Submitted: December tertiary, 2011Published: September 19th, 2012
DOI: 10.5772/48536
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Nader Noroozi Pesyan
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1. Introduction
X-ray crystallography is an important method for determination of the organization of atoms within a crystal of compound in which a axle of 10-rays strikes a crystal and causes the beam of light to spread into many specific directions. From electron density, in the molecule the hateful positions of the atoms in the crystal can be determined, likewise as their chemic bonds and various other information.
The hexamethylenetetramine as an organic chemical compound was solved in 1923 "(Dickinson & Raymond, 1923)". Several studies of long-concatenation fatty acids were followed which are an of import component of biological membranes "(Bragg, 1925; de Broglie & Trillat, 1925; Caspari, 1928; Müller, 1923, 1928, 1929; Piper, 1929; Saville & Shearer, 1925; Trillat, 1926)". In the 1930s, the structures of larger molecules with two-dimensional complication began to exist solved. An important advance was the structure of phthalocyanine "(Robertson, 1936)", that is closely related to porphyrin molecules of import in biological science, such as heme, corrin, chlorophyll and etc.
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ii. Crystal structures of organic compounds
In this chapter, crystal structures of some organic compounds such as organic torsion helicoids, organic compounds consists of intra- and intermolecular hydrogen bond and their some metal complexes and crystal structures of some organic spiro compounds were described.
2.1. Crystal construction of organic torsion helicoids
In recent years, several different interesting organic compounds structures have been found by X-ray crystallography. Helicenes are an extremely bonny and interesting class of conjugated molecules currently investigated for optoelectronic applications "(Groen et al., 1971; Katz, 2000; Rajca et al., 2007; Schmuck, 2003; Urbano, 2003)". They combine the electronic properties afforded by their conjugated organisation with the chiroptical properties "(Bossi et al., 2009; Collins & Vachon, 2006; Larsen et al., 1996)" afforded by their interesting and peculiar helix-similar construction, resulting from the condensation of aromatic (and/or heteroaromatic) rings, all of them in ortho position. For instance, the formula and crystal structures of tetrathia-[vii]-helicene i are shown in Figures 1 and ii, respectively. The compound i has been synthesized in three stride by starting material of benzo[1,two-b:four,iii-b']dithiophene and is shown in Scheme 1 "(Maiorana et al., 2003)" and this compound showed 2nd-guild non-linear optical (NLO) properties and has been investigated (Clays et al., 2003). In particular, carbohelicenes only include benzene rings, and also in heterohelicenes i or more aromatic rings are heterocyclic (pyridine, thiophene, pyrrole and etc.) "(Miyasaka et al., 2005; Rajca et al., 2004)". With increasing number of condensed rings (typically, n > 4), the steric interference of the terminal rings forces the molecule to exist a helicoidal form. For north > 4 the energetic barrier is such that the ii enantiomers tin be separated and stored "(Martin, 1974; Newman, et al., 1955, 1967; Newman & Lednicer, 1956; Newman & Chen, 1972)". Of course, the conjugation of π system decreases with decreasing of planarity; even so, in longer helicenes π-stack interactions can too have place betwixt overlapping rings "(Caronna et al., 2001; Liberko et al., 1993)". All helicenes (more often than not, n > iv) are chiral molecules and exhibit huge specific optical rotations "(Nuckolls et al., 1996, 1998)" since the chromophore itself, in this example the entire aromatic molecule, is inherently dissymmetric (right-paw or left-hand helix), having a twofold symmetry axis, C2, perpendicular to its cylindrical helix (in carbohelicenes), or inherently asymmetric (in heterohelicenes) "(Wynberg, 1971)".
Figure 1.
Formula structures of 1 and 2.
Figure ii.
The helicoid structures of unsubstituted tetrathia-[7]-helicene 1 and unsubstituted hexathia-[11]-helicene 3 "(Caronna et al., 2001)" with the labelling scheme adopted for structural discussion "(Bossi et al., 2009)".
Scheme 1.
The synthesis of one from benzo[1,2-b:four,3-b']dithiophene as a starting textile.
Scheme 2.
Reaction machinery for germination of 5 "Garcia et al., 2009)".
Tetrathia-[7]-helicene 1 accept been used for the synthesis of organometallic complexes "(Garcia et al., 2009)". A series of organometallic complexes possessing tetrathia-[7]-helicene nitrile derivative ligands 5 equally chromophores, has been synthesized and fully characterized by Garcia et al. "(Garcia et al., 2009)". This compound was analyzed by means of 1H NMR, FT-IR, UV–Vis and X-ray crystallography techniques. The spectroscopic data of this compound was shown with in order to evaluate the beingness of electronic delocalization from the metallic middle to the coordinated ligand to have some insight on the potentiality of this compound as non-linear optical molecular materials. Slow crystallization of compound 4 revealed an interesting isomerization of the helical ligand with formation of two carbon-carbon bonds betwixt the two terminal thiophenes, leading to the total closure of the helix five. The reaction mechanism for the germination of 5 is shown in Scheme 2. Crystal structure of 5 is shown in Effigy 3. A selected bond length, angles and torsion angles for chemical compound v is summarized in Table i "Garcia et al., 2009)".
Another case about helicenes is the hexahelicene 2 and its derivatives that is a chiral molecule "(Noroozi Pesyan, 2006; Smith & March, 2001)". A user-friendly road for the synthesis of [7]-helicene (6a) and [7]-bromohelicene (6b) is reported "(Liu et al., 1991)". The crystal structure of 6b is shown in Fig. iv. The crystal construction of 6b and its unusual oxidation reaction product seven (equally a major product) has been reported "(Fuchter et al., 2012)" (Figure four and Scheme 3). Alternatively, compound half-dozen may be an option for a neutral helicene-derived metallocene complex, since the seven-membered benzenoid rings give rise to a scaffold that completes i full turn of the helix with the two terminal rings being co-facial. It has been theoretically predicted and reported that the 6 has potential to demark some metal cation such as Cr, Mo, W, and Pt in a sandwich model "(Johansson & Patzschke, 2009)". Fuchter and co-workers "(Fuchter et al., 2012)" too reported the crystal structure of seven that obtained via unusual oxidation rearrangement of 6. In this structure, The bonds within the pyrenyl unit range betwixt 1.3726(19) and ane.4388(xiv) Å with the exception of one outlier at 1.3512(18) Å for the C(26)–C(27) bond. The C=C double bonds in rings D and East are one.3603(15) and i.3417(16) Å respectively, and the C=O bond is 1.2419(xiv) Å. The structure of 7 revealed the dominant canonical class to have a pyrenyl grouping consisting of rings A, B, C and H linked past single bonds to a C–C=C–C=C–C=O unit of measurement to course rings D and Due east (Scheme three). The pyrenyl unit is apartment, the xvi carbon atoms beingness coplanar. Ring I has 4 unmarried bonds and two effluvious bonds, and has a folded conformation with the methylene carbon lying ca. 0.87Å out of the plane of the other five carbons which are coplanar. Aryl ring Grand forming the five-membered band J, links to ring I. The planes of the five coplanar atoms of band I and the four coplanar atoms of ring J are inclined past ca. 108° to each other. The band of Due east is slightly distorted in a boat-like fashion with the carbon shared just with band D and that shared with rings I and J, out of the airplane of the other four atoms which are coplanar to within ca. 0.01 Å.
The formula structure of Katz's helical ferrocene viii is shown in Effigy five "(Katz & Pesti, 1982; Sudhakar & Katz, 1986)".
Figure 3.
Crystal structure of five.
Bond distances (Å)
Ru(i)–N(1)
2.030(5)
P(2)–C(221)
1.850(7)
Ru(1)–Cpa
i.8595(vi)
P(2)–C(231)
one.829(6)
Ru(1)–P(1)
2.350(2)
N(1)–C(ane)
ane.147(8)
Ru(1)–P(2)
2.353(2)
C(1)–C(2)
1.433(nine)
P(1)–C(111)
one.843(6)
C(2)–C(3)
1.598(ix)
P(1)–C(121)
1.831(7)
C(3)–C(4)
1.535(ix)
P(1)–C(131)
one.817(7)
C(4)–C(23)
ane.519(ix)
P(2)–C(211)
1.846(7)
C(23)–C(2)
one.565(ix)
Bail angles (°)
N(1)–Ru(1)–Cpa
121.79(14)
C(i)–C(2)–C(iii)
115.3(6)
N(1)–Ru(1)–P(ane)
87.93(14)
C(2)–C(3)–C(4)
88.8(5)
North(ane)–Ru(i)–P(two)
90.83(xv)
C(ii)–C(23)–C(four)
90.6(5)
P(ane)–Ru(one)–P(two)
99.84(six)
C(three)–C(iv)–C(23)
91.2(v)
P(1)–Ru(i)–Cpa
124.15(v)
C(3)–C(2)–C(23)
87.2(5)
P(2)–Ru(ane)–Cpa
122.98(5)
C(five)–C(4)–C(23)
106.nine(6)
Ru(1)–N(1)-C(ane)
169.ix(5)
C(4)–C(23)–C(22)
107.7(five)
N(i)–C(1)–C(2)
175.7(7)
C(2)–C(3)-South(1)
119.three(5)
C(1)–C(2)–C(23)
116.iv(vi)
C(3)–C(ii)–Due south(4)
116.five(5)
Torsion angles (°)
Ru(1)–North(i)–C(ane)–C(2)
29(11)
Northward(1)-C(one)–C(2)–C(23)
62(9)
N(1)–C(1)–C(2)–C(three)
-38(9)
C(2)–C(3)–C(4)–C(23)
-eleven.0(5)
N(1)–C(1)–C(2)–S(four)
-175(9)
Table 1.
Selected bond distances and bond and torsion angles for chemical compound five "(Garcia et al., 2009)".
Scheme iii.
The formula structures of 6a and 6b and its unusual reaction for synthesis of 7a (and besides its construction).
Figure 4.
Crystal structures of 6b and 7a.
Effigy 5.
The formula structure of Katz's helical ferrocene 8.
Scheme 4.
Two possible dissimilar torsion helicoids of 9.
Figure 6.
Two independent molecules of 9 in the crystal studied.
Diazepinone dervatives are of pharmaceutical compounds. Another interesting helical diazepinone chemical compound that is discussed in this department, is 1,ix-dimethyl-4,5-dihydro-half-dozenH-pyrido[iii',2':4,5]thieno[2,3-f]pyrrolo[i,2-a][1,four]diazepin-6-one (9). This molecule show two crystallographically independent molecules that form the disproportionate unit of the structure are shown in Figure 6. The X-ray crystallographic analysis shows the molecular structure of the compound ix and reveals an interesting fact that this structure features ii stereochemically unlike molecules (9A and 9B) that can exist understood as different torsion helicoids (Effigy 6). The compound has two stereoisomers (R and S conformers). In each structure the seven-membered diazepinone ring exhibits a boat conformation. The fused pyrido[3',2':4,5]thieno ring moiety has planar geometry. The C3–H3 bond is slightly off the fused pyrido[3',2':4,v]thieno band plane. The hindrance repulsion between the hydrogen atom at C3 on pyridine ring and methyl group on pyrrole band makes the molecule of 9 essentially non-planar (repulsion of C3–H3A with C15 and C3'–H3'B with C15' of methyl groups) (Scheme 4). The torsion angles between the pyrrole and thiophene rings in 9A and 9B are 45.7(half dozen)° and –49.three(vi)°, respectively "(Noroozi Pesyan, 2010)".
The –NH– group of each molecule (e.g. molecule 9A) makes an intermolecular hydrogen bail to the C=O functional group of the molecule of another kind (molecule 9B), and vice versa. For example, the intermolecular hydrogen bond N3–H3····O1' involves the N3 atom from molecule 9A and O1' atom from the carbonyl group of molecule 9B, and viceversa for N3'–H3'····O1 (Effigy 7). The crystal packing diagram indicates zigzag hydrogen-bonded chains forth the crystallographic axes with 2 distinct hydrogen bonds (Figure 7). The intermolecular hydrogen bonds play a principal and important role in the crystal packing diagram of nine "(Noroozi Pesyan, 2010)".
Effigy 7.
Crystal packing diagram of ix showing zigzag H-bonds (shown past dashed lines).
One of the most interesting helical primary structure is sown in Effigy 8 has been reported by Fitjer et al. "(Fitjer et al., 2003)". Helical primary structures of spiro annelated rings are unknown in nature just have been artificially produced, both in racemic and enantiomerically pure grade. The formula construction of one-cyclobutylidenespiro[3.3]heptane (10) as a starting material is shown in Scheme 5. The compound 10 yielded enantiomeric mixture of 11 and 12 in the presence of zinc and 2,2,2-trichloroacetyl chloride. Reductive dehalogenation of 11 and 12 then Wolff–Kishner reduction yielded the desired trispiro[3.0.0.3.2.2]tridecane [rac-(15), (symmetry, C2)]. The crystal structure of the camphanic acid derivative of 15 ((oneSouthward,five'Due south,ten'Due south)-16) is shown in Figure viii "(Fitjer et al., 2003)".
Scheme 5.
Synthesis of the compounds trispiro[3.0.0.3.2.2]tridecane (15) and the formula structure of its derivative (1S,v'S,10'Southward)-16 "(Fitjer et al., 2003)".
Figure 8.
Crystal construction of (1Southward,v'S,x'S)-16.
Helquats, the family of Northward-heteroaromatic cations "(Arai & Hida, 1992)", recently were introduced helical dications that represent a missing structural link between helicenes and viologens"(Casado et al., 2008)". Specifically, bones [seven]-helquat (17) "(Severa et al., 2010)" is a structural hybrid between [7]-helicene and a well-known herbicide diquat (Scheme 6). Synthesis of [7]-helquat (17) starts with bisquaternization of bis-isoquinoline precursor (eighteen) with an excess of 3-butynyltriflate followed past the primal metal catalyzed [two+2+ii] cycloisomerization of the resulting triyne, formed 17 (Scheme vii).
Scheme 6.
Structural relation of [7]-helquat (17) to [7]-helicene 6a and herbicide diquat.
Scheme 7.
Synthesis of 17 via one-pot bis-quaternization of eighteen.
Recently, Nakano et al. accept been reported the helical construction, λ5-phospha [7]-helicenes 9-phenyl-9H-naphtho[1,2-e]phenanthro[3,iv-b]phosphindole-9-oxide (21) and its thio analogue 9-phenyl-9H-naphtho[1,two-eastward]phenanthro[3,4-b]phosphindole-9-sulfide (22) "(Nakano et al., 2012)". The formula structure of 21 and 22 and the crystal construction of 21 are shown in Fig. ten. Phospha [7]-helicenes 21 and 22 take more distorted structures than the other heterohelicenes. In the structure of 21, the sums of the five dihedral angles that are derived from the seven C–C bonds [C(17)-C(17a)-C(17b)-C(17c), C(17a)-C(17b)-C(17c)-C-(17d), C(17b)-C(17c)-C(17d)-C(17e), C(17c)-C(17d)-C(17e)-C(17f), and C(17d)-C(17e)-C(17f)-C(1)] are 95.28 for 21 and 99.68 for 22. These angles are larger than those of hetero[7]-helicenes 23–25 (79–88°). This case can exist attributed to the big angles betwixt the two double bonds of phosphole oxide (l°) and phosphole sulfide (fifty°) relative to furan (32°), pyrrole (35°), and thiophene (45°). Owing to the larger angle, a larger overlap of the two terminal benzene rings was occurred in the λ5-phospha[vii]-helicenes, therefore, a stronger steric repulsion. These larger distortions in 21 and 22 explicate the higher tolerance of 21 and 22 towards racemization.
Figure nine.
Formula and 10-ray single crystal construction of compounds 19 and 20 (Triflate counterions are omitted for clarity) "(Severa et al., 2010)".
Figure x.
Formula structures of λ5-Phospha[7]-helicenes 21 and 22 and crystal structure of 21 equally representative.
2.ii. Inter- and intramolecular hydrogen bonds in the crystal structure of organic compounds
Hydrogen bond plays a fundamental and major role in the biological and pharmaceutical systems and remains a topic of intense current interest. Few selected recent articles exemplify the general telescopic of the topic, ranging from the part of H-bonding such equally in: weak interaction in gas phase "(Nishio, 2005; Wang et al., 2005)", supramolecular assemblies "(McKinlay et al., 2005)", helical structures "(Azumaya et al., 2004; Noroozi Pesyan, 2010)". Important consequences of both inter- and intra-molecular H-bonding have long been recognized in the physicochemical behavior of DNA and RNA "(Jeffery & Saenger, 1991)".
Several kinds of hydrogen bail have been reported. If the donor-acceptor distance to be in the range of; 2.50 ≤ d (O O) ≤ two.65, this kind of hydrogen bond is strong and when shorter than 2.50 Å (d(O O)≤ 2.50), to exist very strong hydrogen bond "(Gilli et al., 1994)".
In very short O H O bonds (2.forty-2.45 Å) the major distribution of the proton are as follows:
The proton is closer to one of the O atoms (asymmetric hydrogen bond).
The proton is located precisely at the centre (symmetric or centred hydrogen bond).
There is statistically disorder of the proton between two positions on either side of the center (the proton is closer to one or the other side in different domains of the crystal).
There is a dynamical disorder between 2 positions as in (iii); the proton jumps between the two positions in the same hydrogen bond "(Gilli et al., 1994; P. Gilli & One thousand. Gilli, 2000; Olovsson et al., 2001; Steiner, 2002)".
For example, the construction of the potassium hydrogen dichloromaleate (26) has been studied by neutron diffraction at 30 and 295 Yard, with the emphasis on the location of the protons. There are ii crystallographically independent hydrogen atoms in two very short hydrogen bonds, 2.437(2) and 2.442(2) Å at 30 K. For the centrosymmetric space group P1, with the hydrogen atoms located at the centres of symmetry, the structure could be refined successfully. Olovsson et al. have and so been applied several different types of refinements on this structure, including unconventional models; with all atoms except hydrogen constrained in P1, just with hydrogen allowed to refine without any constraints in P1, anisotropic refinement of all atoms resulted in clearly off-centred hydrogen positions. The shifts of the two hydrogen atoms from the centres of symmetry are 0.xv(one) and 0.12(1) Å, respectively, at thirty K, and 0.15(i) Å for both hydrogen atoms at room temperature. At 30 K: R(F) = 0.036 for 1485 reflections; at 295 K: R(F) = 0.035 for 1349 reflections (Olovsson et al., 2001)" (Fig. xi).
I of the virtually interesting example about intermolecular hydrogen bond is the heptan-4-yl (2'-hydroxy-[1,1'-binaphthalen]-2-yl) phosphonate (27a) "(Dabbagh et al., 2007)". The phosphonate 27a was existed in dimmer class via ii strong intermolecular hydrogen bonds with centrocymmetric (Ci) 18-membered dimmer grade consisting of two monomers strongly hydrogen-bonded between the oxygen of P=O units and hydroxyl hydrogen atoms (Fig. 12). The crystal structure of 27a was adamant by X-ray crystallography and is shown in Fig. 12. The selected bond lengthes, angles and torsion angles of 27a are summarized in Tables 2-4, respectively. Crystal data indicated the torsion angles (φ) between two naphthalenic rings moieties in BINOL species are 95.28(16)° and are transoid forms (Fig. thirteen). The intermolecular hydrogen bail distance in the structure of 27a was obtained ii.70 Å (potent hydrogen bond) and comparised with other hydrogen bonds P-containing systems (Table 5).
Effigy xi.
Crystal structure of potassium hydrogen dichloromaleate (26).
Effigy 12.
Crystal structure of 27a.
Effigy 13.
Representatively, two strong intermolecular hydrogen bonds with centrocymmetric xviii-membered dimmer class in 27a and 27b.
Entry
Bond
length (Å)
ane
P(1) – O(three)
1.4578(11)
2
P(1) – O(two)
one.5544(12)
3
P(1) – O(i)
ane.5865(11)
iv
P(1) – H(i)
i.295(16)
v
O(1) – C(1)
1.4073(17)
6
O(2) – C(21)
1.5006(19)
7
O(4) – C(12)
1.3634(18)
8
O(iv) – H(four)
0.89(ii)
9
O(3) – H(4)
one.81(2)
10
C(10) – C(11)
1.4942(19)
Tabular array 2.
Selected bail length (Å) of dimmer 27a.
Entry
Bail
Angle (θ, °)
1
O(three) – P(1) – O(2)
118.32(7)
ii
O(iii) – P(1) – O(1)
113.50(vii)
3
O(2) – P(1) – O(1)
102.xvi(half-dozen)
four
O(iii) – P(1) – H(ane)
112.7(7)
5
O(2) – P(1) – H(1)
103.nine(7)
6
O(one) – P(i) – H(one)
104.vii(8)
vii
C(one) – O(1) – P(ane)
122.24(nine)
8
C(21) – O(2) – P(1)
122.27(10)
9
C(12) – O(four) – H(four)
114.4(xiv)
10
C(10) – C(1) – C(2)
123.47(fourteen)
11
C(10) – C(ane) – O(ane)
117.78(13)
12
C(ii) – C(one) – O(one)
118.66(13)
thirteen
C(9) – C(ten) – C(xi)
120.98(12)
14
O(4) – C(12) – C(eleven)
124.08(14)
15
O(4) – C(12) – C(13)
114.68(13)
16
O(ii) – C(21) – C(22)
107.92(12)
17
O(2) – C(21) – C(25)
111.86(18)
xviii
C(22) – C(21) – C(25)
108.84(eighteen)
19
O(2) – C(21) – H(21)
109.4
20
C(22) – C(21) – H(21)
109.4
21
C(25) – C(21) – H(21)
109.4
Table iii.
Selected bond angle of dimmer 27a.
Entry
Bond
Torsion angles (Φ, °)
i
O(3) – P(1) – O(one) – C(1)
51.11(13)
ii
O(2) – P(1) – O(i) – C(1)
179.64(11)
three
O(three) – P(ane) – O(2) – C(21)
58.93(13)
four
O(ane) – P(1) – O(2) – C(21)
-66.49(12)
5
P(1) – O(1) – C(one) – C(ten)
110.03(13)
6
P(one) – O(1) – C(1) – C(ii)
-73.xiii(15)
7
O(1) – C(one) – C(two) – C(3)
-177.12(12)
eight
C(7) – C(8) – C(ix) – C(ten)
178.21(14)
9
C(ii) – C(1) – C(10) – C(xi)
-178.59(12)
10
O(1) – C(ane) – C(10) – C(11)
-2.11(19)
eleven
C(1) – C(10) – C(11) – C(12)
-97.30(17)
12
C(9) – C(x) – C(11) – C(12)
83.69(xviii)
13
C(one) – C(10) – C(11) – C(20)
83.73(17)
14
C(9) – C(10) – C(11) – C(twenty)
-95.28(sixteen)
15
C(twenty) – C(eleven) – C(12) – O(four)
179.63(140
16
C(ten) – C(xi) – C(12) – O(4)
0.6(ii)
17
P(i) – O(2) – C(21) – C(22)
-119.33(13)
eighteen
P(1) – O(2) – C(21) – C(25)
120.97(xix)
19
O(2) – C(21) – C(22) – C(23)
62.75(18)
20
C(25) – C(21) – C(22) – C(23)
-175.66(19)
21
C(21) – C(22) – C(23) – C(24)
166.78(15)
22
O(2) – C(21) – C(25) – C(26)
-68.viii(three)
23
C(22) – C(21) – C(25) – C(26)
172.0(2)
24
C(21) – C(25) – C(26) – C(27)
-173.4(3)
Table 4.
Selected torsion angles of dimmer 27a.
Linkages
Bond distance [Range, donor….H….acceptor] (Å)
Strength
P–O–H....O–P
2.39-2.50
Very strong
P–O–H....O–P
two.fifty-2.65
Strong
P–O–H....O–C
2.41-2.82
Potent
P–H....OH2
2.56-3.15
Moderate
P–O....H–N
2.65-three.10
Moderate
Dimmer 27
2.lxx
Strong
Table 5.
Classification of hydrogen bonds within P-containing systems.
Dimeric centrosymmetric ring structures are quite mutual within phosphorous chemistry: for instance; the structures of 28 and 29 are of 12- and 8-membered structures, respectively "(Corbridge, 1990)". According to spectroscopic testify, esters of (trichloroacetyl) amidophosphoric acid (29) exist equally 29I rather than 29II, which suggests that the hydrogen bond in Due north-H O=P is stable than that of in N-H O=C "(Corbridge, 1990)".
The formula structures of (Due east)-2-benzamido-3-(pyridin-two-yl)acrylic acid (30a) and (E)-two-benzamido-3-(pyridin-four-yl)acrylic acid (30b) are shown in Figure fourteen. The isomer 30a possesses a strong 7-membered ring intramolecular hydrogen bonding and shows quite different physicochemical backdrop, such as solubility and pKa, comparing with its isomer 30b. The p-conjugation betwixt pyridyl and acrylate moieties is extended by intramolecular hydrogen bonding leading to a stiff absorption at near 340 nm. Intramolecular proton transfer facilitates in the excited state, resulting in dual emission at around 420 nm and 490 nm in acetonitrile "(Guo et al., 2011)". Crystal construction of 30a show a strong seven-membered ring intramolecular hydrogen bonding (Effigy fifteen). The intramolecular proton transfer is facilitated by intramolecular hydrogen bond of O–H Northward. Tautomeric forms of 30a is shown in Scheme eight.
Effigy xiv.
Formula structures of 30a and 30b.
Effigy 15.
Crystal structure of 30a.
Scheme 8.
Possible tautomeric forms of 30a.
In that location is hydrogen bonding between the acrylate O(3) and the pyridine N(2) atoms; the distance between these two atoms is 2.483 Å, and the O(3)-H(12)-N(2) angle is 171.3°. The O(iii)-H(12) distance is 1.345 Å (the theoretical distance is 0.920 Å for general carboxyl O-H bail), which is longer than the Northward(2)-H(12) altitude of 1.145 Å (the general altitude is 0.960 Å). The distance difference revealed that H(12) is closer to the pyridine N(2) than it is to the acrylate O(iii). The O(2)-C(9) and O(three)-C(9) distances are 1.233 Å and 1.272 Å, respectively. These results show that H(12) is involved in a stiff intramolecular hydrogen bonding. North(2)-H(12)····O(iii), in which the H(12) interaction with the pyridine N(two) is stronger than that with O(iii) atom. The carboxylic acrid proton moves to the pyridine N cantlet, while an electron delocalizes beyond O(2), O(three), and C(ix) to form two almost equivalent carbonyl groups. These results provide further testify that chemical compound 30a exists mainly as a tautomeric form 30a (NH) in the solid state (30a[Ii]) form "(Guo, et al. (2011)".
Resorcarene derivatives are used as units in self-assembled capsules via hydrogen bonds. Like to calixarenes, resorcarenes are the core to which specific functional groups are attached. These groups are responsible for the hydrogen bonds while the resorcarenes offer the right spatial organisation of them. McGillivray and Atwood constitute that 31 forms in the crystalline land a hexameric capsule with the internal volume of nigh 1375Å3. There are 60 hydrogen bonds in hexameric with the assist of viii molecules of h2o (Fig. xvi) "(McGillivray & Atwood, 1997)".
Effigy sixteen.
Formula structure of 31 unit and crystal construction of (31)half-dozen·8H2O.
Yoshida et al. have besides been reported the germination of a three-dimensional hydrogen bonding network by cocky-associates of the Cu(II) circuitous of a semi-bidentate Schiff base "(Yoshida et al., 1997)". The crystal construction of the Cu(Two) circuitous of Shiff base of operations 32 is shown in Fig. 17. The infinite overall structure of 32 is found to be organized by a three-dimensional hydrogen-bonding network in which the –NHii OtwoS– blazon intermolecular hydrogen bonds play an of import office, every bit shown in Fig. xviii. One complex molecule is surrounded past 4 adjacent complexed molecules through four –NHii O2Southward– hydrogen bonds. These hydrogen bonds would be strong judging from the NH O distances in the range ii.032–ii.941 Å. From the neutron diffraction written report of sulfamic acid (NHiii+And so3-), a comparably potent hydrogen bond has been observed (–Northward+H -O–S– distances in the range 1.95–2.56 Å) "(Jeffrey & Saenger, 1991)". Like hydrogen bonds between sulfone and hydroxyl groups [two.898(6) Å] accept been found in a supramolecular carpet formed via cocky-associates of bis(four,4'-dihydroxyphenyl) sulfone "(Davies et al., 1997)". Furthermore, four weak Br H hydrogen bonds may participate in the hydrogen-bonding arrays "(Yoshida et al., 1997)".
Yang et al. reported the crystal construction of Bis(barbiturato)triwater complex of copper(II). The neutral Cu(H2O)3(barb)2 molecules are held together to form an extensive three- dimensional network via –OH·····O– and –NH·····O– hydrogen-bonded contacts "(Yang et al., 2003)". Hydrogen bonding motifs in fullerene chemistry have been reported past Martín et al. every bit a minireviewe. The combination of fullerenes and hydrogen bonding motifs is a new interdisciplinary field in which weak intermolecular forces allow modulation of 1-, two-, and 3-dimensional fullerene-based architectures and control of their office "(Martín et al., 2005)".
Figure 17.
Crystal structure of 32 unit of measurement.
Effigy xviii.
Crystal packing diagram of 32.
Methyl two,4-dimethoxy salicylate (33) as potential antitumor activity, was synthesized from the reaction of 1,three,5-trimethoxybenzene (the nearly electron-rich aromatic ring) with 2-methoxycarbonyl-5-(4-nitrophenoxy) tetrazole, under solvent-free conditions, a low yield product was obtained (< 2%), while in the presence of a Lewis acrid (AlCl3), the yield was increased to 30% (a kind of trans esterification reaction) "(Dabbagh et al., 2003)".
Crystal construction of 33 is shown in Fig. 19. The carbon-oxygen framework of the molecular structure of 33 is substantially planar; bond lengths and angles are summarized in Table vi, while a structural diagram is shown also in Fig. 20. Planarity is maintained past a strong intramolecular hydrogen bonding interaction betwixt the carbonyl-oxygen and phenolic-H atom [H(1) O(1) = 1.68(4) Å; O(5) – H(1) = i.00(4) Å], and a much weaker intramolecular hydrogen bond of distance 2.535 Å between Me hydrogen's [H(8)] and the C=O group (in what we label a "bisected" conformation with Cs symmetry, Figs. xix and 20). The orientations of the o-OMe and ester-OMe are such to minimize steric interactions. The structure of 33 was also calculated by semi-empirical ab-initio, PM3 and AM1 methods, and information for bond lengths, angles and torsion angles are in skilful understanding together with the experimental ones (Tables 6 and seven), while the corresponding calculated H(one) O(1) bond lengths were 1.57, i.78 and 1.97 Å, and the calculated O(5) – H(i) values were ane.00, 0.980, 0.970 Å, respectively. The ab-initio value for the weaker hydrogen bonding interaction was 2.574 Å. The ab-initio calculation also revealed a one.xl Kcal higher energy, eclipsed conformation with C1 symmetry (Fig. 21 c and d, Fig. xx, Tabular array 7) with an H(eight) – carbonyl bond length of 2.14 Å "(Dabbagh et al., 2004)".
Figure 19.
Crystal construction of 33 with 50% probability ellipsoids.
Effigy 20.
Diagrams showing the favored so-called "bisected" (left) and "eclipsed" (correct) conformations of 33.
Figure 21.
Molecular structures for 33 from ab-initio analysis [side-view: a (bisected); c (eclipsed), and front-view: b (bisected0; d (eclipsed)].
Atoms
Bond lengths (Å)
Atoms
Bond angles(º)
O(1) – C(seven)
ane.247(four)
C(7) – O(2) – C(8)
116.1(three)
O(2) – C(7)
1.325(4)
C(2) – O(3) – C(9)
117.1(3)
O(ii) – C(eight)
1.465(4)
C(4) – O(4) – C(10)
115.eight(2)
O(3) – C(2)
1.363(4)
C(2) – C(ane) – C(6)
116.ix(3)
O(3) – C(9)
1.438(4)
C(two) – C(1) – C(vii)
124.7(3)
O(4) – C(four)
1.362(four)
C(half-dozen) – C(ane) – C(7)
118.3(iii)
O(four) – C(10)
1.443(4)
O(3) – C(2) – C(1)
117.one(three)
C(one) – C(2)
ane.432(iv)
O(three) – C(2) – C(three)
121.9(3)
C(1) – C(half dozen)
1.393(4)
C(1) – C(2) – C(3)
121.03
C(1) – C(7)
1.465(iv)
C(ii) – C(3) – C(4)
119.8(3)
C(2) – C(3)
1.378(iv)
O(4) – C(iv) – C(3)
114.4(3)
C(3) – C(4)
1.406(4)
O(iv) – C(4) – C(5)
125.one(3)
C(four) – C(v)
1.364(iv)
C(iii) – C(4) – C(5)
120.6(3)
C(5) – C(6)
one.402(5)
C(4) – C(5) – C(6)
119.seven(3)
O(five) – C(6)
1.349(4)
O(5) – C(half dozen) – C(1)
122.iii(iii)
-
-
O(5) – C(6) – C(v)
115.7(3)
-
-
C(1) – C(six) – C(5)
122.0(3)
-
-
O(1) – C(7) – O(2)
120.7(3)
-
-
O(i) – C(7) – C(1)
122.0(3)
-
-
O(2) – C(seven) – C(1)
117.3(3)
Table half-dozen.
Bail lengths (Å) and angles (o) of 33.
Bisected
Eclipsed
Relative Energy
Method
Efull
[C=O--H-C]
[C=O--H-O]
Efull
[C=O--H-C]
[C=O--H-O]
(kcal/mol)
Å
Å
(kcal/mol)
Å
Å
(Eeclip -Ebist)
10-Ray
-
two.535
1.68(4)
-
-
-
-
Ab-intio
- 470792.80
2.574
ane.565
-470791.twoscore
2.139
i.557
ane.40
PM3
-2812.fifty
two.647
ane.780
-2811.10
2.309
ane.780
ane.40
AM1
-2813.50
ii.554
1.974
-2812.50
2.186
1.969
1.0
Table 7.
Experimental and calculateda hydrogen bail lengths and energies (kcal/mol) for bisected and eclipsed structure of 33.
Figure 22.
Crystal packing diagram of 34 (a) and 35 (b). Intermolecular hydrogen bond assigned by red dashed line (Carbon: grey; hydrogen: white; oxygen: ruby-red and nitrogen: blue).
Tetrazole ring can be to be an equilibrium mixture of two tautomeric forms (1H and 2H-tetrazoles) "(Dabbagh & Lwowski, 2000)". five-Aryloxy (iH) and/or (2H)-tetrazoles often show intermolecular hydrogen bail "(Noroozi Pesyan, 2011)". For instance, the crystal packing diagram of 5-(2,half dozen-dimetylphenoxy)-(1H)-tetrazole (34) and 5-(two,6-diisopropylphenoxy)-(oneH)-tetrazole (35) prove intermolecular hydrogen bond (Fig. 22). In the compound 34, the crystal structure indicated that the tetrazole and phenyl rings are near perpendicular to each other, forming a dihedral angle of 95.5° (versus 92.06° from calcd. B3LYP/half-dozen-31G(d) and 6-31+G(d)). Because of the conjugation of O1 with tetrazole band, the bond distance C1–O1 [i.322 Å] is slightly shorter than O1–C7 [ane.399 Å]. These bond distances for C1–O1 and O1–C2 were obtained i.333 and i.419 Å with calculation by B3LYP/half-dozen-31G(d) method, respectively and likewise 1.332 and 1.420 Å derived with adding by B3LYP/6-31+G(d) basis set up, respectively. These data are in skillful understanding with experimental results (Table eight). In the compound 35, the crystal structure indicated that the tetrazole and phenyl rings are nearly perpendicular to each other, forming a dihedral angle of 85.91° (versus 107.2° from calcd. B3LYP/6-31G(d)). Because of the conjugation of O1 with tetrazole band, the bail altitude C2–O1 [1.3266(14) Å] is slightly shorter than O1–C7 [one.4257(13) Å]. These bond distances for C2–O1 and O1–C7 were obtained ane.332 and 1.423 Å with calculation by B3LYP/6-31+G(d) method, respectively and are in good agreement with experimental results. These bail distances were as well obtained i.322 and 1.422 Å with calculation by B3LYP/6-31G(d) method, respectively. The torsion angles betwixt phenyl band and each of methyl units on two isopropyl groups are -110.70°, 124.xviii° and 116.15° and 154.12°, respectively (Table 9).The selected parameters of bond length, angles and torsion angles of 34 and 35 derived by experimental and calculated results are shown in Tables 8 and 9.
The crystal packing of 34 exhibits an intermolecular N1–H1 N4 hydrogen bonds and comparized with the calculated at DFT (B3LYP) at 6-31G(d) and vi-31+M(d) ground sets (Table 10). The crystal structure indicated that the bond distance value betwixt donor – hydrogen (N1–H1) and hydrogen-acceptor (H1 N4) were found in results 0.861 and i.959 Å, respectively. For instance, these bond distances were also found in results i.033 for (N1–H1) and 1.814 for (H1 N4) past calculated at B3LYP/6-31G(d) and 1.031 for (N1–H1) and ane.809 for (H1 N4) B3LYP/6-31+G(d), respectively. The donor-acceptor distance value (N1 N4) was obtained two.804 by experimental method. This parameter was found 2.842 and two.838 Å by calculated methods B3LYP/6-31G(d) and 6-31+Thousand(d), respectively. The angle of N1-H1 N4 was plant 169.9, 172.nine and 172.one° past experimental, calculated B3LYP/six-31G(d) and B3LYP/vi-31+K(d) basis sets, respectively. The results of calculated method (specially vi-31+G(d) ground set) are in good understanding with experimental results (Table 10).
Compd. 34
Atom
Ex.
Calcd.a
Calcd.b
O1-C1
1.322
ane.332
i.333
O1-C2
ane.399
1.420
1.419
C1-N1
i.327
1.348
i.348
C1-N4
1.305
1.316
1.315
N1-N2
ane.354
1.362
1.363
N1-H1
0.861
1.01
1.01
N2-N3
ane.285
i.288
1.288
N3-N4
ane.368
i.368
1.368
C2-C3
1.349
1.397
1.396
C2-C7
1.389
1.397
1.396
C3-C9
1.518
one.508
i.508
C7-C8
one.495
i.508
i.508
C1-O1-C2
117.3
117.6
117.6
O1-C1-N1
121.0
120.8
120.viii
O1-C1-N4
129.3
130.05
130.05
C1-N1-H1
126.ane
130.4
130.4
O1-C2-C3
117.8
117.viii
117.8
O1-C2-C7
116.3
117.8
117.8
C2-C3-C9
120.iv
121.2
121.2
C2-C7-C8
123.0
121.2
121.ii
C2-O1-C1-N1
170.0
-180
-180
O1-C1-N1-H1
-0.8
0.0
0.0
O1-C2-C3-C9
4.4
four.9
4.ix
O1-C2-C3-C4
-175.4
-175.6
-175.6
O1-C2-C7-C8
-five.7
-4.9
-4.ix
Tabular array 8.
The selected bond lengths (Å), angles (°) and torsion angles (φ) for 34. Experimental and B3LYP/six-31+G(d) and B3LYP/6-31G(d).
The crystal packing of 35 also exhibits an intermolecular N3–H31 N6 hydrogen bonds and comparized with the calculated at DFT (B3LYP) at 6-31G(d) and 6-31+G(d) footing sets (Tabular array 10). The crystal structure indicated that the bond altitude value between donor – hydrogen (N3–H) and hydrogen-acceptor (H31 N6) were found in results 0.926 and one.919 Å, respectively. For instance, these bail distances were too found in results 1.03 for (N3–H31) and i.91 for (H31 N6) by calculated at B3LYP/6-31G(d) and 1.01 for (N3–H) and i.93 for (H N6) B3LYP/half dozen-31+G(d), respectively. The donor-acceptor distance value (N3 N6) was obtained ii.835 past experimental method. This parameter was institute 2.941 and 2.912 Å past calculated methods B3LYP/half dozen-31G(d) and 6-31+G(d), respectively. The angle of N3–H31 N6 was establish 169.1, 177.0 and 173.0° by experimental, calculated B3LYP/6-31G(d) and B3LYP/6-31+Thousand(d) basis sets, respectively. The results of calculated method (particularly vi-31+G(d) ground set) are in good agreement with experimental results (Tabular array x). Compounds 34 (entry no. CCDC-838541) and 35 (entry no. CCDC-819010) were deposited to the Cambridge Crystallographic Information Center and are available free of charge upon request to CCDC, 12 Wedlock Road, Cambridge, United kingdom (Fax: +44-1223-336033, email: deposit@ccdc.cam.ac.uk).
Compd. 35
Cantlet
Ex.
Calcd.a
Calcd.b
O1-C2
1.327
1.332
i.322
O1-C7
i.426
i.423
1.422
C2-N3
ane.327
one.349
i.348
C2-N6
1.314
ane.316
1.315
N3-N4
i.358
1.362
1.363
N3-H31
0.926
1.01
1.010
N4-N5
1.288
1.288
1.288
N5-N6
i.373
1.368
i.368
C7-C8
i.392
1.401
1.400
C7-C15
1.389
i.404
1.403
C8-C9
1.521
i.525
1.525
C15-C16
i.528
1.527
i.527
C2-O1-C7
114.49
118.64
118.39
O1-C2-N3
121.3
120.47
120.38
O1-C2-N6
128.five
130.51
130.57
C2-N3-H31
129
130.43
130.33
O1-C7-C8
116.8
118.67
118.72
O1-C7-C15
117.ix
117.02
117.08
C7-C8-C9
120.8
123.14
123.08
C8-C9-H91
106.1
108.37
108.29
C10-C9-C11
111.7
111.27
111.41
C7-C15-C16
122.ii
124.82
124.6
C15-C16-H161
106.3
104.94
105.01
C17-C16-C18
111.i
111.52
111.49
C7-O1-C2-N3
-174.eight
178.5
178.vii
O1-C2-N3-H31
-7.5
-0.ii
-0.08
O1-C7-C8-C9
i.5
one.vi
1.nine
O1-C7-C8-C12
-176.5
-177.3
-177.3
O1-C7-C15-C16
-2.0
-1.i
-1.2
C7-C8-C9-C10
154.1
119.45
116.v
C7-C8-C9-C11
-eighty.two
-115.5
-118.5
C7-C15-C16-C17
-110.7
-63.8
-63.eight
C7-C15-C16-C18
124.2
64.7
64.5
Table 9.
The selected bond lengths (Å), angles (°) and torsion angles (φ) for 35. Experimental and B3LYP/half-dozen-31+Grand(d) and B3LYP/half-dozen-31G(d).
D-H····A
D-H
H····A
D····A
D-H····A (degree, °)
Exp.a (34)
N1-H1····N4b
0.861
1.959
2.804
166.9
Calcd.c (34)
1.033
one.814
ii.842
172.nine
Calcd.d (34)
1.031
1.809
2.838
172.1
Exp.a (35)
N3-H31····N6e
0.926
ane.919
2.835
169.1
Calcd.c (35)
1.03
i.91
two.941
177
Calcd.d (35)
1.01
1.93
2.912
174
Tabular array x.
Experimental and calculated B3LYP/half-dozen-31+One thousand(d) and B3LYP/half dozen-31G(d) levels for hydrogen-bond geometry of 34 and 35 (Å, °)
Effigy 23.
Formula and crystal structures of the compounds 36a and 36b.
Nickel(II) complexes containing specific phosphorus– oxygen chelating ligands are very efficient catalysts for the oligomerisation of ethylene to linear form "(Braunstein et al., 1994)". For instance, Nickel(Two) diphenylphosphinoenolate complexes have been prepared from (ortho-HX- substituted benzoylmethylene)triphenyl phosphoranes (10 = NMe, NPh) and [Ni(i,5-cod)2] in the presence of a 3rd phosphine (PPh3 or P(p-Chalf dozenH4F)3) and their crystal structures have been studied by Braunstein et al. (structures of 36a and 36b). Formula and crystal structures of the compounds 36a and 36b are shown in Fig. 23. Crystallographic written report of the complexes 36a and 36b establishes the presence of strong intramolecular hydrogen bonding betwixt the enolate oxygen and the Northward–H functional group "(Braunstein et al., 2005)". The most notable feature in these structures is the strong intramolecular Northward–H O hydrogen bonding: the calculated altitude between the NH hydrogen atom and the oxygen atom of the enolate ligand is brusk: 2.18(5) Å in 36a and ii.00(five) Å in 36b, respectively "(Taylor & Kennard, 1982)".
Intramolecular hydrogen bond is also shown in alkoxyamines. These compounds and persistent nitroxide radicals are important regulators of nitroxide mediated radical polymerization (NMP). The formula and crystal structure of β-phosphorylated nitroxide radical (37) is shown in Fig. 24. Compound 37 prove an 8-membered intramolecular hydrogen bond betwixt P=O····H-O (versus Northward-O····H-O). The hydrogen bond distance for ii enantiomers of 37 is different. The hydrogen bond distances of P=O····H-O in (R)- and (Due south)-37 are 1.570 and 2.040 Å, respectively and favored. Instead, the hydrogen bond distance for Northward-O····H-O in (R)- and (S)-37 are 3.070 and 3.000 Å, respectively and unfavored "(Acerbis et al., 2006)".
Figure 24.
Formula and crystal structure of two enantiomers of compound 37 (O: crimson, N: blue and P: xanthous).
one,8-diaminonaphthalene derivatives such equally; Due north-(8-(dimethylamino)naphthalen-one-yl)-ii-fluoro-N-methylbenzamide (38) is a proton sponge. An unusual stiff intramolecular hydrogen bond was observed in the protonated 38. In compound 38 in which a protonated amine grouping (38-H+) tin human activity as a donor suitably positioned to engage in a strong intramolecular hydrogen bond with the amide nitrogen atom rather than with the carbonyl oxygen cantlet (Scheme 9). Crystal structure of the triflate common salt of 38-H+ is shown in Fig. 25. The unit of measurement cell consists of two molecules of 38-H+, 2 triflate counter ions, and one molecule of water. The dashed line indicates the proposed hydrogen bond between H1A and N2A. Selected bail lengths and angles are N2A–H1A = 2.17(iv), N1A–N2A = 2.869(5), C14A–N2A = 1.369(five) (Å) and N2A–H1A–N1A = 136(three)° "(Cox et al., 1999)".
Scheme ix.
Protonation of 38 in the presence of trifluoromethanesulfonic acid (TfOH).
Figure 25.
Crystal structure of the triflate salt of 38-H+ (l% ellipsoids and triflate counter ion is omitted).
two,4,6-Trisubstituted phenolic compounds such as 2,4,6-tri-tert-butyl phenol are as antioxidant "(Jeong et al., 2004)". Owing to the nature of the catalytic centres of galactose oxidase (GAO) and glyoxal oxidase (GLO), the Due north,O-bidentate pro-ligand, two'-(four',half-dozen'-di-tert-butylhydroxyphenyl)-4,5-diphenyl imidazole (LH) (39) has been synthesized "(Benisvy et al., 2001)". The compound 39 possesses no readily oxidisable position (other than the phenol) and involves o- and p-substituents on the phenol ring that prevent radical coupling reactions. The compound 39 undergoes a reversible one-electron oxidation to generate the corresponding [LH]·+ radical cation that possesses phenoxyl radical graphic symbol. The unusual reversibility of the [LH]/[LH]·+ redox couple is attributed to a stabilisation of [LH]·+ by intramolecular O–H N hydrogen bonding "(Benisvy et al., 2003)". The formula and crystal structure of 39 are shown in Fig. 26. Crystal structure of 39 shows an intra- and intermolecular hydrogen bonds in 39. In respect of the chemical properties of 39, there is a strong intramolecular hydrogen bail between the phenolic O–H grouping and N(5) of imidazole ring. The strength of this hydrogen bond, as measured by the O(i) Due north(5) distance of 2.596(ii) Å and the O(i)–H(ane) N(5) angle of 150.7°. As well, the N–H grouping of imidazole ring in 39 is involved in an intermolecular Northward–H O hydrogen bond [N(ii) O(1S) 2.852(two) Å and North(2)–H(2A) O(1S) 168.8°] to an next trapped acetone molecule (39·Me2CO) "(Benisvy et al., 2003)".
Figure 26.
Formula and crystal structure of 39·Me2CO.
The azamacrocyclic ligand 1,4,7-triazacyclononane or TACN, forty, has attracted considerable interest in recent years for its applications in oxidative catalysis. Another awarding of this chemical compound was discussed by Pulacchini, et al. "(Pulacchini et al., 2003)". The incorporation of the 1,ii-diaminocyclohexane moiety into a 1,4,seven-triazacyclononane macrocyclic ligand was done by this research group, as it is an cheap starting material and both enantiomers are readily bachelor. Moreover, this chiral framework has been included in a number of ligands that have been successfully practical in a range of asymmetric catalytic processes by Jacobsen et al. in metallosalen complexes "(Jacobsen & Wu, 1999)".
Crystal structure of 41 is shown in Fig. 27 and revealed the structure of the macrocyclic ligand in which the six-membered ring has chair conformation (Fig. 27). The asymmetric unit is completed by the ii chloride ions and a water molecule in which all C–C, C–O and C–N bonds are unexceptional. 2 short hydrogen bonding interactions of 2.724(4) Å between Due north(one)–H(01) O(1) and 2.884(5) betwixt N(2)–H(05) O(1) inside the macrocycle are then supplemented past an extensive hydrogen bonding network between the ammonium nitrogen atoms N(one) and N(2) the two chloride ions Cl(1) and Cl(2), besides as the h2o molecule of crystallisation, as shown in Fig. 28. The roles of the two chloride ions in the network are distinct with Cl(one) acting as a direct bridge between ii macrocyclic moieties as well as linking to a third via a h2o molecule. In dissimilarity, the 2nd chloride ion, appears to essentially serve to template the macrocyclic ligand into the conformation observed via hydrogen bonding interactions with Northward(one)–H(01) and North(ii)–H(05). The second chloride ion besides links to other macrocyclic moieties via the h2o molecules.
The following hydrogen bond lengths (Å) were observed from the polymeric hydrogen bonding array in 41·2HCl·H2O.; North(1)–H(06) Cl(i) 3.099(four), North(1)–H(01) Cl(2) 3.185(4), Northward(1)–H(01) N(two) iii.043(v), N(1)–H(01) O(i) 2.724(four), N(2)–H(02) Cl(i)#1 3.103(4), N(2)–H(05) Cl(2) 3.108(3), Due north(two)–H(05) O(1) 2.884(5), O(2)– H(04) Cl(1) 3.271(four), O(2)–H(03) Cl(2)#2 3.217(4) "(Pulacchini, (2003)".
Figure 27.
Formula structures of xl and 41 and crystal structure of 41·2HCl·H2O.
Figure 28.
Polymeric hydrogen bonding network in 41·2HCl·HiiO "(Pulacchini, (2003)".
In all thiohelicene crystals (meet likewise Figs. 1 and 2) specific interactions were found involving sulfur "(Nakagawa et al., 1985; Yamada et al., 1981)" and hydrogen atoms at distances slightly shorter than the sum of van der Waals radii (1.80 Å for S and 1.20 Å for H). They are quite probably attractive, and, in all structures except TH11 (hexathia-[eleven]-helicene 3) they involve just atoms of concluding rings. In the case of the 5-ring system each molecule has two equivalent S S interactions of three.544 Å, while each TH7 (tetrathia-[vii]-helicene ane) molecule is involved in four equivalent S H contacts measuring two.89 Å. All these interactions occur between enantiomeric pairs. Crystal structyre of pentathia-[9]-helicene (TH9, 42) and crystal packing diagram of this compound including South H contacts are shown in Figs. 29 and 30, respectively. For 42, each molecule presents four equivalent S H contacts at 2.87 Å, all with homochiral molecules giving rise to a quasi-hexagonal packing of tilted helices in planes parallel to the ab lattice plane. The crystal construction of TH11 (3) is unusual because the asymmetric unit of measurement is formed by two complete molecules as opposed to half a molecule in all the lower racemic thiohelicenes. The packing environment of each of the ii closely like simply crystallographically independent molecules, and of each of its halves, is unique: thus the Cii axes bisecting the cardinal ring of each TH11 (3) molecule are noncrystallographic. This state of affairs is likely to arise in order to optimize the circuitous network of specific interactions involving South and H atoms. It leads to larger than expected asymmetric units and lower crystal symmetry, common occurrences in hydrogen bonded molecular systems. In the triclinic TH11 (iii) crystals iv nonequivalent short S Southward and an equal number of S H interactions are plant "(Caronna et al., 2001)". The essential geometric features of all these contacts in the racemic thiohelicene series and evidencing a remarkable consistency of the Due south H interaction with expectations for weak hydrogen bonds have been reported "(Desiraju & Steiner, 2000)".
Effigy 29.
Crystal structure of TH9 (42).
Figure 30.
Crystal packing diagram of 42 in which each molecule consists of 4 equivalent S····H contacts.
The fused pyrimidines such as pyrimido[4,5-c]pyridazine-v,7(sixH,8H)-diones, which are common sources for the evolution of new potential therapeutic agents, is well known "(Altomare et al., 1998; Brown, 1984; Hamilton, 1971)". Some of this form of compounds play new heterocyclizations based on {SDue northH} methodology as N(2)-oxide and 3-alkylamino derivatives of 6,8-dimethylpyrimido[iv,5-c]pyridazine-five,vii(6H,eightH)-dione "(Gulevskaya et al., 2003)".
Recently, the synthesis of iii-arylpyrimido[4,v-c]pyridazine-5,7(6H,8H)-diones (43a–d) and their sulfur analogs 3-aryl-7-thioxo-7,eight-dihydropyrimido[4,5-c]pyridazin-5(6H)-ones 44a–d have been reported "(Rimaz et al., 2010)". I of the most interesting intermolecular hydrogen bond in 43a–d take been reported by our inquiry group "(Rimaz et al., 2010)" (Figure 31). Attributable to the less solubility of 43a–d and 44a–d, an attempt to attain the single crystal of these compounds for investigation of the clustered h2o in their crystalline construction was failed. The 1H NMR spectra of 43a–d show two broad singlets in the range of δ = 7.00–viii.00 ppm that correspond to the protons of amassed h2o molecule in the 43a-d. The chemical shift values of two variable protons of h2o in 43a–d in ambient temperature are shown in Table xi. There are some reasons for demonstration and estimation of this criterion. (i) 1 of the evidence is the mass spectra. The mass spectra of the compounds 43a–d bear witness not just the molecular ion fragment (G) only besides the fragment of K+18. Therefore, the strength of hydrogen bail betwixt the proton of H2O (Ha) and oxygen atom of carbonyl group (C5=O Ha–O) and besides hydrogen bond between the N6–H of 43a–d and oxygen atom of H2O (N6–H O–Ha) is considered more that of the hydrogen bonding in the dimer form of 43a–d (judging by the observation of the G+eighteen ion) (Fig. 32) "(Rimaz et al., 2010)". It seems that at least one molecule of water clustered and joined to 43 and 44 by ii potent intermolecular hydrogen bonds and dissociated neither past DMSO molecules every bit a polar aprotic solvent nor in mass ionization bedchamber. Presumably, this intermolecular hydrogen bond is of quasi-covalent hydrogen bond blazon. There are some reports on literatures nigh quasi-covalent hydrogen bonds "(Dabbagh et al., 2007; Gilli et al., 1994, 2000, 2004; G. Gilli & P. Gilli, 2000; Golič et al., 1971; Madsen et al., 1999; Nelson, 2002; Steiner, 2002; Vishweshwar et al., 2004; Wilson, 2000)".
Figure 31.
Formula structures of 43a–d·(H2O) and 44a–d·(H2O).
Figure 32.
Representatively, strong intermolecular hydrogen bond and the chemical shifts of 2 hydrogen bonded protons of clustered water molecule with 43a "(Rimaz et al., 2010)".
Compd.
δ (ppm)
Ha
Hb
43a
7.76
7.57
43b
vii.75
7.61
43c
7.74
7.61
43d
7.75
7.61
44a
4.89
44b
4.90
44c
4.90
44d
4.89
Tabular array 11.
The chemic shift values of the two protons of a clustered h2o molecule in 43a–d and 44a–da at ambient temperature "(Rimaz et al., 2010)".
The proton/deuterium substitution was examined on 43a–d past adding one drib of D2O. Interestingly, from hydrogen to fluorine substituent on phenyl ring in 43a–d the exchange rate was decreased, and no deuterium exchanging of Ha and Hb was observed in 43d while the amide protons were easily exchanged (Fig. 33). This phenomenon attributed to the fluorine atom that has fabricated new intermolecular hydrogen bond with Ha and Hb of clustered water molecule in some other molecule of 43d. The intermolecular hydrogen bond of fluorine with the proton of clustered water (–F····Ha– and –F····Hb–) in 43d inhibited the proton/deuterium exchanging of the clustered water protons. Nevertheless, the electronegativity of fluorine atom caused deshielding of Ha and Hb on 43d and blocked the proton/deuterium exchange (Fig. 33 and Scheme ten). Two conformational forms of IA and IB in 43d are equivalent because of gratuitous rotation of phenyl ring virtually the C3–C9 and C12–F unmarried bonds (Scheme 10) "(Rimaz et al., 2010)".
2.3. Crystal construction of some organic spiro compounds
Spiro compounds are very important and useful compounds and versatile applications. Many of heterocyclic spirobarbituric acids "(Kotha et al., 2005)", furo[2,3-d]pyrimidines "(Campaigne et al., 1969)" and fused uracils "(Katritzky & Rees, 1997; Naya et al., 2003)" are well known for their pharmaceutical and biological effects.
Recently, nosotros take reported new spiro compound based on barbiturates; five-alkyl and/or 5-aryl-1H, 1'H-spiro[furo[ii,3-d]pyrimidine-half dozen,five'-pyrimidine]two,2',4,4',half-dozen'(3H, 3'H, fiveH)-pentaones which are dimeric forms of barbiturate (uracil and thiouracil derivatives) "(Jalilzadeh et al., 2011)". Reaction of i,3-dimethyl barbituric acid (DMBA) with cyanogen bromide (BrCN) and acetaldehyde in the presence of triethylamine afforded one,ane',three,three',5-pentamethyl-1H,i'H-spiro[furo[2,three-d]pyrimidine-half dozen,five'-pyrimidine]-2,2',4,4',6'(iiiH,iii'H,fiveH)-pentaone (46) in excellent yield "(Jalilzadeh et al., 2011)". The formula structures of spiro compounds derived from barbituric acrid (BA, 45), DMBA 46 and i,3-thiobarbituric acid (TBA, 47) is shown in Fig. 34. Attempt for single crystallization of spiro compounds 45 and 47 were unsuccessful. The crystal construction and crystal packing diagram of 46 are shown in Figs. 35 and 36. This compound was crystalized in triclinic system. Selected crystallographic information for 46 is summarized at Table 12.
Figure 33.
Proton/deuterium exchangeability of the Ha and Hb of clustered HtwoO molecule in oneH NMR spectra of 43a (A), 43b (B), 43c (C) and 43d (D). The assigned spectra are shown before (a) and after added DtwoO (b). No exchange occurred in 43d of clustered H2O protons (D) "(Rimaz et al., 2010)".
Scheme x.
Possible various types of intermolecular hydrogen bail of fluorine with a proton of a clustered were (-F····Hb- and -F····Ha-) in 43d. This phenomenon presumably inhibited the proton/deuterium exchangeability of the amassed water protons.
Figure 34.
Formula structures of 45-47.
Effigy 35.
Crystal structure of 46.
Figure 36.
Crystal packing diagram of 46.
Crystal data
Emprical formula
C14HxviNfourO6
M
336.xxx
T
298 K
a (Å)
8.974 (5)
b (Å)
9.539 (5)
c (Å)
10.314 (5)
α ( ◦)
64.782 (5)
β ( ◦)
69.349 (5)
γ ( ◦)
69.349 (5)
V (Å3)
725.8 (7)
Z
2
F(000)
352
Dx (mg m−3)
1.539
λ (Å)
0.71073
μ(mm−ane)
0.12
Data collection
Rint
0.062
θmax
29.0 ◦
θmin
two.3 ◦
Refinement
R[F2 "/> iiσ(Fii)]
0.067
wR(F2)
0.203
Southward
one.04
Table 12.
Selected crystallographic data for 46.
Some other spiro barbiturate compound derived from the reaction of DMBA with BrCN and acetone in the presence of triethylamine is 1,one',3,3',5,5'-Hexamethylspiro[furo-[two,3-d]pyrimidine-6(fiveH),5'-pyrimidine]-2,2',iv,4',6'(iH,3H,1'H,iii'H,vH)-pentaone (48) "(Noroozi Pesyan et al., 2009)". Reaction of aldehydes with (thio)barbiturates is faster than ketones due to the reactivity and less hindrance in aldehydes. The formula and crystal construction of 48 is shown in Figs. 37 and 38, respectively. In Fig. 38, the fused 2,3-dihydrofurane ring has an envaloped conformation, and spiro pyrimidine band has a half-chair conformation. Spiro pyrimidine ring is almost perpendicular to two,3-dihydro furan band moiety as was observed before in the related compound. Torsion angles C2-C1-O4-C7 and C2-C1-C5-C6 are -99.39(3)° and 94.87(three) °, respectively. In the crystal, short intermolecular interaction O C contacts between the carbonyl groups prove an existing of electrostatic interactions, which link the molecules into corrugated sheets parallel to ab plane (Tabular array 13).
C8····O2i
ii.835 (four)
C3····O5ii
2.868 (4)
Table 13.
Selected interatomic distances (Å) in 48.
Figure 37.
Formula structure of 48.
Figure 38.
Crystal structure of 48.
I of another interesting spiro barbiturate compound is the trimeric form of 1,three- DMBA; 5,six-dihydro - 1,3-dimethyl - 5,6 – bis - [l',iii'-dimethyl-2',4',half dozen'-trioxo-pyrimid(5',5')yl]furo[two,3-d]uracil (49). This compound was first reported by electrochemical method "(Kato et al., 1974; Kato & Dryhurst, 1975; Poling & van der Captain, 1976)" and it has been reported the synthesis of 49 by chemic method for a first time two years ago "(Hosseini et al., 2011)". The formula and crystal structures of 49 are shown in Figs. 39 and 40, respectively. Crystals of 49 were obtained by tedious evaporation of a solution of 49 in acetone at room temperature. The data were acquired using a STOE IPDS II diffractometer, data collection and cell refinement were candy using STOE X-AREA "(Stoe & Cie, 2002)" and data reduction was processed using STOE X-Reddish "(Stoe & Cie, 2002)" program. Program(s) used to refine structure was SHELXL97 "(Sheldrick, 1997). Crystal data for 49: Orthorhombic; CeighteenHxviiiNorthward6O9; Yard = 462.38; Unit of measurement prison cell parameters at 293(ii) K: a = 13.2422(4), b = 15.9176(6), c = xix.5817(6) Å; α = β = γ = ninety°; V = 4127.5(two) Åiii; Z = 8; μ = 0.122 mm–one; Total reflection number 4275; 304 parameters; λ = 0.71073 Å; 2916 reflections with I > 2σ(I); Rint = 0.056; θmax = 26.49°; R[Ftwo > two σ(F2)] = 0.048; wR(F2) = 0.112; Southward = i.02, F000 = 1920 "(Hosseini et al., 2011)".
Figure 39.
Formula structure of 49.
Figure xl.
Crystal structure of 49.
Amino acids derived from carbohydrate are of extensive family unit of peptidomimetics "(Businesswoman et al., 2004; Chakraborty et al., 2004)", an of import sub-grade of which incorporate an α-amino acid with a saccharide has anomeric effect. Such carbohydrate amino acids may form spiro derivatives, some of which accept been demonstrated to possess meaning biological action. For instance, the formula and crystal construction of (2'South,3aR,6Due south,6aR)-2,2,6-trimethyldihydro-3aH-spiro[furo[3,four-d][one,iii]dioxole-4,2'-piperazine]-iii',half-dozen'-dione (50) are shown in Figs. 41 and 42 "(Watkin et al., 2004)". This molecule show hydrogen bonds between Northward-H….O=C groups and are shown in crystal packing diagram, viewed along the c axis equally dashed lines (Fig. 43).
Figure 41.
Formula structure of chemical compound 50.
Figure 42.
Crystal structure of chemical compound fifty (Greenish: C, bluish: N and red: O atom).
Figure 43.
Crystal packing diagram of l.
Another interesting spiro linked barbituric acid to the cyclopentane ring moiety (spiro-nucleoside) possessing of hydroxyl and hydroxymethyl groups is (3S,2R)-3-hydroxy-two-hydroxymethyl-seven,9-diazaspiro[4.5]decane-6,viii,10-trione (51) (Figs. 44 and 45). Crystal construction of 51 shows trans stereochemical relationship of the 2 substituents hydroxyl and hydroxymethyl on cyclopentane ring moiety. The barbituric acrid ring is almost planar, while the cyclopentane moiety adopts the C3'-endo-type conformation. Molecules of 51 interconnected past a 2-dimensional network of hydrogen bonds build layers parallel to the ab plane. The hydrogen bond data for 51 is outlined at Table 14 "(Averbuch-Pouchot et al., 2002)".
Figure 44.
Formula construction of 51.
Figure 45.
Crystal structure of 51.
D—H····A
D—H
H····A
D····A
D—H····A
O11—H12····O6v
0.81
2.00
two.809 (two)
173
N7—H8····O10iv
0.86
1.99
2.840 (2)
170
N9—H9····O27
0.85
2.04
2.8620 (x)
161
Table 14.
Hydrogen-bail geometry in 51 (Å, º).
Hydantoins are very useful compounds due to their pharmaceutical behaviour such as; antitumor "(Kumar et al., 2009)", anticonvulsant "(Sadarangani et al., 2012)" and antidiabetic activity "(Hussain et al., 2009)". In the molecules of 52 and 53 (Figs. 46 and 47), the atoms in the hydantoin ring are coplanar. The crystal structures of 52 and 53 are stabilized by intermolecular Due north—H····O=C hydrogen bonds. The hydrogen bond lengthes and angles for 52 and 53 are summarized at Tabular array xv. Crystal packing diagram of these molecules evidence the molecules are centrosymmetric dimer forms. The dihedral angle subtended by the 4-chloro- and iv-bromophenyl groups with the plane passing through the hydantoin unit are 82.98(4)° and 83.29(five)°, respectively. The cyclohexyl band in both molecules adopts an ideal chair conformation and methyl group in an equatorial position "(Kashif et al., 2009)".
D—H····A
D—H
H····A
D····A
D—H····A
52
N2—H2····O4i
0.84 (two)
2.04 (two)
2.8763 (fifteen)
171.5 (19)
53
N2—H2····O4i
0.82 (3)
2.06 (3)
ii.871 (2)
171 (three)
Tabular array 15.
Hydrogen-bail geometry in 52 (Å, º).
Figure 46.
Formula structures of 52 and 53.
Effigy 47.
Crystal structures of 52 (tiptop) and 53 (bottom).
Dihydropyridine are interesting and important systems considering of their exceptional properties as calcium aqueduct antagonists "(Si et al., 2006)" and as powerful arteriolar vasodilators "(Kiowski et al., 1990)". 4',four'-Dimethyl-two-methylsulfanyl-3,4,v,6,7,eight-hexahydropyrido-[ii,three-d]pyrimidine-vi-spiro-ane'-cyclohexane-two',iv,6'-trione, (54), has a markedly polarized molecular electronic structure, and the molecules are linked into a three-dimensional framework by a combination of N–H O, C–H O and C–H л hydrogen bonds (Table 16). Ii contained Due north–H O hydrogen bonds generate a one-dimensional substructure in the form of a chain of rings; these chains are linked into sheets by the C–H O hydrogen bonds, and the sheets are linked by C–H л hydrogen bonds. Crystal packing diagram of 54 show four types of centrosymmetric band. "(Low et al., 2004)" (Fig. 48). Chemical compound 54 tin exist in two zwitterionic forms of 54I and 54II (Scheme 11). For example, the bond lengths of N3–C4 and C4–O4 are both long for their types, the C4–C4A and C4A–C8A bonds are too like in length to be characterized every bit single and double bonds, respectively. Also, the C8A–N8 bond, involving a three-coordinate N atom, is much shorter than the C8A–N1 bond, which involves a two-coordinate N atom. These observations, taken together, finer preclude the polarized form (54I) every bit an effective contributor to the overall molecular electronic structure, instead pointing to the importance of the polarized vinylogous amide form (54II) "(Low et al., 2004)".
Scheme eleven.
Zwitterionic forms of 54.
Effigy 48.
Crystal structure of 54.
D–H····A
D–H
H····A
D····A
D–H····A
N3–H3····O4i
0.88
1.84
ii.715 (2)
176
N8–H8····O65two
0.88
2.10
2.965 (2)
166
C5–H5B....O613
0.99
2.46
three.389 (2)
155
C64–H64A....Cg1iv
0.99
2.87
3.854 (2)
173
Table 16.
Hydrogen-bonding geometry (Å, °) for 54.
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3. Determination
In summary, X-ray single crystal diffraction analysis of the some helicenes and other helix molecules were discussed. In continuation, the crystal structure of some organic and organometallic compounds consists of intra- and/or intermolecular hydrogen bond were described. Finally, crystal structures of some new spiro compounds were analyzed.
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Acknowledgement
The author gratefully admit financial support past Inquiry Council of Urmia University
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