On the Mechanism of Metabolic Reactions of Amino Acids Catalyzed by Vitamin B6 and Related Aldehydes J. Sivý, V. K ettm ann, J. K rätsm ár-Šm ogrovič D epartm ent of Analytical Chemistry, Faculty of Pharmacy, Comenius University, Odbojärov 10, 832 32 Bratislava, Slovak Republic M. B reza Faculty of Chemical Technology, Slovak Technical University, Radlinskeho 9, 812 37 Bratislava, Slovak Republic Z. Naturforsch. 49c, 571-578 (1994); received April 25, 1994 [(N-salicylidene-D,L-glutamato)(pyridine)]copper(II), Crystal Structure, INDO/2 Charges, Metabolic Reactions of Amino Acids, Vitamin B6 Catalysis, Reaction Mechanism The crystal structure of [(N-salicylidene-D,L-glutamato)(pyridine)]copper(II), a model for vitamin B6-amino acid-related metal complexes, has been determ ined by an X-ray analysis. A close examination of the structural data on this and other related complexes combined with quantum-chemical (INDO/2) calculations enabled us to make a clear distinction be tween two mechanisms proposed earlier for metabolic reactions of amino acids catalyzed by the vitamin BA (or salicylaldehyde)-metal system. The results are consistent with a transient formation of a carbinolamine species resulting from the addition of a solvent water or alcohol molecule to the Schiff base double bond, thus supporting the mechanism of the catalysis as proposed by Gillard and Wootton. In tro d u ctio n M etabolic reactions of am ino acids are cata lyzed by m etaloenzym es which require pyridoxal (vitam in B6) (form ula 1, Fig. 1) or its phosphate as a cofactor (G u ira rd and Snell, 1964). The com m on featu re of these reactions is a heterolytic cleavage of one of the th re e bonds to the a-carb o n atom of the am ino acid. O f p articular biochem ical im p o rt ance are tran sam in atio n , racem ization and a,ßelim ination reactions which are d ep en d en t on cleavage of th e C a - H bond. T he first in term ed iate of the catalytic reaction is a Schiff base b etw een pyridoxal and an am ino acid which subseq u en tly coordinates (as a trid en tate ligand) to th e m etal ion of the enzym e to form chelate 2 (these steps may proceed in a concerted m a n n e r or even be reversed). In the next step a pro to n is released from the a-carb o n of the am ino acid m oiety to form a planar, highly reactive carbanion. T hen th e fate of the carbanion depends on its electronic stru ctu re which can be described by canonical form ulas 3 a - c . S tructure 3 a predom i- R eprint requests to J. Sivy. Telefax: (7) 60388. 0939-5075/94/0900-0571 $ 06.00 nates at pH higher than pK a of the pyridine n itro gen w hen the carbanion is u n p ro to n ated so that subsequent rep ro tonization on the a-carb o n leads to racem ization of the am ino acid. O n the other hand, transam ination, which requires protonation on the azom ethine carbon, is the m ajor reaction in the system in an acidic environm ent; structure 3 b, a pred o m in an t form of the p ro to n ated pyrid oxal carbanion, is th erefo re an interm ediate of the transam ination reaction. M ost of these enzym atic reactions have been duplicated by non-enzym atic m odel reactions (L ongenecker et al., 1957; H olm , 1973) in which pyridoxal (or an o th er ap p ro p riate aldehyde) and a suitable m etal ion serve as catalysts. A s the p h e nolic and form yl groups are sufficient structural req u irem en t for catalytic activity of the cofactor (the presence of the heterocyclic nitrogen en hances the rate of the catalytic reaction and the hydroxym ethyl group functions to link the cofac to r to the enzym e), pyridoxal m ay be replaced by salicylaldehyde so th a t the system salicylaldeh y d e -a m in o a c id -m e ta l (4, Fig. 2) represents a relatively sim ple m odel to study enzym atic reac tions of am ino acids. C atalytic reactions in the m odel system 4 also proceed through interm ediate © 1994 Verlag der Zeitschrift für Naturforschung. All rights reserved. Unauthenticated Download Date | 6/18/17 10:57 PM 572 J. Sivy et al. • Mechanism of Vitamin Bft-Catalyzed Reactions 3a 3c Fig. 1. General structures of the compounds derived from pyridoxal. form ation of the carbanion 5 with th e only excep tion th at the transam ination reactions are not o b served. This is m ost likely caused by the fact that the carbanion 5 cannot exist, due to the lack of the ring nitrogen, in the form analogous to 3 b (or 3c). The key question is: W hat is the m echanism of the rate determ ining step of the catalytic reaction, i.e. form ation of the carbanion from chelate 2 or 4. T here have been a nu m b er of rep o rts dealing with this question. The first attem p t to rationalize the literatu re data on these system s was m ade by M etzler et al. (1954), w ho p roposed a m echanism (h ereafter m echanism A ) according to which the labilization of the C ct- H bond was a ttrib u ted to the direct displacem ent of an electron pair from the Ca - H bond to the a -C atom , a displacem ent which is facilitated by the presence of the planar conjugated system and fu rth er intensified by the electron-accepting capability of the m etal ion. This idea was then m odified by P erault et al. (1961) in the sense that the driving force for the release of the a-p ro to n was an increase in the delocalization energy of the system, since after form ation of the carbanion the a-C atom becam e a p art of the con jugated system. Several years later, G illard and W ootton (1970) have found that: a) in nucleophilic solvents the rate of the racem ization reaction of am ino acid esters 6 is by several orders of m agnitude higher relative to the corresponding free acids, b) by using deuterioethanol exchange of hydrogen for deuterium takes place at position Ca, and c) the rate of the reaction can be enhanced by addition of a base. Based on these facts the authors concluded that in nucleophilic solvents (w ater, alcohols) the nucleophile can add accross the azo- Unauthenticated Download Date | 6/18/17 10:57 PM J. Sivy et al. ■Mechanism of Vitamin B6-Catalyzed Reactions 573 RPH Fig. 2. General structures of the compounds derived from salicylaldehyde. :B represents any base present in solution. m ethine d ouble bond to form a reactive carbinolam ine 7 and su b sequent base-catalyzed elim ina tion led to form atio n of the carbanion. G illard and W ootton advanced a hypothesis th at in system 4 a sim ilar addition-elim ination m echanism (m echa nism B) m ay also be involved in form ation of the carbanions, the higher rate of racem ization in ch e late 6 (com pared to th at in 4) being explainable in the follow ing way: in the carbinolam ine 7 free ro tatio n aro u n d the N - C “ bond can bring the a -p ro to n into a position which favours its rem oval by the leaving alkoxy group during the elim ination step; on the o th e r hand, in the carbinolam ine which w ould result from 4 coordination of the carboxy group fixes th e conform ation of the groups on the chelate ring so that the a-p ro to n is in a less favourable position for rem oval by the leaving O R 3 group. A lthou g h the experim ental d ata available in the literatu re seem to be consistent with m echanism B, th ere are still tw o groups of w orkers which in cline to eith e r of th e above m echanism s (see, e.g., B kouche-W aksm an et al., 1988). Consequently, the aim of this w ork was to test which of the tw o m echanism s fits reality. To achieve this, we have ad o p ted a sim ple strategy based on the fact th at upon chelation of the Schiff base the rate of race m ization is enhanced by several orders of m agni tude; for divalent cations the reaction rate in system 4 (or 6) increases in the follow ing order: Z n 2+ < C o2+ < P d2+ < N i2+ < C u2+ (O ’C onnor et al., 1968; N unez and E ichhorn, 1962). It is also well docum ented th at the catalytic effect of the m etal ion is observed just after (and n ot before) the form ation of the Schiff base (N unez and E ich horn, 1962; M artell, 1982). It is obvious th at in the case of m echanism A the system (Schiff base) shifts, due to m etal activation, along the reaction coordinate tow ards the final state 5, i.e. the com plex should be closer to the species 5 th an the free, u n coordinated Schiff base. This should be reflected in redistribution of the charge density (enhanced electron density on the a-carb o n accom panied by an ad eq u ate lowering of this density on the a-h ydrogen) and in the geom e try around the a -C atom (change of the bond angles due to rehybridization from sp3 to sp2, a tendency of the Ca - H bond to becom e p erp en dicular to the salicylaldim ine plane coupled with a planarization of the Ca -C ß bond). O n the o th e r hand, according to m echanism B the Schiff base is in the first (rate determ ining) step activated by the m etal ion tow ards nucleophilic attack by R 3O H so that, in agreem ent with Unauthenticated Download Date | 6/18/17 10:57 PM 574 J. Sivy et al. ■Mechanism of Vitamin B6-Catalyzed Reactions the theory of charge controlled A d N2 reactions (Flem ing, 1976), one would expect an en h an ce m ent of the positive charge on the azom ethine carbon upon introduction of the m etal ion. From the above it is clear th a t in o rd er to study the m echanism of the catalytic (e.g. racem ization) reaction it is necessary to m o n ito r changes in geom etry and distribution of the electron density associated with the transfer of th e Schiff base into the chelate. In this w ork, single-crystal X -ray dif fraction and quantum -chem ical calculations w ere chosen for this purpose. The crystal structure of one derivative belonging to class 4 was investi gated in this p a p e r and the rem aining w ere re trieved from the C am bridge Structural D atabase (A llen et al., 1979). The salicylaldehyde chelates w ere chosen over pyridoxal chelates since the for m er m ore readily provide good crystals, and C u ” was chosen over o th e r m etals because of the high reaction rate for copper-catalyzed reactions (N unez and E ichhorn, 1962; M artell, 1982). Experimental Selection o f the com pounds All com pounds selected for this study are listed in Table II. They differ in the n atu re of the am ino acid and of the additional ligand L. The glycinato chelates w ere not included in th e analysis because of uncertainty which of the tw o C “ - H bonds is actually cleaved in the catalytic reaction. Since, to our know ledge, no Schiff base of salicylaldehyde and an am ino acid has been studied crystallographically, we have chosen for this purpose the know n structure of ch lo ro -trip h en y l-(0 -ethyl-N salicylideneglycinato) Sn,v (L ee et al., 1990) in which the O -ethyl-N -salicylideneglycinato ligand is m onodentately coord in ated via the ph enolate oxygen to the tin atom , i.e. it contains an un coordi nated azom ethine nitrogen and hence may be re garded, to a good approxim ation, as the m etal-free Schiff base. X-ray structure o f 4 e The com plex [C u (sal-g lu )(p y rid in e)] (4e) (s a l-g lu = N -salicylideneglutam ate) was p repared by allowing of [C u (sa l-L -g lu )(H 20 ) 2]. H 20 to react with an equim olar am o u n t of pyridine in a stirring ethanolic solution at 6 0 -6 5 °C for 0.5 h. A fter cooling to room tem p eratu re the precipitate was collected by filtration and recrystallized from ethanol to give w ell-developed dark-green crystals. Analysis for C i7H 16N 20 5Cu (394.89) Calcd C 51.71 H 4.08 N 7.09, Found C 51.52 H 4.12 N 6.99. A crystal of size 0.3 x 0.2 x 0.2 mm was selected for the structure analysis. The unit cell param eters were refined by a least-squares fit of positional angles of 15 reflections with 5 < 2 0 < 26°. The intensities were m easured on a Syntex P2] dif fractom eter using graphite-m onochrom atized C u K a radiation and the 0 - 2 0 scanning technique in the range 0 < 20 < 100°. The scan speed in the interval 4.88-29.3° m in -1 was controlled a u to matically, with each reflection scanned 1° (in 2 0 ) above and below the K a doublet. The background was m easured at each end of the scan for one half of the scan time. Two standard reflections m oni tored after every 98 scans showed th at no correc tion for instrum ent instability or crystal decay was required. O f the 1696 unique reflections recorded, 1410 with I > 1.96o(I) w ere classified as observed and used for the structure analysis. Crystal data: Form ula weight M x = 394.9, m o n o clinic, space group P 2 x!n, a = 8.128(2), b 10.649(3), c = 19.113(5) A , ß = 95.47(2)°, V = 1646.7(7) Ä 3, Z = 4, [i = 2.19 m m “ 1, qx = 1.59 g- cm “3, F(000) = 804, M oK a, X = 0.71069 Ä , room tem perature. The structure was solved by P atterson and F ou rier m ethods and refined on F by block-diagonal least-squares with anisotropic therm al param eters assigned to all non-hydrogen atoms. Positions of the H atom s H 1 - H 9 , which w ere found on a difference Fourier map, were refined while the rem aining (H 1 0 -H 1 6 ) were fixed at calcu lated positions; therm al param eters of all the H atom s were set to 0.5 A 2 higher than Beq of the associated C or O atoms. The function Z w (IF0 l - IFc I)2 was minim ized by using unit weights (w = 1) for all the observed reflections. Final residuals were R = 0.062, wR = 0.059, S = 1.22. In the final cycle (A /o)max = 0.043, (AQ)max = 0.30, (A0 )min = -0.45 e • A -3. The scattering factors for the neutral atom s w ere taken from In te r national Tables, 1974. All crystallographic calcu lations w ere carried out with the X R C 83 program package (Pavelcik et al., 1985). Prelim inary results Unauthenticated Download Date | 6/18/17 10:57 PM J. Sivy et al. ■Mechanism of Vitamin B6-Catalyzed Reactions 575 of the crystal stru ctu re of 4 e have been reported previously (K rätsm är-Sm ogrovic et al., 1985). Table I. Final atomic coordinates (xlO4) and equivalent isotropic thermal parameters Beq (A2) with E.S.D.'s in parentheses*. Beq = 4/3 YZ. BVj c?j, ctj. 'j M O calculations Atom E lectronic stru ctu res in term s of total atom ic charges, W iberg indices and orbital energies were o btained from a local version of the IN D O /2 p ro gram (Boca, 1989) by using a fixed geom etry constructed on th e basis of know n X-ray struc tures - for all six chelates studied. Initial geo m etries of the m etal-free Schiff bases were derived from the X -ray stru ctu re of the corresponding che late p aren ts by rem oval of the copper atom and com pleting the freed valencies on the phenolate and carboxylate oxygens by H atoms. Subsequent optim izations using A M I (D ew ar et a l, 1985) have revealed only slight torsional rearrangem ent indicating th at the p lanar conform ation of the Schiff base ligand observed in the chelate is also a low -energy conform ation for the ligand itself. CO(l) 0(1) 0(2) 0(3) 0(4) 0(5) N(l) N(2) C(l) C(2) C(3) C(4) C(5) 0(6) C(7) 0(8) 0(9) 0(10) 0(11) 0(12) 0(13) 0(14) 0(15) 0(16) 0(17) R esults and D iscussion Final atom ic coordinates for 4 e are given in Table I. R elevant structural p aram eters and the total atom ic charges in the catalytically interesting p art of the chelates studied are com pared in Tables II and III, respectively. A s the atom ic charges calculated for the six m etal-free Schiff bases w ere alm ost identical, only the m ean values are given in Table III. y X 1450(2) 2117(7) 986(7) 1122(7) -3793(7) -1977(8) 512(8) 2223(8) -617(11) -1231(11) -745(13) 399(13) 1001(11) 1299(10) 1930(11) 668(11) -1079(11) -2300(12) 3102(10) 3604(10) 4672(11) 5227(11) 4732(11) 3694(11) 3108(11) 1301(1) 61(5) 2585(5) 2983(6) -412(6) -1393(8) 2430(6) 358(6) 3315(8) 4117(8) 4017(9) 3106(9) 2333(8) 2303(8) 949(8) 233(8) 346(9) -581(9) -876(8) -1263(8) -2305(8) -2968(9) -2611(9) -1600(8) -630(8) z Beq [A2] 4547(1) 5238(3) 3813(3) 2683(3) 2671(3) 2100(4) 5251(3) 3781(3) 5036(5) 5523(6) 6219(5) 6435(5) 5941(5) 3201(4) 3082(4) 2591(4) 2843(5) 2477(5) 5146(4) 4496(4) 4456(5) 5049(6) 5692(5) 5756(4) 3847(4) 6.52(4) 5.57(18) 5.85(17) 6.51(19) 7.18(21) 9.82(28) 5.07(20) 5.41(21) 5.92(31) 6.77(35) 7.38(33) 7.13(35) 5.97(29) 5.63(27) 5.82(28) 5.66(27) 6.31(30) 6.50(30) 5.23(25) 5.15(25) 6.06(26) 6.70(32) 6.55(31) 5.81(28) 5.58(26) * Anisotropic thermal parameters, H-atom coordinates, F0/Fc tables, and complete lists of geometrical param eters are available at the authors. The overall geom etry of 4 e (Fig. 3) shows the usual features of this type of com plex, perhaps with the exception th at the coordination around the Cu atom is exactly square-planar. This is sub- Table II. List of compounds3 studied here and their relevant geometric parametersb. Compound N -C a -C N -C a -CP C -C a-CP C=N C = N -C a-CP C = N -C a-H Ref. 4a 4b 4c 4d 4e 4f usbd 107.4 108.5 107.3 107.5 109.6 105.3 111.8 109.5 112.3 112.7 111.7 112.6 108.3 109.1 110.2 108.3 109.1 110.0 114.8 1.270 1.275 1.286 1.285 1.267 1.288 1.303 83.3 70.6 73.7 72.8 75.9 74.0 -39.8C -46.6C -48.8 -47.7C -50.3 -41.8 18 19 20 21 this work 22 13 a The compounds are designated as follows (see also Fig. 2): 4a: R i = CH3, L = pyrazole; 4b: R, = CH3, L = NCO; 4c: R, = CH2Ph, L = NCO; 4d: R, - (CH2)2COOH, L = H20 ; 4e: Rj = (CFb)2COOH, L = pyridine; 4f: R, = CH(CH3)2, L = h 2o. b E.S.D.’s for the bond angles range from 0.2 to 0.6°, for the C=N bond length from 0.003 to 0.011 Ä, and for the torsion angles from 0.3 to 0.7° (C =N -C “- C P) and from 0.6 to 1.0° (C = N -C “-H ). c Position of the hydrogen calculated, i.e. not actually found in the difference Fourier synthesis. d Uncoordinated Schiff base (see text). Unauthenticated Download Date | 6/18/17 10:57 PM J. Sivy et al. ■Mechanism of Vitamin B6-Catalyzed Reactions 576 Table III. INDO/2 net atomic charges. Compound3 Qc Qn Ra-C qa-H 4a 4b 4c 4d 4e 4f usbb 0.26 0.25 0.25 0.26 0.26 0.26 0.20 -0.02 -0.01 -0.03 -0.05 -0.05 -0.02 -0.22 0.05 0.06 0.07 0.05 0.03 0.06 0.11 -0.01 -0.02 -0.02 -0.01 -0.02 -0.01 -0.02 a For designation of the compounds see the footnote of Table II. b Atomic charges for the uncoordinated Schiff base (usb) are means of six values (see text). stantiated by the fact th at no atom occurs at a dis tance sho rter than 3.3 A in the axial direction and by the coplanarity of Cu w ith the four donor atoms. The p ro to n a te d side chain carboxyl group is not involved in the coordin atio n to th e copper atom , but it form s a strong hydrogen b ond with the carbonyl oxygen 0 3 [ 0 —0 = 2.593(5) A] of a n o th er m olecule at ( - 0 .5 - jc, -0 .5 + y, 0.5 - z), thus form ing chains going along the diagonal of the unit cell. A s the space group (P 2 \/n) is centrosym m etrical, the crystal structure of 4 e is a racem ic m ixture of [Cu(sal-D ,L-glu)(pyridine)] even though an optically active p aren t com plex [C u(sal-L -glu)(H 20 ) 2] was used in the reaction with pyridine (see above). This again d em o n strates that the racem ization of the Schiff base ligand readily occurs under mild conditions even in neutral or weak acidic aqueous or alcoholic solutions (K rätsm är-Sm ogrovic et al., 1991). A s can be seen in Table II, bond angles at the a-C atom for the six chelates studied range from 105.3 to 114.8° with the m ean value of 109.7° cor responding exactly to the tetrah ed ral (sp3) value. M oreover, the N - C a - C angle in all six chelates is even sm aller than that found in the u n coordinated Schiff base (111.8°). Similarly, as shown by the to r sion angles presented in Table II, it is the C a - C |3 bond rath er than the Ca - H bond which tends to be oriented perpendicularly to the jt system of the molecule. Inspection of Table III fu rth e r shows th at although chelation of the Schiff base causes a low ering of the positive charge on the a-carb o n , the lowering is not at the expense of reduced elec- Fig. 3. A perspective drawing of the 5-enantiomer of 4e derived from the X-ray coordinates. Unauthenticated Download Date | 6/18/17 10:57 PM J. Sivy et al. ■Mechanism of Vitamin B6-Catalyzed Reactions tron density on th e a-hydrogen. H ow ever, as the sem iem pirical quantum -chem ical m ethods of IN D O type are generally know n to underestim ate the charge polarization, the results of the charge d istribution should be taken with caution. N ever theless, this draw back of the IN D O m ethods is supposed to affect the C - H polarization in both the m etal-free Schiff bases and the corresponding chelates in a sim ilar m anner. From the above it is clear th a t o u r results are not consistent with reaction m echanism A, which predict a direct activation of the am ino acid by the ji system o f the Schiff base and the m etal ion. In contrast, according to m echanism B the catalytic reaction is in itiated by nucleophilic attack of R 3O H on the azom ethine carbon of the Schiff base. A s show n in Table III, the characteristic fea ture of all the com plexes studied is an 0.05 to 0.06 increase in the positive charge on this atom rela tive to the m etal-free Schiff bases. C om parison of the charges on the azom ethine nitrogen (Table III) shows th at the enhanced positive charge on the azom ethine carb o n results from electron w ith draw al by the co p p er atom. It is notable th at the azom ethine b ond shortens from 1.303 to 1.2671.288 A upon co p p er introduction (Table II). This interval corresp o n d s to the range 1.27-1.29 A generally accepted for a pure C=N double bond (B urke-L aing and Laing, 1976). It should be em phasized in this context that IN D O /2 was unable to rep ro d u ce th e observed increase in the C=N 577 bond o rd er so th at the m etal-induced en hance m ent of the positive charge on the azom ethine car bon is probably even higher than that indicated by IN D O /2. The above electron distribution coupled with the high double-bond character in the azom ethine group is in line with enhanced susceptibility of this carbon tow ard nucleophilic attack by a solvent w ater or alcohol m olecule (Flem ing, 1976). That the addition of the nucleophile to the Schiff base double bond is indeed charge controlled was veri fied by com parison of the fro n tier orbital energies: the L U M O energy for the six chelates studied here was calculated by IN D O /2 to range from 1.7 to 2.0 eV while the H O M O energy of w ater or al cohols is know n to be < - 1 0 e V (Flem ing, 1976); this indicates that the H O M O /L U M O energy sep aration is large enough for the fro n tier orbital interactions to be neglected. In conclusion, the results of this study strongly indicate th at the catalytic effect of the copper ion resides in electron w ithdraw al from the azo m ethine linkage and in increase in the C=N bond polarization. B oth these electronic effects enhance the electrophilicity of the im ine carbon. 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