbitz & Etter, 1992). The maleic acid molecule exists in the mono-ionized state (i.e. as a semi-maleate anion). In the semi- maleate anion, a nearly symmetric intramolecular hydrogen bond, with a proton shared between the O3 and O5 atoms, is observed as in the crystal structures of complexes of maleic acid with dl- and l-arginine (Ravishankar et al., 1998) and l- histidine and l-lysine (Pratap et al., 2000). However, in the

also been published (Hoang et al., 1992). The metal atoms in these complexes are also six-coordinate, and the pym ligands bidentate (binding through the N and O atoms). Each of these complexes is also stabilized by a strong intramolecular hydrogen bond, but in these cases either the carbonyl O or N atoms of the saccharinate or salicylate anions are the accep- tors.

angles (Allen et al., 1987) are within normal ranges. The nitro group is essentially coplanar with the aromatic ring forming a dihedral angle of 3.4 (3)° with the ring. The amine H atom forms an intramolecular hydrogen bond with a nitro O-atom acceptor (O2) (Table 1). In the crystal structure, intermolecular aromatic C—H···O and C—H···N hydrogen bonds link the molecules (Fig. 2) while also present are weak aromatic ring π–π interactions [minimum ring centroid separation, 3.9841 (16) Å].

(Wattanakanjana et al., 2012). As in all other complexes with S-only coordination of thiosemicarbazides the ligand is in the anti-conformation, which is stablized by an intramolecular N—H···N hydrogen bond between N1—H1A and N3 (graph set designator as S(5) (Bernstein et al., 1995)). Another intramolecular hydrogen bond, between the hydrazine N2 —H2 group and the chloride anion, orients the hyrdrazide N—H group towards the chlorine atom and, through this, influences the arrangement and orientation of the ligands around the Cu I center. Neighboring complexes are connected

The molecular structure of (I) in the gas phase was optimized by the density-functional theory at the B3LYP/6–31 G(d,p) level, using the computer program GAUSSIAN09 (Parr & Yang, 1989; Frisch et al., 2009). Calculations were performed using the X-ray coordinates as the input structure. The calculated geometry of the sulfonamide group allows for intramolecular hydrogen-bond five-membered ring formation (H1···N1 = 2.618 Å; N2—H1···N1 = 100.3°; N1—C2— S1—N2 = -35.2°) (Fig. 3). In the crystal structure of quinoline-2-sulfonamide (I) an intermolecular hydrogen bond is more difficult to break than comparable intramolecular hydrogen bond formed between the the sulfamoyl NH 2 group and

The title compound, (I), adopts the keto±imine tautomeric form, with a strong intramolecular N1ÐH1 O1 hydrogen bond (Fig. 1). The rather short C1ÐO1, C18ÐO2 and C2Ð C3, C5ÐC6, C7ÐC8 bonds can be considered as C O and C C double bonds, respectively. This suggests the presence of a signi®cant quinoidal effect. A similar effect was observed in 1-[N-(p-hydroxyphenyl)aminomethylidene]naphthalen- 2(1H)-one propan-1-ol hemisolvate [C O = 1.292 (2) and 1.295 AÊ; OdabasËogÆlu et al., 2004] and N-n-propyl-2-oxo-1- naphthylidenemethylamine [C O = 1.277 (2) AÊ; Kaitner & Pavlovic, 1996].

Compounds (1) and (2) were synthesized in moderate/high yields by a one-pot reaction using 4-oxo-4H-chromene-3- carboxylic acid as the starting material. Chromone-3-carb- oxylic acid was initially activated with benzotriazol-1-yl-oxy- tripyrrolidinophosphonium hexafluoridophosphate (PyBOP). Then the in situ formed intermediate reacts with the hetero- amine (stoichiometry 1:1) giving rise to 5H-thiazolo[3,2-a]- pyrimidin-5-one derivatives (1) (68%) and (2) (81%). From a mechanistic point of view, the 6-(2-hydroxybenzoyl)-5H-thia- zolo[3,2-a]pyrimidin-5-one derivatives may have been obtained by a nucleophilic attack of primary heteroamine to the 2-position of the activated chromone with a subsequent opening of the pyran ring. Then, the heterocycle entities were obtained by a process involving an intramolecular reaction assisted by the nitrogen atom of the heterocycle moiety (see scheme below). Crystals were obtained by recrystallization from (1) in AcOEt (m.p. 454–456 K) in the form of colourless

In both molecules, there is an intramolecular O—H O hydrogen bond involving the hydroxyl substituent and the carbonyl O atom of the adjacent acetyl group. In the crystal structure, molecules A and B are linked via a C—H N interaction. There are also some weak C—H interactions involving the phenyl ring of molecule A and H atoms of the acetyl groups of both molecules.