The structure of CDGSN at RT was determined using direct methods as implemented in SHELXS [21]. The atomic parameters so obtained were subjected to a series of isotropic and anisotropic full matrix least square refinements using SHELXL97[21]. All the reflections were used for refinement. In the initial stages of refinement, reflection weight (w) was taken to be 1/ σ(Fo2), which was derived using counting statistics. All the hydrogen atoms were located from the difference Fourier map and refined isotropically. Crystallographic and refinement details for CDGSN are summarized in Table 1. The asymmetric unit consists of glycine in the zwitter ionic form, a silver ion(Ag+) and a nitrate ion(NO3−) [figure 1]. The bond distances in the C1gO2gO1g group (C1g-O1g = 1.262(2)Å & C1g-O2g = 1.248(3) Å) of glycine indicated that the group appears as a carboxylate, -COO..
It is important to mention here that GSN and NDGSN are more light and X-ray sensitive[5] as compared to that of FDGSN and CDGSN. The crystals when exposed to light and X-rays change in color form white transparent to brown colour, hence the data quality of NDGSN is not that good as compared to that of CDGSN even though they have been collected under same conditions.
The structure of NDGSN at RT was determined using direct methods as implemented in SHELXS SHELXS97 and SHELXL97. University of GoÈ ttingen, Germany[21]. The atomic parameters so obtained were subjected to a series of isotropic and anisotropic full matrix least square refinements using SHELXL97 [21]. All the reflections were used for refinement. In the initial stages of refinement, reflection weight (w) was taken to be 1/ σ(Fo2), which was derived using counting statistics. Hydrogen atoms belonging to C and N of glycine molecule were refined using AFIX instruction as they could not be refined unlike the case of CDGSN Crystallographic and refinement details for NDGSN are summarized in Table 1. The asymmetric unit consists of glycine in the zwitter ionic form, a silver ion(Ag+) and a nitrate ion(NO3−) [figure 2]. The bond distances in the C1gO2gO1g group (C1g-O1g = 1.27(1)Å & C1g-O2g = 1.22(1) Å) (Table 3a)of glycine indicated that the group appears as a carboxylate, -COO.
Crystallographic and refinement details for CDGSN and NDGSN are summarized in Table 1. .
Table 1
Crystallographic and Refinement details for CDGSN and NDGSN
| CDGSN | NDGSN |
CCDC No. | 2264620 | 2264621 |
Empirical formula | C2D2H3AgN2O5 | C2H2D3AgN2O5 |
Formula weight | 244.95 | 244.95 |
Temperature (K) | 300K | 300K |
Wavelength (Å) | 0.71073 | 0.71073 |
Crystal system | Monoclinic | Monoclinic |
Space group | P 21/c | P 21/c |
Unit cell dimensions | | |
a (Å) | 5.4603 (13) | 5.5441 (9) |
b (Å) | 9.060 (2) | 19.475 (3) |
c (Å) | 11.586 (3) | 5.4468 (9) |
β(°) | 91.696 (10) ° | 99.947 (5)° |
Volume (Å3) | 572.9 (2) | 579.25 (16) |
Z | 4 | 4 |
Calculated density (Mg m-3) | 2.840 | 2.809 |
Absorption coefficient (mm-1) | 3.48 | 3.44 |
θ range for data collection (°) | 30.5° | 30.6° |
Limiting indices | -4 ≤ h ≤ 7 -12 ≤ k ≤ 12 -16 ≤ l ≤ 16 | -4 ≤ h ≤ 7 -25 ≤ k ≤ 27 -7 ≤ l ≤ 6 |
Reflections collected/unique | 10321/1729 Rint = 0.043 | 4237/1670 Rint = 0.025 |
θ max(°); Completeness to | 30.5/0.992 | 30.5/0.941 |
Data/restraints/parameters | 1729/112 | 1670/92 |
Goodness-of-fit on F2 | S = 1.09 | S = 1.389 |
Final R indices R[F2 > 2σ(F2)] | R1 = 0.025 wR(F2) = 0.062 | R1 = 0. 0.083 wR(F2) = 0.215 |
Table 2
Comparison of cell parameters in GSN [5], NDGSN, FDGSN[20], CDGSN
| GSN[5] | NDGSN | FDGSN[20] | CDGSN |
Crystal system | Monoclinic | Monoclinic | Monoclinic | Monoclinic |
Space group | P 21/a | P 21/c | P 21/c | P 21/c |
Unit cell dimensions |
a (Å) | 5.451 | 5.5441 (9) | 5.4372 (1) | 5.4603 (13) |
b (Å ) | 19.493 | 19.475 (3) | 9.0488 (2) | 9.060 (2) |
c (Å) | 5.541 | 5.4468 (9) | 11.5456 (3) | 11.586 (3) |
β (°) | 100.2 | 99.947 (5)° | 91.926 (1) | 91.696 (10)° |
Volume (Å3) | 579.46 | 579.25 (16) | 567.72 (2) | 572.9 (2) |
From Table − 2 it is observed that the structural parameters of GSN and NDGSN are similar and NDGSN crystallizes in P21/c space group and that of FDGSN and CDGSN are similar. Between GSN and NDGSN, there is increase in lattice parameter a and decrease in c with very little change in the volume, whereas a comparison in FDGSN and CDGSN, there is increase in lattice parameters a, b and c and decrease in β in CDGSN compared to FDGSN, and there is appreciable increase in volume in CDGSN. A comparison of the bond distance and bond angles for FDGSN and CDGSN is given in Table 3a & Table 3b respectively.
Table 3
a. Comparison of Bond Distances in FDGSN[20] and CDGSN
Atoms | Bond distance (Å) | Atoms | Bond distance (Å) |
| FDGSN[20] | CDGSN | | FDGSN[20] | CDGSN |
Ag1—O1g | 2.2901 (9) | 2.296 (2) | C1g—O1g | 1.258 (1) | 1.262 (2) |
Ag1—O2gi | 2.417 (1) | 2.428 (2) | C1g—C2g | 1.519 (1) | 1.521 (3) |
Ag1—O1n | 2.534 (2) | 2.539 (3) | C2g—N2g | 1.468 (2) | 1.469 (3) |
Ag1-O3N | 2.651 | | | | |
Ag1-O2N | 2.739 | | | | |
Ag1-O1G | 2.732 | | | | |
N1—O1n | 1.237 (2) | 1.241 (3) | C2g—H4g | 0.95 (2) | 0.96(4) |
N1—O3n | 1.249 (2) | 1.253 (3) | C2g—H5g | 0.98 (2) | 1.04(4) |
N1—O2n | 1.250 (1) | 1.249 (3) | N2g—H1g | 0.86 (3) | 0.79(5) |
C1g—O2g | 1.250 (1) | 1.248 (3) | N2g—H2g | 0.91 (3) | 1.03(5) |
N2g—H3g | 0.90 (3) | 0.91(4) | | | |
Table 3
b.. Comparison of Bond angles FDGSN[20] and CDGSN
Atoms | Bond angle (º) | Atoms | Bond angle(º) |
| FDGSN[20 | CDGSN | | FDGSN[20] | CDGSN |
O1g—Ag1—O2gi | 117.60 (3) | 117.70 (6) | C1g—C2g—H4g | 110 (2) | 111 (2) |
O1g—Ag1—O1n | 114.41 (4) | 114.25 (7) | N2g—C2g—H5g | 106 (1) | 106 (2) |
O2gi—Ag1—O1n | 127.90 (4) | 127.96 (6) | C1g—C2g—H5g | 114 (1) | 114 (2) |
O1n—N1—O3n | 120.5 (1) | 120.5 (2) | H4g—C2g—H5g | 108 (2) | 109 (3) |
O1n—N1—O2n | 120.6 (1) | 120.5 (2) | C2g—N2g—H1g | 114 (2) | 118 (4) |
O3n—N1—O2n | 118.9 (1) | 119.0 (2) | C2g—N2g—H2g | 112 (2) | 112 (3) |
N1—O1n—Ag1 | 97.7 (1) | 97.53 (17) | H1g—N2g—H2g | 103 (2) | 98 (4) |
O2g—C1g—O1g | 125.7 (1) | 125.9 (2) | C2g—N2g—H3g | 110 (2) | 110 (3) |
O2g—C1g—C2g | 117.4 (1) | 117.35 (18) | H1g—N2g—H3g | 108 (3) | 110 (4) |
O1g—C1g—C2g | 116.9 (1) | 116.76 (19) | H2g—N2g—H3g | 110 (3) | 109 (4) |
N2g—C2g—C1g | 112.00 (9) | 112.26 (17) | C1g—O1g—Ag1 | 113.60 (8) | 113.64 (14) |
N2g—C2g—H4g | 107 (2) | 105 (2) | C1g—O2g—Ag1ii | 121.53 (8) | 121.61 (14) |
Symmetry codes: (i) 1 + x, y, z (ii) -1 + x, y, z.
Equation of plane was calculated for the zwitter ionic glycine, the nitrate ion and the silver coordinated oxygens in FDGSN and CDGSN. It was observed that the nitrate ions are planar in both the structures. The zwitterionic glycine is nonplanar in both FDGSN and CDGSN, and the deviations[Table 4] are also same in both the structures. Similary the equation of plane Ag coordinated with oxygen in nonplanar, with similar deviations of atoms from the plane in both FDGSN and CDGSN
Table 4
Deviation of atoms form the plane in FDGSN[20] and CDGSN
atoms | Deviation of atoms from plane | atoms | Deviation of atoms from plane | atoms | Deviation of atoms from plane |
| Nitrate ion | | Zwitterionic Glycine | | Ag coordinated |
| FDGSN[20] | CDGSN | | FDGSN[20] | CDGSN | | FDGSN[20] | CDGSN |
N1 | 0.0 | 0.0 | N2G | 0.132 | 0.132 | AG1 | 0.012 | 0.013 |
O1N | 0.0 | 0.0 | C2G | 0.164 | 0.164 | O1G | 0.028 | 0.027 |
O2N | 0.0 | 0.0 | C1G | 0.018 | 0.018 | O1N | 0.067 | 0.066 |
O3N | 0.0 | 0.0 | O2G | 0.103 | 0.103 | O3N | 0.073 | 0.072 |
| | | O1G | 0.053 | 0.053 | O2G | 0.046 | 0.046 |
A comparison of the bond distance and bond angles for GSN and NDGSN is given in Table 5a & Table 5b respectively.
Table 5
a. Comparison of Bond Distances in GSN[5] & NDGSN
Atoms | Bond distance (Å) | Atoms | Bond distance (Å) |
| GSN[5] | NDGSN | | GSN[5] | NDGSN |
Ag1—Ag1i | 2.877(6) | 2.815 (2) | O1N—N1 | 1.28(3) | 1.27 (1) |
Ag1—O2G | 2.25(2) | 2.227(8) | O2N—N1 | 1.26(3) | 1.24 (1) |
Ag1—O1Gi | 2.22(2) | 2.282 (8) | O3N—N1 | 1.25(4) | 1.25 (2) |
Ag1—O1Gii | 2.37(2) | 2.412 (9) | N1G—H1G | | 0.8900 |
O1G—C1G | 1.28(3) | 1.27 (1) | N1G—H2G | | 0.8900 |
O2G—C1G | 1.25(3) | 1.23 (1) | N1G—H3G | | 0.8900 |
N1G—C2G | 1.50(4) | 1.49 (2) | C2G—H4G | | 0.9700 |
C1G—C2G | 1.54(4) | 1.53 (2) | C2G—H5G | | 0.9700 |
Symmetry codes: (i) 1, 1, 2; (ii) 1,, ; (iii) -1,, .
Table 5
b. Comparison of Bond Angles in GSN[5] & NDGSN
Atoms | Bond angle (º) | Atoms | Bond angle(º) |
| GSN[5] | NDGSN | | GSN[5] | NDGSN |
O2G—Ag1—O1Gi | 163.1(7) | 164.7 (3) | O2N—N1—O3N | 123(2) | 122.9(12) |
O2G—Ag1—O1Gii | 120.8(6) | 120.3 (3) | O2N—N1—O1N | 120(2) | 118.4 (13) |
O1Gi—Ag1—O1Gii | 76.0(7) | 75.0 (3) | O3N—N1—O1N | 116(2) | 118.6 (11) |
O2G—Ag1—Ag1i | 84.7(4) | 86.9 (3) | C2G—N1G—H1G | | 109.5 |
O1Gi—Ag1—Ag1i | 79.1(5) | 78.2 (2) | C2G—N1G—H2G | | 109.5 |
O1Gii—Ag1—Ag1i | 149.9(4) | 148.3 (2) | H1G—N1G—H2G | | 109.5 |
C1G—O1G—Ag1i | 130.0(17) | 126.9 (8) | C2G—N1G—H3G | | 109.5 |
C1G—O1G—Ag1iii | 123.8 | 125.8 (7) | H1G—N1G—H3G | | 109.5 |
Ag1i—O1G—Ag1iii | 104.04 | 105.0 (3) | H2G—N1G—H3G | | 109.5 |
C1G—O2G—Ag1 | 120.8(15) | 119.3 (7) | N1G—C2G—H4G | | 109.4 |
O2G—C1G—O1G | 125(2) | 127.3 (10) | C1G—C2G—H4G | | 109.4 |
O2G—C1G—C2G | 119(2) | 119.1(10) | N1G—C2G—H5G | | 109.4 |
O1G—C1G—C2G | 116(3) | 113.5 (10) | C1G—C2G—H5G | | 109.4 |
N1G—C2G—C1G | 110(3) | 111.1 (10) | H4G—C2G—H5G | | 108.0 |
Equation of plane was calculated for the zwitter ionic glycine, the nitrate ion and the silver coordinated oxygens in NDGSN and GSN. It was observed tht the nitrate ions are more planar NDGSN. The zwitterionic glycine is nonplanar in both NDGSN and GSN, and the deviations (Table 6) are also similar in both the strutures. Similary the equation of plane Ag coordinated with oxygen in nonplanar, with similar deviations of atoms from the plane in both NDGSN and GSN.
Table 6
Deviation of atoms form the plane in GSN[5] and CDGSN
atoms | Deviation of atoms from plane | atoms | Deviation of atoms from plane | atoms | Deviation of atoms from plane |
| Nitrate ion | | Glycine ion | | Ag coordinated |
| GSN[5] | NDGSN | | GSN[5] | NDGSN | | GSN[5] | NDGSN |
N1 | 0.046 | 0.004 | N2G | 0.099 | 0.099 | AG1 | 0.127 | 0.128 |
O1N | 0.015 | 0.001 | C2G | 0.118 | 0.127 | O1G | 0.096 | 0.103 |
O2N | 0.015 | 0.001 | C1G | 0.025 | 0.005 | O2G | 0.206 | 0.218 |
O3N | 0.016 | 0.001 | O2G | 0.083 | 0.076 | Ag1b | 0.206 | 0.217 |
| | | O1G | 0.038 | 0.043 | O1B | 0.225 | 0.232 |
Table 7 gives the comparison of torsion angle amongst the four complexes. It is observed that the conformation of glycine is similar in GSN & NDGSN. Similarly the conformation of DGSN and CDGSN are similar. But between the two there is difference in the conformation as shown in Fig. 3.
Table 7
Comparison of torsion angle amongst GSN[5], FDGSN[20], CDGSN and NDGSN
atoms | Glycine |
| GSN[5] | FDGSN[20] | CDGSN | NDGSN |
O2G-C1G-O1G | 124.9 | 125.7 | 125.9 (2) | 127.3 (10) |
O1G-C1G-C2G | 115.8 | 116.89 | 116.8 (2) | 113.5 (10 |
O2G-C1G-C2G | 119.2 | 117.4 | 117.4 (2) | 119.2 (10) |
C1G-C2G-N1G | 109.8 | 112.00 | 112.3 (2) | 111.1 (10) |
O2G-C1G-C2G-N1G | -166.18 | 161.61 | 161.62 | -166.7 |
O1-C1G-C2G-N1G | 12.72 | -19.57 | -19.58 | 15.67 |
H3G-N1G-C1G-C2G | | 52.35 | 48.19 | -41.76 |
Silver coordination:
The distances of the atoms less than 3 Å to the silver atom are shown in Fig. 4 and tabulated in Table 8. The oxidation state of silver ion is + 1. In FDGSN and CDGSN the silver ion is mononuclear and it is coordinated to four oxygen’s, of which two are from the same nitrate ion forming a bidenate coordination, and the other two are oxygen’s of the symmetry related glycine. All these four oxygens are in the same plane. There is also a hydrogen atom, H5g in this plane. Ag ion is also coordinated to O1G & O2N above and below this plane. The coordination of the Ag-O bond distances in the axial plane are longer compared to that in the equatorial plane. The four oxygens in the plane form a distorted triangular coordination [23]. In CDGSN and FDGSN, only the Ag-O2g distance differ more than the standard deviations,.
The coordination of silver in NDGSN is similar to that of GSN. The silver ion is binuclear with oxidation state of + 1. The silver ion is coordinated to Ag and oxygens of zwitter ionic glycine. There is considerable change in the Ag-Ag coordination between NDGSN and GSN. Unlike FDGSN and CDGSN, here the Ag is coordinated to only oxygens of the zwitter ionic glycine in the equatorial plane, and is coordinated to only one of the nitrate oxygens in the axial plane. There is no coordination to the Hydrogen atom of zwitter ionic glycine in GSN and NDGSN. Incidentally the Hydrogen coordination to Ag in FDGSN and CDGSN is through the deuterated Hydrogen connected to C alpha carbon of glycine.
It is basically the coordination of Ag ion which brings about a change in the structure. It is also necessary to mention here that it is the fully deuterated DGSN and CDGSN which produces a new isotope polymorph of GSN, whereas partially deuterated GSN and NDGSN doesn’t result in a new polymorph. Hence it can be said that it is the C-deuteration of glycine which brings about change in the structure.
Table 8
Silver coordination IN GSN, NDGSN, FDGSN and CDGSN
Atoms | Bond distance (Å) | Atoms | Bond distance (Å) |
| GSN | NDGSN | | FDGSN | CDGSN |
Ag1—Ag1i | 2.877(6) | 2.815 (2) | Ag1—O1g | 2.2901 (9) | 2.296 (2) |
Ag1—O2G | 2.25(2) | 2.227 (8) | Ag1—O2gi | 2.417 (1) | 2.428 (2) |
Ag1—O1Gi | 2.22(2) | 2.282 (8) | Ag1—O1n | 2.534 (2) | 2.539 (3) |
Ag1—O1Gii | 2.37(2) | 2.412 (9) | Ag1—O3N | 2.6506(1) | 2.653(3) |
Ag1—O1N | 2.86(2) | 2.857(9) | Ag1—O2N | 2.7392(1) | 2.748(2) |
Ag—O2giii | 2.85(2) | 2.833(9) | Ag1-O1G | 2.7318(1) | 2.738(2) |
| | | Ag1-H5G | 2.81(2) | 2.78(4) |
Molecular interaction
i) CDGSN
Packing of the molecule is shown in Fig. 5. Like FDGSN in CDGSN too, the nitrate ion, the silver ion and the zwitter ionic glycine form a layered structure in the ab plane. and are stacked along the c-axis.. Two of the hydrogen H1G and H3G form N-H…O hydrogen bonds to the nitrate in the plane, the third hydrogen H2G forms N-H…O hydrogen bonds to nitrate ion as well as the zwitter ionic glycine to the plane above. There are C-H..O hydrogen bonds, C2G-H5G is hydrogen bonded to O1G of glycine in the plane, whereas C2G- H4G forms bifurcated hydrogen bonds with oxygen of the nitrate ion and zwitter ionic glycine to the plane below. Two of the oxygens of the nitrate ion(O1N and O3N ) are coordinated to the same silver ion. The total crystal structure is built up from these repeating units to give 2-dimensional polymeric structure extended along the c-axis. Figure 5 CDGSN looking down a-axis. A comparison of hydrogen bonding parameters between FDGSN and CDGSN is given in Table 9. It is observed that the D…A distances have increased in all the hydrogen bonds in CDGSN.
Table 9
Comparision of hhydrogen bonding papmeters between FDGSN[20] and CDGSN (Å, °)
| D—H | H...A | D...A | D—H...A |
N2G—H1G...O3Ni(FDGSN) | 0.86 (3) | 2.19 (3) | 3.046 (2) | 174 (2) |
CDGSN | 0.79(5) | 2.26(5) | 3.054(3) | 178(5) |
N2G—H1G...O2Ni(FDGSN) | 0.86 (3) | 2.40 (3) | 3.028 (2) | 130 (2) |
CDGSN | 0.79(5) | 2.49(5) | 3.038(3) | 127(4) |
N2G—H1G...N1i(FDGSN) | 0.86 (3) | 2.64 (3) | 3.447 (2) | 157 (2) |
CDGSN | 0.79(5) | 2.73(5) | 3.456(3) | 154(4) |
N2G—H2G...O3Nii(FDGSN) | 0.91 (3) | 2.34 (3) | 2.986 (2) | 128 (2) |
CDGSN | 1.03(5) | 2.29(5) | 2.994(3) | 124(4) |
N2G—H2G...O2Giii(FDGSN) | 0.91 (3) | 2.45 (3) | 3.175 (2) | 136 (2) |
CDGSN | 1.03(5) | 2.38(5) | 3.188(3) | 134(4) |
N2G—H2G...O1Niii(FDGSN) | 0.91 (3) | 2.52 (3) | 3.121 (2) | 123 (2) |
CDGSN | 1.03(5) | 2.45(5) | 3.139(3) | 124(4) |
N2G—H3G...O2Niv(FDGSN) | 0.90 (3) | 2.02 (3) | 2.907(2) | 166 (3) |
CDGSN | 0.91(4) | 2.03(5) | 2.921(3) | 164(4) |
C2G—H4G...O1Nv(FDGSN) | 0.95 (2) | 2.43 (2) | 3.222 (2) | 140 (2) |
CDGSN | 0.96(4) | 2.45(4) | 3.231(3) | 138(3) |
C2G—H4G...O2Gv(FDGSN) | 0.95 (2) | 2.63 (2) | 3.388 (2) | 137 (2) |
CDGSN | 0.96(4) | 2.61(4) | 3.401(3) | 140(3) |
C2G—H5G...O1Gvi(FDGSN) | 0.98 (2) | 2.55 (2) | 3.457 (1) | 155 (2) |
CDGSN | 1.04(4) | 2.51(4) | 3.474(3) | 155(3) |
Symmetry codes: (i) -1 + x, -1 + y, z; (ii) -x, -y, -z; (iii) -1-x, -y, -z; (iv) x, -1 + y, z; (v) -1-x, -1/2 + y, 1/2-z; (vi) -1 + x, y, z.
ii) NDGSN
Packing of the molecule is shown in Fig. 6. The Nitrate ion the silver ion and zwitterionic glycine form a three-dimensional network unlike the case in CDGSN. The N-H…O hydrogens bonds are all to the nitrate ions unlike the case in CDGSN where the hydrogen bonds are to nitrate as well as the zwitter ionic glycine. Two of the hydrogen’s H1G and H2G form bifurcated hydrogen bond to nitrate, whereas H3G forms single N-H…O hydrogen bond to nitrate ion. The C-H…O hydrogen bonds are also to the nitrate ion, Both the oxygen’s O1G and O2G are coordinated to the Silver ion, and hence do not participate in any hydrogen bond as acceptor unlike the case of CDGSN. A comparison of hydrogen bonding parameter between GSN and NDGSN is given in Table 10.
Table 10
Comparision of hydrogen bonding papmeters between NDGSN and GSN[5] (Å, °)
| D—H | H...A | D...A | D—H...A |
N1G—H1G...O1Ni(NDGSN) | 0.89 | 2.50 | 3.12 (2) | 127.2 |
GSN | | | 3.14 | |
N1G—H1G...O3Ni | 0.89 | 2.05 | 2.94 (2) | 176.4 |
| | | 2.97(4) | |
N1G—H1G...N1i | 0.89 | 2.62 | 3.45 (2) | 155.5 |
| | | 3.40 | |
N1G—H2G...O2N | 0.89 | 2.47 | 3.11 (1) | 129.6 |
| | | 3.12 | |
N1G—H2G...O2Nii | 0.89 | 2.10 | 2.86 (1) | 142.7 |
| | | 2.88(3) | |
N1G—H3G...O1Niii | 0.89 | 2.19 | 2.97 (2) | 145.7 |
| | | 2.93(4) | |
C2G—H4G...O3Niv | 0.97 | 2.44 | 3.41 (12) | 173.8 |
| | | 3.06 | |
C2G—H5G...O1Ni | 0.97 | 2.37 | 2.97 (1) | 119.6 |
| | | 2.95 | |
Hirshfeld surface Analysis
The size and shape of the Hirshfeld surface is ideal for use in comparing different structure having the same molecules [24, 25]. Crystal explorer [26, 27] was used to generate Hirshfeld surfaces and 2D finger plots using the cif files obtained using the single crystal X-ray diffraction data of the FDGSN[20], CDGSN and NDGSN determined by us, and for GSN the Cif file (REFCODE: GLYAGN [5], was obtained from CCDC Cambridge Structural Database [28] using ConQuest database.
The following parameters were calculated using Crystal explorer [24] and are described below:
Globularity is a meaure of the degree to which the surface area differs from the value for a sphere of the same volume and is defined as
$$G=\frac{{\left(36\pi {V}_{H}^{2}\right)}^{1/3}}{{S}_{H}}$$
Where VH and SH denote molecular volume and surface area, and is 1.0 for a sphere and less than one as the molecular surface becomes more structured [24].
Globularity (Table 11) has been calcuated for nitrate and glyine molecule independently and also for the enitire comlex. The globularity for nitrate and glycine molecules when calculated independently follows the trend with maximum for GSN followed by NDGSN, CDGSN and FDGSN. It is also observed from structural data that the nitrate ions are planar in FDGSN and CDGSN, unlike the case with GSN and NDGSN reflecting more structured molecular surface of nitrate in FDGSN and CDGSN. In GSN [5] the hydrogen atoms have not been located and refined the volume and area reflects this, hence showing the lowest volume and area. The globularity parameter is similar in all the strutures. When the entire complex is considered, it is observed that FDGSN and CDGSN has similar values, which is lower than that of GSN and NDGSN.
Asphericity, Ω is measure of the anisotropy of an object and when applied to the atomic positions and is defined as
$$\text{}=\raisebox{1ex}{$1$}\!\left/ \!\raisebox{-1ex}{$2$}\right.\left(\sum _{i\ne j}{\text{( }\text{}}_{i}{-{\text{}}_{j})}^{2}\right){\left(\sum _{i}{\text{}}_{i}\right)}^{-2}$$
where λi are the three principal moments of inertia of the molecule. Ω has a value of zero for an isotropic object, 1.0 for a prolate object and 0.25 for an oblate object. [24]
Asphericity parameter ((Table 11) )for nitrate molecule is similar in all the four strutures with a value close to zero showing the isotropic nature of nitrate molecule. In the case of glycine, NDGSN and GSN have similar values and FDGSN and CDGSN have similar values. When the entire molecule is considered it is observed that NDGSN and GSN are close to 0 indicating the isotropic natrure wheres as FDGSN and CDGSN indicae oblate nature .
Table 11
Comparsion of Hirshfeld parameters
Crystal structure | | Volume (Å3) | Area (Å2) | Area/volume (Å−1) | Globularity | Asphericity |
CDGSN | nitrate | 40.32 | 63.19 | 1.567 | 0.900 | 0.040 |
NDGSN | nitrate | 43.45 | 65.93 | 1.517 | 0.907 | 0.035 |
FDGSN | nitrate | 39.97 | 62.92 | 1.574 | 0.898 | 0.038 |
GSN | nitrate | 49.57 | 71.55 | 1.443 | 0.912 | 0.038 |
CDGSN | glycine | 69.55 | 92.04 | 1.323 | 0.889 | 0.071 |
NDGSN | glycine | 69.82 | 92.02 | 1.318 | 0.891 | 0.048 |
FDGSN | glycine | 68.95 | 91.50 | 1.327 | 0.889 | 0.071 |
GSN | glycine | 61.55 | 84.01 | 1.364 | 0.897 | 0.063 |
CDGSN | Entire crystal | 137.27 | 167.85 | 1.222 | 0.767 | 0.366 |
NDGSN | Entire crystal | 138.86 | 157.43 | 1.134 | 0.824 | 0.044 |
FDGSN | Entire crystal | 135.99 | 166.92 | 1.227 | 0.766 | 0.366 |
GSN | Entire crystal | 138.56 | 155.41 | 1.122 | 0.833 | 0.038 |
Hirshfeld surfaces are mapped using the normalized contact distance (dnorm), which is defined as:
$${\text{d}}_{\text{n}\text{o}\text{r}\text{m}=}\frac{{\text{d}}_{\text{i}}-{\text{r}}_{\text{i}}^{\text{v}\text{d}\text{w}}}{{\text{r}}_{\text{i}}^{\text{v}\text{d}\text{w}}} +\frac{{\text{d}}_{\text{e}}-{\text{r}}_{\text{e}}^{\text{v}\text{d}\text{w}}}{{\text{r}}_{\text{e}}^{\text{v}\text{d}\text{w}}}$$
The various parameters given are dnorm, which is a ratio encompassing the distances of any surface point to the nearest interior (di) and exterior (de) atom and the van der Waals radii of the atoms [ 24,25,29,30]. The negative dnorm visualized by red colour in the Hirshfeld surfaces indicates the sum of di and de is shorter than the sum of the relevant Van der Waals radii considered as the closest contact. The dnorm equal to zero visualized by white colour denotes intermolecular distances close to Van der Waals whereas contacts longer than the sum of Van der Waals radii with positive dnorm values are colored with blue. The surfaces are shown as transparent to allow visualization of the different moieties. The dnorm values when compared for nitrate molecules(Table 12 Fig. 7) in all the four structures shows that, FDGSN and CDGSN has more red spots compared to that in the case of NDGSN and GSN indicating more intermolecular interactions in CDGSN and FDGSN. The same when compared for glycine molecule(Table 13 Fig. 8), it is observed that in NDGSN and GSN has more red spots compared to that in FDGSN and CDGSN. When the entire complex is considered, it is observed that mean dnorm (Table 14 and Fig. 9) value of CDGSN is more than that of FDGSN. The number of red spots are also more in CDGSN indicating more numbar of intermolecular interactions in CDGSN. Comparing GSN and NDGSN shows more red spots in NDGSN.
Shape index S is a dimensionless measure of shape and is s defined as
$$\text{S}=\frac{2}{{\pi }}\text{a}\text{r}\text{c}\text{t}\text{a}\text{n}\left(\frac{{}_{1}+{}_{2}}{{}_{1}-{}_{2}}\right)$$
where principal curvatures are \({}_{1}\) and \({}_{2}\). Mapping is in the range-1.0 (concave) through 0.0 (minimal surface) to + 1.0 (convex)[24, 25]
The shape index is extremely sensitive to the change in surface shape giving a visual identification of the regions using complementary pairs of red and blue colored schemes. The concave red-colored region on the shape index represents the cluster of the surface around the acceptor atoms and the blue-colored bumps represent the cluster of the surface around the donor atoms. In the case of nitrate molecule (Table 12, Fig. 7) it can be seen that the concave red coloured regions are more in GSN and NDGSN compared to that of FDGSN and CDGSN, this is basically because the two of the nitrate oxygens are coordinated to the Ag ion in FDSN and CDGSN. In the case of glycine molecule(Table 13, Fig. 8), it is observed that GSN and NDGSN has more red coloured regions. The mean value of shape index is minimum in NDGSN, compared to other three structures and shows more number of red and blue spots.
Curvedness, C is defined,
$$\text{S}=\frac{2}{{\pi }}\text{ln}\sqrt{\frac{{{}_{1}}^{2}+{{}_{2}}^{2} }{2}}$$
where principal curvatures are \({}_{1}\) and \({}_{1}\). Mapping is in the range − 4.0 (flat) through 0.0 (unit sphere) to + 0.4(singular) [24, 25]
The curvedness is a measure of the shape of the surface area of the molecule.The flat areas of the surface correspond to low values of curvedness, whereas sharp curvature areas correspond to high values of curvedness and usually tend to divide the surface into patches, indicating interactions between neighbouring molecules. The curvedness map displays large regions of green (relatively flat) separated by dark blue boundaries (large positive curvatures),. In the case of nitrate molecule(Table 12 Fig. 7) NDGSN shows more sharp curvatures followed by CDGSN. In the case of glycine molecule(Table 13 Fig. 8) and the entrire complex(Table 14 Fig. 9) NDGSN and GSN shows more sharp curvatures followed by CDGSN.
A plot of di versus de is a 2D fingerprint plot which recognizes the existence of different types of intermolecular interactions. Figure 10 shows the 2D Finger plots of C..H, N..H, O..H, H..H, Ag…o and Ag…Ag interactions. The Table 15 gives the percentage of different contacts. It can be from the Table 10 that C…H. N…H and O… H interactions are higher in CDGSN and FDGSN as compared to NDGSN. The H…H interactions are higher in NDGSN. NDGSN and GSN have higher Ag…O interactions compared to that of CDGSN and FDGSN. NDGSN and GSN have Ag…Ag interaction, which is totally absent in CDGSN and FDGSN.
Table 15
percentages of different contacts in CDGSN, NDGSN, FDGSN and GSN
Refcode | N…H | C…H | O…H | H…H | Ag-O | Ag-Ag |
CDGSN | 0.2 | 0.3 | 65 | 1.1 | 14.0 | 0.0 |
NDGSN | 0.1 | 1.1 | 61.3 | 2.3 | 17.7 | 2.0 |
FDGSN | 0.2 | 0.3 | 65.3 | 0.9 | 13.9 | 0.0 |
GSN | | | | | 24.8 | 2.1 |
Spectroscopic results
Since the x-ray doesn’t directly show the deuteration in the compound, Raman scattering experiments were carried out for NDGSN and CDGSN. Lattice modes of GSN and FDGSN were also recorded (Fig. 11). Modes below 200 corresponds to vibrational modes of lattice modes, as observed form the Table 16a, it can be seen that GSN and NDSN have similar modes and FDGSN and CDGSN have similar modes confirming the similarity of structure as obtained from single crystal X-ray diffraction studies.
Table 16
a: Raman modes in NDGSN & CDGSN in the lattice region
Raman modes | GSN (cm− 1) [8] | NDGSN (cm− 1) | FDGSN (cm− 1) [20] | CDGSN (cm− 1) |
Lattice modes | 83 | 83 | 94 | 87 |
107 | 106 | | |
118 | 119 | 120 | 121 |
144 | 145 | | |
193 | 188 | | |
Raman spectra corresponding to the internal modes of NDGSN and CDGSN is shown in Fig. 12 and Fig. 13 respectively. The assignment of the internal modes for NDGSN and CDGSN was achieved by comparing the Raman frequencies of the parent molecules i.e.N-deuterated glycine 31, 32,33,34], C deuterated glycine[ [32, 33, 35] silver nitrate[36, 37, 38], GSN [8] and FDGSN [20] reported earlier as one expects close correspondence between the internal frequencies of these molecules. The vibrations corresponding to nitrate ions could be identified by comparing with the Raman spectra of AGNO3 and also with that in GSN and FDGSN and have been listed in Table 16b. The internal vibrations of the zwitter ionic glycine can be considered as vibrations belonging to NH3+, CH2 and COO− groups. For identifying the Raman modes due to glycine in NDGSN and CDGSN, the Raman modes in N deutertaed glycine[31, 32, 33, 34] and C deuterated glycine[33, 34, 35] was used respectively. The modes corresponding to backbone N-C-COO, ND3 and CH2 for NDGSN are enumerated in Table 16c. The appearance of various modes associated with ND3 and CH2 group in Table 16c confirms the N deuteration in NDGSN. The modes corresponding to ND stretch were identified using the modes of ND stretch in FDGSN[20], since the same were not recorded in NDGLY in the References 31, 32, 33, 34. The modes corresponding to backbone N-C-COO, NH3 and CD2 for CDGSN are enumerated in Table 16d., similarly the various modes associated with CD2 and NH3 group in Table 16d confirms the C-deuteration in CDGSN. It can be observed from the Raman spectra in the region between 1900 to 3500 cm− 1, there are also modes corresponding to ND3, showing there is partial deuteration of hydrogens attached to Nitrogen of glycine. This again shows that the importance of C-deuteration alone is important in bringing about isotopic polymorphism.
Table 16
b Raman Modes corresponding to nitrate molecule in CDGSN and NDSN
Raman modes | AGNO3 (cm− 1) [ 36, 37,38] | GSN(cm− 1) [ 8] | NDGSN(cm− 1) | FDGSN(cm− 1)[20] | CDGSN(cm− 1) |
ν4 NO3− ion | 711 | 706 | 706 | 715 | 714 |
ν4 NO3− ion | 731 | 721 | 720 | 725 | 725 |
ν 2 NO3− ion | 807 | 825 | 822 | 825 | 825 |
ν 1 NO3− ion | 1047 | 1050 | 1050 | 1046 | 1046 |
ν 3 NO3− ion | 1305 | 1329 | 1319 | 1336 | 1331 |
ν 3 NO3− ion | 1350 | 1354 | 1359 | 1362 | 1361 |
Table 16
c: Raman modes in NDGSN due to Zwitter ionic glycine
Raman modes | NDGLY (cm− 1) [31, 32, 33, 34] | NDGSN(cm− 1) |
Internal vibrations of the zwitter ionic glycine |
δ NCC (CCN bend) | 330 | 336 |
CO2 rock (r(COO)) | 493 | 525 |
CO2 wag (γ(COO)) | 595 | 589 |
CO2 bend (δ(COO) | 666 | 654 |
C-C stretch | 1001 | 998 |
C-N stretch | 1017 | 1020 |
νs COO ( symm str) | 1403 | 1416 |
νas COO( symm str) | 1592 | 1571 |
Raman modes corresponding to ND3+ vibrations |
ND3 rock | 763 823 | 749 835 |
ND3 symm defor | 1166 1176 | 1146 1167 |
ND3 Asymm defor | 1187 | 1180 |
ND3 ν(S) | | 2205 2220 |
ND3 νa(S) sym. str. | | 2367 |
Raman modes corresponding to CH2 vibration |
CH2 ρ rock | 964 | 971 |
CH2 torsion | 1269 | 1280 |
CH2 wag ω | 1323 | Merged with NO3 |
CH2 bend δ | 1441 | 1448 |
CH2 v(S) sym. str | 2972 | 2972 |
CH2 ν(A) sym str | 3007 | 3011 |
Table 16
d: Raman modes in CDGSN due to Zwitter ionic glycine
Raman modes | CDGLY(cm− 1) [33, 34, 35] | CDGSN(cm− 1) |
Internal vibrations of the zwitter ionic glycine |
δ NCC (CCN bend) | 355 | 329 |
CO2 wag | 539 | 532 |
CO2 bend | 668 | 667 |
C-C stretch | 914 | 903 |
C-N stretch | 1187 | 1186 |
νs COO ( symm str) | 1396 1413 | 1395 1413 |
νas COO( asymm str) | 1568 | 1556 |
Raman modes corresponding to NH3 + vibrations |
NH3 tor | 462 | 476 |
NH3 rock | 1111 | 1095 |
NH3 symm defor | 1498 | 1495 |
NH3 Asymm deformation | 1629 1663 | 1611 1650 |
NH3 ν(S) sym. str | | 3069 |
NH3 ν(S) sym. str | | 3105 |
Raman modes corresponding to CD2 vibrations |
CD2 ρ rock | 809 | 798 |
CD2 wag ω | 867 | 873 |
CD2 torsion | 941 | 933 |
CD2 bend δ | 1039 | 1030 |
CD2 ν(S) sym. str | 2160 | 2158 |
CD2 ν(A) sym str.. | 2255 | 2267 |