D-Alanine is Analogous to D-Valine or L-Valine That is a Question.doc

Series of Selected Papers from Chun-Tsung Scholars,Peking University (2002)D- Alanine is Analogous to D- Valine or L- Valine: That is a Question Wei Min, Wen-Qing Wang and Zhe-Ming Wang(College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China)Li-Ying Wang, Lei Chen and Feng Deng(Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.O. Box 71010, China)AbstractThe contribution of PVED in phase transition process of D-/L- alanine and valine crystals was confirmed by solid state 1H CRAMPS NMR experiments. It was found that the proton nucleus behaviors of D-alanine are similar to that of L-valine crystal instead of D-valine in this specific phase transition. The X-ray diffraction study indicates that the energy of L-alanine contributed by electroweak force is lower than D-alanine in the crystal situation, but it would be difficult to judge which eantiomer of valine is more stable because of its two kinds of conformations. These facts suggest that the sign of PVED values in alanine and valine crystal systems may be opposite, which also questions the earlier calculations on amino acids that all the naturally occurring L-form is stablized by electroweak force. Keywords:D- and L-alanine and valine, origin of homochirality, phase transition, parity-violating energy difference, 1H CRAMPS NMR spectra1. IntroductionWhile the phenomenology of parity-violating (P-odd) effects in atoms has been observed more than a decade ago,1 interest in parity-violating weak neutral current (WNC) at the molecular level have focused on the calculation2-6 and experimental search for parity-violating energy difference (PVED) between enantiomers of a chiral molecule, and a link between the asymmetry of biochemisty and the homochiral scenario under terrestrial and extraterrestrial conditions has been intensively searched for.7-11 In 1998, a novel theoretical discovery,2 reconfirmed by independent computational techniques,3,5,6,12 that PVED for several molecular examples is calculated by configuration interaction singles (CIS) and other more advanced theoretical methods to be larger by one to two orders of magnitude than anticipated by the earlier single determinant excitation-restricted Hartree-Fock (RHF) methods, has led to a renewed interest in experimental testing P-odd effects in molecules. Research focused on amino acids is especially important because these substances were presumably present on the prebiotic earth. Among these molecules, alanine has been repeatedly used as a prototype for parity violation calculation in L-amino acids because of its relative simple structure. While all earlier studies on amino acids reported the naturally occurring L-form to be stabilized by WNC, 13,14 two recent contributions dealings with electroweak quantum calculations of alanine have convincingly defied this long held belief.15,16 Quack et al. introduced the multi configuration linear response (MC-LR) approach to parity-violating effects for alanine in gas and solution phase, and proposed that there is no direct relation between Epv and the mechanism of selecting a given homochiral form.15 These results were fully supported by the complementary study by Schwerdtfeger et al.,16 and once again, the conclusive statement is that nothing can be said about the relative thermodynamical stability of the L- or D- forms of an amino acid. The question “D- or L- alanine, which is lower in energy” is now a discussion reopened by theoretical physicists. 16 Theoretical calculations on PVED values of D-/L-alanine and valine in condensed phase have not been reported so far. To avoid the complicated conformational changes and solvent effects, we select alanine and valine single crystal to search for the P-odd effects between enantiomers of amino acid molecules. 2. Experimental2.1 Sample preparation and characterization.D-/L-alanine and valine single crystals were characterized by elemental analysis (C, H and N) and a good agreement was shown between the theoretical and experimental data. By using X-ray diffraction crystallography at 293K, the cell dimensions of D-/ L-alanine crystals were determined as the same space group P21P21P21, orthorhombic, a = 6.0250 , b = 12.3310 , c = 5.7841 , V = 429.72 3, It indicates that D-alanine and L-alanine are pure single crystals containing no crystal water. The rotation angle z of the D- and L- alanine and valine solution were measured on Polarimeter PE-241 MC at 293 K with the wavelength of 589.6 nm. By using the formula of a = z /(L C), the corresponding a values of eantiomers were shown to be the same.2.2 1H CRAMPS solid state NMR measurements. 1H NMR multipulse spectra were run on a Varian InfinityPlus400 spectrometer with resonance frequency 400.12 MHz. A 4mm Chemagnetics double probe was used for the variable temperature CRAMPS experiment. A BR-24 multiple sequence was employed with a p/2 pulse width of 1.6 ms and 64 scans with a 2s recycle delay to acquire CRAMPS spectra. Spin rate was 2.5 kHz and the number of scans was 64. Chemical shifts were referenced to tetramethylsilane (TMS) for 1H NMR measurements.2.3 X-ray diffraction studies.X-ray diffraction data were measured at Nonius B.V. Demo Lab in Peking University. Data were collected on a nonius KappaCCD diffractometer with graphite monochromated Mo-K radiation. Cell parameters were obtained by the global refinement of the positions of all collected reflections. Integration was carried out by the program DENZO-SMN, and data were corrected for Lorentz-polarization effects and for absorption using the program SCALE-PACK. Solution was obtained by direct methods and followed by subsequent Fourier-difference synstheses (SHELXL97). A total of 12922 was collected, of which 3526 (R1= 0.0359 and wR2 = 0.0787) was unique; equivalent reflections were averaged. All non-hydrogen atoms refined anisotropic, while all hydrogens were assigned to calculated positions. The structure was refined by a full-matrix least-squares technique to find the results R1 (0.496) and wR2 (0.0840), using the weighting scheme. In the case of alanine and valine crystal, the carboxyl groups are ionized and the molecules exist as a zwitterion. The present crystal of valine contains two crystallographically independent molecules A (trans form) and B (gauche form) in the asymmetric unit, which are the rotational isomers with two kinds of conformation.3. Results and Discussions3.1 Evidence of chiral discriminating phase transition Novel parity-violating and chiral discriminating phase transitions of D/L-alanine and valine crystals were first recognized by specific heat measurement with differential scanning calorimetry, DC-Magnetic susceptibilities and laser Raman experiments. 17-21 The experimental results were repeated for the same samples after several thermal cycles from 77K 300K. The shape and magnitude of the specific heat jump and the peak position are approximately the same for different pairs of D-/L- samples, which shows that the phase transition is reproducible and reversible. 3.2 1H CRAMPS solid state NMR measurements results Fig 1. Temperature dependence of peak widths of -H, -H of D-/L-alanine crystalsIn these specific phase transitions, for the sake of investigating the temperature-dependent proton nuclei dynamics of valine and alanine molecules further, solid state 1H CRAMPS NMR experiments were performed and the widths of proton peaks of D-/L-alanine and valine samples are shown in Figure 1 and 2. Figure.1 displays that four peaks widths of a-H and b-H of alanine samples experience distinct maximum in the temperature range of 230240K. So we suppose that both D-/L-alanine may undergo a phase transition in this temperature range. As for D-alanine, the values of -H peak width agree with those of L-alanine, however, the variation degree of -H peak width is much fiercer than that of its enantiomer in the transition process. Similar phenomena, that D/L-samples undergo a phase transition and the behaviors of -H nucleus are much different between the two enantiomers, are also discovered in valine molecules (shown in Figure.2). Fig2. Temperature dependence of peak widths of -H, -H and -H of D-/L-valine crystalsFrom the above data, the peak linewidth represent spin-spin relaxation times T2. The half height linewidth is given by D1/2 = 1 / p T2. R2 = T2-1 is the sum of several contributions, which corresponding to the different mechanisms, namely quadrupolar R2Q, dipolar interaction R2D, chemical shift anisotropy R2CSA and spin-spin coupling (J-coupling) R2J. In the CRAMPS experiment, the dipolar interaction R2D and the chemical shift anisotropy R2CSA are averaged out to zero. By choosing a spin 1/2 nucleus (1H), the nuclear quadrupole moment is equal to zero, thus R2Q cancels out. The J-coupling R2J might be the predominant contribution. This part of study indicates the obviously different J-coupling R2J values between D- and L- amino acids in the phase transition process, and suggests that the parity-violating WNC may contribute to the sudden decrease of spin-spin relaxation time of -H nucleus in alanine and valine molecules in the transition processes. It is noteworthy that there are also much differences among the variation degrees of -H, -H and -H peaks of valine molecules. The width of -H peak changes little with the temperature varying; on the other hand, -H peaks width varies the most violently of all in the transition process. In the case of D/L-alanine, the changes of -H peak widths are much more sensitive than that of -H, too. These experimental results and the phenomena discussed above, that -H nucleus but not -H or -H show some clues for the WNC playing a parity-violating role in the J-coupling R2J values of D- and L-alanine and valine molecules, indicate that the smaller the distance between the proton nucleus and the asymmetric carbon atom, the more precipitously its spin relaxation times decrease in the phase transition process, and -H nucleus may be the molecular active parity-violating effects centers compared with other two kinds of proton nucleus.3.3 The possibly opposite sign of PVED values in alanine and valine crystal systems Recently Quack et al. showed that Epv as a function of the conformational angle of the carboxylato plane with respect to the Ca-CO2 -Ha for the gas and solution properties of alanine, which provide no support whatsoever for a systematic accessible conformations.15 Meanwhile, calculation parity-violating energy shifts for the 13 stable conformers of gaseous alanine by Schwerdtfeger et al. 16 also indicated that the stabilization of a certain enantiomer is strongly dependent on its flexible and highly dynamic structure of the biomolecule and unknown effects of its environment (naturally occurring L-alanine is preferred for only seven of the investigated structures), which allows no definite conclusion on the relative stability of the two chiral forms to explain the origin of homochirality in living organisms. However, either magnitudes or the directions of any PVED values in solid state amino acids crystals have not been obtained in theoretical or experimental studies. Meaningfully, in our transition process, the variation of -H peak width of D-alanine width is much fiercer than that of L-alanine; in the case of valine, the -H peak width of L-valine are clearly much wider than those of its enantiomer. These mean that in the condensed matter which has no flexible and highly dynamic structure and unknown effects of its environment, the proton nucleus behaviors of D-alanine are similar with that of L-valine crystal instead of D-valine in this specific phase transition, and suggest that the sign of PVED value in alanine and valine crystal systems may be opposite. COONHHHHHHH Fig 3(a) Conformatin of the alanine molecule with explicit definition of the angle COONHHMetHHHMet Fig 3(b) Conformatin of the valine molecule with explicit definition of the angle To investigate the proton nuclear behavior difference between the alanine and valine systems, we measured the structure of D- and L-alanine and valine by using X-ray diffraction. We found that the crystal structures of eantiomers are almost the same. Quack et al. have showed that while all values of a correspond to the L-configuration of alanine, the sign of DEPV changes repeatedly from negative (that is, L-alanine is more stable than the D-alanine) to positive values (D-alanine is more stable than its L-form) through the complete range between 0 and 360. The PVED between two enantiomeric structures at a given angle (a) can be formulated as the following equation. PVED = D EPV (a) EPV, L (a ) - EPV, D (a ) = 2 EPV, L (a ) Fig 4. Epv of valine molecule as a founction of the orientation of carbixylato group of zwitterionic L-valine obtained with the EXT/CHF basis set 4In the case of crystal, the rotational angle and the crystal conformation are fixed. So we calculated the conformational angle of alanine and valine, respectively, applying the obtained crystal structure data. Unit-cell dimensions of D-valine and D/L-alanine crystals at 270K are shown in table 1. The of alanine crystal in 270K is calculated to be 45.20 (54), and the corresponding Epv is about -410-20 Eh by the calculation of Quack et al.15 This means that in the crystal situation, the energy of L-alanine contributed by electroweak force is lower than D-alanine. However, the X-ray diffraction results show clearly that the present crystal of D-valine contains two crystallographically independent molecules A (trans form) and B (gauche form) in the asymmetric unit, which are the rotational isomers with two kinds of conformations, and two dihedral angle are 20.08 (51) and 48.26 (52), respectively (shown in Fig 3). According to the EXT/CHF results performed on valine molecule by Zanasi et al.4, Epv is negative when=20.08 but positive when =48.26 ( shown in Fig 4). Therefore, the obtaining of the exact sign and magnitude of PVED in valine crystal should take into account the conformational distribution of valine molecules in real crystal environment. Thus, it would be difficult to judge which eantiomer of valine is more stable because of its two kinds of conformations. Table 1 Unit-cell dimensions of D-valine and D/L-alanine crystal at 270K Samples D-Alanine L-AlanineCrystal systemOrthorhombicSpace groupP212121Unit cell Dimensions ()a = 6.0073(5)6.0095(5)b = 12.3030(7)12.3388(7)c = 5.7732(4)5.7904(3)Volume (3)426.69(5)429.36(5)Z4Atomic coordinatesXYZXYZ O(1)0.7280(1) 0.08419(6) 0.3723(1)0.4489(1) 0.18494(6) 0.2388(1) O(2)0.4488(1) 0.18497(6) 0.2388(1)0.7279(1) 0.08414(6) 0.3725(1) C(1)0.4744(2) 0.16118(8) 0.6442(2)0.4746(2) 0.16115(8) 0.6445(2) C(2)0.5591(2) 0.14146(7) 0.3978(1)0.5593(2) 0.14146(7) 0.3980(2) H(4)0.441(2) 0.237(1) 0.656(2)0.440(2) 0.238(1) 0.656(2)Dihedral angle(degree)-45.52(50)45.20(54) SamplesD-ValineCrystal systemMonoclinicSpace groupP21Unit cell Dimensions ()A=9.6686(5)b=5.2556(3) c=11.9786(6) Volume (3)608.64(6)Z4Atomic coordinatesXYZXYZ O(1)0.8550(1)0.4668(2)0.3961(1)O(3)0.3715(1)0.10696(2)0.3997(1) O(2)0.7742(1)0.758(2)0.3687(1)O(4)0.2922(1)0.7003(2)0.3366(1) C(1)0.6347(1)0.4253(2)0.3084(1)C(6)0.1330(1)0.10441(2)0.3459(1) C(2)0.7646(1)0.3098(3)0.3638(1)C(7)0.2771(1)0.9284(2)0.3632(1) H(4)0.5612(15)0.3090(30)0.3078(12)H(15)0.657(13)0.9310(30)0.3781(10)(degree) 20.08(51) 48.26(52)4. ConclusionThe X-ray diffraction study indicates that the energy of L-alanine contributed by electroweak force is lower than D-alanine in the crystal situation, but it would be difficult to judge which eantiomer of valine is more stable because of its two kinds of conformations. This phenomenon, together with the similarity of proton nucleus behaviors between D-alanine and that of L-valine crystal unraveled by temperature-dependent 1H CRAMPS NMR experiments, questions the idea that, as one naively might assume, D-alanine is analogous to D- valine. And it seems decreasingly likely that the cause for the preference to biochemical evolution on earth can be assigned to the intrinsic chirality present at the elementary particle level. 22. AcknowledgmentsThis research was supported by the grant of 863 program (863-103-13-06-01) and National Natural Science Foundation of China (29672003). 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