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THE CRYSTAL AND MOLECULAR STRUCTURE OF TRIS(ORTHO- AMINOBENZOATO)AQUOYTTRIUM(III)
SHARON MARTIN BOUDREAU
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Bo u d r e a u , S h a r o n M a r t in
THE CRYSTAL AND MOLECULAR STRUCTURE OF TRIS(ORTHO- AMrNOBENZOATO)AQUOYTTRIUM(III)
University o f New Hampshire PH.D. 1979
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University M icrailm s Irternarjonal 300 N ZEES RD.. ANN AR30R Ml J8106 '313) 761-4700 THE CRYSTAL AND MOLECULAR STRUCTURE OF TRIS( ORTHO-AMINOBENZOATO)AQUOYTTRIUM( I I I )
Ly
SHARON MARTIN BOUDREAU
B.A. , Wheaton College
Norton, Massachusetts, 1975
A DISSERTATION
Submitted to the University of New Hampshire
In Partial Fulfillment of
The Requirements for the Degree of
DOCTOR OF PHILOSOPHY
in C hem istry
September, 1979 ; This thesis has been examined and approved.
O — t — 4 Helmut M. Haendler, Thesis Director Professor of Chemistry
C. L. Grant Professor of Chemistry
• y y i f j v Y w ^ Jamek D. M o rriso n B^jfessor of Chemistry
C h a rle s W. Owens Professor of Chemistry
M. Wayne M y B easley U Associate Professor of M aterials Science
/ ? 7 y TO MY HUSBAND, PARENTS, AND FAMILY who, through their love and support,
made this thesis possible Ac knowledgeme nts
The author wishes to express her sincere appreciation
to her research director, Dr. Helmut M. Haendler, for his guidance,
support, and friendship during the course of this research and for
the opportunity to share a unique learning experience.
Gratitude is expressed to Dr. C.L. Grant and the faculty of the Department of Chemistry for providing the opportunities to teach chemistry. The experience of teaching was very important in
the professional development of the author..
In addition, thanks is extended to my father whose own chemistry background set the stage for my career, and to my mother for her never ending love and encouragement.
The author is grateful for the financial assistance of
the Lester Eratt Fellowship, two University of New Hampshire Summer
Fellowships, Dissertation Year Fellowship, and teaching assistantships. TABLE OF CONTENTS
List of Tables ...... v i i
List of Figures • • viii
A b s tra c t ...... ix
The Crystal and Molecular Structure of Trisfortho-aminobenzoato)aquoyttrium(III)
P a r t One
The Synthesis of Metal Complexes of Ortho-aminobenzoic Acid ...... 1
I. Introduction ...... 1
II. Experimental ...... 7
A. S t a r t in g M a te ria ls ...... 7
B. Preparation of Sodium Ortho-aminobenzoate Reagent ...... 7
C. Preparation of Metal Anthranilates ...... 7
D. Preparation of Single Crystals of Cadmium(ll), Cobalt(ll), Zinc(ll), Y ttrium (lll), and Lanthanum(lll) Anthranilates 8
E. X-Ray Powder Diffraction Patterns ...... 11
F. Elemental Analyses ...... 11
1. Carbon, Hydrogen, and N itrogen ...... 11
2. Determination of Yttrium and Lanthanum ...... 11
G. Determination of the Existence of Coordinated Water Molecules in Zn(ll), Y (lll), and La(lll) Anthranilates .. 12
III. Results and Discussion ...... 13
A. Single Crystal Growth ...... 13
B. Characterization of the Compounds ...... 17
C. Suggested Future Research ...... 18
v P a r t Two
The Crystal and Molecular Structure of Tris(ortho-aminobenzoato) a q u o y ttr iu m ( lll) , YtHgNCgH^COO)^ • HgO ...... 20
I. Introduction ...... 21
A. Coordination Number Six ...... 23
B. Coordination Number Seven ...... 23
1. Capped Trigonal Prism ...... 24
2. Capped Octahedron ...... 27
C. Coordination Number Eight ...... 28
1. Square Antiprism ...... 28
2. Dodecahedron ...... 28
D. C o o rd in a tio n Number Nine ...... 29
E. Higher Coordination Numbers ...... 30
II. Experimental ...... 31
A. Preparation of Single Crystals of Tris(ortho-aminobenzoato) aquoyttrium( III) ...... 31
B. Determination of the Space Group, Unit Cell Dimensions, and Density of Tris(ortho-aminobenzoato)aquoyttrium(III) ...... 31
C. Intensity Measurements ...... 33
III. Solution and Refinement of the Structure ...... 43
IV. Results and Discussion ...... 65
Appendix ...... 87
A. X-Ray Powder Diffraction Patterns ...... 88
B. Computer Programs ...... 96
Bibliography ...... 104 LIST OF TABLES
I. Synthesized Metal Complexes of Ortho-aminobenzoic A cid ...... 16
II. Crystal Data for Y^NCgH^COO)^ • H20 ...... 36
III. Outline of the Structure Determination for a Compound Containing a Heavy Atom ...... 44
IV. Co-ordinates of Equivalent Positions for Space Group, C2/c..4?
V. Selected Patterson Map Peak Heights and Locations ...... 49
VI. Final Positional and Thermal Parameters for y( h2mc6h |>coo)3 ■ h20 ...... 57
VII. Summary of Refinement Stages ...... 62
VIII. Calculated and Observed Structure Factors f o r Y(H2NC6H^C00 )3 ■ HgO ...... 63
IX. Characteristic Parameters of the Coordination Polyhedron ...7 1
X. Bond Distances and Angles in Y(H 2NG^H^C00)3 ■ HgO...... 77
XI. X-Ray Powder Diffraction Data for Zn(H 2NC^H^C00)2 ...... 89
XII. X-Ray Powder Diffraction Data for Y(H 2NC^H^C00)3 • K^O 90
XIII. X-Ray Powder Diffraction Data for La(H 2NC^H^C00)3 ...... 91
XIV. X-Ray Powder Diffraction Data for Mn(H 2NC^H^C00)2 ...... 9 2
XV. X-Ray Powder Diffraction Data for Co(H 2NC^H^C00)2 ...... 93
XVI. X-Ray Powder Diffraction Data for Ni(HgNC^H^COO )2 ...... 94
XVII. X-Ray Powder Diffraction Data for Cd(H 2NC^H^C00)2 ...... 93
v i i LIST OF FIGURES
1 . Molecular Structure of Bis(ortho-aminobenzoato)copper(II) ...... 5
2 . Diffusion Apparatus for Single Crystal Growth ...... 9
3- Photograph of the Diffusion Apparatus in Use ......
k. TGA Curve for YCHgNC^COO)^ • HgO ......
5 . Idealized Polyhedra Observed in Yttrium Compounds ...... 2 5
6 . Microscopic View of the Y^gNC^H^COO)^ * H^O Crystals ...... 3 2
7. Zero Level Weissenberg Photograph of Y^gNCgH^COO^ * H^O .. •••3 3
8. F irst Level Weissenberg Photograph of Y^gNC^H^COO)^ . H^O .. ... 3^
9- C rystal Morphology of Y^gNCgH^COO)^ • H^O ...... 3 8
1 0 . Molecular Geometry of Y^gNC^H^COO)^ * H^O ...... 6 6
1 1 . Coordination Around Yttrium in Y^^NCgH^COO)^ • H^O ......
12 . Polymeric Structure in Y^^NCgH^COO)^ • H^O ......
13- Stacking of the Phenyl Rings in Y^gNCgH^COO)^ * H^O ...... •••7 5
Ik. Photograph of the Unit Cell for Y(H 2HC6fyC 00)3 ■ HgO ...... 8 1
v i i i ABSTRACT
THE CRYSTAL AND MOLECULAR STRUCTURE OF TRISf ORTHO-AMINOBENZOATO)AQ.UOYTTRIUM( I I I )
"by
SHARON MARTIN BOUDREAU
University of New Hampshire September, 1979
The crystal and molecular structures of tris(ortho-aminoben zoato )aquoyttrium( III) have been determined using three dimensional x-ray diffraction data gathered on multiple-film, equi-inclination, integrated Weissenberg photographs taken about the [ 010] crystal axis.
Further data were collected with integrated precession photographs.
The intensities were read using a Welch Densichron. The compound crystallizes in the monoclinic space group, C2/c, with eight molecules o o o in a unit cell of dimensions: a = 30.89(l)A, b = 9.09(l)A, c = l4.85(l)A, and >6 = 109 »3(1)°« The structure, excluding hydrogen atoms, was solved from Patterson and electron density maps and refined by least squares methods to a final conventional R factor of 8.1%. The yttrium atom is at the center of a distorted octahedron of chelate oxygen atoms (aver- o age Y—Ogheiate = 2 .^ 2 ( 2 )a) capped on one face by the water molecule
(Y— = 2.30(2)a). Each ortho-aminobenzoate ligand acts as a bi- dentate ligand, but the two sites of attachment are not associated with the same yttrium atom resulting in six ortho-aminobenzoate residues coupled to each yttrium atom. This bonding configuration generates a structure in which each yttrium atom in the ( 100) plane is attached to two other yttriums via carboxylate bridges to give parallel sets of polymeric chains coincident with the (100) plane. It is suggested that this polymeric character accounts for the extreme insolubility of the tris(ortho-aminobenzoato)aquoyttrium(III). This model appears to be the best one based on the available data.
Single crystals of zinc(ll) and lanthanum(lll) anthranilates have also been grown and current research is involved in the structure determination of these complexes for a direct comparison with the yttrium complex.
x PART ONE
THE SYNTHESIS OF METAL COMPLEXES
OF ORTHO-AMINOBENZOIC ACID PART ONE
I . INTRODUCTION
Ortho-aminobenzoic acid (anthranilic acid) is an important pre cursor to tryptophan, one of the twenty biologically important -amino
acids. In addition, this acid forms stable, highly insoluble compounds with a variety of divalent and trivalent metals and may be used as a 1 2 reagent for quantitative determinations of these metals. '
This first part of the research involves the synthesis and cha racterization of a series of metal chelates of anthranilic acid. These metal anthranilates include manganese(ll), cobalt(ll), nickel(ll), zinc(ll), cadmium(ll), yttrium (lll), and lanthanum(lll). Copper(ll) chelates of some aromatic amino acids have been shown to have anti inflammatory and anti-ulcer activity, not exhibited by the parent acid alone. This suggests the possibility of a template or mimicry effect, related to the molecular structure. In order to determine the struc tural skeleton of these anthranilate complexes, single crystals must be made available. Until some structures are known, considerations of the biological effects will be hindered. Thus the first objective was the growth of single crystals.
A diffusion apparatus specially designed to minimize solution convection during crystal growth and simplify crystal removal, has made possible the growth of single crystals of many of the studied complexes of the ortho-aminobenzoate ligand. Single crystals of zinc,
1 2
manganese, cobalt, cadmium, yttrium , and lanthanum complexes of the ortho-aminobenzoate were successfully grown. Many of these crystals were well formed suitable for single crystal x-ray diffraction studies.
The details of the employed diffusion apparatus w ill be described in detail latter in this thesis.
Research in the area of structural determinations is of interest because some metal chelates exhibit anti-inflammatory activity. A re- 3 port by Sorenson ^ suggested that copper might be a component of the active metabolite of clinically used anti-inflammatory agents, and that copper chelates were active metabolites. There was a marked increase in activity by copper chelates of chelating agents which themselves exhibited no activity. Anti-ulcer activity has also been demonstrated, and it was reported that there was a decrease in toxicity relative to the parent substance. A subsequent report listed the activity data h for a number of copper compounds. Included in this list were com- paritive studies of cupric acetate, observed to be more active than hydrocortisone in the carrageenan foot edema model of inflammation, with the activities of L- and D-tryptophan, anthranilic acid, and 3»
5-diisopropylsalicylic acid copper complexes. In all cases the copper coordination compounds were more active.
If the formation of a chelate is necessary for the enhanced activ ity of the parent compounds, such formation should be demonstrated. The observed activity is apparently not due to the parent ligand, nor to the metal ion itself. If transport of the metal is a factor, then the effect of the unchelated complexes should equal those of the chelated complexes.
Such does not seem to be the case, which strongly suggests that the ac tivity is somehow related to the type of coordination and stereochemistry 3
associated with the complex. Results ^ suggest the possibility of a
template or mimicry effect, related to the molecular structure. Until
some structures are known, considerations of such effects will be hin
d e re d .
The lim ited amount of stereochemical and structural information
available for several of the divalent metal ortho-aminobenzoates are at
variance. Sandu et al.^ propose a structure in which the ortho- amino
benzoate acts as a tridentate ligand, giving rise to a distorted octa- 7 hedral coordination about copper. Khakimov et al. also conclude in g favor of the distorted octahedral structure. Hill and Curran , Decker 9 10 11 and Frye , Inomata , and Ismailov all advocate a square planar
structure in which the ortho-aminobenzoate is bidentate. 12 13 Lange and Haendler ’ have in fact confirmed the distorted
octahedral coordination for bis(ortho-aminobenzoato)copper(II) using
three dimensional X-ray diffraction data. C^HgNC^H^COO)^ crystallizes , o in the monoclinic space group P2^/c, with cell dimensions a = 12.95A, b = 5.25#, c = 9-39A, and = 93*3 • Anisotropic temperature refine ment gave a conventional R = 3.1%. Each copper atom has distorted octa
hedral coordination. Four equatorial positions are occupied by two
amino nitrogens and two carboxylate oxygens with both the nitrogens and
oxygens in trans positions. The axial positions are occupied by two
carbonyl oxygens, each of which belongs to a different ortho-aminoben-
zoate ligand. The resulting mode of coordination is that each copper
in th e ( l 00) plane is attached to four other coppers via carboxylate
bridges to give a two-dimensional polymeric sheet coincident with the
(100) plane. This polymeric network probably accounts for the extreme
insolubility of the complex, adequate for analytical gravimetry. The 4
molecular structure is shown in Figure 1.
The copper(ll) anthranilate complex is one of a rare group of amino acid complexes in which both oxygens of the carboxylate group 14 are active in bonding, and is unique in that each carbonyl oxygen belongs to a different ligand. How important these variations are, in terms of activity, s till needs to be answered. Lange and Haendler have also reported the sim ilarity between the powder patterns of the copper and zinc complexes. Intuitively, one would surmise that the Zn—0 dis tance would be shorter than the Cu—0 distance. Preliminary investiga tions have shown that the bis(ortho-aminobenzoato)zinc(II) also belongs to the space group TZ^/c. It is possible that a similar but tetrahedral coordinated structure exists in the zinc anthranilate complex.
The purpose of this part of the research was to synthesize a series of metal chelates of anthranilic acid. A number of these complexes have been reported, but in many cases the descriptive material and data leave something to be desired. Two objectives were kept in mind: (l) to grow single crystals of as many varieties of metal anthranilates as possible; and ( 2 ) to utilize available single crystals for a series of structural studies on the complexes formed between ortho-aminobenzoic acid and metal ions. Many of these compounds axe insoluble in water so that diffusion methods offer good possibilities for single crystal growth.
The ultimate goal of this study is to relate structural and bond ing properties of these compounds to their biological activity. The testing of anti-inflammatory activity in animals is beyond our capabili ties, but if the structure can be related to the mode of action, or if a template mechanism can be substantiated, the significance for the de velopment of improved agents would be considerable. 1
F ig u re 1
The Molecular Structure of Bis(ortho-aminobenzoato)copper(II)
(copied by permission of Lange and Haendler, 1975) a
0 (2) 0 (1) I I . EXPERIMENTAL
A. Starting Materials
Reagent grade manganese sulfate, cobalt sulfate, zinc sulfate,
G.P. grade cadmium nitrate and analytical grade nickel sulfate were ob
tained from Fisher. Analytical grade yttrium nitrate and reagent grade lanthanum nitrate were purchased from Alfa. The analytical grade ortho- aminobenzoic acid, obtained from Eastman, was used without further pu rification. The purity of the ortho-aminobenzoic acid was confirmed by its excellent melting point (1A6-1A7 ° C). ^
1 B. Preparation of Sodium Ortho-aminobenzoate Reagent
Ortho-aminobenzoic acid (3*0 S» 0.0218 mol) was dissolved in
0.1 N sodium hydroxide (22 ml). The resulting solution was filtered and then diluted to 100 ml with distilled water. Small amounts of the ortho-aminobenzoic acid were added to the solution until it was just acid to litmus. The reagent was light yellow in color and was stored in a tightly stoppered, light-proof container.
C. Preparation of Metal Anthranilates
The metal anthranilates were prepared according to a precipi- tation method given by Prodinger. A 0.01 M solution of the appropriate metal salt (200 ml) was heated to boiling in an Erlenmeyer flask. The anthranilic acid reagent ( 25-30 ml) was added dropwise to the flask, resulting in a precipitate of the metal anthranilate. The solution was digested for ten minutes and then allowed to cool before filtration.
7 8
The precipitates were collected under vacuum on a sintered glass filte r, washed with a dilute solution of anthranilic acid reagent (0.001 M) and
10 ml of ethanol. The compounds were then dried in a vacuum desiccator for twenty-four hours.
D. Preparation of Single Crystals of Zinc(ll), Gobalt(ll), Cadmium(ll),
Manganese(ll), Y ttrium (lll) and Lanthanum(lll) Anthranilates
Single crystals of insoluble compounds'can sometimes be grown by diffusion of two. solutions which interact to form a solid by metathesis.
Minimization of convection and removal of crystals without further mixing of the solutions are often difficult. These two problems have been avoid ed by a modification of the gel-diffusion apparatus of Armington and
O'Connor. ^
The apparatus (Figure 2) consists of two 125 ml round-bottom flasks which serve as reservoirs for the reactant solutions. Medium porosity fritted-glass disks are mounted in the side arms, and the flasks are connected, through spherical joints, by a diffusion tube. The dif fusion tube is held in place by the use of clamps and the entire appa- 16 ratus is supported With tripods or ring stands.
In use, the apparatus is assembled, and the reservoirs are filled to the level of the bottom of the diffusion tube with the reagent solutions. A solution of sodium anthranilate (0.002 M) is in one reser voir and a solution of the metal salt (0..001 M) in the other. D istilled water is added through the center tube and the reservoirs are filled to capacity. The apparatus is stoppered to prevent evaporation and protect ed from exposure to light to avoid decomposition of the anthranilic acid reagent. Growth requires 2-3 weeks for well-shaped crystals suitable for X-ray work. After the formation of crystals in the diffusion tube, F ig u re 2
Diffusion Apparatus for Single Crystal Growth 6 mm I.D. T 8 cm
□\ 3 L 15 cm— - GLASS FRIT 11
the reservoirs are slowly drained simultaneously through the stopcocks
until the levels are below the center tube, thus avoiding further mix
ing. The apparatus is disconnected and the crystals are removed, fil
tered, washed and air dried.
E. X-ray Powder Diffraction Patterns
All X-ray powder diffraction photographs were taken with o either nickel-filtered copper radiation (wavelength = 1•541?8A) or man
ganese-filtered iron radiation (wavelength = 1.9373A). Both the 57*3 mm
and 114.56 mm Philips cameras were utilized. All films were read with
a Norelco film reading scale and films having back reflection lines
were corrected for shrinkage. The intensities were estimated visually for qualitative identification. The d-spacings were calculated using a 17 Hewlett-Packard HP 55 program.
F. Elemental Analyses
1. Carbon, Hydrogen, and Nitrogen
All carbon, hydrogen, and nitrogen analyses were done
using an F and M model I 85 CHN Analyzer. All the samples analyzed
were dried in a vacuum desiccator 24 hours prior to analysis.
2. Determination of Yttrium and Lanthanum
The metal anthranilates synthesized, with the exception
of the yttrium and lanthanum complexes, can be used for quantitative a 0«*2O determinations of these metals. Yttrium and lanthanum were
determined as the metal oxide. Weighed samples of the metal anthra
nilates were heated in a muffle furnace at 700° c for three hours.
The products were weighed as the oxide (M = Y or La). 12
G. Determination of the Existence of Coordinated Water Molecules
in Zinc(ll), Y ttrium (lll), and Lanthanum(lll) Anthranilate Complexes
D ifferential thermal analyses were run on a Fisher DTA,
Model 260F. A 2 mm i.d. quartz capillary was packed with a ground
sample of the complex. The heating rate in all cases was 10°/min.
Platinel and chrome-alumel thermocouples were used with the reference
junction immersed in an ice-water bath. In the case of the yttrium complex, further analyses were run on a Perkin-Elmer D ifferential Thermo-
gravimetric Analyzer using a differential scanning calorimeter, DSC 2.
Runs were made using a nitrogen atmosphere and measured weight loss over the range 25~500° C. A heating rate of 10°/min. was used. I I I . RESULTS AND DISCUSSION
A. Single Crystal Growth
Single crystals of cobalt(ll), zinc(ll), cadmium(ll), man- ganese(ll), yttrium (lll), and lanthanum(III) anthranilates were suc cessfully obtained from the diffusion method. Time of growth varied anywhere from 2-3 weeks, resulting in crystals ranging from 0.05 mm x
O.O5 mm to 2.0 mm x 0.1 mm in size. These crystals were found to be comparable in quality to the single crystals used to determine the struc- 1 ? ture of bis(ortho-aminobenzoato)copper(ll).
Attempts to synthesize single crystals of nickel(ll) an- thranilate were unsuccessful, and crystals of the manganese species were twinned in many cases. The general appearance of the diffusion ap paratus during crystal growth is shown in Figure 3»
The science of growing crystals is really an art, but con siderable progress has been made in establishing a theoretical basis of 21 "23 crystal growth. The shape of the single crystals grown (Refer to
Table i) depend to a certain extent upon the process of growth. In molecular diffusion the transport of matter to the crystal is much slow er than under other diffusion conditions. With time, the thickness of the boundary layer increases and the concentration gradient decreases.
Larger amounts of matter tend to reach projecting parts of a crystal
(edges or corners) resulting in supersaturation gradients appearing along faces. If these gradients and the dimensions of the crystal are small; a flat-faced crystal is obtained. Increasing the size of the crystal and the supersaturation gradients lead to a situation where the supply
13 F igu re 3
Photograph of the Diffusion Apparatus in Use ■,.'i m T able I
Synthesized Metal Complexes of Ortho-aminobenzoic Acid
A nalyses Compound Physical Appearance M.P. C C alcd. Obsd.
Mn(H 2NC6H4 C00)2 tan hexagonal shaped 350°; chars 51-39 C 5 1 .4 4 twinned crystals 3 .7 0 H 3-78 8.56 N 8 .4 5 c o ( h 2n c 6h ^ c o o )2 red spherical shaped > 3 5 0 ° 50.77 C 50.65 c r y s t a ls 3.69 H 3-79 8 .46 N 8 .5 4
Ni(H2NC6H^C00)2 light blue powder >350° 50.81 C 50.12 3 .6 5 H 3-95 8.46 N 8 .4 8
Zn(H2HC6H^C00)2 white hexagonal shaped 310° ; c h a rs 4 9 .8 0 C 4 9 .2 0 crystals, some twinning 3 .5 8 H 3 .7 8 8.29 N 8.26
Cd(H2NC6H4C00)2 white needle crystals 285 ° ; c h a rs 43.71 C 4 3 .5 2 3 .1 4 H 3 .3 4 7 .2 8 N 7.10
white needle crystals, 330° 4 8 .9 5 C 4 8 .3 0 some skeletal forms 3.91 H 3 .9 4 8 .1 5 N 8 .2 4 17.26 Y 17 .3 4 2 6 La(H HC H^COO), tan needle crystals, 325°; chars 46.09 C 45.98 some skeletal forms 3 .3 2 H 3 .4 7 cr\ 7.68 N 7 .7 5 2 5 .3 8 La 25.62 17
of matter to the middle parts of the faces decreases, so much that the
cavities appear. Subsequent layers cover this cavity, and an inclusion
of the solution may be captured by the crystal. At even greater gra
dients and dimensions of the faces, the deposition of matter occurs
mainly at the corners, resulting in the formation of branched crystals 2k known as corner skeletal forms. Unlike dendrites, skeletal forms
are single crystals.
The formation of needle-like crystals in which the planes of
the rings are more or less normal to the needle axis, is a common occu
rence for molecules containing planar aromatic ring systems. Such is
the case as the synthesized cadmium, yttrium, and lanthanum anthranilates.
The relatively strong interaction between the Tf clouds of the rings
causes more rapid growth in the stacking direction along the needle axis
than at right angles to it.
B. Characterization of the Compounds
The metal to ligand ratio was found to be 1:2 in all cases
except yttrium and lanthanum where it was 1:3. Powder films gave clean
sharp lines which aided in indexing. Sim ilarities were noted between
the powder films of cobalt(ll) and nickel(ll) as well as zinc(ll) and
cadmium(ll) complexes. Powder film data are given in the Appendix with indexing for the yttrium, zinc, and lanthanum complexes.
Elemental analyses are tabulated in Table I. Differential 25 thermal analyses J revealed no endothermic peaks indicative of coordi
nated water molecules for the zinc(ll) or lanthanum(lll) complexes. On
the other hand, the yttrium (III) complex exhibited an endothermic peak between 105-125° C, suggesting coordination of water. For comparison, 18
a dta of the reported para-GufH^NC^H^COO• 2H20^^ showed a sim ilar,
hut greater endothermic peak between 133-168° C, representing the loss
of two coordinated water molecules. D ifferential thermogravimetric
analysis showed a weight loss of 3*30^ between 1 09- 129° G, i n com p ariso n
to the calculated weight loss of 3 *^ 9% for one molecule of water, fur
ther supporting the existence of yttrium (lll) anthranilate as the mono
hydrate. Refer to Figure k. This observation is in disagreement with
the report by Surgutskii stating that the yttrium (lll) complex was
not hydrated. The author's analyses and method of preparation are the
same as the work presented here. An X-ray structural determination
should clarify this discrepancy.
C. Suggested Future Research
The growth of a number of single crystals suitable for X-ray
studies obviously directs this research toward structural determinations.
As many structures as possible should be determined in order to estab
lish some criteria for their biological activity. These structures will hopefully be useful to biologists and biochemists of the future.
The diffusion apparatus has several possibilities open for in
vestigation. Attempts at growing single crystals in different media, such as gels, might prove interesting. Also studies in optimizing con ditions by changes in temperature and/or concentration are feasible.
Comparative studies on the meta and para aminobenzoate complexes are also possible if single crystals can be grown. This method of crystal growth may not only prove valuable in this work, but may be important in the research of others needing single crystals for molecular determinations. F ig u re k
Thermal Gravimetric Analysis Curve for Tris(ortho- amino'benzoato)aquoyttrium(lll) illustrating the coordination of a molecule of water. PERCENT WEIGHT LOSS
vjx •£- ^ ro m- o
t— i r “ i — I------r
o o S 1-3 o t?d n s ►t) Hj n w H* > t-3 3 ro a O s ■P- w ro o o o t?d o o
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02 PART TWO
THE CRYSTAL AND MOLECULAR STRUCTURE OF TEIS( OR THO-AMINOBENZOATO)AQUOYTTRIUM(III) PART TWO
I . INTRODUCTION
Yttrium is a member of the second transition metal series, but is frequently associated with the lanthanide group elements. This element has a tripositive ion with a noble gas core, and as a result of the lan thanide 'contraction', has both atomic and ionic radii lying close to 27-29 the corresponding values for terbium and dysprosium. In nature, it is also generally found with members of the lanthanides, and resembles terbium (lll) and dysprosium(lll) in its compounds. 30 A review of the literature prior to 19^5» shows almost a com plete lack of structural data for complexes of the lanthanide ions. In more recent years, the number of published reports in this area has vast- 31 -34 ly increased, largely as a result of the increased availability of advanced methods for collecting X-ray intensity data and of computing facilities. Nevertheless, although many complex derivatives of the lan thanide ions have been described, the total number known is much less than the number characteristic of the d transition metal ions.
Apparently there are several factors which lim it the number of lan thanide complexes and hinder formation. To an approaching ligand, the
Ln n+ ion in the ground state represents a completely paired, noble gas configuration. Ligand field stabilization energies axe only of the or- -1 -1 d e r o f 1 kcal mol , in comparison to 100 kcal mol for valency-shell 3 c orbitals of the d transition metals. The lanthanide ions axe typical
21 22
"hard" acids in the Pearson sense. J The majority of the complexes
that can he isolated from aqueous systems contain ligands with oxygen 37 donor sites. Ligands with pure oxygen donors (e.g., oxalate and Op pQ /3-diketonate * ) or mixed oxygen nitrogen donors (e.g., ethylene- 4 0 \ diamine-N,N,N',N'-tetraacetate ) are known. Also a limited number . Zjq . of ligands with only nitrogen donor sites (e.g., 1 , 1 0 -phenanthroline ) have been reported. The water molecule is also a very strong ligand toward the lanthanide ions and competes effectively for coordination sites. Under alkaline conditions, the hydroxyl ion is an even stronger ligand. The solubilities of the lanthanide hydroxides or Oxides are small enough that precipitation of these compounds prevents complexation by many lig a n d s .
In general, the coordination number of the lanthanides is only lf.2 rarely six, and higher coordination numbers appear to be the rule.
This is a consequence of the comparatively large size of the lanthanide ions. Definitive data for coordination numbers and molecular geometry of yttrium compounds, available from X-ray diffraction methods, is il.3 -.Z4i4, still quite meager. The molecular geometry of known yttrium compounds however is quite varied, and the present discussion seeks to coordinate some of the recent findings. 23
A. Coordination Number Six
Six coordination in an octahedral geometry has been estab- / \ ^ lished for hexakisantipyrineyttrium tri-iodide (1). In this struc- +3 ture the Y ion occupies a symmetry centre at the origin of the unit +3 cell. Six antipyrine molecules are octahedrally disposed about the Y ion which is in keeping with the stereochemical arrangement predicted by valence-bond and ligand field theories. Coordination via the car- o bonyl groups results in Y — 0 bond, lengths of 2 . 19A.
O C © N • 0 Q*
(i)
B. C o o rd in a tio n Number Seven
A large number of polymeric lanthanide compounds contain metals in seven coordinate environments, with yttrium being no exception.
Two of the three ideal polyhedra have been shown to exist: the capped trigonal prism (C* 2 V)» and the capped octahedron (C^). To date, no 24-
yttrium compounds have exhibited the third possible polyhedron, the pentagonal bipyramid. This may be due to the less efficient packing of the pentagonal bipyramid geometry in comparison to the capped octa hedron, which can provide much denser three-dimensional packing in p o ly m ers. 31 Muetterties and Wright point out that the energy dif ferences between the idealized shapes are probably small compared with the intermolecular forces generated by ordering. Therefore, great care is necessary in the consideration of the specific seven-coordinate geometry considering the rather small differences of spatial arrange ment. Figure 5 illustrates the idealized polyhedra observed in yttrium compounds.
1 . Capped Trigonal Prism
Three-dimensional X-ray diffraction studies have shown the tris(acetylacetonato)aquoyttrium (lIl) molecule, (Y^H^COCHCOCH-P^HgO), 48 to exist as a monocapped trigonal prism. The yttrium ion is bonded to seven oxygen atoms, six from the chelating ligand and one from the ad- duct molecule. The water molecule occupies a position above a rectangu lar face. Individual trigonal prismatic groups are hydrogen-bonded to each other through the adduct molecules, and the chelating ligands span the triangular faces. 4-9 The structure of is also characteristic of a capped trigonal prism. There are ten independent yttrium atoms. This is an example of a mixed six-fold and seven-fold coordinate structure.
Four of the yttrium atoms are seven-coordinate, as capped trigonal prisms, and six are as six-coordinate octahedra. Another mixed system exists 50 with YgTiOj.. The yttrium atoms are surrounded by oxygen atoms which F igure 5
Coordination Polyhedra of Yttrium Compounds
O ctahedron
Capped Octahedron
Capped Trigonal Prism 26
Figure 5—Continued.
Square Antiprism
Dodecahedron (symmetry related, edges are labelled)
Tricapped Trigonal Drism 27
form irregular trigonal prisms capped through one triangular face, and the groups of polyhedra are held together by titanium ions which are five-coordinate, with four oxygen ligands from one group and one from the next group at the corners of a square pyramid.
2. Gapped Octahedron
Monocapped octahedral geometry is characteristic of qo the tris(benzoylacetonato)aquoyttrium(lIl) molecule (2). The octa-
O c • 0
( 2 ) hedron is substantially distorted. The /3 -diketonate ligands wrap asymmetrically about the coordination polyhedron, with two phenyl groups 'up' and one 'down1. The water molecule is coordinated above a triangular octahedral face. 28
G. Coordination Number Eight
Both the square anti prism (D^) and the triangularly faced dodecahedron (Bg^) are characteristic polyhedra for this common coordi- 51 nation number. Refer to Figure 5* Goulombic energy differences be tween the polyhedra are very small and a preference for one or the other is probably dictated by chelate ligand requirements or molecular packing f o r c e s .
1. Square Antiprism
The first reported X-ray crystallographic study of a tris-rare earth(lll) chelate exhibited this eight-fold geometry. The ffp yttrium ion in yttrium acetylacetonate trihydrate, Y(C ■ 3^ °• is bonded to eight oxygen atoms contributed by three bidentate acetyl acetonate groups and two water molecules. The third water molecule associated with each complex is not coordinated to the yttrium ion, but takes part in a chain of hydrogen bonds to link the molecules in pairs.
The authors attribute the distortion of the polyhedron to two chemically different ligands bonded to the same central metal atom. 53 Diyttrium silicon beryllate, Y^SiBegO^ also shows eight-fold geometry. The yttrium atoms lie within distorted square oxygen antiprisms and the silicon atoms lie in isolated SiO^ tetrahedra.
The beryllium atoms occupy distorted tetrahedra linked at one corner to form double BegO,-, pyramids oriented upward or downward relative to the c - a x is .
2. Dodecahedron
The first tetrachelate metal atom to show eight-fold coordination was the cesium tetrakis(hexafluoroacetylacetonato)yttrate
(ill) compound (3)» Eight essentially equidistant oxygen atoms (2.31- 29
- 2 .3 5 a) surround the central yttrium atom in a slightly distorted dodecahedral configuration. In contrast with other dodecahedral ML^
(L = hidentate ligand) structures, each ligand in this structure spans four 'g' edges rather than the 'm' edges of the polyhedron resulting in overall symmetry. Refer to Figure 5 f ^ symmetry related edges.
Cs w © Y • 0 O C F
(3 )
D. Coordination Number Nine
N ine c o o rd in a te s tr u c tu r e s a re common among m o lecu lar com plexes of the lanthanides. The most frequent polyhedron is the symme trically tricapped trigonal prism (D^) which is sustained by a hybridi zation of one s, three p, and five d orbitals. The double oxalate of yttrium and ammonium, * HgO is nine-fold coordinate, in volving eight oxygen atoms from the oxalate ions and one oxygen from the o water molecule. The Y—0 bonds range from 2.3^~2.4lA with the yttrium and water situated on a two-fold axis of symmetry. 30
E. Higher Coordination Numbers
Higher coordination spheres have been established for a few lanthanide compounds. Coordination numbers of ten, eleven, twelve, four teen, and sixteen have been reported. ^ The size of the metal ion and the compactness of the ligands is important if higher coordination poly hedron are to be generated. To date, there are no published reports of higher coordination compounds involving yttrium.
In summary, the coordination of yttrium compounds is quite varied.
The few X-ray crystallographic studies reported exhibit coordination numbers six, seven, eight, and nine. In part one of this thesis, the investigation of metal complexes of ortho-aminobenzoic acid resulted in the growth of single crystals of trisfortho-aminobenzoato)aquoyttrium(III) suitable for three-dimensional X-ray studies. Considering the variable coordination around the yttrium atom which could exist, a structure determination seemed worthwhile. Furthermore, since this compound was the only member of the synthesized series which was hydrated, a fact 26 contrary to the composition reported by Surgutskii, a study of the molecular structure would determine unequivocally the existence of w a te r. I I . EXPERIMENTAL
A. Preparation of Single Crystals of Tris(ortho-aminobenzoato)
aquoyttriumfIII)
Single crystals of Y^NCgH^COO)^ * H^O were prepared by reaction of solutions of yttrium nitrate (0.001 M) and the sodium salt of anthranilic acid (0.002 M) in a diffusion apparatus as reported in part one of this thesis. The tan needle-shaped crystals were washed with a dilute solution of the sodium salt of anthranilic acid and air dried. Figure 6 represents a microscopic view of the synthesized sin gle crystals.
B. Determination of the Space Group. Unit Cell Dimensions, and
Density of Tris(ortho-aminobenzoato)aquoyttrium(III)
Preliminary precession and Weissenberg photographs showed the crystal to be monoclinic. Centering was indicated by the observa tion of a 'diamond pattern' produced by festoons composed of reflections alternating with extinctions, and the observation that photographs of successive levels (h 0 1 , hll), rotated about the b-axis, when superim posed showed no two reflections coinciding. Weissenberg photographs of the zero and first level of the crystal rotated about the b-axis are illustrated in Figures 7 and 8 . The spacings observed along the a* and c* axes in the zero level photograph are actually half of that indicated by the reflections due to the systematic absences of the space group.
Observed reflections of hkl with h + k = 2n, hOl with h = 2n and 1 = 2n, and OkO with k = 2n indicated the space group, C2/c, number 15 in the
31 jLi^ijLaa
F ig u re 6
Microscopic View of the Y^M^H^COCOy HgO single crystals Figure 7
f'f5'"
Zero Level Weissenberg Photograph of Y(HoNG.H,,G00)o ■ Ho0 D 4 j 2 3^
F ig u re 8
1/M
F irst Level Weissenberg Photograph of Y^^NCgH^COO)^ ■ H^O 35
57 International Tables. According to a survey of space groups found
in organic crystal systems, the assigned centrosymmetric space group 58 is quite common. ^
The unit cell dimensions were determined using zero level
Weissenberg photographs (Figure 7) and rotation photographs taken about * the [010] . In addition, zero level precession and cone axis photo
graphs were taken of the a*b* and b*c* reciprocal nets. In both cases,
exposures were taken with nickel-filtered Cu-ko< radiation (A = 1. j&l 78A).
The cell constants were appropriately calculated from film measurements,
and the computer program REDCEL calculated the reduced cell from the
direct cell parameters. ^ The direct cell was the reduced cell.
All measurements were made at 21° G. These dimensions along with other
pertinent crystal data are given in Table II.
The observed density of Y^gNC^H^COO)^ • H^O corresponds to
eight formula units per unit cell. Density measurements were obtained
by two techniques. The first involved the flotation of a single crystal
in a solution of carbon tetrachloride/diodomethane. The second technique
measured the density by pycnometry using an aqueous soap solution of
known density to ensure the wetting of the single crystals.
G. Intensity Measurements
Intensity data for Y^^NCgH^COO)^ • H^O were collected with
nickel-filtered Cu-k c* radiation (A = 1.5^178$) using m ultiple-film , equi-
inclination, integrated Weissenberg photographs for layers 0-5 of a crystal mounted on the b-axis, and multiple-film integrated precession photographs for layers 0-2 of the a*b* reciprocal net. The crystal used for data collection was a fragment of dimensions 0 .0 5 x 0 .^ 5 x 0 .0 9 mm T able I I
Crystal Data for Tris(ortho-aminobenzoato)aquoyttrium(lIl)
fo rm u la w eig h t = 515*315 amu V = 3940.1 t 3 a = 30.89(1) A Z = 8 b = 9*09(1) A D en sity 0 flot. l.?4 g c = 14-.85(1) A pycn. 1 .6 8 g 0 c a lc . 1 .7 3 7 { * = 9 0 . 0 ( 1 ) -1 0 /« = 46.97 cm 1 J3= 109.3(1) Fooo = 2a* y= 9 0 . 0 ( 1 )° space group = GZ/c 3?
cut from a larger rodlike crystal. The relationship of the real axes
(a,b,c) and the reciprocal axes (a*,b*,c*) to the morphology of the
crystal is depicted in Figure 9* Phi represents the dial setting on
the spindle axis. The dimensions of the crystal faces were measured
with the aid of a Leitz microscope equipped with a x and y translational
micrometer stage. Five Kodak No-Screen medical X-ray films were used
for each individual layer, the average film absorption factor being 3 * 8 .
This absorption factor was determined by comparison of the intensities
of the same reflections on different films of the pack within the same
level. The intensities of the reflections were measured with a Welch
Densichron for which a 0.5 mm aperture was made. The optical densito
meter was calibrated with a standard density wedge and a calibration
curve was obtained via a polynomial regression treatment available on 6l the University of New Hampshire's DEC-10 system.
The method for evaluating the intensity of each visible reflection on the exposed films proceeded as follows. Three measure ments were taken for every reflection, two background measurements (one
on either side of the reflection) and a measurement of the total inten
sity of the diffraction spot. Each reading was corrected by the cali bration polynomial, and the net corrected intensity was calculated by
averaging the two corrected background readings and subtracting this
average from the corrected peak intensity. This procedure was repeated for any reflections with sufficient intensity to be visible on the sec
ond, third, fourth, and fifth films within the multiple-film pack of
each level. All net corrected intensities at this point were multiplied
by the appropriate film absorption factors. Intensities which were mea sured on more than one film within each level were averaged to give a F igure 9
Relationship of the Real Axes (a, h, c) and the * * * . Reciprocal Axes (a , h , c ) to the Morphology of the Crystal +a a*
~xc 0 = 50° (100)
Rotation 0.09 mm ( 001) Axis b (b)
+ c
0 = 140 ( 001) Rotation +a Axis b(b*) ( 100) 0.05mm 1
-c -c 0.45mm *i VO 40
final net intensity. These raw intensity data were corrected for Lorentz
and polarization factors.
In equi-inclination Weissenberg geometry, the Lorentz factor,
L, depends on the precise method of measurement. The expression may be
g iv en as
s in 0 L = ------s in 20 ( s i n 20 - s in ^ u ) 2 w h ere /i is the equi-inclination setting angle. For zero-level reflec
tions this expression reduces to
1 L = sin©
The polarization factor is a function of 20 and is expressed as
1 + c o s 2 20 P =
This term arises because of the nature of the x-ray beam and the way its reflection efficiency varies with the reflection angle.
Data reduction of the Weissenberg raw intensity measurements initially involved calculating the value of sin 0 for each reflection.
The relationship is expressed as
2 s in 0 p p p p p p —-— = (ha* + k b* + 1 c * + 2hka*b*cosi(* + 2hla*c*cos/3 *•: + A 1. 2 klb*c*cosot*) 2 where h,k,l are the indices of the reflection and a*, b*, c*, y* are the reciprocal lattice constants. The resultant sin© value for each reflection enabled immediate calculation of Lorentz and po larization factors. Data reduction was completed by multiplying the raw intensity data by the factor l/Lp. 41 Corrections on the integrated precession data involved 62 superimposing a transparent chart showing the relative value of l/Lp on the reciprocal lattice net. The Lorentz-correction factor for precession motion is radially symmetrical for each level and varies from level to level. The Lorentz factor for one recorded spot on a precession photograph is given by the complex expression: A ^ sin/I sin r\ 1 + tan^ ;u sin^(£ + t\) 1 + tan^ ju s in ^ (£ - t \) wke re A - angular velocity of precession t , C - cylindrical reciprocal lattice coordinates M - inclination angle of the reciprocal lattice plane from a position normal to the x-ray beam sin >u + § ^ _ si n2 y r\ - cos A = ------^------2 £ s in Jl A calibration curve of the corrected precession integrated intensities vs. Weissenberg integrated intensities was used to bring the intensity d a ta to a common s c a le . The value of the linear absorption coefficient,yU with copper radiation for Y^gNC^H^COO)^’ HgO was calculated as 46.97 cm from the expression A = djp( £ ) where d = density p = proportion of each element in the compound {M/e) = mass absorption coefficient. In view of the small magnitude calculated, no absorption correction was applied. A scale factor to place the reduced intensity data on an ab solute scale and an overall temperature factor, B, were derived from a Wilson plot. The Wilson calculation involves plotting ln(lre]/£]fj ) 2 2 v s. ( s i n 0 )/A , where f represents the scattering factors of the 42 various atoms. The temperature factor is obtained from the slope, -2B, and the intercept is In G where C is related to the scale constant, k, needed to convert | Fre-^ | to Fabs | ^ rela’ti°nship: 1 kv r where | Fahs I k Frel A total data set of 1871, observed and unobserved reflections was recorded from Weissenberg levels zero through five. This represented 1159 non-zero reflections, a non-zero reflection being defined as a dif fraction spot visible on any film. This data set encompassed the entire reciprocal lattice up to a sin 0 maximum of 0.80. Further data reduction, limiting the sin 0 cutoff to 0 .7 0 resulted in a final data set of 1393 reflections; 915 of these being non-zero reflections. I I I . SOLUTION AND REFINEMENT OF THE STRUCTURE The process of a structure determination consists of a series of well-defined steps with each step depending on the accuracy and proper interpretation of the preceeding steps. An outline of the general method CO can be found in almost any textbook on crystallography. ’ In this work the heavy atom method was used, and a summary of the method, with appropriate computer programs, is outlined in Table III. The flow diagram unfortunately does not indicate the difficulty encountered after the in tensity data collection. The structure factor, F^-^, expresses the distribution of the scattered radiation in reciprocal space in terms of the electron density distribution in real space. The electron density at any point XYZ in the unit cell may be calculated, given a knowledge of the amplitudes and the phases of the scattered waves in reciprocal space by the equation: + c o + c o + 00 PXYZ = T £ £ £ Fhklexp ' 2?7i(hX + kY + 1Z) h=-*"k=-«ol= - p = electron density V = volume of cell = structure factor The process appears quite straightforward. It seems only necessary to measure as many values of F^^^ as possible, perform the appropriate cal culations to produce an electron density map, and locate atoms in posi tions of high electron density to solve the structure. The main problem, however, involves the condition "given a know- 43 kb Table I I I Structure Determination Outline for a Compound Containing a Heavy Atom Experimental Information Crystallographic P ro ced u re Program s a Crystal Mounting Precession Photo Orientation and Axes Selection Oscillation Photo U n it C e ll * Reduced Cell I P aram eters (REDCEL) Weissenberg Photos Space Group Powder Pattern I QpOMP (UNH-23) I n te n s ity Measurements ------^ Integrated Intensities \ Lorentz and Polar i- zation C orrec tions (Hewlett-Packard) Corrected Intensities Observed and Unobserved reflec tio n s (NR2.MAN) F « F o-bs !OC obs b Data Tape (NRC-2) Temperature Factor I Scale Factor 4— - Wilson Statistics (NRC-5A) Center of Symmetry Sign Determination - -> F o u r ie r (N R C -8 ) Electron Density Map■ Approximate Atomic Block Diagonal P o s itio n s ------Least Squares Refinement (NRC-10) Structure Factors Error Analysis (NRC-1*0 Bond Distances and Angles, Coordination Bond Scan (NRC-12) Publication Table 4— -> Structure Factor ! Table (NRC-23) Stereo Drawing UNH Identification Code k5 ledge of amplitudes and phases". The amplitudes are calculated from thq intensity measurements, since they are proportional to the square root of the corresponding measured intensities. But there is no way to mea sure the phase angles experimentally. This is known as the "Phase ProB- lem ".: The electron density expression for centrosymmetric structures Gk sim plifies to one with cosine terms only: PxYz = - f + f +S +E Fh ia co s ^ + kY + l z >' h=oo k="oo l= ‘oo The phase angle associated with F^-^, which in a general case can have any value#, Becomes either 0 o r j f . Therefore the summation can cover waves that are either exactly in phase or exactly out of phase; i.e. + F^kl for waves with oi-0 and - F^kl for waves with o i = I t . F o r a centrosymmetric case, the phase prohlem thus reduces to one of sign de termination. To overcome this question of signs, a trial structure must Be postulated and the phases from this trial structure are used as input to the electron density expression. In this research a trial structure was developed By the heavy atom method. This system works on the assump tion that an atom with a large atomic scattering factor will determine the phase angles of the whole structure. One of the key techniques used in this method involves the Patterson function. Although it is not pos sible to compute directly, due to the uncertainty of the phases of the F values, there is no uncertainty about J F j ^ v a lu e s . A Patterson map, which is always centrosymmetric, can Be computed directly from the function, The peaks of the resulting map repre sent interatomic vectors. In other words, a peak at UVW implies that 46 there are two atoms in the crystal structure at , y^, z^ and x^, ygi Zg such that x^ - x^ = U; y^ - y^ = V; Zg - z^ = W. Furthermore, the + 00 +CO‘w +oO 1 Puw = Y ^£ £ £ [ Fhkl | 2 cos 27T(hU + kV + 1W). h="«o k="«® l=-oo height of the peak will he proportional to the product of the number of electrons in each of the two atoms involved. A three-dimensional unsharpened Patterson map was calculated in an attempt to locate the yttrium atoms. The resulting map revealed nu merous peaks of high vector density. Peak heights of approximately 5000 were located at x,y,z = 0,0,0; x,y,z = ■§■,■§,0; x,y,z = 0,0,y and x,y,z = TtTitT’ Although the origin (0,0,0) represents the summation of all atomic vectors, there existed the possibility that the true yttrium- yttrium vector was lying at the origin. In space group CZ/c there are five sets of special positions including (0,0,0). These positions are tabulated in Table IV. Three cycles of block diagonal least squares refinement with isotropic temperature factors assigning the yttrium atoms to special positions 4a and 4b gave a reliability index, R = 0.535» where ^ = D K I “ K || /£ K I * ®ie ^eoretical value for a centrosymme- c;0 trie model with atoms placed randomly would be O. 8 3. Although the R factor obtained was lower than the random value, a better value was sought for a trial structure. An attempt was made to locate the eight yttrium atoms in general positions (8f), x,y,z = 0.0,0.44,0.09. This position was later found to be incorrect. After four cycles of block diagonal least squares refine ment with isotropic temperature factors the R value was 0.330» suggest ing a starting point for a trial structure. A Fourier electron density 4? Table IV Co-ordinates of Equivalent Positions for Space Group C2/c, Second Setting Wyckoff Notation and Number of Symmetry Co-ordinates of Equivalent Positions Positions (0,0,0; 0) + 8 f 1 x,y,z; x,y,z; x,y,f--z; x ,y ,f-+ z. 4 e 2 o,y,-jj-; o,y,-jp *TLl a. A J. 1 3- 3. 1 . 3 3- rv 4 C 1 VtTtT* 4 b 1 ®»2’»2’* 4 a -I 0,0,0; 0,0,-|. 4-8 map was calculated to locate further atomic positions. High electron densities were observed at the origin but were ignored since tests of the origin position had already proven false. These peaks did not dis appear during the refinement, indicating an obvious error. Possible atomic positions for the remaining atoms were few, due to the small elec tron density peaks on the map. A total of twenty-two positions were located and refined in ten cycles of least squares isotropic refinement to an R = 0.289. A Fourier map of these refined positions suggested no further locations for the remaining ten non-hydrogen atoms. In addition, approximate bond distance calculations of known carbon positions revealed no phenyl rings in the postulated structure. The Patterson map was reexamined for any particular concentrations of vector points which could lead to a better choice of the yttrium atom position. A summation of the various peak heights found on the Patter son map is in Table V. These concentrations, commonly known as Harker lines and planes, arise because the vectors between corresponding atoms of molecules related by symmetry elements other than centers, have one or two constant coordinates. Tabulation of all vectors generated from the eight equivalent symmetry positions of C2/c resulted in several Har ker locations: + 2x , 0 , ■§■ + 2 z ; + 2x , + 2y , + 2 z ; and 0 , + 2y , •§■. Initially, the yttrium atom was assigned to x,y,z = 0.25,0.22,0.20, a position represented on the Patterson by vectors of peak heights 500 and 1700. Three cycles of least squares refinement with an isotropic temperature factor resulted in an R index of 0,^3^' The Fourier map drawn from this refined heavy atom location showed no origin peak, peaks of maximum densities at the positions above, and another sizable peak nearby. A different trial position was assigned using this other peak 49 T able V Patterson Map Locations of Important Vectors Peak Height ^5000 0. 0, 0. 0, 0.0 0 . 5 , 0 .5 1 0 .0 origin vector locations 0 . 0 , 0 . 0 , 0 .5 0 .5 , 0 .5 , 0 .5 Peak Height r * 2000 0 . 0 0 , 0 . 5 2 , 0 .0 9 0 . 5 0 , 0 . 00, 0 .0 9 0 . 0 0 , 0 . 5 0 , 0.40 * 0 . 5 0 , 0 . 00 , 0.40 ± 2x , 0 , •§■ ± 2 z ; ± 2x , ± 2y, ± 2 z 0 . 0 0 , 0 . 5 0 , 0 .5 6 0 .5 0 , 0 . 0 0 , 0 .5 6 0 . 0 0 , 0 . 5 0 , 0 .8 9 * 0 . 5 0 , 0 . 0 0 , 0 .8 9 Peak Height 900 0 . 0 0 , 0 . 5 0 , 0 .2 4 0 . 5 0 , 0 . 0 0 , 0 .2 4 0 . 0 0 , 0 . 5 0 , 0 .7 3 0 . 5 0 , 0 . 0 0 , 0 .7 3 location of Y- -Y v e c to rs Peak Height a^OO 0 . 0 0 , 0 . 5 0 , 0 .0 0 0 . 0 0 , 0 . 5 6 , 0 .0 0 0 . 0 0 , 0 . 5 0 , 0 . 5 0 -— 0 . 0 0 , 0 . 5 6 , 0 . 5 0 ------0 , + 2y , | 0 . 5 0 , 0 . 0 7, 0 .5 0 0 . 0 0 , 0 .4 4 , 0 . 5 0 ^ ^ ^ 0 . 5 0 , 0 . 0 7, 0 .0 0 0 . 0 0 , 0.44-, 0 .0 0 50 o f maximum d e n s ity . The y ttr iu m atom was a ssig n e d to x ,y ,z = 0 .2 5 ,0 .4 9 ', 0.20. In the Patterson map this position was supported by two vectors of peak heights around 1700. Isotropic least squares refinement result ed in an R index of 0.3 7^ after three cycles. The generated Fourier map showed a peak density 1 .5 times any peaks previously recorded for the yttrium atom. Also numerous other electron density concentrations repre sentative of the remaining non-hydrogen atoms were apparent. The posi tions of the oxygen and nitrogen atoms were located with some difficulty due to the complexity of the map. Three cycles of isotropic least squares refinement of the yttrium, 0(l), 0(2), 0(3)* 0(4), 0(5), 0(6), 0(7), N(l), N(2 ), and N(3) gave an R = 0.329. Repeated cycles of the structure-fac tor and Fourier calculations were necessary to locate the remaining car bon atoms. The new atom locations do not, unfortunately, appear as strong ly as do those of the phasing model, so their identification can some times be difficult. The fragments of the phenyl groups were located more easily by making use of known bond lengths and angles. ^ With all thir ty-two non-hydrogen positions located, the block diagonal least squares isotropic refinement gave an R = 0.259 after six refinement cycles. The postulated structure was quite likely, but an alternative yt trium position at x,y,z = 0.25*0.01,0.20 was also a possibility. This other position arises from an analogous ± 2x, + 2y, + 2z vector. In the space group C2/m (the symmetry of the Patterson map), x,y,z vs. x,y,z are related by symmetry. This means that the initially assigned yttrium position at x,y,z = 0.25*0.49,0.20 is equivalent to x,y,z = 0 . 2 5 , 0 . 0 1 , 0 .2 0 . In OZ/c the corresponding atomic positions are not related by symmetry such that the second position represents another possible site for the yttrium atoms. The symmetry constraints in CZ/c are x,y,z vs. x»y*■§■ + z. After four cycles of least squares isotropic refinement, the 51 R factor was O. 3 8 8. The resulting Fourier map showed numerous concen trations of electron density, not as sharp as the previous trial-struc- ture. Repeated cycles of structure factor calculations and Fourier maps were carried out until all 32 non-hydrogen atoms were located. The R index could he reduced no further than O. 32 O. This trial structure was abandoned in favor of the postulated structure with x,y,z = 0 . 2 5 , 0 .^ 9 i 0 . 2 0 , for the atomic position of the yttrium atom. A Fourier difference map was generated of the structure which had refined to R = 0.259- Several carbon atoms were noted to be slightly misplaced as their assumed position was on a steep gradient not far from a zero contour with a large negative region on one side and a large pos itive region on the other. To correct these atomic positions, the atoms were moved up the steepest gradient by an amount proportional to the gradient at the center. ^ Further refinement, using full matrix least squares calculations ^ with isotropic temperature factors for the non-hydrogen atoms and yt trium scattering factors corrected for anomalous dispersion lowered R to 0.256. Anomalous dispersion is caused by atoms which have an absorp tion edge close to the frequency of the incident radiation, thus intro ducing an additional phase change. In the case of the yttrium the effect is almost negligible, but for some atoms the simple scattering factor, fQ, must be modified to take account of the interaction of the incident x-rays with the bound electrons. The simple scattering factor becomes: f anom* = f + Af* + iA f" o o where A f' and iA f" represent the terms that introduce the phase dif ference. Scattering factors used during this analysis were those of Hanson et al. Anomalous dispersion corrections for yttrium, both 52 r e a l (a f 1 = - 0 . 70e ) and Imaginary (A f" = 2 . 3 e“) parts applied to the 68 structure amplitudes were those given in the International Tables. The refinement of the trial structure continued with all thirty- two non-hydrogen atoms being refined anisotropically by the block diag onal least squares method. After six cycles of refinement, the R factor had been lowered to 0.112. All temperature factors were positive, with no abnormal values. At this stage in the structure solution, a Fourier difference map was generated to locate the hydrogen atoms. Fifteen of the twenty hydrogen atoms were readily located. The average amplitude of the peaks located was 1.0e/A^. The remaining hydrogen atoms distrib uted on the water molecule and the amine groups were assigned positions on the basis of a constructed model of the unit cell. Refinement of all fifty-tw o atoms by the block diagonal method, assigning anisotropic temperature factors to the non-hydrogen atoms and isotropic temperature factors of 5*0 to the hydrogen atoms resulted in R = 0.079* The R factor did not improve when the isotropic temperature factors of the hydrogen atoms were allowed to refine. A final Fourier difference map showed some small peaks, the largest of which was l.jje/k?. These peaks are somewhat higher than would be expected for the best pos sible model, and may be a result of the available crystal data, since the peaks are dispersed at random. If the model was a perfect match to the real crystalline lattice, the difference map would be featureless. An error analysis of the final structure factors showed no systematic errors as a function of sin^0 or | Fq | . Systematic errors manifest them selves as systematic shifts in results and may be inherent in the method of observation. The error analysis also indicated that reflections with R-values more than twice the final R-value were the weakest reflections. 53 Calculation of the bond distances and angles in the postulated o structure revealed several C—C bonds of magnitude 1.6-1.8 A. These o values were much greater than the reported C —C bond of 1.4 A in a benzene ring. Because of this discrepancy in bond distances in the postulated model, attempts were made to find other structural solutions. The availability of a recently developed crystallographic program, en- 69 t i t l e d 'SHELX' , i n i t i a t e d th e s e in v e s tig a tio n s . There existed the possibility of the true structure being of lower symmetry, namely belonging to the noncentrosymmetric space group, Cc. Although the Wilson test had indicated that the data suggested a centro symmetric model, a borderline case was possible. The space group Cc has four general symmetry positions (^a) represented by: x,y,z; x,y,-§+z; i+x, -|+y,z; |"tx,|-y,f+z. In order to locate the eight yttrium atoms, two sets of ^-a assignments were made: x,y,z = 0 . 2 5 , 0 .^ 8 , 0 .2 0 and x,y,z = 0.75»0.52,0.80. After six cycles of full matrix isotropic refinement R was 0.525. The generated correlation matrix indicated the amount of correlation among the various positional and thermal parameters of the atoms. High correlation coefficients ranging from 0 .9 to 1.0 between all parameters of the supposedly unrelated yttriums indicated the im proper selection of space group Cc. The two sets of yttrium atoms were actually related by a center of symmetry and the structure was of a high er symmetry, namely the postulated C2/c space group. An attempt was made to solve the structure on the basis of the "Direct Method". This approach involves generating an adequate set of phases by consideration of the structure amplitudes. One starts with a very lim ited number of phases and builds on this pyramid to a set of phases large enough to give a recognizable Fourier representation of the 54 - structure. The key to the succes of this method is the correct choice of starting phases, hut modern methods of computing enable the investi gation of several starting phase sets to see which is best. The failure of this approach to the solution of the yttrium an- thranilate structure was due to the lack of necessary parities for a set of starting phases. The space group C2/c has a limited number of re flection parities: eee, eeo, ooe, ooo. The phases of eee reflections are always positive so that they are fixed by the structure (structure invariants) and cannot be given values at w ill. All the remaining pari ties are positive for four origins and negative for four. The phases must be assigned properly in order to fix the origin, but the rules for bid the combination of two or three reflections whose indices add to eee. Therefore, according to parity arithm etic, eeo+ooe+ooo = eee which is not allowed. The only means for solving this structure might be the transformation of the centered cell to a primitive cell which would pro vide the necessary parities to build a set of starting phases. The other alternative would be to subtract the heavy atom contribution from the observed structure factors, obtaining the magnitude and sign of the light atom contributions for these reflections, and solving the remaining or- 70 game part of the structure. Both of these methods are complex and require computer programs which are not available to us at this time. Since the alternative methods of solution had prompted no new pos tulated structure, work was resumed with the final model. Further com putations were carried out with 'SHELX' crystallographic programs. Six cycles of full matrix least squares refinement with isotropic tempera ture factors of the thirty-two non-hydrogen atoms resulted in R = 0 . 2 7 7. This value was in agreement with the previously reported R factor from 55 the full matrix calculation of the ORXFIS program. The slight difference in the values was due to the method of calculation of the structure fac tors. Similarly, a full matrix anisotropic calculation of all non-hydro gen atoms gave R = 0.099* This calculation was not possible with the ORXFIS program because of the large arrays needed for computation which could not be handled by the University's DEC-10 computing system. At this stage the option of fixing the carbon atoms into a regular hexagon o was attempted. The C—C bond distances were assigned to 1.395 A, and the benzene ring was refined as a rigid group. After four cycles of full matrix refinement, assigning anisotropic temperature factors to non hydrogen atoms, the R factor had increased to 0.122. These parameters were input into the National Research Council's block diagonal least squares program and the rings were allowed to refine independently. After four cycles of least squares refinement, the R factor was 0.099 but the carbon atoms of the rings were found to be drifting toward the original positions in the postulated model. The benzene rings s till could not be clearly defined. Further refinement would only result in a model like the one already postulated. Thus far the refinement had included only the observed reflections. It was thought that the addition of the unobserved reflections might add additional phasing to the model and improve the quality of the bond dis tances. Four cycles of block diagonal least squares refinement includ ing all 1393 reflections, both observed and unobserved, gave an R index o f O.O9 8. No noticable improvement in the bond distances of the benzene rings resulted. All attempts to improve the bonding distances within the benzene rings were fruitless. The error apparently lies in the quality of the 56 data set. For better bond parameters a larger data set should be col lected with an automatic diffractometer. Nevertheless, the photographic data set has given the basic skeletal structure of the compound. Block diagonal least squares refinement was continued with anisotropic temper ature factors until a final R-value of 0.081 was reached for the thirty- two non-hydrogen atoms. A final difference map showed several small °3 peaks of intensity 0.85-1.2 e/A . These undoubtedly are locations of hydrogen atoms. The quality and size of the data set, however, does not permit the accurate assignment of these hydrogen positions. The values of the refined parameters are given in Table VI along with their estimated standard deviations (in parentheses). A summary of the successful stages of the refinement is given in Table VII and a tabulation of the observed structure factors and the final calculated structure factors is given in Table VIII. Table VI cL b Final Positional and Thermal Parameters ’ f o r Y( H^NCgH^C0 0 )^ ’ HgO I Positional Parameters Atom X y z Y 0 . 2 5 1 6 ( 1 ) 0 .4 8 8 4 (3 ) 0 .20 5 7 (2 ) 0 (7 ) 0 . 2 5 5 2 ( 6 ) 0 . 5 2 1 6 ( 2 9 ) 0 .0 547(12) Ligand 1 0 (1 ) 0 . 197( 1 ) 0 .6 7 3 (4 ) 0 . 3 85 ( 1 ) 0(2) 0 . 1 5 4 ( 1 ) 0 .6 1 1 (4 ) 0 .4 3 5 (1 ) 0 (3 ) 0 . 1 5 3 ( 1 ) 0 .4 6 9 (4 ) 0 .4 7 7 (1 ) c (4 ) 0 . 111( 1 ) 0 .4 0 1 (4 ) 0 . 5 16 ( 2 ) 0 (5 ) 0 . 071( 1 ) 0 .4 7 8 (4 ) 0 . 5 26 ( 2 ) c(6 ) 0 . 074 ( 1 ) 0 .6 2 1 (5 ) 0 .4 8 6 (2 ) 0 (7 ) 0.114(1) 0.692(4) 0.445(2) 0 (1 ) 0 . 2 2 7 6( 4 ) 0.6075(20) 0.3422(8) 0 (2 ) 0 . 1983( 6 ) 0 . 8160( 2 5 ) 0.3836(11) n ( i ) 0 . 1917( 8) 0 . 3 8 0 9( 2 7) 0 .4 663(15) Ligand 2 0 (8 ) 0 . 3 3 1 ( 1 ) 0 .7 4 5 ^ ) 0 .2 0 4 (2 ) 0 (9 ) 0 . 3 7 8( 1 ) 0 .7 2 4 (4 ) 0 .1 8 7 (2 ) 0 (1 0 ) 0 .4 0 0 ( 1 ) 0.820(4) 0.234(2) 0 (1 1 ) 0.44-8(1) 0 .8 0 2 (6 ) 0 .2 1 8 (3 ) 0 (1 2 ) 0 .4 7 0 (1 ) 0.736(5) 0.147(3) 0 (1 3 ) 0 .4 5 1 (2 ) 0 .6 1 7 (5 ) 0 .1 0 0 (3 ) 0(14) 0.401(1) 0 .6 1 7 (5 ) 0 .1 1 5 (2 ) Positional Parameters - Continued Atom x y z 0 (3 ) 0 .3 1 1 3 (6 ) 0 .6 3 7 4 (1 8 ) 0 . 1739( 1 1 ) 0 (4 ) 0 . 3022( 5 ) 0 .8 2 9 0 (2 0 ) 0 .2 5 2 9 (1 1 ) N(2) 0 .3 7 9 (1 )' 0 .8 8 8 (4 ) 0 .3 1 5 (2 ) Ligand 3 c ( l 5 ) 0 .3 1 1 (1 ) 0 .2 7 0 (2 ) 0 . 3 0 5 ( 2 ) 0 ( 1 6) 0 .3 5 5 (1 ) 0 .3 3 5 (3 ) 0 .3 1 1 (1 ) 0 (1 7 ) 0 .3 5 6 (1 ) 0 .4 6 2 (3 ) 0 .3 5 7 (1 ) C ( l8 ) 0 .4 0 0 (1 ) 0 .5 1 3 (4 ) 0 . 363( 2 ) c ( l 9 ) 0 .4 3 8 ( 1 ) 0 .4 2 3 (3 ) 0 .3 2 3 (2 ) C(20) 0 .4 3 6 ( 1 ) 0 . 3 0 2 ( 4 ) 0 .2 7 7 (2 ) 0 (2 1 ) 0 . 3 9 4 ( 1 ) 0 .2 5 7 (4 ) 0 .2 7 4 (2 ) 0 (5 ) 0 .2 8 2 1 (6 ) 0 . 3623( 1 6) 0.3044(12) 0 (6 ) 0 .3 0 6 9 (5 ) 0 . 1391( 1 7) 0 . 3030( 1 1 ) n(3 ) 0 . 3201( 8 ) 0 .5 6 1 9 (3 0 ) 0 .3 992(15) Table VI—Continued / ? ° 2\ Anisotropic Thermal Parameters (xl(K A ) Atom U33 U11 U22 L?12 U13 u23 Y 1 5 -5 (1 .3 ) 4 0 .6 ( 2 .1 ) 8 .4 ( 1 .0 ) 1 .7 ( 2 .0 ) -5 0 .1 (9 .0 ) 0 . 9 ( 1 . 6 ) 0 (7 ) 5 4 .7 (1 2 .5 ) 146.2(23.2) 9 - 1 (9 - 8 ) 1 1 .4 (1 6 .2 ) - 9 9 .6 (9 .8 ) 2 2 . 0 ( 1 3 . 9 ) L igand 1 c ( i ) 2 3 .3 (1 6 .0 ) 106.4(29.3) -2 9 .8 (9 .9 ) 3 3 .3 (1 6 .8 ) -20.2(10.4) -20.4(12.9) 0 ( 2 ) 8 1 .0 (2 4 .1 ) 108.7(29.3) - 2 5 .8 (9 .9 ) 3 3 -8 (2 0 .2 ) -106.1(15.5) 5 .3 (1 5 .8 ) 0 (3 ) 6 7 .2 (2 0 .3 ) 100.2(32.3) - 2 0 .7 (9 .9 ) -13-5(20.2) -68.6(10.4) 1 3 . 8( 1 6. 2 ) c (4 ) 3 0 .6 (1 7 .2 ) 9 1 .9 (2 9 .3 ) 8 .9 (1 5 .9 ) 2 4 .4 (1 7 .5 ) -100.5(15.5) - 1 2 . 7( 1 6. 8) 0(5) 85.4(23.7) 7 0 .5 (3 1 .8 ) 4 7 .4 (2 0 .9 ) -20.6(24.2) -119.3(20.7) 3 0 .3 (2 1 .3 ) c ( 6 ) 3 4 .5 (2 0 .3 ) 176.3(41.9) 23.1(19.9) 24.7(24.2) - 8 0. 8( 1 7. 6 ) 1 . 6( 2 2 . 6 ) 0 (7 ) 5 3 -0 (2 1 .5 ) 8 3 .6 (2 9 .3 ) 1 1 .7 (1 5 .9 ) -1 .7 (2 0 .2 ) -97.6(16.6) - 3 9 . 8( 1 7. 8 ) 0 ( 1 ) - 5 . 2 ( 8 . 6 ) 74.4(15.1) - 3 2 .1 (5 .9 ) - 1 5 .3 (8 .7 ) - 4 . 8( 6 . 0 ) - 4 7 . 8( 7 . 8 ) 0 (2 ) 2 5 . 0 ( 1 1 . 2 ) 118.4(20.9) 1 4 .6 (9 .9 ) 4 .7 ( 1 2 .1 ) - 4 .1 ( 9 .3 ) - 9 0 . 8( 1 1 . 9 ) K (l) 6 0 .3 (1 7 .2 ) 3 3 .9 (1 8 .7 ) 2 9 .3 (1 3 .9 ) - 0 .9 (1 3 .4 ) -106.4(10.4) - 2 4 . 9 ( 1 2 . 9 ) Anisotropic Thermal Parameters—Continued Atom J33 U11 U22 U12 U13 D23 Ligand 2 C(8) 23.2(17.2) 6 9 .9 (2 9 .3 ) 2 9 .4 (1 9 .9 ) - 3 .8 (1 3 .4 ) -27.1(14.9) 2 0 . 8( 1 9 .4 ) C(9) -12.9(12.9) 108.8(33-5) 3 5 .4 (1 9 .9 ) - 3 .8 (1 3 .4 ) -55-1(10.4) - 1 . 2 ( 1 9 .4 ) G(10) 3 4 .9 (1 9 -8 ) 63.9(29.3) 50.1(19.9) 1 0 .1 (2 0 .2 ) - 8 9. 1 ( 1 0 . 4 ) - 3 2 . 0 ( 1 9 . 4 ) c (n ) 6 8 .9 (2 5 .9 ) 189.8(50.3) 7 9 .9 (2 9 .9 ) 18.7(30.2) -99.7(13.4) - 7 4 . 1 ( 3 2 . 3 ) C(12) 8 1 .0 (2 5 .9 ) 163.2(46.1) 9 0 .5 (2 9 .9 ) - 1 . 1 ( 3 0 . 2 ) -104.2(18.2) - 6 0. 8( 3 2 . 3 ) C(13) 124.1(37.5) 111.4(41.9) 9 7 .4 (3 4 .2 ) -12.7(33.6) -39.9(18.8) - 6 5 . 8( 3 2 . 0 ) C (l4 ) - 6 . 0 ( 1 7. 2 ) 151.2(39.5) 70.6(19.9) -27.1(18.8) -43.4(15.5) - 7 5 . 3 ( 2 5 . 8 ) 0 (3 ) 5 7 -3 (1 2 .9 ) 1 . 6( 1 6. 8 ) 2 2 .8 (9 .9 ) -10.5(10.1) -8 8 .1 (9 .3 ) -1 8 .2 (9 .7 ) o(4) 1 9 .8 (1 0 .8 ) 5 7 .1 (1 6 .8 ) 1 9 .2 (9 .9 ) -6 .9 (1 0 .1 ) -9 0 .3 (9 .3 ) 1 1 .1 (1 0 .6 ) N(2) 48.7(17.2) 1 8 5 . 8( 3 7.?) 8 4 .6 (1 0 .9 ) - 1 .8 (2 0 .2 ) -121.8(12.9) -21.7(22.6) Ligand 3 0 (1 5 ) 5 6 .5 (1 7 .2 ) -71.4(16.8) 1 2 .9 (9 .9 ) - 4 .9 (1 3 .4 ) -81.5(10.4) - 1 4 .7 (9 .7 ) G(l6) 1 5 .5 (1 2 .9 ) 1 1 -9 (2 0 .9 ) - 2 .7 ( 9 .9 ) 3 3 .4 (1 3 -4 ) -93.6(10.4) 1 .7 (1 2 .9 ) 0 (1 ? ) 2 9 .3 (1 7 .2 ) 4 3 .4 (2 5 .2 ) - 3 .1 ( 9 .9 ) 3 9 .3 (1 3 .4 ) -84.7(12.7) - 6 .7 (1 3 .9 ) C (l8 ) 7 2. 4 ( 2 0 . 7 ) 5 2 .9 (2 3 .0 ) 3 1 -5 (1 8 .3 ) 2 8 .0 (2 2 .3 ) -122.0(17.4) -47.2(20.2) 0 (1 9 ) 56.5(23.?) 35.9(23.9) 1 2 1 . 0( 3 2 . 0 ) 4 .9 (1 8 .0 ) - 1 6 1. 5 ( 2 5 . 2 ) - 4 .9 (2 1 .4 ) C(20) 3 7 .9 (1 9 .4 ) 3 5 -8 (2 7 .8 ) 57.9(22.3) ■27.5(17.7) -96.9(18.?) -13-3(18.6) 0 (2 1 ) 2 5 .0 (1 7 .2 ) 8 8 .5 (3 1 .3 ) 0 0 . 0 ( 1 3 . 9 ) - 2 .6 (1 7 .5 ) -48.3(13.7) - 3 . 8( 1 6. 2 ) Anisotropic Thermal Parameters—Continued Atom U33 Uu U22 U12 ”13 u23 0(5) 8?.5(15-1) -71-4(11.7) 62. 4(12.9) -9 .3(8.7) -118.2(11.4) -2 .3(8.3 ) 0(6) 38.8(11.2 ) -17.3(13-*0 39.8(10.9) 1.9(8.7) -105.0(9.3) -12.8(9 .0) N(3) 7^.6(17.2 ) 116.1(28.3 ) 13.9(9.9) -28.9 (13.4 ) -116.7(10.4) 63.9(12.9) 3. The anisotropic thermal parameter is defined as: f = f exp£-2tr 2 (U .,h 2a *2 + U00k2b *2 + U„_l2 c *2 + 2U. -hka*b* + 2U._hla*c* + 2U 0 „k lb * c* )3 o 11 22 33 12 13 23 Estimated standard deviations are given in parentheses, x, y, and s are fractional coordinates Table VII Summary of Refinement Stages M e th o d o f A to m s A tom M e th o d o f Temperature C y c l e s o f L o c a t i o n R e f in e m e n t F a c t o r s Refinement R-value P a t t e r s o n Block Diagonal I s o t r o p i c 0.37^ Y,0(l),0(2),0(3), % o( 4 ) , o( 5 ) , o( 6 ) , o( 7 ) , N(1),H(2),N('3) F o u r i e r Block Diagonal I s o t r o p i c 3 0.329 A ll non-H-atoms F o u r i e r Block Diagonal I s o t r o p i c 6 0.259 A ll non-H-atoms F o u r i e r Full Matrix I s o t r o p i c 3 0.256 ORXFIS A ll non-H-atoms F o u r i e r F ull Matrix I s o t r o p i c 6 0.277 SHELX A ll non-H-atoms F o u r i e r Full Matrix A nisotropic k 0.099 D i f f e r e n c e SHELX Y(anom. disp.)» F o u r i e r Block Diagonal Anisotropic 6 0.081 A ll non-H-atoms D i f f e r e n c e Table V III Calculated and Observed Structure Factors f o r Y(H2NC6H^GOO)3 • HgO 7*91 6C*1 • IC8S- 89*5 0 tC 8 l l » * 6 9 9 1 - Z19V 9 i / o z r s • c c r s * c s 2 * 5 - 995 C Z2/Z 9997 9 775- *95 ft 1 * 9 - / 1 / Z CI61 9*91 * 9 2 9 - BOB Z a y * 9 1 - aH 60Z 1P9 * ay *01 aH C991- CC*1 Z o r / - 056 Z . t/01- 6001 B 9PAT- 1402 9 ay * 2 - aH 1 a* •!*- «M 79*— 669 9 6/91- t6*l Z Z*C Z /2 1 11* - c o s c 9ZS 5 * 6 t C * 0 2 - Z*1C 9 CPA— *02 I 66*1 C5*l 5 t* 6 f 6* 9 **rt otci o 0091 95*1 9 6 9 9 - 119 Z 0 9 * 296 21 6992 SSS2 0 0097 IAAZ 5 1817 6/C2 9 *8*1 PC41 * 1P9T 7 /C t 71 « t« 111 C 1«C» z / c z ay *61 *H 7 r* on* z 9 / / 0 9 / 1 2 6 6 - 0*6 01 6911 zrci * 5*B— 176 5 - 6 5 - 645 C 6 1 / 1 - ?AOt 01 IZZ Z9Z 0 z ay '9 1 - *H TOO- 19/ S z o z r O/OC 0 *26 Z** 6 a y * 0 - #H */ 0- *66 r PA S t- 0061 * 66 I — 1451 7 0167 T/62 8 I a y w 99*- 669 01 i r o m * c Z*B 999 9 2061- 9*21 Z 209- ZC/ C A*/ SOP 1 6 * 6 - 466 9 6 a y * 12- aH CAS C6Z 9 l*r- ABC z rspi /roz z ay « Z t- BH C96 /1 9 6 6 6 5 - SC9 S B 26- IBS 1 1*81 B1B | 2 1 1 9 - 609 0 •I 6 0 /1 * i t t • / / • 906 066 2 690 569 5 l / P t CB2T | 9 9 6 - 2*6 • 9C9- 6*5 / *1* 725 1 A l* r B6*C Z -3 * * o c z e e z ZZC 606 9 *0C - Z9C 1 2B9 6201 • • *021- *621 0 92*1- 12*1 9 1101 /1 6 C C l* - CZ* 9 ay • / aH I £95— SACS 0 / p s - i t t e IOC- 9C» Z 6221— *121 0 2AC1— 1*51 Z 9P01- 5001 5 S 5 * t 6ZCI 2 60S 209 5 ay *5 aH VO 299— *601 9 •*ri ii*t o a y •*1 aH •CO CP/ * 9P01- 9901 1 •7S T26 • ft/8- 670 01 60P *1/ Ot ay *2 aH e ay •**- *H *66 C*0t 9 ay * 9 1 - aH SC*2- 1/92 Z 0C9C- *C5C 0 2 /2 - *67 C Z /9 869 6 509 066 IT C P21- 4471 9 *901- 6001 Z ay «9! aH /C6 9001 Zl 6621- 20*1. 1 02*1- 2961 Z / o n t e n b 5 6 6 - 005 6 9 n r - o i r / 51 5 e r s 6 4«f* ft*9 0 6 IZ 629 0 z o e — i / * • r * z - *09 o i ZB2C 7B5C 0 ay * 0 1 - aH /P S 026 1 6 9 6 - 629 * 766 96P B 616 1 210 1 4 / * 9 ‘ 4»S 8 c * * * e r c CBZ- 906 21 BOO IBS B 699Z 6*/Z 0 202 661 C 1C02- 22/1 9 OfAt- /*/| * 6 8 / - 2 7 / / O a y »9 Z aH C ay *17- aH C6Z1 6 /Z t Z 195 S t9 01 o r n t 0*61 2 ay *21 aH /OS 26* 6 CP* I *6C1 7 B 92- 2*2 5 296 154 C r / n i - 1111 9 545 — 906 I 169— ZAZ 9 •90C- 501C 0 9901 9601 9 ay «S aH CIS- tZ* 1 126 o 16 * / O d 0 /2 1 7 8801 1701 5 ♦ 85- 6/9 9 6271- 9621 0 106 065 9 1C6- 21P1 Zl /SCI- 2*21 z / 5 0 2 - CPOZ 0 B IST - 9661 2 * 9 4 - 696 0 266 0 /8 * AC/ 6*01 • /911- //Ot 2 a y * * | - *H 9 * / / 9 / 01 rezi 09*1 5 6671- 9CCI 71 125 IPS 1 4711- 749 C 9 * 9 - CQ9 7 a y MZ *H ay *91 aH CCZC 9662 0 BOZ- PRO 9 C92I- /6*1 • 600 1 0C6 0 1 ay * 9 - 8H ay •r- aH ZA6- 5*9 2 O Prt 6601 P C * !t 2CPI * 919- C5Z. C 5 6 6 - /0 9 6 ay * 5 - *M C M *57- aH tf C 66C 9 *26 196 21 a y * 9 1 - aH /60? 0662 O 9501- 7/6 2 9H02 9CCZ Z 666- 6001 0 909 226 6 r / » 265 P 999— 9 1 / 9 0 / 5 - 0 6 / 01 16 1 2 - SI 22 * 6021 I CZ 1 0 or«r- «»qc o P tS - CP* 6 6P9 508 8 irei 1691 01 z * r * / r / Z/S — 9CA 9 6 6 * - 96* 6 999 Z/B 9 9671- C/01 9 0**2 AAC2 2 SftS— 0*5 C 091 162 9 * 0 6 - 2*0 A 6 - CI 9 9 /69 — 4*6 P r t t 9C0T * /* 9 6C9 * * * r - 025 6 /OCC C9tC * *90C — / SIC 0 • y »ot 9CI2- 9/A I Z SCSI— 1P51 * 0661- 9007 B 10/1 A t / t * 625 rC 6 / •lo t' Z96 Z 2CB- * 1 / 2 CC9- Z05 * 5*92— 9192 Z •*9 119 1 • 06* C 62/- 26/ / 2** SB* C C641 21p t 9 6 2 / *09 0 * /0 t 916 Z cczc srtr o 01P- 020 g 9 /S 699 21 srrc soic o •OCt 0261 2 0//Z 6C0C O 2 0 0 7 - C4AT 2 1 4#- t n 6 t ay *5*- *H 9991- *roi 0 C 1P1- AC01 9 966 01 2602- 5/61 0 9 P S 2 - 0 /6 2 5 r r * o p s i 9001- mot * ay « tZ - BH 9 1 P - 6 /P 01 IP21 9C71 • /PZI 6621 9 ay *fl- aH PS* 6 /* • * 4 9 - 6*9 0 218 498 C 6 9 9 - { ft/ Z a y *9 1 - aH 050 r z o 9 6021 9171 0 299- 5*0 - » ay *9 aH 1497 »*IC 7 8 5 / 0 7 / 2 5602- 0Z61 • 6 6 * - 905 9 iro i- 5601 9 CS2- 25/ 0 5P0Z 0701 01 0*6 6901 t «y * r bh * ay «»Z- *H 96C1 *911 Z • 9 6 1 - 0961 * 606 196 9 TOO f 66 * ay *71 aH t e n - ** 2 t 6 /•Cl 2221 21 ay *1 a M 6 2 / 609 0 22/1 5/ZI 2 6 / 0 - 629 • Z2Z - pnz 2 0 ay » 0 1 - BH £ 0 9 - ILL 0 IPA- 2*01 01 / 1 *— 58C 6 9991- 96/1 0 / / * 106 Z 0*2 992 0 902 9 i r 01 22*1- **61 5 299 579 6 20*1 - 67*1 8 / I P - 016 01 ay *IZ aH /C 9 — CIO P * 0 /1 - 09*1 01 0161 9922 * to o t p e n 9 76*1 71*1 01 ifCZ PP02 9 CPC1 PC*I P 7 a y *91 aH 5 ay *S 1- aH a y *C1- *H 6R6 966 / BI92 66*2 9 OIC SOC C •* 6 — 298 9 6 / 6 - C6* 6 90/ CA/ 5 C20C- 1CCC 9 0 9 * - *96 9 C66 */Pt 9 DCS— 9601 9 C I6 2 - 2CCC 7 2 2 2 - 1R2 * osrt- zr*t r C /6 - 8*8 • 1141 29*| » 922 60C 9 699 9*6 Z t CC21 01CI 9 0 7 / - 029 * P i l l - Z0C1 * 5CCC *9CC 0 0C71 C901 C B/O **4 * B*5 119 r 6/C l- 5121 C 6 6 f 6Cr * 0 5 6 - /0O 0 1 o n e - 60* s /Itt 6*01 2 65/1 9161 2 CPBl A941 2 7 / 2 - 1C? C A/t2 r«17 2 6 A M - *PO! 7 T66- 7101 Z 6*C - 09* 9 11C1- 1 /P I * 0 P 2 - CSC 0 CSZ- 600 0 1 90- 695 1 9 / 8 - * 2 / 2 x 9 o r i- c*ii i 0 - 1 - 017 1 C2ZI 6C11 0 9201 066 Z ay *5! *H C06 5 /6 C 65CC- /OCC 0 e r c i o n i o * 6* ZS* 0 a y « * Z iH 2/12- Z10Z 0 6 * 9 - n r s t ay * 1 1 - *H ay «0t aH 209- CC6 Zl ay »0Z - aH 10* S6C 01 0*7 IBP 0 91* 5ZC 01 a y * 9 - aH ay • * - «H Z6 Ot ay * B t- aH oir- to* o 0*61- 2PB1 9 6*C OS* 6 1021- 951 I 9 0*11- 9*11 8 it 9 a / / o»n 9 ay « r l all ZP2 C67 S B29 206 fi POD 2*9 * 5 0 1 2 - 6761 01 / 18 9 /P 01 / r z - AC9 II *42t *rrt / Z 5 * t- Z0S1 • 9 6 2 - 69C 5 07C1 /SSI * 0 2 5 - 60* Z 6CZ- * 0 / Z 60*1 2221 6 08*- COS 6 7iii- ms oi 8/*2 *P*2 4 0 a» «*Z- aH 16*1 *6C1 2 2*9- SCS * * 9 2 - 7PC 01 ri6- /601 C 6 9 9 - 269 9 •602 ZPP2 R P**- CIS 8 94*1 erci 6 4 0 P - *?p 5 ay *02 aH 2/12- 0922 0 11/ 5 /9 C OB* 2 /5 B io n - o r / z 225 52* 5 0 ay *B — aH CO/ 9 2 / / 015 9P» S 6591 r s n i B p * t t - p i o i * 9 Z S I- OOCt Z Z1Z C2S 2 0 0 6 - *10 9 CAOT 0 56 * “■ r coo 5 0871 *821 * 6P P 7- C6B2 9 068 S /9 C «Z* 259 0 1 29*— AS* 0 POE- SOC C 016- /IS Z *26 B /6 01 B0C1- CR*1 • 606- 69t1 C e*5C 690* * *1* 66r t 0 ay **J •» 9 * 9 - 1*9 9 6 1 0 - 5 /5 2 S2C 20C 0 9 6 5 2 - Z66Z 6 o r / i / / c IC P- /* 6 7 1« 6 2 - 60CC c 929 2 0 / 9 99C 09* 9 • y ‘ S t - aH. 000 1 P66 t 1 / 0 - 629 9 **9i srot 9 0/02 C/17 7 *6* BC9 1 1/ 9 - 669 7 r * / - /I B Z 9 1 9 - 929 9 5 6 * - 995 0 C 12 1 696 9 ay * 6 - BH 2C9 665 • B P /- COB 1 ecci 09C1 o *6* C6C 0 2661 6061 O 60* C l* S 6621- 0911 Z PP21- 9/01 * SCSI- BIZI Z 65CC- 89*C 0 8 *9 t SF9 I 8 C 79- 6 6 / 9 660 0ZZ • 1291- *601 9 a y « C f- aH *9P- ZP? C 022 9SZ Z a y *C *H 1711 5411 / 966 Z16 Z ay * 0 2 - aH CCC- 05* C 696 C0C1 5 0/21 6921 2 /CCZ SC2Z 9 ay *B al ay *9 aH 12/2- Z//2 9 699— Z9S 0 C /Z - Z0B 2 AM *09 • /191- 2*51 9 6621- 29C1 1 9*0Z- *012 • 6021- 2*01 21 04*— /C* It 1/41- 9*61 5 1211 9/11 * 0 0 6 - 006 C 6201 1B6 Z z c * * * r o 5101 0601 2 ZZC- / • * 6 656 166 71 19* CAS 1 1 1221- 8001 01 “ ' 1 ACZ * 60*1- 99C1 Z • 1 ' / 1 — *H '* - 692 2 *162 5062 9 CZZ- 6C0I 6 15 1 1 - 9*11 01 1*11 e?u 01 51* 604 6 85*1 1*21 C *16 01* 1 o / r - oac t 0 6 / — 1 / / 5 ay *6 bh CS01 5101 9 S2B 566 9 ROB- 1 /9 6 P*A COOt 9 • r o t - 66/1 7 2551 0961 0 C1C- CCC 01 2 9 * - r o * o 9 9 * 7 - 0A*Z * 2 06— 205 5 ’CM- SOZt * 9B01- 6/01 P tn*- /** / 2/ / - PfO I 69C 94C 9 OAM 69*1 C 060 109 6 226 516 9 C161— StCt * .Zl *07 2 U S 5* 6 4 944 A9/ C 2 . a y *0Z aH * 0 /- Z*9 9 C ay *51 aH 660 S /P Z 9661 5691 B O SCI- 2271 9 AC* BC* f 2 * 0 £ - C60C 0 trit t'.?i s 7*11 /071 2 • 1 - t ay * rz m B U 019 * P69 2*9 1 9/6- troi Z P561 5PS1 • 519 C9S 7 6221 9/21 a 2/ r A ir i Z65- 299 21 6 / 6 - C*6 2 o r* Z l* 11 66*- *0O 0 * • 6 2 - A*>A2 O OSS- 509 C 0 ay * 9 - aH on*- tor c CC9- 074 o 8 /* 2P5 11 9 0 / / R9 9 11/ 6CZ 01 ♦*5 C15 0 6 6 6 - 6 r / 9 P121 /n?i 6 t n * t- *6C1 2 S ay • / - a *nrz- *noz z /P 6 OI 6 * 6 - 099 • 96P— ZIP Z •601 0/61 9 a y * r t bh • r p 7 p / i p * » 96* I AS*- ftSS 01 * 2 6 - 766 1 ay * 7 - mu *9A I — 6*61 8 C921 61 f 1 Z CS*2 9122 0 ay *21 — *H Z*HI - 7291 • /AA 1- * 072 2 5 * / CCZ 0 IfO t B*01 B 0A02 1/02 8 2 6 /2 6*/2 0 PCS- 70S / / 6 9 - 0C9 I o r s t 17/*1 Z A*9 7A4 P 509* 0 /6 1 965- *66 Z *AHI— 2/6 1 9 41/1- 9*4| 01 29*2 ft/C2 4 ay * 0 2 - BH 6561 CO/1 9 120 6 0 / I or/ I- AT9| 9. /C * 72* 0 ay *6- *H 5 6 /1 - C/01 9 0 5 1 2 - 67*7 * ay • * - aH * 2* i r s B S4f»r 47A7 6 t ay »CZ- aw 6 9 / - 269 5 0 9 5 - 119 0 P/02 /1 A1 * 7 t6 t RPA1 « z*rr zosr z t o t 1 1411 4 C12*- *9C* * 09*1 16C1 • 6 * 9 - 0P9 * BP*- /16 C ay *11 al 6161- 2661 « • C6— SCI I 2 Z*0C— / / t c 0 179 8* 6 I t 90/- *rp 6 4«-ni- 2/71 C t / 9 - ZC9 Z 6CZ2- 0*02 Z 2 0 f - 692 C / 0 1 2 - CCA1 2 . * 1*6 / r.r/ i 71/ t oi 4 / s t - s r d * 4TZ- A/P 2 C5*2 6/CZ 0 6 /9 CCZ 2 •o 9A5 1 9 * 6 - C6R 9 12*2 2/*2 9 ay *9 aH 279 tit A zr-4- sro i C / I - *5? I I ay *CZ aH * •6 01 * 0 066 1T21 B i p r o s c o n r o t * 2r t * 0/ 1 1- r r n 5 note, oric b fir*- oi4 o ay * 0Z aH 6262- *6/2 9 2fin— OP 9 6 0 7 2 - 61T2 * 6901 1 262- CO* 01 z n r i - 2* s t 4 ay •1 aM Z9C /6C 9 ay #Z t BH Ct*l- 11*1 5 l ay • C l- *H pent- P591 * 6*6 5*6 C 9291 C991 1 IS* *26 6 A te B** 5 ay *2 aH 9911 zrzi z 0 /Z - Z6* 9 6972 2/12 * 606 SPA 2 9*61 2902 2 S9*— *9* 1 0/1 262 B 25*2 16/2 * • fif 0** II SAC 1 Z102- 9281 1 CSZ- *02 / zooi **rt r 2611 5PM 71 8411 7711 01 66*- 666 t 0C9 **9 9 /A 9 * 990 6 9/C 69* C 612- 7CM B 9 * 9 - 6 9 / 1 2 /4 II 62*1- 99CI 0 1 6*- CSS 6 66C 90* 9 2*C2- 0062 2 6*1 OSC I Z 6* / 228 0 2001 5001 I rcn - 1621 9 /5 P 2 - s r e e 2 4*B- 2 5 7 - 91C 4 i - 606 • 96*1- 6261 9 2PC /6 * t 06 IP //1C 9 ///I C191 ; 229 210 6 014 624 i 2 6 P - *«" 01 / / 4— ft?/ 9 9 / c • • * r 1771- /61 1 Z 9 0 5 - Z /S 0 2*/- O */ 5 ay *6 *H 6 2 2 - 5 /2 ( AC * 1 * / 2 1 * 26/2 9*6 2 0 £75 *.54 A /AO / 7 /* *69 Z *191- PC/1 • 1 / 9 - 10/ 6 0 2 6 - *16 C ' * 1 0/ * 1 B o * r - a / c 9 o o * - CO* c I/CZ 0*22 B 5 /* - CP* Zl y • / - 8 0 6 - 0 9 / 7 6*.r * r s / 9 r 9 — 616 6 606- C6C 0 S22I 9*11 e 172 972 0 6 1 4 - r s s 4 569 2 /6 2 / *«2— C*62 6 r.ppj -7 /1 1 6 ay * 6 1 - aH 91CZ 0 0C2 9 60/- *66 01 0PI1 /6I 1 1 1111 5121 5 0 6 * - 625 / BSC— 51* 01 11 1 1 - T4A 21 * ay *ZZ aH C6« 9 0 / 5 “'2 . *P* 6 to r ZP6 0 o z r o r r r S f 6 1- C95I 9 9591 10/1 9 ay » 5 - *H *nci rori ot 501 I - 7*71 * 9272- *902 • APB / * 6 9 o / r - c * r z f201 *201 6 OZR- *69 / 60 / 660 * */6t 0751 C fR9t //SI • 2992- 02/2 9 OCC- *5C 6 * 9 9 1 - C4S1 7 “ o r 2502 2 ay *0 * H 2*6 C60 9 10/t 56/1 Z • 2 6 - 9 15 * ay «C1 aH 6 P * — *15 1 6 6 4 - 0 6 / 1 * 2 « - t / 2 9 6 9 * - • /* 1 C6C COS C 9 6 2 - 62* 0 SC9- 109 Z 6A2I 26*1 6 06P— 608 B 9 * * 9 / * 6 2C61 zr*1 z 26B 9AB 01 29C 92* I zort r6Ct * OCZ POO / / RS7— I4C2 0 /in - rftft zt 7 0 9 - ay */1 aH 1 6 /- 6 1 / R ay a || z o r - 206 c 2151 6251 9 66* ASC II /6 9 6*9 Z 999 PA*— 206 1 *11 a y * 2- lU 9 /* P Ot s i n - *i:\ o 1*2 61C 6*6t- 5091 0 /•AC PO* * ay * 6 - aH 9861- 6891 Z 2*5- CA* 6 CAA 1911 01 /4ft 0C6 2 f9 669 01 1 0 9 - 2*5 C 6 * / - OPR 01 6 2 2 - C62 0 5/21- 0841 • 0 * 9 2 - C902 8 2 * 4 — 0P4 P 965 9 •701 626 01 2*5 /AC r 9**— 6 /6 * 629- 675 II 294 OCZ 9 0 5 6 - / 69 • 0 0 - 11/ 9 POO 1 — 1601 2 . 226 *251 *701 2 5 9 1 1 - /r .’ | 41 AB/ 2 5 / 6 606 66* 96C /*C * /PR 2 9 / T 9 9 / - C*Z O 0211 *201 6 ay • / aH 9C82- 862C 7 n o t - r i 6 2 09* ZOS 9 06CZ 0*C2 0 21/- 1R9 • 8C2Z- *222 B 5 8 6 - BIO t 26A— /7 6 A StC 267 * •SCI 6/21 0 9 / 9 - 2 0 / * 2fi* I I * r 6B11 6601 Z C95 96* 71 2PI1 7511 9 62/2 - 99 P7 C 600 109 C 0 /P 0/fl 2 6922 66*2 9 6/ * - 2/* 11 ay *5 aH 16/ SCO I 9 1* 11 AT 11 2 Z ay * z r IH 6C6 996 a y * 9 1 - aH 2161 0691 2 P 20— 0 0 / 1 2651- 5/91 5 6C9 209 A 18* / FS 01 0C 6- 176 6 C29 / I / 1 * 1 0 1 269 Z9*— 99C 1 act- 69p z 0A52- /9rz 0 2 0 / - Z /9 * C 06- 6CZ B 865— 2A* 01 //•- 7*6 6 //O f- 841 1 * 0621 2P2t e 9Z9- 929 01 7 C * - zee C26 Z /S • 5 * 6 1 - 2*61 0 o /* o r* s 619 019 C 1957 6*12 9 6101 /C01 B 9ft*- 925 P 14/1- 8CP7 C 6 1 * 2C5 9 44C - BOC C 920 1 *POT * * ay *01- BH C99 t 1602 Z 1/*- *8* 5 2 9 * 2 - 90C2 9 I f * 994 / 9201 1/ 6 1 2 ay *0 aH 2001- 2021 * 2**1 — 71*1 2 * ay * * t aH 6*6— AT * C 959 6 6 / 1 120- OCZ • 62* C/C 5 _ II C5II 9 ZP62- 5152 0 till- **91 0 200 266 1 P6P2- PA02 Z A611 /021 9 906 SCA C 6CC7 6602 * 7071- 1111 6 P9BI- 0*/T Zt 6 1*- 006 9 • SC 1 60*1 0 61* *99 ZT o s r z oapz o 669 *P* / ay *6 aH 1851 59*1 7 189- 9PC C 6*21- /BU • ay •2 aH C//I 2CP1 01 996 z r o t o COP- Z06 01 12* 6SC 9 6**1- 5071 1 9S91— 12*1 Z r* 6 C60 C • • 6 1 - C651 8 OCCt - n e t * ay *91 aH 0 /9 065 9 ay *21 BH *2 51 — 19/1 • P9S *19 01 51* 50* 1 C**t r.SII 7 Z9M A m 21 91C1 7621 4 1 9 9 - 126 » 6601 *601 z o o r - *92 5 *9* *1* C 6 6 0 - 1*6 B a y • / - aH 11 9 - 9 5 5 0 oact — e/*t oi 66*1 2*91 • 9911 6Z11 Z 166- *29 Zt IB * - Bn* « Ars- 966 Zl 0212 2012 2 26C 916 9 C ay * 5 - *H . 2*51 IB*I 9 80/*- 9*C* 7 rz/t- *9/1 0 00/ Z/B 01 */r. a/ s z o c r PC6 o t /S O - 129 1 ASC 11C 5 5 ay *C— aH 6 * 7 7 - AC77 * 2 /9 — O f/ 9 *921- *621 0 P 5 9 - ZCZ 9 0652- *292 0 ' CCZ Z */ * flit *101 Ot 5252 2CC7 2 ay «0 aM 3d 0 / 3d OJ 3 d Od 3 ‘ 3d Od 3d Od 3 3d Od IV. RESULTS AND DISCUSSION The molecular geometry and the light-atom numbering scheme are shown in Figure 10, while Figure 11 depicts the coordination around the yttriums. These drawings show the yttrium atoms as seven-coordinate — n o t s u r p r is in g s in c e t h i s i s one o f th e m ost common c o o rd in a tio n geom etries for yttrium. Of the several possible seven-coordinate geometries, even the more symmetrical ones differ little from one another, and the geometry observed in any one molecule may reflect the constraints placed on the complex by ligand steric requirements and packing considerations. 31 In the present case, the coordination polyhedron of the oxygen atoms (0(l) -0(7) ) about the central metal atom may be described as a distorted monocapped octahedron symmetry). The oxygen atom of the water of hydration lies above the center of one face (O^-O^-O^) of the distorted octahedron consisting of six oxygen atoms from the ortho-aminobenzoate ligands. Each ortho-aminobenzoate group functions as a bidentate ligand, but the two sites of attachment are not associated with the same yttrium atom. This is similar to the oxygen bonding found in the bisfortho- 12 aminobenzoato)copper(II) compound. In tris(ortho-aminobenzoato)aquoyttrium(III) the octahedron is distorted by a spreading apart of the atoms defining the capped face: Og, 0^, and 0g. The greatest amount of distortion is caused by 0g. As a result, the angles O^-Y-O^, O^-Y-O^, and O^-Y-Or, measure 53*5 1 5 7 .9» and 99.^ ° respectively, in comparison with the idealized 5^*7°* More over, there is an expansion of the angles O^-Y-O^, O^-Y-O^, and Og-Y-O^ to 6 9 . 7 * 1 0 7* 2 , and 150.6°, while 0^-Y-0^, 0^-Y-0^, and 0^-Y-0^ contract 65 E igure 10 M olecular Geometry of Y^^NCgH^COO)^ '£g£3g?S5 0 (3 ) ,0 (7 ) C(12) C(13) 68 F ig u re 11 Coordination Around Yttrium in Y^gNC^H^COO)^ • H^O 70 t o 6 9.O, 71-1» and. 8 1 .0 ° , respectively. The dimensions of the distorted polyhedron are given more fu lly in Table IX. The equatorial positions of the distorted octahedron are occupied by four oxygen atoms, each from a different ortho-aminobenzoate ligand. The oxygens 0(2) and 0 ( 3 ) are cis to each other, as are 0(l) and 0(4). Axial positions are occupied by 0(5) and 0(6), again belonging to dif ferent ortho-aminobenzoate ligands. Thus a total of six ortho-amino- benzoate residues are associated with each yttrium atom. The result of this mode of coordination is that each yttrium atom in the (100) plane is attached to two other yttriums via carboxylate bridges to give two polymeric parallel chains located at an x coordinate of 0 .2 5 f o r th e yttrium atom. A similar set of parallel chains is located at an x co ordinate of 0.75 for the central metal atom. A total of four polymeric chains are within the unit cell. Figure 12 is a representation of one half the unit cell in the ^100J direction, showing one set of these parallel chains. A two-dimensional polymeric network has been reported 1 P for the bis(ortho-aminobenzoato)copper(ll) compound. In this mole cule, the copper atoms in the (1 0 0 ) plane are attached to four other copper atoms via carboxylate bridges. The result is a network of poly meric sheets. As with the copper compound, the aromatic rings of the ortho-aminobenzoate ligands in the yttrium compound extend nearly per pendicular on either side of the polymeric chains and may provide lateral stab ility. This polymeric arrangement probably is the source of the compound's extreme insolu b ility. For packing efficiency, the aromatic rings of the ortho-amino benzoate ligands are nested in the unit cell nearly perpendicular to the b-c lattice direction. The rings stack in a close packed array tilted 71 Table IX Characteristic Parameters of the Coordination Polyhedron cl Atoms Distances(A; Atoms Angles(deg) o 0 1 CM 94.1(7) 5-32(3) °2"03"°l o d* 1 c-\ 4.99(3) °3“° r 04 89.5(7) 1 0 o 3 .68(2 ) 9 1 .2(6 ) ON 01"°4_02 3 .06(2 ) °2-°3 V °2-°3 82.2(7) V °5 3.07(2) °2-°6-°4 62.5(7) V °3"°5"°1 4.14(2) °r°3 °2-°6 4.88(3) 3.66(3) °3_06 °2“y“°7 53.5(7) 2 .91(2 ) V °6 °3-y- ° 7 57.9(7) O Cl I CM IN- 2.35(3) °6-y- ° 7 98.9(7) o O 1 £>- 2.28(3) °2"Y-°3 69.7(5) °6~°7 3.45(3) 03-Y -°6 107.2(6) °2“Y“°6 150 .6(6) ° r Y"°4 69.0(5) V y"°5 71.1(7) 81.0(7) °l"Y"°5 °5"y"°6 127.4(7) Estimated standard deviations are given in parentheses and are calculated from those derived for the positional parameters F ig u re 12 Polymeric Structure in Y^^NC^H^COO)^ • H^O 73 csin£ c O O © Y 74 at 40-50° angles with respect to the a-b plane. An alternating pattern of three rings sloping toward the [d o ] direction, then three rings slop ing toward the [ 010 ] direction is observed throughout the unit cell. Figure 13 illustrates this close molecular packing of the phenyl groups of the ortho-aminobenzoate ligands in the yttrium complex. The bond distances and angles found in tris(ortho-aminobenzoato) aquoyttrium(III) are listed in Table X. The axial bond lengths of Y—0(5) and Y—0(6), 1.86 and 2.24A, respectively are noticeably shorter than the equatorial bond lengths of Y—0(l), Y—0(2), Y—0(3), Y—0(4)s o 2.6l, 2.82, 2.46, and 2.55A, respectively. These are what would be ex pected with the Jahn-Teller effect in operation. The magnitudes of the observed bond distances in Y**’N(l), Y,,,N(2), and Y‘*'N(3); 3*64, 4.03, o and 3.23A, respectively are too large for coordination of the yttrium atom to the nitrogens of the ligands. The C-0 distances in the carbonyl group are significantly different especially in Ligands 1 and 2. This is an indication that the pi delocalization between these two bonds is not equal— possibly as a consequence of the bonding arrangement. The bond angles C(l)-0(2)-Y and C(l5)-0(5)-Y.(126(2)° and 128(2)°) support 2 sp hybridization of 0(2) and 0(5). The remaining bond angles: C(8)- 0(3)-:Y, C(l5)-0(6)-Y, C(l)-0(1)-Y, and G(8)-0(4)-Y (136(2)°, 134(2)°, 157(l)°» and 164(2)°) are of magnitudes somewhat larger than would be 2 expected for sp hybridization and may result due to the rigidity of the organic ligand. The bond lengths of the aromatic rings differ in many instances from the idealized G—G bond of 1.395^* In each ligand, there appears to be an elongation of at least two C—G bonds on opposite sides of the ring. The difference map indicated no other possible locations for the assigned atoms, but the high standard deviations of the parameters F igure 13 Stacking of the Phenyl Rings in x o N(3) b Table X Bond Distances and Angles in Y(HgN C 00 ) ^ • HgO5 ,o Distances (A; Ligand 1 Ligand 2 L igand 3 1 .3 0 (4 ) 1 .1 5 (4 ) 1 .2 3 (3 ) G1 “ °1 C8 - ° 3 C15 _ °5 1 .4 3 (3 ) 1 .4 1 (4 ) 1 .1 9 (3 ) G1 “ °2 C8 - ° 4 C15 ~ °6 1 .8 1 (4 ) 1 .6 0 (4 ) 1 .4 5 (4 ) C1 ~ C2 G8 C9 C15 Cl 6 1 .4 4 (5 ) 1 .1 8 (5 ) 1 .3 4 (4 ) C2 “ C3 C9 _ G10 Cl 6 - C17 1 .5 1 (4 ) 1 .6 6 (4 ) 1 .7 1 (4 ) c 3 “ N1 G10 ~ N2 C17 ~ N3 1 .6 7 (4 ) 1 .5 8 (5 ) 1 .4 2 (4 ) C3 “ C4 G10 _ G11 C17 ~ C18 1 .4 7 (5 ) 1 .5 5 (6 ) 1 .6 7 (5 ) c 4 “ C5 G11 ~ C12 C18 ~ C19 1 .4 5 (6 ) 1 .3 1 (7 ) 1 .3 0 (5 ) C5 “ c 6 C12 ~ C13 C19 ~ C20 1 .6 8 (5 ) 1 .5 9 (6 ) 1 .3 6 (4 ) c 6 ~ C7 C13 ~ Cl4 C20 C21 1 .4 9 (5 ) 1 .7 7 (5 ) 1 .6 3 (4 ) °7 ~ C2 Cl4 — C9 C21 - Cl 6 N2 - ° 4 2 .1 6 (3 ) ■ n3 - o5 2 . 36( 2 ) N1 - ° 1 3 -1 9 (3 ) 2 .1 6 (3 ) N2 - ° 7 3 .6 5 (3 ) 4 .7 8 (3 ) N1 “ °7 N3 °7 Estimated standard deviations are given in parentheses and are calculated from - Bond Distances and Angles in Y(H 2NCgH^C00) 3 ’ H2° b o Distances (A) Y-----0^ 2 . 61( 1) Y ...O ^ 2 .55 ( 2 ) Y , \ 3 -6 4 (3 ) y..* o2 2 .8 2 (2 ) Y-----0^ 1 .8 6 (2 ) Y , N2 4 .0 3 (2 ) 2.46(2) Y*'* 06 2 .2 4 (2 ) Y , N3 3 .2 3 (2 ) M 3 Y-----0? 2 .3 0 (2 ) Angles (deg.) Ligand 1 C3 -C 4 -C 5 1 28(3) °1 “ C1 _ °2 113(2) G1 “ c 2 - C7 12?( 2 ) O a a 1 1 CM T—I \ — 137(2) c3 - c 2 — c ? 105 ( 2) 102(3) 1 C4 - c 5 “ C6 110( 2 ) C2 - C3 - N± 106( 2 ) 131(3) °2 ~ dl " °2 C5 " C6 - C7 127( 2 ) Ck - C3 - Nj_ 125 ( 2 ) c6 - c ? - c 2 G1 “ C2 “ C3 125(3) c2 ~ c3 r \ 128( 3) ^ The dotted line represents a bond between a yttrium atom and the carbonyl oxygen of a ligand attached to a different yttrium atom. T able X—C ontinued Angles (deg.) L igand 2 T c 0 * d 1 1 00 112(3) C8 " C9 " C14 139(3) 1*H(4) °3 C8 C9 103(3) G10 - C9 “ Ci4 120(3) 118(4-) °^ - C8 ~ C9 144(3) c9 “ G10 ” N2 115(3) 101 (4) C8 - C9 - G10 101(3) G11 - G10 - N2 139(3) 133(3) C9 ” G10 ~ G11 102(3) Ligand 3 127( 2 ) 125(2) °5 ~ C15 _ °6 C15 “ Gl6 " C21 126( 3) 113(2) 131(2) °5 ” C15 “ Cl6 C17 “ Cl6 “ C21 13M 3) 120(2) 138(2) °6 _ g 15 _ C 16 C16 ” g17 ~ N3 9 8 (3 ) 104.(2) 122(2) C15 " C16 - C17 C18 ~ C17 “ N3 132(3) 100(2) Cl6 ” C17 ~ C18 Table X—Continued Angles (deg.) 01—Y . . . 0 ^ 6 9 .0 (5 ) 0 , — Y . . . 0 C 8 1. 0( 7) 1 5 02 — Y ...03 6 9 -7 (5 ) °2 — Y . . . 0 6 150 . 6( 6) 0 O 1 1 CM o- 5 3 .5 (7 ) ° 3 - y . . . o6 107. 2 ( 6) 0 l 1 5 7 .9 (7 ) 0 0 >1 1 ■ • • 7 1 .1 (7 ) °5 “ y . . . ° 6 1 2 7 .M 7 ) °6 - Y - °? 9 8 .9 (7 ) oo o 81 F ig u re 1^ Photograph of a Model Depicting the Unit Cell of YtiyK^H^COCOy HgO 82 reflect the poor quality of the data set. The significant deviation from the idealized bond lengths of an aromatic ring may be in part contributed by the quality of the data set. A sim ilar type of sevenfold coordination for a yttrium atom has oo been reported for tris(1-phenyl-1,3-butanedionato)aquoyttrium(III). In this structure, the molecules are monomeric with two molecules per unit cell. The /3-diketonate ligands wrap asymmetrically about the co- o ordination polyhedron with the average Y—C>cdelate distance = 2.28A. o The water molecule caps one face with a bond distance Y—0 = 2.24A. These bonds are in general agreement with those found in the Y^gNC^H^ GOO• H^O model. The Y—Oo^eiate bonds of the yttrium compound are o also comparable with the corresponding average values of 2.36(6)A and o 2.323(8)A obtained from the few reported yttrium (lll) complexes with 52 54 amino acids. ’ A monocapped octahedron has also been reported for a closely re lated lanthanum element in the tris(diphenyl-propanedionato)aquoholmium 71 compound. In this structure, the water molecule is located on a crystallographic threefold axis passing through the holmium atom, and the remaining six oxygens from the ligands are at the corners of an octa hedron which has undergone substantial trigonal distortion. For the tris(ortho-aminobenzoato)aquoyttrium(III) molecule, however, there is no threefold axis because one of the ortho-aminobenzoate ligands (C^ reverses its mode of chelation as illustrated in Figure 10. This struc tural feature probably reflects both intra- and intermolecular packing requirements. Although most crystallographic structure analyses proceed fairly smoothly, this one proved to be the exception. Nevertheless, we feel 83 that the postulated structure is the best model based on the available data. The structural refinement was complicated for several reasons, some of which contributed to the amount of error witnessed in the final s tr u c tu r e . The first complication was an overwhelming contribution of the heavy atom (yttrium) to the phasing of the structure. The net result was that the light-atom contributions could not be determined very ac curately and in the case of the hydrogen atoms, not at all. This fact is supported by the accurate determination of the positional parameters of the yttrium atom in comparison with the remaining atoms of the struc ture. This problem is not entirely unusual, and recent developments in the area of neutron diffraction have led to the determination of light- atom positions in the presence of heavy ones, which may have been dif ficult or impossible from X-ray data. The present data set is also entirely too small for reasonable hydrogen atom locations. For overdetermination of the structure, it is suggested that there be four or five reflections for every adjustable parameter. This amounts to approximately 1900 observed reflections as the number necessary to assign accurate hydrogen positions. A-. d a ta s e t twice the current size would be needed. Therefore due to the size and quality of the existing data set, the positions of the hydrogen atoms can only be inferred from indirect evidence such as probable bonding schemes. The copper compound exhibits hydrogen bonding, suggesting a similar pattern for the yttrium compound. It is entirely possible that there is hydrogen bonding between the amino nitrogens and the oxygen of the water molecules, although the present data is not accurate enough to enable verification. The bond distances between N(l)—0(7) and &h o N (2)— 0( 7) are 2.16 and 3»^5A, respectively. These lengths are outside the range found for hydrogen bonds between amine groups and oxygen (2.57- o 3.22A) but a better data set may prove otherwise. Further complications were caused by the centered space group, C2/c The yttrium atoms located in eight general positions were supported by corresponding vector locations on the Patterson map. However, the remain der of the Patterson map was extremely crowded with numerous overlapping peaks enabling further identification as impossible. With a centered space group it proved fruitless trying to solve the structure by "Direct Methods". The only successful method for a solution by this means would have been to convert the centered cell to a primitive cell. At the time, this conversion process was beyond our computing capabilities. Consequent ly, the assigned space group led to a very complex unit cell containing 256 non-hydrogen atoms as shown in Figure Ik. In addition to the centering in the structure, the yttrium complex contains a large anisotropic element. This is apparent in the radical decrease in the R-factor from 0.259 for all atoms with isotropic temper ature factors, to an R-factor of 0.081 with anisotropic temperature fac tors. Unfortunately, a thermal ellipsoid drawing of the yttrium complex is not available to further support this claim. Such a drawing represents each atom as an ellipsoid, the dimensions of which show the extent of an isotropic vibration for the atom. It is postulated that a drawing of this type would show the yttrium atom as a very elongated ellipsoid since the thermal motion of the yttrium is undoubtedly related to its nature of coordination. The remainder oxygen, nitrogen, and carbon atoms would also exhibit a fair amount of anisotropy. The atoms of the phenyl rings would have different shaped ellipsoids depending on their location within 85 the ring. For example atoms on the outskirts of the molecules, i.e ., G(^), C(5), C(6) would exhibit large thermal displacements, generally with the largest dimension of the ellipsoid parallel to a bond. Where the number of bonds to an atom increases (bonds to hydrogen not included), the ellipsoid would be more spherical in shape (c(2) and C(3)) due to a decrease in thermal vibration. Ihe structure of tris(ortho-aminobenzoato)aquoyttrium(III) is unique in that it represents a very uncommon coordination geometry— seven coordinate. In addition, the rarity of reported structures of yttrium makes the knowledge of the bonding in this model even more valu able. The structure of this yttrium complex probably represents one of the first reported yttrium amino acid, complexes where both oxygens of the carboxylate are active in bonding. An unusual feature is that each of the six bonding chelate oxygens of the distorted octahedron belong to a different ortho-aminobenzoate ligand. Preliminary investigations of other members of the synthesized metal anthranilate group are currently in progress. The bis(ortho-amino- benzoato)zinc(ll) crystallizes in the space group P2^/c with four mole cules per unit cell. This is not surprising since the powder diffraction pattern of the zinc complex is extremely similar to, but not identical with that of the copper complex. The lattice cell constants measure: ° ° o 0 a = 9.3QA, b = 5-23A, c = 26.25A, and ft = 90.86 . A data set of approx imately ^00 observed reflections has been collected with a Syntex P2^ automatic diffractometer using Mo radiation. This is an improvement over the collection of intensity data from photographic films and should introduce less error into the structure analysis. The unit cell parame ters of the tris( ortho-aminobenzoato)lanthanum(III) have also been mea sured. Unlike, the previous complexes, the lanthanum complex appears to 86 crystallize in a hexagonal space group, P6^22 or P6ym with eight mole- o o cules per unit cell. Ihe lattice constants ares a = b = 21.62A, c = 7.6?A, °< = P = 9 0 . 0°, and y = 60.0°. The solution of this structure would provide an interesting comparison with the reported structure of the tris(ortho-aminobenzoato)aquoyttrium(III) complex. APPENDIX X-Ray Powder Patterns 89 Table XI X-ray Powder D iffraction Data for Z^HgNCgH^COO)^ a I n te n s it y h k l I n te n s ity h k l dh k l A "hKL X 13.23 VS 002 2 .0 8 VW 225 10 .8 0 VVW - 2 .0 5 w 414 6.65 M 004 1.986 w 415,322 4 . 83 VW 012 1.926 VW 324 4 .4 7 VS 111,202 1.886 W ' 325 4 .0 7 W 113 1.854 w 502 3 .8 5 M 204 1 .7 2 5 w 422,513 3 .4 8 M 210 1.681 w 133,424 3 .3 5 S 212 1.617 VW 232 3 .0 5 W 214 1.511 VW 332 2.91 W 215 2 .5 7 M 313 2 .4 9 M 314 2.38 M 315 2 .2 8 W 220 2 .2 4 M 222 2.12 .S 412 S = strong; M = moderate; W = weak; V = very 90 % l % ’’k % | Table XII X-ray Powder D iffraction Data for Y^gNC^H^COO)^ ■ HgO <3-1.71h k l A I n te n s ity h k l 14 .7 8 VS 200 12.06 S (b ro a d ) - 7-94 VS I l l 6 .9 5 M 002 6.01 W 402 5 .4 5 S 312 4 .9 5 M 510 4 .4 4 - S 402 3.62 S 512 3-3 7 M 223 2 .9 4 M 132 2 .7 3 W 115,423 2 .5 5 M 514 2.36 W 334 2.17 W 440 2 .1 0 w 242 1.992 VW 243 1.930 VW 444 1.705 VW 352 1.512 VW 155 Table X III X-ray Powder D iffraction Data for La(HoNCrHi.C00) o o I n te n s ity h k l Intensity hkl ^ h k l A dh k l A 8 .8 0 VS 34-1,311 2 .21 W 242,113 6 .2 3 S 300 2 .1 3 W 104 5-4- 3 S 101,220 2 .0 8 W 332 4 .6 6 M 400 2.03 W 305,335 4 .0 5 S 140,510 1.9 4 2 VW 506,556 3*74- M 500 1 .8 4 2 VW 352,215 1 o 3-58 M 1 .7 0 4 VW 054 3.4-2 M 414,434 1 .6 5 7 VW 125 3 .1 9 S 102,112 3-09 M 112,333 2 .9 5 S 042,122 2.81 W 241,352 2.6 9 w 440 2.54- M 434 2.4-5 M 341 1 O CM 2 .3 7 M 2.26 W 244 92 Table XIV X-ray Powder D iffraction Data for Mn(HgNG^H^G00 I n t e n s i t y I n t e n s i t y d hKL A d»h t k n l A 12.98 VS 2.17 M 9.70 M 2.12 M 6.62 M 2.07 M 5-49 VW 2.03 M 4 .5 3 VS 1.986 M 42 M 1.917 M 4.0 7 M 1.867 M 3.91 M 1.764 VW 3.53 S 1.693 VW 3.42 VS 3.16 w 2.92 w 2.80 w 2.71 M 2.61 M 2.52 M 2.45 M 2.38 M 2.25 W 93 Table XV X-ray Powder D iffraction Data for Cot^HgNCgH^COO^ o o I n t e n s i t y I n t e n s i t y d h k l A d h k l A 13-33 VS 2.24- M 6.59 M 2.21 W 4-.84- W 2.12 M 4-.4-6 VS 2.09 M 4-.31 S 2.04- W 3.99 M 2.01 W 3.84- M 1.936 W 3.4-6 M 1.889 W 3.36 S 1.861 M 3.15 VW 1.776 VW 3.03 VW 1.728 w 2.93 VW 1.684- w 2.80 VW 1.631 w 2.69 M 1.599 VW 2.56 M 1.575 VW 2.4-9 M 1.512 VW 2.4-1 W 1.4-91 VW 2.37 M 1.4-53 VW 2.28 M 1.328 VW 94 Table XVI X-ray Powder D iffraction Data for N^HgNCgH^COO)^ ° o A Intensity ^hkl ^ Intensity 13.17 VS 2.68 M 10.51 M 2.5 8 W 6.59 M 2.54 M 4 .8 4 M 2.48 M 4.46 VS 2.36 M 4.30 S 2.26 M 4.09 M 2.23 M 3.99 w 2.19 W 3.81 S 2.10 VS 3.45 S 2.06 M 3.34 VS 1.971 M 3.21 VW 1.912 VW 3.14 VW 3.03 W 2.89 W 2.79 w 95 T a b le X V I I X-ray Powder D iffraction Data for Cd^gNCgH^COO)^ o o d^j^ A Intensity ^hkl ^ Intensity 12.97 VS 2.11 VW 6.69 S 2.05 M 5.79 M 1.868 M 5.11 M 1.814- M 4.83 M 1.769 M 4.56 VS 1.714 w 3.97 M 1.472 VW 3.56 M - 1.371 W 3.45 S 3.24 W 2.93 W 2.70 M 2.53 M 2.42 M 2.26 S 2 .1 7 M Computer Programs 97 The purpose of this section is to aquaint the crystallographer with a few basics of the computer to enable rapid and convenient data manipulation on disk. Currently all needed crystallographic computer programs are stored on cards and may be run with magnetic tapes on batch, if the user wishes. This method is suggested if the program needs only to be run once or twice. For multiple runs of the same program, for example NRC10, the least squares block diagonal program, the most efficient method is to store the program and any data files on disk. This avoids unnecessary wear and tear on the card decks, frequent card reader errors due to poor card reader equipment, and time wasted waiting for magnetic tape drives. The NRC10 program requires three magnetic tapes in order to run. Initially, any card program in the crystallographic computing file can be read into the user's disk area with the following control cards. $ JOB $ PASSWORD $DECK NRCIO.FOR See Note 1 Program Source Deck $EOD $T0PS10 .LOAD NRCIO.FOR See Note 2 $EOJ — Note 1 — Ihe program name is entered here. — Note 2 — This step com piles the program and stores both the FORTRAN and REL file in the disk area. Once the program is on disk, the only cards needed for the computation are the data cards. To illustrate the manipulation of data files by this method, three examples of the most frequently used programs w ill be pre sented. The user should note that these instructions are in addition to the instructions outlined in the crystallographic computing manuals. It 98 is hoped that the storage of intermediate data files on disk, rather than magnetic tape, w ill save lo th time and money. The first example is the Data Reduction and Tape Generation pro gram, NRC2M.F0R. This program has been modified to read the data file from disk. The program arranges all the data of a given crystal struc ture into appropriate lists which are recognized by the other NRG crystal lographic programs. This data file is stored as a permanent record on magnetic tape, but may also be stored on disk during all intermediate stages of the structural refinement. Depending on the number of stored reflections, the program deck may involve 3000-4000 cards. For this reason, it is suggested that the program be loaded in three stages. 1. Load the main program, NRC2M.F0R into the user's disk area. 2. Prepare the data cards according to the user's manual and divide into three files, loading each separately. Once loaded these files are strung together as one file. File 1 - all data cards except the reflections. File 2 - all reflection cards. File 3 - stopper card for reflection data. Example: $ JOB $PASSW0RD $DECK FOR01.DAT YTTRIUM ANTHRANILATE NRC2M PROGRAM TAPES 0 0 17 070201 0 070001DIRECT0RY 06 0101 0201 0301 0401 0501 0601 07O1O1CELL 30.898 9 .O96 14.854 9O.OlO9 .3 9 O.Ol.54 i 8 F ile 1 070201SYMMETRY 02 03 1 7 2 01 1 0 0 0 1 0 001 0/1 0/1 0/1 02 -1 0 0 0 1 0 0 0-1 0/1 0/1 1/2 01 1 02 01 02 02 1 01 01 070201SYM. 03 0 02 01 02 23136. 21725. I 8563. 153^1- 12279- 10406. 8128. 6577. 5710. 4302. 3388. 2720. 2187. 1750. 1407. 1133. 921. 758. 99 —Continued— O7O3OIFORMFAC TORS 08 Y-CURVE 0 1 39.O 37.93 35.62 33-20 3O.93 28.79 26.79 24.96 23-34 Y-CURVE 0 2 20.61 18.39 16.44 14.66 13.02 11.56 10.29 9 .2 3 8 .3 5 YAD-CURVE 0 1 3 8 .3 37-23 3 4 .9 4 32.50 30.23 28.09 26.09 24.26 22.64 YAD-CURVE 0 2 19.91 17-69 15-74 13.96 12.32 10.86 9.59 8.53 7.65 YAD-CURVE 1 1 2.3 2.3 2.3 2.3 2 .3 2 .3 2 .3 2 .3 2 .3 YAD-CURVE 1 2 2 .3 2 .3 2 .3 2 .3 2 .3 2 .3 2 .3 2 .3 2 .3 0-CURVE 0 1 8.0 7.805 7.276 6.538 5.728 4.944 4.243 3.645 3.153 0-CURVE 0 2 2 .2 2 4 2.017 I .757 I .592 1.477 1-385 1.304 1.227 1.151 C-CURVE 0 1 6 .0 5.757 5.141 4.383 3.662 3.0 6 3 2.601 2.261 2 .0 1 7 C-CURVE 0 2 1.719 1.553 1.436 1.332 1.229 1.127 1.026 O.929 0.837 N-CURVE 0 1 7.0 6 .7 8 4 6.211 5.453 4.667 3.954 3.355 2.875 2.505 N-CURVE 0 2 2.012 1.736 1.571 1.457 1.361 1.273 1.185 I .099 1.014 H-CURVE 0 1 1 .0 O.947 0.811 0.641 0.481 0.350 0.251 0.180 0.130 H-CURVE 0 2 0.071 0.04 0.024 0.015 0.01 070401 PARAMETERS 1 0 070401 Y 1 0.25 0.48 0.20 070601S.F.LEAD 2096 915 123 2242244 1111 2 1 01 2 10 $EOD $E0J $ JOB $PASSWORD $DECK FOR21.DAT File 2 Input deck of reflections here $E0D $E0J $ JOB $ PASSWORD F i l e 8 $DECK F0R22.DAT J 070601 99 99 99 $E0D $EOJ While the user is logged into a terminal, the three data files are strung together with the command: .COPY F0R20.DAT = FOR01.DAT, F0R21.DAT, 100 F0R22.DAT. By typing .TYPE FOR20.DAT and .TYPE NRC2M.F0R, the user may obtain an immediate display of the entire data file and a copy of the FORTRAN listing of the program. Data files not needed at this point may be d eleted by typing .DELETE F0R01.DAT, F0R21.DAT,F0R22.DAT. To generate the data tape for a permanent record input the following: $ JOB $ PASSWORD $ TORSI 0 .MOUNT MTA:17/REELID:X0 /WE See Note 3 $DATA 20 See Note $E0D $T0PS10 .EXECUTE NRC2M.F0R .DISMOUNT 17: $E0J — Note 3 — The proper tape number assigned by Computer S ervices i s in serted . — Note 4 — The number o f the data f i l e (FOR20. DAT) is punched in columns 1 and 2. The second example illustrates the block diagonal least squares refinement program, NRCIOM.FOR. This modified program is a fifty-tw o atom version which calculates structure factors, refines positional and thermal parameters, occupation factors and the overall scale by the block diagonal least squares approximation. To eliminate the mounting of three magnetic tapes, the program has been altered to operate entirely from disk except for the initial run which sets up the data file. This elimi nates retyping or punching the parameters data deck after each cycle. Once again the program NRCIOM.FOR is loaded into the user's disk area. One magnetic tape drive is needed for the NRC2M input, but the other tapes are assigned to the disk by using ASSIGN statements. $ JOB $ PASSWORD $T0PS10 101 —Continued— .MOUNT MTA:l6/REELID:X0 /WE See Note 5 .ASSIGN ESK 1? .ASSIGN E6K 18 $DATA 0221 See Note 6 Y-ANTHRANIIATE ISOTROPIC REFINEMENT TAPES 1 0 16 070201 18 17 071009 See Note 7 070001DIRECTORY 07 0101 0201 O3 OI 0*U1 0*H2 0501 0612 07 SFIS 1 11 12 111111000 1.0 2520. 6.01 07 SFIS 2 0.80 289 00 1000 5 1 4 $E0D $T0PS10 .EXECUTE NRCIOM.FOR .DELETE F0R18.DAT .COPY F0Rl6.DAT / ! = F0R17.DAT See Note 8 .DELETE F0Rl6.DAT ’ .DELETE F0R17.DAT .DISMOUNT 17 $E0J — Note 5 — Insert the proper tape number of the NRC2M output tape. — N ote 6 — This represents the code given to input and output data files for the parameter c a rd s . 02 means the input parameters are on cards, 21 means the output file is F0R21.DAT on disk. — Note 7 — The tapes card must have the appropriate codes for the input NRC2M tape and the o u tp u t NRC10M ta p e . — Note 8 — The output data file should he copied to another PPN with adequate storage space. The output file is F0R17.DAT and is changed to F0Rl6.DAT for the next input file. Subsequent cycles of NRCIOM.FOR require only a few modifications for operation to be entirely on disk. The mount and dismount tape cards are removed. An ASSIGN DSK 16 and a .COPY F0Rl6.DAT = F0R1 6. DAT £ > ! are needed to transfer the new NRC10M data file to the user's disk area. The tapes card must have the proper code for the input from NRC10M, i . e . O7IOO9 . The only other change is the appropriate code for the parameters card file. The card which would be input into the cycle following the example would read 2122, meaning input from File 21 and 102 output on File 22. These files alternate since the output file of one cycle becomes the input file for the next cycle. Any time the user wishes to have a punched card output of the parameter cards, the following com mand must be given on a term inal: .CPUNCH F0R21.DAT. The last example illustrates the Fourier summations program which computes a 3-0 Patterson, Fourier, or Fourier difference map for all space groups. All operations are carried out on disk using the data file F0Rl6.DAT from the NRCIOM.FOR program. The program, NRC8.F0R is loaded into the user's area, the appropriate data cards are punched, and the last file from NRC10M is copied into the user's PPN from another PPN which contains more storage capacity. $ JOB , $ PASSWORD $T0PS10 .COPY F0Rl6.DAT = F0Rl6.DAT 4 , ' See Note 9 .ASSIGN E6K 16 See Note 10 $DATA FOURIER DIFFERENCE MAP Y-ANTHRANILATE TAPES 16 071009 See Note 11 070702FOURIER MAP 0 1 3 01 OO5 .9 0.98 04 000.40 0 01 04 070702PARITY GROUPS 2 2 12121212 2096. 11 070702SIGNS OF TERMS 3 1 2 00 10 070702SIGNS OF TERMS 3 2 2 10 11 0707021^10 FUNCTIONS 4 1 2 111 212 070702TRIG FUNCTIONS 4 2 2 221 122 070702REJECT + PRINT 5 0 0 150 070702MESH n o .1 612250123 0.00 0.00 0.00 0.25 0.50 0.50 $E0D $T0PS10 .EXECUTE NRC8.F0R .DELETE F0Rl6.BAT .DELETE NRC8.CTL $E0J — Note 9 — Pf "the data file exceeds 150 blocks, it must be stored under a research PPN. 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