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The electron bonded cytosine–guanine complex
Chemical Physics Letters 420 (2006) 221–224 www.elsevier.com/locate/cplett
The electron bonded cytosine–guanine complex Abraham F. Jalbout *, Ludwik Adamowicz Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA Received 2 November 2005; in final form 29 November 2005 Available online 19 January 2006
Abstract In this work, we have performed quantum chemical calculations on a new form of the guanine–cytosine anion, in which the excess electron is suspended between the two systems. The vertical detachment energy calculations performed with the MP2 method yield a value of 0.40 eV, showing a stability relative to the addition of this excess electron. The effects of removing the excess electron are also presented, whereby a significant change in the structure occurs. In these geometry optimizations of the neutral structure initiated with geometry of the anion, we obtain a hydrogen-bonded dimer with energy lower than the anion. Ó 2005 Published by Elsevier B.V.
1. Introduction In this work, we have investigated a new form of the cytosine–guanine (C–G) anion complex based on the ability of this molecule to form a solvated electron system [1– 4]. From our previous studies on this system [5], we have come to the conclusion that this molecule resulted in a stable covalent as well as dipole bound anionic state. From this study, it has been shown that these anions should exist in the gas-phase, and that the p and orbital density was primarily concentrated near the cytosine ring. It was also shown that an excess electron would probably first be attracted and captured in a dipole-bound state, due its interaction with the dipole-field of the dimer. Although, the covalent and dipole-bound anions of the C–G system are relatively stable, the excess electron can potentially be captured in another form. Other previous studies on the calculations of uracil Æ H2O, uracil Æ HF [6] and the uracil dimer [7] show that an alternative form exists were by stabilization of the excess electron occurs inbetween the molecular species. These computed systems contain electron density inside the cluster and not on the surface, as is the case of dipole-bound anions. *
Corresponding author. Fax: +1 520 621 8407. E-mail addresses: [email protected], [email protected] (A.F. Jalbout). 0009-2614/$ - see front matter Ó 2005 Published by Elsevier B.V. doi:10.1016/j.cplett.2005.11.117
Therefore, the diffuse electron, has two points of contact, in which the molecules are held together only by their attraction to the excess electron. These structures are formed through two important steps. First, a dipole-bound anion is formed through the attachment to one of the subunits. Then, the second molecule will attach to the dipolebound electron on its opposite side relative to the point of contact between the first molecule and the excess electron. After this you obtain a system that is connected via a suspended electron. These systems have subsequently been labeled as ‘anions with internally suspended electrons’ or AISE for short. The weak interaction between the two as a result of the electron attachment is similar to hydrogen bonding and we therefore, have labeled this as an e-bond. These AISE molecules belong to a group of anions that are labeled as solvated electrons, since the excess electron is trapped between two molecules. Although they are higher in energy than typical dipole-bound or covalent anions, our previous studies have shown [4] that their stability in the gas phase is probably due to kinetic factors, and that they can form at elevated temperatures [8,9]. We attempt to explore the AISE of the cytosine–guanine (C–G) system in this Letter. This is part of our ongoing exploration of alternatives to dipole-bound anion formation, since many nucleic acid bases do not have the necessary dipole moments for this to occur. In our previous calculations of the uracil dimer system [6] we have shown
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that the excess electron is trapped in-between the molecular framework. However, in this work, we show that a relatively stable bound state of the excess electron is formed, in spite of the fact that no hydrogen bonding, occurs in the C–G system. We have concluded that instead electrostatic and dispersion forces act together to stabilize this excess electron. 2. Calculations and discussion The purpose of our presented calculations has to do with the location of a minimum of the cytosine–guanine (G–C) anion potential energy surface that corresponds to the AISE and then the calculation of the vertical detachment energy (VDE). The VDE is important due to the fact that it is a value that can be extracted from photoelectron spectroscopy (PES) experimental procedures [8]. The quantum chemical calculations performed in this work have been carried out with the GAUSSIAN03 [10] software package and the 3D plots of the molecular orbitals were carried out with the MOLDEN package [11], for which the results will be described below. The geometry optimizations were performed with the MP2 method and with the basis set consisting of the standard 6-31++G** basis augmented with six diffuse Gaussian sp-shells with exponents equal to 0.01, 0.002, 0.0004, 0.00008, 0.000016 and 0.000032, and a p-shell with exponent 0.036. This special basis set will be described as 6-31++G**X in our following discussions in the next sections. These additional orbitals were placed at the hydrogen atom located closest to the position direction of the molecular dipole on the cytosine molecule. Therefore, by using these Gaussians with small exponents in the basis, we allow the excess electron to escape from the system if this would allow for lower system energy of the system. We have seen that this basis set will not preferentially change the geometry of the calculated structures. When basis sets chosen are very diffuse (as in this case), it really does not make a difference where you put the extra basis functions. In our experiences with these systems, the geometries obtained will not change from the position of the basis set. Preferentially, the electron may attach to the outside of the molecular framework (as in dipole bound anions). However, the molecules in this work have their dipoles facing each other, making the excess electron favoring a position between the two molecules. As previously mentioned, the major cause of the stability of the C–G AISE system will probably be due to the electrostatic in addition to dispersion forces [12]. Therefore, one must be careful to adequately describe these effects with an appropriate method that we have tested in the past. In addition, the geometry of the structure is almost identical to the default one. Fig. 1 depicts the structure and HOMO of the AISE C–G system. It can be seen from this figure that the rings are almost perpendicular to one another, and are separated by distance of around ˚ , with the excess electron occupying the region 4.5 A
Fig. 1. Two views of the equilibrium MP2/6-31++G**X structure of the C–G AISE and the HOMO of the excess electron occupied by the system plotted at a counter spacing value of 0.02 bohr 3/2.
between the molecules. This intermolecular distance is ˚ of the more than two times the distance of around 1.7 A neutral C–G dimer shown in Fig. 2 (which will be discussed later). It is interesting to note, that while our previous studies on the covalent and dipole-bound anion of the hydrogen bonded C–G system [5] show a hydrogen bonded structure, our new calculations reveal that the guanine molecule interacts with the excess electron that is dipole-bound to cytosine, forming a weak bond. Thus, the guanine molecule performs this task via a ‘spectator’ relationship. After we finished the optimization of the anion structure, we wanted to calculate the vertical detachment energy (VDE) for this molecule. In this computation, we took the MP2 geometry from the previous calculation, and calculated the MP2/6-31++G**X energy of the neutral molecule at the anion geometry. Table 1 shows the results of these calculations. As we can see the VDE value of 0.40 eV shows a strong interaction of the dimer with the excess electron for a solvated electron system. This is similar to our previously calculated [5] VDE value of 0.565 eV for the covalent cytosine–guanine anion, and 0.95 eV for the electron affinity of the dipole-bound anion of this molecule. Our new cytosine–guanine AISE complex shows good correlation to the uracil–uracil AISE system which has a VDE of 0.47 eV [6], and is typical for these systems.
A.F. Jalbout, L. Adamowicz / Chemical Physics Letters 420 (2006) 221–224
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Fig. 2. MP2/6-31++G**X equilibrium structure of the C–G complex obtained in the geometry optimization initiated with the AISE equilibrium geometry.
Table 1 Calculations of the vertical electron detachment energy (VDE) of the AISE of the cytosine–guanine complexa Method HF//MP2c HOMO/LUMO MP2//MP2 Methods MP2//MP2
Anion 932.0604667 0.01540 934.8937859
Neutral//anionb
VDE
932.0517428 0.00826 d 934.8790609 Neutral//neutrale 934.9224789
0.2374 0.4004
a Calculations performed with the 6-31++G**X basis set. Total and HOMO/LUMO energies in hartrees (Eh); VDE in eV. Only the valence electron correlation has been included in the calculations. b Calculations performed at the equilibrium anion geometry. c This notation denotes the level of theory used in the calculation//the level of theory used in optimizing the geometrical structure. d The difference between the HOMO of the anion molecule and the LUMO of the neutral species at the anion geometry. e Calculations performed at the equilibrium geometry of the neutral complex obtained in the geometry optimization initiated with the equilibrium geometry of the anion.
Our final set of calculations was performed to see what happens when the excess electron is removed from the anion. To calculate this effect, we performed MP2/631++G**X geometry optimizations of the neutral C–G structure initiated from the equilibrium geometry of the AISE system. The result was the system in Fig. 2. The molecule appears to be planar, and is very different from the AISE structure. Similar results have been seen for the uracil dimer system [6] for which the only way the AISE is a local minimum on the potential energy surface if it has an excess electron suspended between the two rings. In addition, Table 1 presents the energy of this minimum structure. It can be seen that the energy is around 0.78 eV lower than the AISE energy. It can be concluded that based on this energy difference the C–G AISE system is metastable, and should probably transform to the neutral molecule or another type of anion such as a dipole-bound anionic state or a covalent anionic state under certain conditions.
3. Conclusions We have computed a stable guanine–cytosine (G–C) dimer that is connected by an excess electron forming a stable anion. In our computed anion, the excess electron is solvated by the cytosine and guanine molecules, in a nonhydrogen bonded fashion therefore stabilized by electrostatic and dispersion forces. This so-called e-bond is similar to an H-bond in the fact that it is weak, but it is perhaps more interesting due to the way in which it is formed. The potential energy surface around the minimum has not yet entirely been explored, however, due to the strength of the interaction of the cytosine and the guanine molecules with the excess electron and their orientation, suggests that the minimum probably has a considerable depth. As our calculations also showed, the adduct complex has a higher energy than the neutral complex at its geometry obtained from the optimization initiated with the anion geometry used to initialize the calculation. The global minimum is expected to be a hydrogen bonded system, however, we have explored the orientation in which the excess electron is stabilized in a perpendicular molecular position, with the cytosine and guanine dipoles facing each other, trapping the excess electron. The structure that we have obtained is a minimum for the AISE anion potential energy surface. Our present calculations suggests that the AISE is a relatively metastable form of the anion, at least when the excess electron attachment occurs between two molecules. Similar behavior has been predicted with the uracil dimer system [6], as well as the hydrogen fluoride trimer anion system. For these systems it has been argued both theoretically and experimentally that certain conditions in the PES experiment [8] allow for these molecular complexes to form. The purpose of this work was not to explore the potential energy surface around the minimum, rather than ponder on the potential of the two systems forming a stable
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solvated anionic state. The present calculations pose a very interesting problem for experimental verification. For this type of study, an advanced form of photoelectron spectroscopy (PES) can be applied to help combat this problem of whether this type of system can exist or not. Our calculations can be used as a starting point for these experiments. Acknowledgments We thank the University of Arizona for valuable resources as well as Jesus Mungia for interesting conversations. References [1] E.J. Hart, M. Anbar, The Hydrated Electron, Wiley-Interscience, New York, 1970.
[2] W.L. Jolly, Metal-Ammonia Solutions, Dowden, Hutchinson, and Ross Inc., Stroudburg, PA, 1972. [3] R.N. Barnett, U. Landman, C.L. Cleveland, J. Chem. Phys. 88 (1988) 4429. [4] J. Schnitker, P.J. Rossky, J. Chem. Phys. 85 (1987) 3462. [5] J. Smets, A.F. Jalbout, L. Adamowicz, Chem. Phys. Lett. 342 (2001) 342. [6] A.F. Jalbout, C.S. Hall, L. Adamowicz, Chem. Phys. Lett. 354 (2002) 128. [7] C.S. Hall, L. Adamowicz, J. Phys. Chem. A 106 (2002) 609. [8] M. Gutowski, C.S. Hall, L. Adamowicz, J.H. Hendricks, H.L. de Clercq, S.A. Lyapustina, J.M. Nilles, S.-J. Xu, K.H. Bowen Jr., Phys. Rev. Lett. 88 (2002) 143001. [9] A.F. Jalbout, C.A. Morgado, L. Adamowicz, Chem. Phys. Lett. 383 (2004) 317. [10] M.J. Frisch et al., GAUSSIAN03, Revision B.05, Gaussian Inc., Pittsburgh, PA, 2003. [11] G. Schaftenaar, J.H. Noordik, J. Comput.-Aided Mol. Des. 14 (2000) 123. [12] D.M.A. Smith, A.F. Jalbout, J. Smets, L. Adamowicz, Chem. Phys. 260 (2000) 45.
The electron bonded cytosine–guanine complex Abraham F. Jalbout *, Ludwik Adamowicz Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA Received 2 November 2005; in final form 29 November 2005 Available online 19 January 2006
Abstract In this work, we have performed quantum chemical calculations on a new form of the guanine–cytosine anion, in which the excess electron is suspended between the two systems. The vertical detachment energy calculations performed with the MP2 method yield a value of 0.40 eV, showing a stability relative to the addition of this excess electron. The effects of removing the excess electron are also presented, whereby a significant change in the structure occurs. In these geometry optimizations of the neutral structure initiated with geometry of the anion, we obtain a hydrogen-bonded dimer with energy lower than the anion. Ó 2005 Published by Elsevier B.V.
1. Introduction In this work, we have investigated a new form of the cytosine–guanine (C–G) anion complex based on the ability of this molecule to form a solvated electron system [1– 4]. From our previous studies on this system [5], we have come to the conclusion that this molecule resulted in a stable covalent as well as dipole bound anionic state. From this study, it has been shown that these anions should exist in the gas-phase, and that the p and orbital density was primarily concentrated near the cytosine ring. It was also shown that an excess electron would probably first be attracted and captured in a dipole-bound state, due its interaction with the dipole-field of the dimer. Although, the covalent and dipole-bound anions of the C–G system are relatively stable, the excess electron can potentially be captured in another form. Other previous studies on the calculations of uracil Æ H2O, uracil Æ HF [6] and the uracil dimer [7] show that an alternative form exists were by stabilization of the excess electron occurs inbetween the molecular species. These computed systems contain electron density inside the cluster and not on the surface, as is the case of dipole-bound anions. *
Corresponding author. Fax: +1 520 621 8407. E-mail addresses: [email protected], [email protected] (A.F. Jalbout). 0009-2614/$ - see front matter Ó 2005 Published by Elsevier B.V. doi:10.1016/j.cplett.2005.11.117
Therefore, the diffuse electron, has two points of contact, in which the molecules are held together only by their attraction to the excess electron. These structures are formed through two important steps. First, a dipole-bound anion is formed through the attachment to one of the subunits. Then, the second molecule will attach to the dipolebound electron on its opposite side relative to the point of contact between the first molecule and the excess electron. After this you obtain a system that is connected via a suspended electron. These systems have subsequently been labeled as ‘anions with internally suspended electrons’ or AISE for short. The weak interaction between the two as a result of the electron attachment is similar to hydrogen bonding and we therefore, have labeled this as an e-bond. These AISE molecules belong to a group of anions that are labeled as solvated electrons, since the excess electron is trapped between two molecules. Although they are higher in energy than typical dipole-bound or covalent anions, our previous studies have shown [4] that their stability in the gas phase is probably due to kinetic factors, and that they can form at elevated temperatures [8,9]. We attempt to explore the AISE of the cytosine–guanine (C–G) system in this Letter. This is part of our ongoing exploration of alternatives to dipole-bound anion formation, since many nucleic acid bases do not have the necessary dipole moments for this to occur. In our previous calculations of the uracil dimer system [6] we have shown
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that the excess electron is trapped in-between the molecular framework. However, in this work, we show that a relatively stable bound state of the excess electron is formed, in spite of the fact that no hydrogen bonding, occurs in the C–G system. We have concluded that instead electrostatic and dispersion forces act together to stabilize this excess electron. 2. Calculations and discussion The purpose of our presented calculations has to do with the location of a minimum of the cytosine–guanine (G–C) anion potential energy surface that corresponds to the AISE and then the calculation of the vertical detachment energy (VDE). The VDE is important due to the fact that it is a value that can be extracted from photoelectron spectroscopy (PES) experimental procedures [8]. The quantum chemical calculations performed in this work have been carried out with the GAUSSIAN03 [10] software package and the 3D plots of the molecular orbitals were carried out with the MOLDEN package [11], for which the results will be described below. The geometry optimizations were performed with the MP2 method and with the basis set consisting of the standard 6-31++G** basis augmented with six diffuse Gaussian sp-shells with exponents equal to 0.01, 0.002, 0.0004, 0.00008, 0.000016 and 0.000032, and a p-shell with exponent 0.036. This special basis set will be described as 6-31++G**X in our following discussions in the next sections. These additional orbitals were placed at the hydrogen atom located closest to the position direction of the molecular dipole on the cytosine molecule. Therefore, by using these Gaussians with small exponents in the basis, we allow the excess electron to escape from the system if this would allow for lower system energy of the system. We have seen that this basis set will not preferentially change the geometry of the calculated structures. When basis sets chosen are very diffuse (as in this case), it really does not make a difference where you put the extra basis functions. In our experiences with these systems, the geometries obtained will not change from the position of the basis set. Preferentially, the electron may attach to the outside of the molecular framework (as in dipole bound anions). However, the molecules in this work have their dipoles facing each other, making the excess electron favoring a position between the two molecules. As previously mentioned, the major cause of the stability of the C–G AISE system will probably be due to the electrostatic in addition to dispersion forces [12]. Therefore, one must be careful to adequately describe these effects with an appropriate method that we have tested in the past. In addition, the geometry of the structure is almost identical to the default one. Fig. 1 depicts the structure and HOMO of the AISE C–G system. It can be seen from this figure that the rings are almost perpendicular to one another, and are separated by distance of around ˚ , with the excess electron occupying the region 4.5 A
Fig. 1. Two views of the equilibrium MP2/6-31++G**X structure of the C–G AISE and the HOMO of the excess electron occupied by the system plotted at a counter spacing value of 0.02 bohr 3/2.
between the molecules. This intermolecular distance is ˚ of the more than two times the distance of around 1.7 A neutral C–G dimer shown in Fig. 2 (which will be discussed later). It is interesting to note, that while our previous studies on the covalent and dipole-bound anion of the hydrogen bonded C–G system [5] show a hydrogen bonded structure, our new calculations reveal that the guanine molecule interacts with the excess electron that is dipole-bound to cytosine, forming a weak bond. Thus, the guanine molecule performs this task via a ‘spectator’ relationship. After we finished the optimization of the anion structure, we wanted to calculate the vertical detachment energy (VDE) for this molecule. In this computation, we took the MP2 geometry from the previous calculation, and calculated the MP2/6-31++G**X energy of the neutral molecule at the anion geometry. Table 1 shows the results of these calculations. As we can see the VDE value of 0.40 eV shows a strong interaction of the dimer with the excess electron for a solvated electron system. This is similar to our previously calculated [5] VDE value of 0.565 eV for the covalent cytosine–guanine anion, and 0.95 eV for the electron affinity of the dipole-bound anion of this molecule. Our new cytosine–guanine AISE complex shows good correlation to the uracil–uracil AISE system which has a VDE of 0.47 eV [6], and is typical for these systems.
A.F. Jalbout, L. Adamowicz / Chemical Physics Letters 420 (2006) 221–224
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Fig. 2. MP2/6-31++G**X equilibrium structure of the C–G complex obtained in the geometry optimization initiated with the AISE equilibrium geometry.
Table 1 Calculations of the vertical electron detachment energy (VDE) of the AISE of the cytosine–guanine complexa Method HF//MP2c HOMO/LUMO MP2//MP2 Methods MP2//MP2
Anion 932.0604667 0.01540 934.8937859
Neutral//anionb
VDE
932.0517428 0.00826 d 934.8790609 Neutral//neutrale 934.9224789
0.2374 0.4004
a Calculations performed with the 6-31++G**X basis set. Total and HOMO/LUMO energies in hartrees (Eh); VDE in eV. Only the valence electron correlation has been included in the calculations. b Calculations performed at the equilibrium anion geometry. c This notation denotes the level of theory used in the calculation//the level of theory used in optimizing the geometrical structure. d The difference between the HOMO of the anion molecule and the LUMO of the neutral species at the anion geometry. e Calculations performed at the equilibrium geometry of the neutral complex obtained in the geometry optimization initiated with the equilibrium geometry of the anion.
Our final set of calculations was performed to see what happens when the excess electron is removed from the anion. To calculate this effect, we performed MP2/631++G**X geometry optimizations of the neutral C–G structure initiated from the equilibrium geometry of the AISE system. The result was the system in Fig. 2. The molecule appears to be planar, and is very different from the AISE structure. Similar results have been seen for the uracil dimer system [6] for which the only way the AISE is a local minimum on the potential energy surface if it has an excess electron suspended between the two rings. In addition, Table 1 presents the energy of this minimum structure. It can be seen that the energy is around 0.78 eV lower than the AISE energy. It can be concluded that based on this energy difference the C–G AISE system is metastable, and should probably transform to the neutral molecule or another type of anion such as a dipole-bound anionic state or a covalent anionic state under certain conditions.
3. Conclusions We have computed a stable guanine–cytosine (G–C) dimer that is connected by an excess electron forming a stable anion. In our computed anion, the excess electron is solvated by the cytosine and guanine molecules, in a nonhydrogen bonded fashion therefore stabilized by electrostatic and dispersion forces. This so-called e-bond is similar to an H-bond in the fact that it is weak, but it is perhaps more interesting due to the way in which it is formed. The potential energy surface around the minimum has not yet entirely been explored, however, due to the strength of the interaction of the cytosine and the guanine molecules with the excess electron and their orientation, suggests that the minimum probably has a considerable depth. As our calculations also showed, the adduct complex has a higher energy than the neutral complex at its geometry obtained from the optimization initiated with the anion geometry used to initialize the calculation. The global minimum is expected to be a hydrogen bonded system, however, we have explored the orientation in which the excess electron is stabilized in a perpendicular molecular position, with the cytosine and guanine dipoles facing each other, trapping the excess electron. The structure that we have obtained is a minimum for the AISE anion potential energy surface. Our present calculations suggests that the AISE is a relatively metastable form of the anion, at least when the excess electron attachment occurs between two molecules. Similar behavior has been predicted with the uracil dimer system [6], as well as the hydrogen fluoride trimer anion system. For these systems it has been argued both theoretically and experimentally that certain conditions in the PES experiment [8] allow for these molecular complexes to form. The purpose of this work was not to explore the potential energy surface around the minimum, rather than ponder on the potential of the two systems forming a stable
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solvated anionic state. The present calculations pose a very interesting problem for experimental verification. For this type of study, an advanced form of photoelectron spectroscopy (PES) can be applied to help combat this problem of whether this type of system can exist or not. Our calculations can be used as a starting point for these experiments. Acknowledgments We thank the University of Arizona for valuable resources as well as Jesus Mungia for interesting conversations. References [1] E.J. Hart, M. Anbar, The Hydrated Electron, Wiley-Interscience, New York, 1970.
[2] W.L. Jolly, Metal-Ammonia Solutions, Dowden, Hutchinson, and Ross Inc., Stroudburg, PA, 1972. [3] R.N. Barnett, U. Landman, C.L. Cleveland, J. Chem. Phys. 88 (1988) 4429. [4] J. Schnitker, P.J. Rossky, J. Chem. Phys. 85 (1987) 3462. [5] J. Smets, A.F. Jalbout, L. Adamowicz, Chem. Phys. Lett. 342 (2001) 342. [6] A.F. Jalbout, C.S. Hall, L. Adamowicz, Chem. Phys. Lett. 354 (2002) 128. [7] C.S. Hall, L. Adamowicz, J. Phys. Chem. A 106 (2002) 609. [8] M. Gutowski, C.S. Hall, L. Adamowicz, J.H. Hendricks, H.L. de Clercq, S.A. Lyapustina, J.M. Nilles, S.-J. Xu, K.H. Bowen Jr., Phys. Rev. Lett. 88 (2002) 143001. [9] A.F. Jalbout, C.A. Morgado, L. Adamowicz, Chem. Phys. Lett. 383 (2004) 317. [10] M.J. Frisch et al., GAUSSIAN03, Revision B.05, Gaussian Inc., Pittsburgh, PA, 2003. [11] G. Schaftenaar, J.H. Noordik, J. Comput.-Aided Mol. Des. 14 (2000) 123. [12] D.M.A. Smith, A.F. Jalbout, J. Smets, L. Adamowicz, Chem. Phys. 260 (2000) 45.