ALBERT

Notes: A method of expansion of molecular orbital wave functions into valence bond (VB) functions is extended to molecular fragments. The wave function is projected onto a basis of mixed determinants, involving molecular orbitals as well as fragment atomic orbitals, and is further expressed as a linear combination of VB functions, characteristic of structural formulas of the fragment but whose remaining bonds are frozen. Structural weights for the fragment are deduced from this expression. Delocalized molecular orbitals are used as a startpoint, as they are after an ordinary SCF calculation. Wave functions of medium-sized molecules may be analyzed with reasonable storage requirements in a computer.

Notes: The generalized branching diagram (GBD) spin representation is defined as the method of sequentially coupling together a number of subsystem spin eigenfunctions using the general rules of angular momentum coupling. It is shown that any GBD representation may also be obtained by Schmidt orthogonalizing a set of cannonical spin-paired (SP) functions, provided the SP basis is suitably ordered. The ordering procedure used is well suited to computer implementation. This is a generalization of results known in the literature for the Yamanouchi-Kotani and for the Serber spin representations.

Notes: In the present work the total energy of a Ne atom at T = 0 K is calculated as a function of a spherical container radius. The calculation is based on the Thomas-Fermi (TF) equation, which is solved approximately by an equivalent variational principle. The effect of an approximate exchange correction on the variational TF energy values is investigated.

Notes: Diagonal hypervirial relations are applied to enclosed one-dimensional systems when wave functions obey Dirichlet boundary conditions. A general formula for the energy is derived and it shows a striking difference with the usual formulas through an “extra” term. It constitutes a generalization of previous ones for the virial theorem when there exist nonusual boundary conditions. The values obtained are compared with other approximate methods. Several extensions are proposed.

Notes: Exact formulas for 147 overlap integrals between Slater-type orbitals with equal screening constants are presented in the most simplified form. This represents all combinations of orbitals with quantum numbers: 1 ≤ N ≤ 5, 0 ≤ L ≤ 3, and M ≤ L. The formulas are automatically generated by computer using the “C-matrix” single-center expansion method. There are no limitations to the applicability of this method to orbitals of higher quantum numbers.

Notes: A simple method is described for the calculation of resonance energies (RE) of linear acenes based on their number of Kekulé structures. The values obtained for the first five linear acenes are used to graph-theoretically calculate RES of a wide variety of benzenoid hydrocarbons. Excellent linear relationships are found between RES and each of A-II, graph-theoretical (GT), Hess-Schaad (HS), and Dewar resonance energies (SCF). These relations apply to 42 hydrocarbons and lead to the following equations: A-II = 0.084RE + 0.080 (0.9999); GT = 0.072RE + 0. 135 (0.9832); HS = 0. 106RE + 0. 169 (0.9889); and SCF = 0.316RE + 0. 166 (0.9899). Correlation coefficients are shown in parentheses. A linear relation also exists between RES and the square roots of the wavelengths of the UV spectra of hydrocarbons of the linear acenes and phene series. Least-squares analysis of the data leads to the following equation: RE= 0.412(λ)½ -15.479, with a correlation coefficient equal to 0.9903, in which λ is the wavelength of the β band of the UV spectra of these hydrocarbons. The method predicts no resonance energies for both open chain polyenes and the radialenes.

Notes: A direct method for calculating resonant states in reactive scattering is suggested, permitting us to obtain the characteristics of multichannel resonances (partial width amplitudes). The method is based on the construction of a Laurent expansion of the scattering matrix S(∊ -iΓ/2) in the complex plane. The position of the poles of the S matrix are derived by solving the dynamical problem with complex energy values. The residue at the pole gives all the information concerning the partial widths. The method is applied to a linear triatomic reactive scattering problem. The properties of the resonant states in the H + H2 system are calculated as an example. Two broad resonances are found which have not been reported in previous calculations. The interference of overlapping resonances is shown to have a profound effect on the energy dependence of the transition probabilities.

Notes: An approximate technique of generating orthonormality-constrained one-electron orbitals for the description of open-shell systems is suggested. The “off-diagonal Lagrangian-multiplier problem” is circumvented by using a common potential for both the closed- and open-shell electrons. This common potential is generated by a scaling of the usual exchange potential of Hartree-Fock theory. The problem of choosing an appropriate scaling parameter (μ) is considered from both variational and perturbative points of view. The relationship of the present method with some other approximate open-shell theories is explored. The numerical results of computations carried out at the semiempirical MO level are presented in order to bring to light the dependence of computed molecular properties on the magnitude of the scaling parameter.

Notes: Ab initio and INDO LCBO-MO calculations are carried out on glyoxal, 1,3-butadiene, and acrolein in order to analyze the qualitative failure of INDO-like methods to describe conformation energies in these molecules. Following the method of Brunck and Weinhold for ethanelike systems we identify the principal bond-antibond interactions contributing to the glyoxal barrier, their dependence on dihedral angle and substituent, and their relative magnitudes as calculated by ab initio and INDO SCF-MO theory. We find a gross disparity in the INDO representation of π* interactions which leads to a grossly exaggerated estimate of the stability of gauche conformers in these molecules. These findings appear to have serious implications for the applicability of INDO-like theories to conformational problems in π-bonded molecules, including those of biological interest.

Notes: The localized MO's (LMO's) of 1,2-dioxethane in its ground state and along the dissociation reaction path (to formaldehyde products) are generated using Boys' criteria for localization. The total charge density in each LMO is partitioned into atomic and overlap densities and the binding or antibinding character of each LMO is discussed in terms of the forces exerted on the nuclei by these densities. The driving force for the dissociation reaction is shown to arise essentially from the atomic dipole forces exerted on the oxygen nuclei by their lone-pair LMO's. The characterization of a saddle point on the potential energy surface has been discussed in terms of the electrostatic equilibrium between forces exerted by the electron clouds “incomplete following” and “preceding.” The differences between the LMO's obtained from the two Hartree-Fock solutions to which the SCF procedure converges have been discussed.

Notes: Based on the all-valence ZDO SCF approximation a procedure for estimating the basis set superposition error (BSSE) in semiempirical CNDO/INDO methods has been proposed. The results of the calculation show that the BSSE effect may improve the results obtained from the standard CNDO/INDO supermolecule calculation. The estimated BSSE effect enables one to explain some recently reported artificial structures for water and ethylene dimers.

Notes: In this paper a variational principle has been formulated for obtaining an approximate solution of Poisson's equation for the potential of a donor ion embedded in Si. A comparison of a two parameter approximate analytical potential with the exact numerical potential shows excellent agreement for several electron concentrations. It is also found that the present theory, using the concept of a “spatially variable dielectric constant,” leads to a donor-ion potential which deviates significantly from the potential of Dingle, which has been the traditional starting point of calculations of electron mobility limited by ionized-impurity scattering.

Notes: Chemists do not take the view that chemistry can be derived from quantum mechanics by computations too literally; the difficulties are illustrated by the double bond concept. Quantum mechanics is very useful, but recent calculations have been mainly concerned with physical properties rather than chemical processes. In general, the chemical formula plays a central role in all interpretation of quantum-chemical results, thus suggesting that the chemical bond is a preexistent notion. Moreover, the Born-Oppenheimer approximation seems to be necessary for deriving the existence of bonds between atoms previously assigned to suitable positions. Recent analyses by Claverie and Diner, Woolley, Primas, and others are briefly recalled, concluding with an expression of hope that use of more general Hamiltonians can lead to progress in obtaining a fully independent quantum theory of chemistry.

Notes: An SCF LCAO MO calculation on the methane-methane-methane system is presented, in order to analyze the deviation from pairwise additivity of the interaction energy. Three-body terms are shown to be remarkably similar to those of noble gas trimers both in magnitude and in their dependence on the geometrical arrangements of the three molecules.

Notes: Making use of different information measures, the Pauli exclusion principle and the first Hund rule were found to be related to a trend toward acquiring a maximum information content of the atoms and molecules, and more generally, for any fermion system. The bosons conversely always have a minimum (zero) information content with respect to the permutation symmetry of their wave functions. Some new interpretations of the Pauli principle are presented.

Notes: A first principles method based on an APW-k · p band structure calculation is derived in order to obtain the self-consistent eigenenergies, crystal potential, and electronic density. The simplicity and extensions of the method are discussed, including comparison with the results obtained by the use of the Chadi and Cohen special points technique.

Notes: An analytic atomic active electron model potential adjusted to experimental single-particle energy levels is used to generate wave functions for the valence and excited states of O1+, F2+, Ne3+, Na4+, and Mg5+. Using these wave functions in conjunction with the Born approximation and the LS-coupling scheme, we calculate optical oscillator strengths for excitations from the 1s22s22p3(4S3/2) ground state. The results are compared to experimental data and other calculations. Systematic trends along the isoelectronic sequence are discussed.

Notes: Ab initio computations have been performed on the compounds AlH2BH4 and AlH2C3H5 in order to achieve a better understanding of the peculiar characteristics of the metal to ligand bond. Our results suggest a bidentate coordination for the tetrahydroborate complex and an η3 coordination for the allyl complex. Due to the nonrigidity of the BH4- and allyl complexes, possible interconversion paths between different coordination modes have also been analyzed.

Notes: Synchrotron radiation has been used to determine the fluorescence decay parameters of a tryptophan-containing oligopeptide, Lys-Trp-Lys, bound to nucleic acids. All fluorescence decay curves can be fitted by a sum of two exponentials. The two lifetimes very likely correspond to two conformational states of the oligopeptide. The mean fluorescence lifetime of the peptide is not markedly affected upon binding to nucleic acids even though the fluorescence quantum yield is strongly reduced. A model is presented that accounts for the existing fluorescence data: two consecutive complexes are formed both involving electrostatic interactions. In one of the complexes the tryptophyl ring is stacked with the nucleic acid bases and its fluorescence is completely quenched. The other complex emits a fluorescence having characteristics which are similar to those of the free peptide.

Notes: The molecular size is found to play an important role in carbonic anhydrase (CA) inhibition by sulfonamides. Significant correlation is obtained between the inhibitory power of meta-substituted analogs and the van der Waals volume (Vw) of the substitutents. This provides a theoretical basis to map the active sites in enzyme and find the nature of sulfonamide-receptor binding. It is inferred that in addition to well known binding of sulfamyl group with Zn2+ ion of the enzyme, the meta substituent of sulfonamides interacts with some secondary binding site and this interaction is argued to be of van der Waals type.

Notes: The paper reports comparison of electrostatic charge and energy distribution on the basis of the CNDO/2 method for six forms of prostaglandins-PGF2α, PGF1β, PGE1, PGE2, PGB1, and PGA1-having diverse physiological action. The isopotential mapping done in three dimension showed that the lower value of electrostatic potential and proximity of the two low energy regions around O9 and O11 in PGE2 and PGF2α is probably responsible for their higher abortificient activity. We also compare here the variation of the long- and short-range interaction between ring-chain and chain-chain portion of different forms and compared them with the variation in their action.

Notes: The conformational energy of acetylcholine is minimized with respect to the distances between nonbonded atoms with the help of the Bremermann method of unconstrained global optimization. The set of distances for which the energy is the absolute minimum is then used to calculate the coordinates of all the atoms and hence the conformation of the molecule. The simplest type of potential function, namely the classical potential function is chosen for the calculation. The major advantages of this method are (i) that the starting point need not be close to the actual solution, (ii) that it gives the global minimum, irrespective of the starting point, (iii) that it is very general and can be used for any type of potential function, and (iv) that it does not require the computation of gradients. The results obtained are in very good agreement with those of other workers.

Notes: Some aspects of the use of simplified formulas for the evaluation the interaction energy between two molecules is discussed. This energy is obtained as the sum of four terms: electrostatic, polarization, dispersion, and short-range (exponentially decreasing) repulsion. The effect of using several approximations is considered (i) for representing the charge distributions of the isolated molecules (which determine the electrostatic and polarization terms), and (ii) for evaluating the short-range repulsion term. The various charge distributions considered are semiempirical atomic net charges (Del Re + Pariser-Parr), atomic charges and dipoles (CNDO) and corresponding “effective” atomic charges, and many-centered multipole distributions obtained from ab initio SCF calculations (charges, dipoles, and quadrupoles located on the atoms and the middles of segments joining pairs of atoms, whether chemically bonded or not). As concerns the short-range repulsion, the various procedures considered are a sum of atom-atom terms, a sum of bond-bond terms, and the use of anisotropic van der Waals radii for heteroatoms (oxygen and nitrogen). In all cases, the dispersion energy is obtained as a sum of atom-atom terms (of the R-6 type). These various procedures are checked in the case of the interactions between nucleic acid bases, for two rather different kinds of configurations, namely, hydrogen bonded and stacked. This comparison reveals a rather complicated picture, namely the results got from the various levels of approximation of the molecular charge distribution lead to different degrees of agreement according to different situations, e.g., for guanine-cytosine interactions, qualitative agreement is found between the various methods as concerns the relative order of stacked and hydrogen bonded situations, while agreement is much less satisfactory for adenine-uracile interactions. One of the main conclusions is that a sufficiently sophisticated representation of the molecular charge distribution is required in order to get reliable results for all possible configurations of a complex. Such comparative studies should bring significant help as concerns the development of the reliable simplified procedures for evaluating intermolecular interaction energies.

Notes: pKa(NH3+) values of N,N-dihydroxyethylglycine (bicine) and N-[tris(hydroxymethyl)methyl]-glycine (tricine) have been determined by the Irving-Rossotti method in an aqueous medium at 25, 30, 35, 40, 45, and 50°C and at different ionic strengths (I = 0.1, 0.5, and 1.0). Plots between pKa(NH3+) and 1/T for various ionic strengths have been obtained and the values of slopes have been used to calculate the ΔH, ΔS, and ΔG for the dissociation reactions of bicine and tricine. The ΔH, ΔS, and ΔG values for bicine were found to be 10.6 ± 0.6 kcal mol-1, -1.9 ± 1.8 e.u., and 11.1 ± 0.06 kcal mol-1, respectively, and for tricine 11.2 ± 0.6 kcal mol-1, 1.6 ± 1.6 e.u., and 10.7 ± 0.06 kcal mol-1, respectively. The pKa(NH3+) values decrease with rise in temperature but the influence of ionic strength is not significant.

Notes: Infrared spectroscopy has been employed to study possible base pair interactions, in nonpolar media, between O6-methylguanine and uracil, cytosine and adenine; and between derivatives of N4-hydroxycytosine and adenine. The association constants of O6-methylguanine with uracil, cytosine, and adenine are well below 1M-1, whereas those for interaction of 1-methyl-N4-methoxycytosine and its 5-methyl derivative with adenine are identical, K = 14M-1. The significance of the latter finding is discussed in relation to the conformation of the exocyclic N4-methoxy group. Quantum chemical calculations, with the aid of the perturbation method, were carried out for the interaction of O6-methylguanine with uracil, cytosine, and adenine, to establish the most energetically favoured configurations for interactions of the free bases, and of the same base pairs in the B form of DNA. The role of the conformation of the exocyclic  - OCH3 group in O6-methylguanine is discussed. The relevance of both the experimental and theoretical results to mutagenesis by O6-methylguanine and N4-hydroxycytosine is examined.

Notes: The laser microprobe mass analyzer (LAMMA) is a new type of analytical instrument. It is a combination of a laser microscope with a time-of-flight (TOF) mass spectrometer. By focusing an UV pulse laser beam onto the specimen positive and negative atomic and molecular ions are formed which are detected by the TOF mass analyzer. The detection limits reach 10-20 g for some elements in an excited sample volume of 10-13 cm3. With the aim of finding out whether the LAMMA instrument is capable of quantitative measurements on very small biological samples the 23Na+ and 39K+ contents of single mycobacterial cells (M. tuberculosis H 37 Ra) were measured and the results were compared with those obtained from “integral” methods (AAS, NAA, tracer). Furthermore, the influence of different temperatures applied during the washing procedure of the bacteria on the distribution of the Na+/K+ ratio within the cell population was investigated. First attempts to trace isonicotinic acid hydrazide (INH) in bacteria were made by comparison of the LAMMA spectra of INH treated and untreated cells.

Notes: Proton affinities, geometries with optimized parameters, and net atomic charges are reported for guanidine-, methyl-, amino-, and fluoro-substituted guanidines. The results are obtained using the ab initio SCF method as implemented by the GAUSSIAN-70 computer program with a 6-31G basis set. Basicity is discussed in terms of electron distribution and intramolecular attraction forces.

Notes: The electronic density of states for d bands was calculated accurately in the tight-binding approximation for a simple cubic lattice. Numerical values of the density of states for five subbands as well as of the total density of states were tabulated for the set of values of two-center integrals of the magnitudes corresponding to those estimated for real crystal.

Notes: New theoretical developments based upon hypervirial analysis of enclosed systems are given. Systems which obey unsymmetrical boundary conditions are analyzed. Several results which were given by the authors in two previous communications are generalized.

Notes: Ab initio MODPOT/VRDDO/MERGE calculations were carried out on carcinogenic 3-methylcholanthrene (3-MCA) and its metabolites. The results for 3-MCA were compared to our earlier similar calculations for carcinogenic benzo(a)pyrene (BP). Both compounds 3-MCA and BP are carcinogenic and are metabolically activated by similar mechanisms but in different positions. Both the calculated wave functions for 3-MCA and BP and the electrostatic molecular potential contour maps generated from these wave functions correctly reflect the similarity of mechanisms of metabolic activation and the differences in position. Our calculated results both for BP and for 3-MCA reflect accurately their experimentally observed behavior. Thus this combination of theoretical techniques can be used with confidence to describe the behavior of the polycyclic aromatic hydrocarbons (PAH's) and their metabolites. The ab initio MODPOT/VRDDO method incorporates two very desirable options into our fast ab initio Gaussian programs: MODPOT-ab initio effective core model potentials - and a charge-conserving integral prescreening approximation which we named VRDDO (variable retention of diatomic differential overlap). For orbital energies and population analysis the MODPOT/VRDDO results agree to essentially three decimal places with completely ab initio calculations using the same valence atomic basis set. For this series of very closely related congeners our recent MERGE technique which allows reuse of integrals from a common skeletal fragment was used. The ab initio MODPOT/VRDDO/MERGE calculations were carried out for 3-MCA, 3-MCA oxides, 3-MCA dihydrodiols, and 3-MCA dihydrodiolepoxides. The metabolites investigated were 3-MCA 9,10-oxide; 3-MCA 7,8-oxide; 3-MCA 9,10-dihydrodiol [trans(axial, axial); trans(equatorial, equatorial); cis(axial, equatorial); cis(equatorial, axial)]; and 3-MCA 9,10-dihydrodiol-7,8-epoxide [for both conformations A and B of the dihydrodiol and for all stereoisomers of the dihydrodiolepoxides relative to below and above the plane: ααα, and ααβ αβα αββ βαα βαβ ββα and βββ (most stable)]. Calculations were also carried out for opening of the C7—O—C8 epoxide ring both towards C7 and C8 for the most stable isomer Aβββ (above the ring). Opening the epoxide ring between C7 and O leads to a more stable intermediate than opening the epoxide ring between C8 and O. Again, however, as with opening the epoxide ring in BP 7,8-dihydrodiol-9,10-epoxide there is no buildup of positive charge on C7 in the 3-MCA metabolites as postulated by some cancer researchers, but rather the C7 becomes slightly more negative. Nor is there a buildup of negative charge on the O atom, but rather it becomes slightly more positive. As the epoxide ring is opened further than 90° for the O—C7—C8 or O—C8—C7 angles, there appears to be a possible mixing of configurations that is being investigated further.

Notes: Both short-range and long-range intermolecular interaction energies between two prophin molecules, both in their ground state, separated by a range of interplanar distances from 3 to 4.5 Å, are estimated using the standard perturbation theory. The results indicate that a 60° rotated sandwich structure is the most stable conformation for the dimer. Certain translated as well as the perfect sandwich forms are other favoured structures. The stability of the dimer is mainly due to the van der Waals interactions with no significant contribution from the charge-transfer interactions. Biochemical implications of these findings are discussed.

Notes: The electrostatic molecular potential contour maps were calculated for carcinogenic 3-methylcholanthrene (3-MCA) and a number of its metabolites {3-MCA 7,8-oxide and 3-MCA 9,10-oxide; 3-MCA 7,8-dihydrodiols[several stereoisomers: A trans(equatorial, equatorial) and A cis(equatorial, axial)]; 3-MCA 9,10-dihydrodiol-7,8-epoxide A βββ and 3-MCA 9,10-dihydrodiol-7,8-epoxide A αβα}. The maps were generated from our ab initio MODPOT/VRDDO/MERGE wave functions calculated for these species. The results of these maps for 3-MCA [similarly to our results for the maps we generated for benzo(a)pyrene (BP)] show that these electrostatic molecular potential contour maps can be used to indicate favored positions of attack for electrophilic species, such as “electrophilic” oxygen to form an epoxide as well as for positive ion attack. The 3-MCA maps indicate the favored site for attack and the pathways. The maps around 3-MCA 9,10-oxide and around 3-MCA 9,10-dihydrodiol-7,8-epoxide indicate the directional preferences for proton assisted epoxide ring opening. The maps around the 3-MCA dihydrodiols indicate that while for certain stereoisomers the “electrophilic” oxygen will prefer to attack from below, for other isomers it will prefer to attack from above. This gives great insight into the stereochemical preference for formation of different 3-MCA 9,10-dihydrodiol-7,8-epoxides.

Notes: Infrared spectra in the NH, OH, and C=O stretching regions are reviewed for various methylated and halogenated 2(4)-oxopyrimidines and uracils, as well as other nucleic acid derivatives, in the vapor phase and in low-temperature matrices. The 2-oxopyrimidines are predominantly in the enol form both in the vapor phase and in low-temperature matrices. By contrast, the 4-oxopyrimidines exhibit comparable populations of the keto and enol forms, with KT ≈ 1-2, and a difference in chemical binding energy between the two forms in the gaseous phase of the order of 1-2 kcal/mol. The observed tautomeric equilibria in the gas phase point to the need for a drastic revision of interpretations of theoretical methods, and simultaneously provide the appropriate quantitative data necessary for testing the results of quantum mechanical calculations. In sharp contrast to other heterocyclic systems, several of the bases found in natural nucleic acids were found to exist predominantly in the keto or amino forms, as in the solution phase. In particular, uracils exist predominantly in the keto form. This has made possible, for this class of compounds, to evaluate the heats of sublimation and vaporization, and to relate these data to hydrogen bonding and stacking interactions in the condensed phases. Examples are presented of base analogs which do exhibit appreciable tautomerism in solution. Some biological implications of the foregoing are presented in relation to the types of heterocyclic bases found in natural nucleic acids, and to concepts of spontaneous and induced mutagenesis.

Notes: Nonbonded interaction energies have been calculated for various conformations of the diester giving explicit consideration to the lone-pair electrons. As suspected from an earlier calculation on the dipeptide, such inclusion of the lone-pair effect leads to significant differences in the conformational potential energy map. The diester is shown to be more constrained than the dipeptide. The impact of this constrained geometry and the possible occurrence of cis residues on configuration statistics of poly(lactic acid) chains have been studied. Contrary to expectation the inclusion of cis isomers does not explain the paradoxical high negative temperature coefficient of ln C∞.

Notes: The single excited doublet states of some small molecule cations calculated by CI method in the framework of semiempirical CNDO and INDO models are correlated with the photoelectron spectra of the parent molecules. The purity of the Koopmans transitions is used to discuss the one-particle interpretation of photoelectron bands by comparison with nonempirical many-body calculations. Furthermore, empirical relations are applied with respect to the evaluation of shake-up energies.

Notes: The ab initio valence bond method has been used to study the ground and the lowest vertical valence ionized states of pyridine. On the basis of our calculations the first two ionization potentials are assigned to π and n electron removals, respectively. The final wave functions have been interpreted in terms of valence bond structures by means of an appropriate population analysis.

Notes: The Racah method, proposed for the evaluation of coefficients of fractional parentage (CFP) for single shell configurations, is generalized for the cases of two and more than two shells. On the basis of the generalized Racah method, we have evaluated one-particle CFP for all states of svpμ electronic configurations. Two-particle CFP are expressed through one-particle CFP and Racah coefficients.

Notes: The FSGO molecular fragment technique has been employed to perform ab-initio SCF-MO calculations on morphine and naloxone in the free-base and N-protonated forms. Particular features of electronic structure which have been investigated are molecular-orbital (MO) density distributions, energies and ordering, as well as the correlation of specific orbitals between different molecular species. It has been found that high-energy occupied and low-energy unoccupied MOS are centered on the aromatic moiety of both drugs, enabling the ring to act either as an electron donor or as an acceptor in a charge-transfer interaction. Comparison of corresponding MOs in the free base and the acid cation of both morphine and naloxone demonstrates that the field of the cationic head causes a dramatic downward shift in orbital energies. Thus in the N-protonated drugs the acceptor capability of the benzene ring is greatly enhanced at the expense of its suitability as a donor. Furthermore, the allyl group of naloxone becomes highly activated as an electron acceptor through N-protonation. Investigation of the molecular electrostatic potential of the free-base species has revealed preferred avenues of approach for electrophilic and nucleophilic entities. However, the N-protonated species shows no regions of attraction for electrophiles. In both the free base and the acid cation, the vicinities of the nitrogen atom and the 3-hydroxy group are found to be favorably disposed for electrostatic interactions with receptor entities possessing the proper charge or polarity. Based on the findings with regard to electronic structure, a simple model has been suggested to explain the binding of morphine and naloxone at the opioid receptor.

Notes: Hemoglobin-catalyzed hydroxylation of aniline may be taken as a model for similar reactions catalyzed by cytochrome P-450. Using ultraviolet-difference spectroscopy and 1H nuclear relaxation techniques, the binding of aniline to hemoglobin was examined. From the magnitude of paramagnetic effects of ferric iron on aniline protons, using the correlation time determined from the magnetic field dependence of water proton relaxation rates, aniline was found to bind to methemoglobins such that the aromatic protons are 8.5 ± 0.7 Å, away from the high-spin Fe3+. A mode of binding is proposed where the aniline molecule is hydrogen bonded to the distal histidine of hemoglobin.

Notes: The solution conformations of two DNA octanucleotides, (GGAATTCC)·(GGAATTCC) and (AAAGCTTT)·(AAAGCTTT), have been investigated by theoretical calculations of NMR shifts. The calculations of proton chemical shifts have been made, taking into consideration the ring current effects and the atomic magnetic anisotropies of the bases. The computed shielding constants for B-DNA, alternating B-DNA, the Levitt propeller-twisted model and the Dickerson propeller-twist model (based on crystallographic data) have been compared with experimentally available shifts. For the (AAAGCTTT)·(AAAGCTTT) double helix the experimental data are available only for the exchangeable protons HN1 and HN3; thus a complete and detailed evaluation is impossible for this system. For (GGAATTCC)·(GGAATTCC) the results indicate that the A·T pairs are propeller twisted à la Levitt and Dickerson.

Notes: Neocarzinostatin, an antitumor protein antibiotic containing an essential nonprotein chromophore, causes single-strand breaks in DNA in vitro. Mercaptans are required for the DNA-cleavage activity, and irradiation of the protein by ultraviolet light destroys this activity. Observations are reported from optical, fluorescence, EPR, and 1H NMR spectroscopy on the irreversible changes induced in neocarzinostatin, and where possible in the isolated chromophore, by ultraviolet irradiation and treatment with mercaptans. For the first time it was found that EPR-detectable short-lived chromophore-dependent radicals are formed during ultraviolet inactivation and mercaptan activation of neocarzinostatin. Mercaptan-induced chromophoric radicals detected in this study may participate in DNA cleavage, but decay unproductively in the absence of DNA. 1H NMR and fluorescence results are consistent with the idea that dissociation of the chromophore from aromatic groups in the protein accompanies inactivation and activation. Both inactivation and activation of the drug involve substantial changes in the structure of the chromophore.

Notes: A model has been proposed to account for many of the intracellular actions of insulin. This model is called the insulin transduction system and consists of coordinated stimulation by insulin of the sodium pump and the Na:H exchange system in the plasma membrane. The primary end result of stimulation of the insulin transduction system is an elevation of intracellular pH, pHi. This model is a biophysical system which depends upon thermodynamic gradients across the plasma membrane and thus is a property only of the intact cell. Insulin is one of several agents that produce mitogenesis, that is, stimulate DNA synthesis and division in cultured cells. Arguments are presented that mitogenesis is triggered by activation of the insulin transduction system with a resulting elevation of PHi.

Notes: The energetics of the α-chymotrypsin charge triad, taking into account the interaction energies of the components of the charge relay system and its surrounding environment, have been calculated. These results are compared with corresponding ab-initio MO energies and thermodynamic values as taken from the literature. The following conclusions can be drawn from this analysis. The ab-initio and interaction calculations yield results which are in good agreement, suggesting that the latter, while computationally easy for implementations, is reliably good for the study of large systems such as enzymes. The theoretical prediction for the most stable state of the charge relay system depends upon the model assumed for the environment. In keeping with available crystallographic data, and thereby allowing for partial hydration of the serine residue, the zwitter ionic state is found to be the most stable.

Notes: Largely derived from experiments in molecular evolution, a theory of the origins of protein synthesis cycles has been constructed. The sequence begins with ordered thermal proteins resulting from the self-sequencing of mixed amino acids. Ordered thermal proteins then aggregate to cell-like structures. When they contained proteinoids sufficiently rich in lysine, the structures were able to synthesize offspring peptides. Since lysine-rich proteinoid (LRP) also catalyzes the polymerization of nucleoside triphosphate to polynucleotides, the same microspheres containing LRP could have synthesized both original cellular proteins and cellular nucleic acids. The LRP within protocells would have provided proximity advantageous for the origin and evolution of the genetic code.

Notes: Highly angularly dependent axial Gaussian-lobe orbitals (AGLO) (up to L = 5) are presented. The angular and radial optimizations of these functions have been realized on the ground of theoretical frameworks, previously reported in the literature and somewhat extended here. The numerical difficulties that can appear in the recombination of elementary integrals over lobes are particularly investigated. It is shown that it is necessary to limit the angular accuracy, i.e., the relevant YLo character, in order to preserve the accuracy of atomic integrals. The proposed p, d, f, g, and h AGLOS satisfy this condition, and can be used with confidence in LCAO-MO-SCF calculations. Their advantages, e.g., for the treatment of large symmetrical inorganic systems containing transition metal atoms, are emphasized.

Notes: The strong-coupling correspondence principle has been used to calculate the T-V transition probabilities in the collinear collision of He and Kr with CO2. For a harmonic CO2 potential the results for He agree well with published quantum mechanical probabilities. For Kr the agreement is less satisfactory but at worst the ratio of quantum to semiclassical transition probability is approximately 0.2. Introduction of anharmonicity in the CO2 potential was found to increase the semiclassical transition probabilities but this may just be due to the lowering of the vibration frequencies.

Notes: A compact and efficient scaled single-zeta basis set has been developed for use in conjunction with the coreless Hartree-Fock silicon effective potential. The scale factors were determined by minimizing the electronic energy of the disilane molecule. Based upon a generalized valence bond computation using this basis, we conclude that the classical concept of localized σ bonds is adequate to fully explain the electronic structure of disilane in analogy to the ethane molecule.

Notes: The coupled-cluster approach to obtaining the bond-state wave functions of many-electron systems is extended, with a set of physically reasonable approximations, to admit a multiconfiguration reference state. This extension permits electronic structure calculations to be performed on correlated closed- or open-shell systems with potentially uniform precision for all molecular geometries. Explicit coupled cluster working equations are derived using a multiconfiguration reference state for the case in which the so-called cluster operator is approximated by its one- and two-particle components. The evaluation of the requisite matrix elements is facilitated by use of the unitary group generators which have recently received wide attention and use in the quantum chemistry community.

Notes: A formalism for dealing with noncanonical Hartree-Fock spin orbitals is presented within the framework of many-body perturbation theory. A test calculation on the planar methyl radical is carried out which displays certain features of open-shell calculations and which demonstrates the viability of using noncanonical spin orbitals. Results are found to be in good agreement with a previous configuration interaction calculation.

Notes: A scheme for obtaining approximate solutions of the electronic Schrödinger equation is formulated within the context of the method of moments. The flexibility of the method of moments is utilized in the construction of a model based on an antisymmetric product of geminals (APG). This APG model is compared with a model based on an antisymmetric product of strongly orthogonal geminals (APSG). As a test example the advocated APG model is applied to the ground state of ammonia. Our best APG function recovers 37% of the total molecular correlation energy to be compared with an estimated 31% for the best APSG function.

Notes: Static dipole and quadrupole polarizability (αd and αq, respectively) values of coupled Hartree-Fock quality have been calculated for the alkaline earth atoms Be(2s), Mg(3s), Ca(4s), and Sr(5s) using a method based on the many-body perturbation theory. The present values of αd and αq for Be and αd for Mg are in excellent agreement with the other available results of similar accuracy. The CHF calculations of αd for Sr and αq for Mg, Ca, and Sr are being reported for the first time.

Notes: Computation of exchange-polarization and electrostatic-polarization interaction energies between ions is the most expensive step in ab initio investigations of the properties of perfect and imperfect ionic crystals. In the present paper approximate formulas are proposed for these quantities. They save about 95% of the computation time and give these values with an error less than 0.2 kcal mol-1 as compared to ab initio results. The formulas for the exchange- and electrostatic-polarization energies involve the generalized overlap integral between the one-determinantal wave functions of the deformed ions. The approximations are tested in the calculations of the interactions of deformed ions in LiF and NaF crystals.

Notes: Parameters for the OH (sp2) and NH3 (planar, sp2) pseudopotential-FSGO molecular fragments have been established in this paper. Calculations for the molecules of formic acid, formaldehyde, and formamide show good agreement with experiment.

Notes: The group theory for nonrigid molecules is used for studying the internal dynamics of the two equivalent C3v rotor “bent” molecules. Special emphasis is given to the deduction of the symmetry basis vectors which represent in box form the Hamiltonian operator. It is shown that these basis vectors may be advantageously employed in order to simplify the resolution of the two-rotor equation. The procedure is applied to the acetone molecule. It is found that the lowest solutions are clustered into groups of four. The four lowest levels are related to vibrational states, the upper 64 to vibro-rotational states, in which the rotors are rotating in a restricted manner. Only few states show some cogwheel effect. Internal rotation contributions to the principal thermodynamic parameters of acetone are also computed.

Notes: A procedure has been developed for automatic optimization of molecular structures in the EHT method with possible inclusion of electrostatic correction terms, operating with analytical formulas for the first derivative of the total energy in Cartesian coordinates in the s, p, d basis of Slater orbitals. Illustrative examples are given of optimization of the structural parameters of FeCl3, Fe2Cl6, FeCl4, FeCl4-, FeCl2, and FeCl2+ and of optimization of the reaction pathways of the dissociation of Fe2Cl6 yielding the other species of the above set. The values are in good argreement with the available experimental data; this agreement is discussed briefly in connection with the general applicability of the EHT method combined with automatic geometry optimization to theoretical study of compounds containing transition metal atoms.

Notes: Gradient optimized constrained (2s ≠ 2p) and unconstrained (2s ≠ 2p) Gaussian 3G basis sets are reported for the first-row atoms and ions XO, for Q = -2 to +4. Analytic equations have been fitted to the logarithm of the exponents as a function of the nuclear charge Z and formal charge Q. Consequently only two parameters Z and Q have to be specified in order to completely define a basis set.

Notes: The Fermi surface (FS) of beryllium has been calculated using the augmented plane wave energy bands for the material. The extremum area and the FS caliper distances are in excellent agreement with the de Haas-van Alphen measurements, and are better than existing ab initio calculations.

Notes: The exact (nonadiabatic) nuclear and electronic factors of a molecular wave function are expanded in the basis of eigenfunctions of the electronic Hamiltonian according to the Rayleigh-Schrödinger perturbation theory of Born and Huang. Thus it is shown that, with rare exceptions, the exact nuclear factor (a marginal amplitude) is a nodeless function. The nodes in vibrationally excited nuclear wave functions within the Born-Oppenheimer approximation become node-avoiding minima in the exact nuclear wave function. Corresponding to each node-avoiding minimum in the nuclear wave function the exact (nonadiabatic) effective potential for the nuclear motion has a spiky barrier superimposed upon the Born-Oppenheimer (adiabatic) eigenenergy of the electronic Hamiltonian. These barriers are the result of nonadiabatic coupling between electronic states, which is strongest in the vicinity of the nodes in the Born-Oppenheimer-approximation nuclear (vibrational) wave function.

Notes: Unitary transformations of operators and variables are considered for those cases when a Hermitian operator in the expression U = exp (iS) explicitly depends on the projection operators. Some simple examples of such transformations are given and the equations obtained which define projectors (among special sets of them), thus bringing forth better estimations for upper and lower bounds. The unitary transformations are also applied to the reduced resolvent operator and equations are presented for the operators U that minimize the energy functional.

Notes: A class of multilocal functions called n-local energies, which can serve as accuracy criteria on approximate wave functions, are defined. Their interpretation is discussed and their multilocal form is shown to be a result of the holistic character of the quantum description. The analogy with the reduced local energy of Thomas, Javor, and Rothstein is demonstrated. The explicit formula for the simplest n-local energy capable of measuring the deviation from the exact solutions of the Schrödinger equation is obtained in the one-determinantal case.

Notes: The barrier to predissociation of the first excited states of NH3 (3s1,3 A″2) is computed from a truncated first-order wave function using the iterative natural orbital method. The results show that the barrier is lower than when calculated with RHF and the CI wave functions, where single and double replacements to a truncated virtual space are carried out. These findings are used to interpret experimental data.

Notes: The accuracy of a new effective one-body potential is assessed by the study of the electronic structure of atoms from He to Kr. The exchange part of this potential is obtained from a local approximation. Several simplified representations of the electronic density which lead to analytic Coulomb potentials are tested. It is shown that the introduction of the shell structure of the density is necessary, at least for third row atoms. The screening parameters of the potential are variationally optimized with respect to the total energy of the atom. With the most elaborate form of the Coulomb potential which contains one screening parameter for each shell, the comparison of the results with exact Hartree-Fock calculations is very promising. The relative difference is on the order of 10-5 for the total energy and on the order of 10-2 for the orbital energies. Multiplet splitting is reproduced accurately and F- is predicted to be stable (in contrast some others local potentials) by an amount of 0.046 a.u., compared with 0.050 a.u. for an exact Hartree-Fock calculation.

Notes: The nature of problems connected with binding which arise in the everyday work of experimental physicists and material scientists is illustrated by reference to two different experimental studies. (i) Sliding in crystals of group V elements is found to take place not only along planes cutting the quasimetallic bonds, but also along planes apparently cutting their “covalent” bonds, thus suggesting that a more elaborate picture of the two types of bonds and of their interrelation is necessary. (ii) The physisorption of linear pentatriacontane on alkali chlorides indicates alignment of the paraffin molecules along the [110] directions. This may be associated with polarization of methylene groups by ions in the substrate. This hypothesis must be substantiated by suitable quantum-theoretical calculations, which in turn must be based on an adequate description of the adsorption bond.

Notes: This paper is intended to provide an experimentalist's contribution to a critical discussion of adsorption energies and their significance. The experimental requirements, with special reference to the limitations and the quality of the information provided by the various techniques are briefly reviewed. The significance of the measurements, and the background theoretical (phenomenological and model) schemes which experimentalists use for interpreting their results, are discussed in order to show that the interpretations of surface measurements must be carefully analyzed by theoreticians intending to contribute to an understanding of surface bonding.

Notes: The point of view of a physical chemist interested in metal clusters because of their connection with heterogeneous catalysis is illustrated. The analogies and differences between clusters and surfaces are given special attention. After a review of experimental techniques and of types of clusters studied, very important questions of theory are briefly considered, with special reference to Lauher's rules for predicting the stoichiometry of clusters. The relevance of clusters to surface studies is discussed also with reference to fluxionality and reactivity.

Notes: The status of theoretical calculations on polymers is illustrated by two specific problems. The first one is the interpretation of ESCA results on polymers by suitable ab initio calculations. The second problem is the very timely one of bond alternation in polymers. The reliability of theoretical calculations at various levels and the possible central role of electron correlation are discussed.

Notes: The excited states of molecules can be divided into three categories: valence-shell, Rydberg, and intermediate. Reasons are given why this classification is important for photochemistry. The photolytic primary steps should be different for excited states falling into these different categories. Rydberg states should be taken into account when the photochemical reaction path is interpreted in terms of orbital symmetry conservation or diradical intermediates. They might play a role in certain photobiological events.

Notes: A bond model directly derived from an LCAO Hamiltonian is applied to the study of Group IV elemental semiconductors. The derivation has been made through suitable approximations of the interaction integrals. The average and the lowest energy gaps of C, Si, Ge, and α-Sn are then computed with the use of just one parameter. The overall reliability of the model has been checked by computing the lattice dilatation contribution to the temperature coefficient of the lowest energy gap of Ge. The result is in excellent agreement with the experiment.

Notes: A novel model of interaction between peptide backbone and nucleic acid base pairs, proposed earlier on the basis of model building studies has been theoretically investigated. Interaction energies for two different schemes of H-bond interaction between peptide backbone and base pairs A—U and G—C have been calculated for different conformations of peptide backbone. The different H-bond parameters have been calculated. The importance of such an interaction in specific recognition has been discussed in light of the results of theoretical calculations.

Notes: The model developed by Sanyal, Kumar, and Roychoudhury has been applied to some very important aspects of transcription such as (i) a rapid elongation of the newly synthesized RNA chain; (ii) simultaneous release of the nascent RNA; (iii) base sequence directed (or p independent) termination of RNA transcription; and (iv) absence of thymine in RNA. It has been found that the model successfully explains most of the aspects mentioned above. Also, as a consequence of these studies, a new insight to the unwinding mechanism during replication has been developed using intermolecular association studies.

Notes: Possible conformations of two mannotetraoses and several milk oligosaccharides have been studied by an energy minimization procedure using semi-empirical potential functions. Changes in the terminal residue at the reducing end (cyclic to acyclic form) of these molecules do not affect the favored conformations of the remaining oligosaccharide moiety. However, differences in the overall shape of the native and reduced forms of the mannotetraose, mannose α(1-3) mannose α(1-2) mannose α(1-2) mannose are much less marked than between the native and reduced forms of lacto-N-tetraose. These differences are related to the effectiveness of the native forms as inhibitors of antibodies produced using synthetic antigens. Changes in the linkage of the residues at the nonreducing end of these molecules affect significantly the overall shape of these molecules. These differences also are related to their effectiveness as inhibitors. In the fucose-containing milk oligosaccharides the additional fucose residues only restrict the orientation of the backbone tetrasaccharide and do not push it into a totally new conformation. The fucose residues come on a surface of the molecule which is away from the region which may be important for binding. The present studies show that it is the overall shape of the molecule which is important in determining its inhibitory properties and give information as to how best to use the immune method for identification of unknown oligosaccharide sequences by specially prepared antibodies.

Notes: The mode of action of sulfonamides is evaluated and described and the structural dependency of the inhibitory effect of sulfonamides against isolated enzymes as well as against whole cell bacteria is quantitatively described as a function of the variation of electronic and steric influences of the various substituents. In addition the structural dependence of various pharmacokinetic properties as rate of absorption, distribution, metabolism, and excretion on structural changes in the sulfonamide molecules is quantitatively derived. In contrast to the preconditions for inhibitory activity, changes in lipophilicity play the dominant role in pharmacokinetics of sulfonamides.

Notes: The quantum chemical model for predicting the optimal molecular environment exerting the highest catalytic activity on transition complex has been proposed. It was applied for the CO2 hydration reaction at the nonempirical LCAO MO SCF level. The possible use of the resulting optimal charge distribution of environment for design of new synthetic catalysts and explanation of the carbonic anhydrase action was discussed. In addition, a simplified approach based on the difference electrostatic molecular potentials evaluated within the many center multipole expansion is presented. It may enable us to perform corresponding estimations even by means of a programmable calculator.

Notes: Introducing the concept of the “dinucleotide” as the helical repeat, theoretical attempts have been made to determine possible single and double stranded helical structures by using helical parameter calculations and model building investigations. By virtue of its flexible framework, the dinucleotide repeat offers a much greater scope of finding new secondary structural forms for nucleic acids. Considering only those conformations which show tendency for at least partial base overlap as does the dinucleotide helical repeat, it has been possible to predict poly(dinucleotide) helical models in which successive phosphodiesters as well as nucleotide conformations alternate. More important, the recently found left-handed Z-type polynucleotide helix is characterized rather uniquely on the helical parameter plot. The results further suggest the possibility of other Z-type helices obtainable by alternative conformations for the exocyclic C4'-C5' bond and sugar pucker. Near neighbor long range conformational correlations between the dinucleotide repeat and the phosphodiester linking them have been established similar to poly(mononucleotide) helices. Need for considering higher repeats such as trinucleotide has been suggested to obtain models for looped out helical conformations.

Notes: The potential energy curves for the intermolecular proton transfer in complementary base pairs and respective hydrogen bonded model systems have been studied at the semiempirical all-valence and ab initio STO-3G level. The proton transfer probability was found to be markedly greater in excited electronic states than that of the ground state. Substantial lowering of the potential barrier height for the coupled double proton transfer in model (HCOOH)2 system has been observed when the dynamics of zero-point vibrational deformations of the heavy atom skeleton and the environmental effects were taken into account in nonempirical STO-3G calculations. The results of quantum-chemical calculations indicate on the possibility of the double proton transfer in complementary base pairs corroborating the submolecular Löwdin hypothesis on the mechanism of spontaneous mutations.

Notes: PCILO computations have been carried out on the conformation of 3'-deoxyadenosine (cordycepin) and 3'-amino-3'-deoxyadenosine. These nucleoside antibiotics results as a consequence of modification in the sugar part of adenosine. Both C(2')-endo and C(3')-endo sugar puckerings have been considered in the computations and the results obtained indicate that these nucleoside antibiotics have very similar conformational preferences as compared to those of the parent nucleoside adenosine. This similarity which is quite marked in aqueous solution has important biological significance.

Notes: Based upon a stereochemical guideline, both right- and left-handed duplexes were generated for A, B, and D forms of DNA using a mononucleotide as the repeat. Structure factor amplitudes were computed following two methods: (i) one employed an infinite helix as the motif and (ii) the other had an exact crystallographic repeat (e.g., 10 b.p. for B-DNA) as the motif. Both the procedures showed that DNA in either handedness for A, B, and D forms of DNA are consistent with the observed fiber data. This observation is attributed to the fact that fibre pattern (resolved only upto 3 Å) only gives the image of the gross structure of the molecule. Thus, when the gross structure is suitably fitted to match the observed pattern, it is immaterial as to what the precise stereochemistry of the repeating unit (fine structure) and handedness of a model are. Sequence specific helical conformations were obtained using dinucleotide as the repeating unit. Helices fell into two classes: (i) right-handed uniform (RU) and (ii) left-handed zig-zag (LZ) structures. A few aspects concerning the scattering profile of these helices are discussed.

Notes: Minor modifications or substitutions in the sugar or in the base part of pyrimidine and purine nucleosides have a profound effect on their biological activity. These modified nucleosides usually become antiviral, antibacterial, or cancerostatic agents and they are collectively called nucleoside antibiotics. The conformational properties of some of these nucleoside antibiotics have been studied by the PCILO method. The results obtained from such study indicate that the conformational preferences of these nucleoside antibiotics are very similar to those of their parent nucleosides and especially so in the situations that occur in aqueous solutions. The important biological significance of these results is that these nucleoside antibiotics can easily get incorporated into growing chains of DNA and RNA by mimicking their parent nucleosides and can interfere with the protein synthesis of RNA or DNA synthesis.

Notes: Based on in vitro culture studies, it has been proposed that the photochemical generation of superoxide in the intraocular chambers provides a significant cataractous insult. Rat lens when maintained in medium generating excessive O2. -  is damaged as indexed by deterioration of the cation pump. If O2. -  levels are low (ambient levels), peroxidative degradation of lipids has been observed. These reactions are intuitively deleterious to tissue physiology and may contribute to the manner through which light may be toxic to lens in the long run, giving rise to senile cataracts. It was interesting to note that these deleterious reactions could be attenuated greatly by physiological levels of ascorbic acid. The significance of these in vitro studies to the in vitro situatiion as offered by the diurnal habitat of mankind remains yet to be known, but studies simulating such situation in experimental animal models are in progress.

Notes: The ascorbate reduction reaction of the native and urea-perturbed forms, 0-8M urea, of horse heart ferricytochrome c is found to be a three-step process: a urea-dependent equilibrium step between a reducible and an irreducible form with a midconcentration of urea of 7.4M, a binding step with a binding constant of 5.9M-1, and a reduction step with a urea-independent rate constant of 2.9 ± 0.3 s-1 [J. Biol. Chem. 255, 9666 (1980)]. The effect of adding urea, in addition to the generation of an irreducible form, is a slight lowering of the ascorbate-protein binding constant, 5.9 to 2.7M-1, which is limited to the 0-5.5M concentration range. The thermodynamics of the ureadenaturation process also yields a three-step mechanism, N—X1—X2—D, with midconcentrations of urea of 2.5-3M, 6.2M, and 7.5M, respectively, where N, D, and the Xs are the native, the 9-M-urea, and the intermediate forms. The three processes are described as the loosening of the heme crevice opening, the solvent exposure of the polypeptide backbone, and the disruption of the tryptophan-porphyrin interactions, respectively [Biochemistry 19, 199 (1980)]. The reaction of the protein with 2,3-butanedione, a group-specific reagent for the guanidinium groups and an electron donor for this protein, is inhibited in the presence of ascorbate, but only one of the two functional groups is involved [J. Biol. Chem. 255, 11094 (1980)]. A correlation of kinetic and thermodynamic observations led to the conclusion that the ascorbate reduction of the protein is independent of the state of the heme crevice opening and of the polypeptide organized structures; instead, it is determined by the integrity of the tryptophan indole-porphyrin interactions. This information, when taken in conjunction with the selective inhibition of the reaction of the arginine side chains by ascorbate, establishes the binding site of ascrobate as one of the two arginyl side chains, and not the opening of the crevice or its vicinity. From the three-dimensional structure of the protein, and taking into consideration the variability of the protein sequence, it is suggested that Arg-38 is the ascorbate binding site, and that the electronic interaction between the indole of Trp-59 and the porphyrin moiety must constitute, at least in part, the electron-transfer path to heme iron.

Notes: A brief thermodynamic analysis of transport processes in open systems is presented. It is shown that the concept of an active transport in the usual sense of the existence of a flow against the direction of its conjugate force is operationally unrealistic. The so-called metabolically coupled active transport has been shown to be mathematically falacious. The experimental establishment in favor of the active transport process by the use of metabolic inhibitors has been logically disproven. From this analysis it is naturally concluded that all transport processes in the living organisms can be reduced to passive ones if one recognizes all the possible potential gradients existing in the system. Assuming the existence of active transport process is as erroneous as taking for granted a vital force explaining the life phenomena. It simply indicates our lack of knowledge about the pattern of superposition of a complete set of driving forces or about the nature of a yet unknown physical driving force and the generating mechanism of such a force.

Notes: The calculus of the overlap integral for two states represented by the vibrational wave functions ψν′a and ψν″b is reduced to that of the Franck-Condon integral ℒ(0, x) = ∫0x ψν′aψν″b (t) dt. It is proved that for “numerical potentials” (as well as for a Dunham potential), this integral is given on each interval by a simple analytic expression in terms of the two potentials. The Franck-Condon factors are well determined by “coupling constants” related uniquely to the coordinates of the turning points of the potentials. An application to the band system BII—XΣ of Nα2 is compared with the usual numerical methods.