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Notes: Cholesterol and phospholipids are major components of biological membranes. The role of cholesterol in membranes is not metabolic and is known to be a regulator of membrane fluidity which in turn regulates various biological phenomena. We have studied the nature of cholesterol and phospholipid interaction in artificial membranes using 13C NMR spectroscopy. This involved preparation of phospholipids specifically labeled with 13C in the ester carbonyl group. Though the chemical shift data did not provide very useful information the T1 and T2 measurements indicated that previously proposed H bonding between the ester carbonyl group and hydroxyl group of cholesterol seems unprobable.

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: Which information on the properties of the adsorption complex can be obtained from the application of the standard methods in experimental surface science is discussed. None of the methods gives all the information necessary for a complete description of the chemisorption bond so that the results delivered by as many methods as possible should be taken into account.

Notes: For the purpose of illustrating methods for treating the chemisorption problem, which take into account bulk properties of the crystal, it is shown how the single-particle Green's function may be used to solve the self-consistent Schrödinger equations for an adatom-substrate system. The absorption problem is then reduced to the solution of a set of integral equations in terms of the infinite crystal Green's function. The method is illustrated using the interaction between an impurity level and surface states in a semiconductor gap and using sp hybridization of an alkali atom on a metal.

Notes: Some aspects of studies on organic solids, polymers, and solid surfaces are discussed in connection with the suggestion that local interactions can constitute an important common feature of these quite different systems, which allows a common treatment of certain properties in cluster-type calculations. The examples of molecular crystals, of the influence of different side groups bound to the backbone of a regular polypeptide, and of the interactions of fluorine and chlorine atoms with a silicon surface are treated in order to illustrate this thesis, with special emphasis on the reduction of a variety of bonding situations to local interactions rather than on details of computations.

Notes: Standard ab initio quantum chemical computations are quite effective in throwing light on binding features of biomolecules, in particular, hydrogen bonds. This is illustrated by a brief survey of recent work, including some interesting preliminary results on dipeptides, tripeptides, and tetrapeptides. Differential-energy maps for analyzing results are presented and discussed. Basic theoretical questions, such as the significance of minimal-basis calculations and localization on a subsection of a macromolecule, are also discussed.

Notes: Analysis of available data on atoms has led to a relatively simple empirical relationship between the correlation energy and second moment 〈r2〉, a measure of the size of the electron density. With the aid of this simple relationship it is possible to predict correlation energies with fair accuracy given the SCF or Hartree-Fock limit values for the size of the electron density. Preliminary extensions of this work to two- and ten-electron molecules indicate that it may be possible to predict molecular correlation energies to semiquantitative accuracy from SCF data on the electronic distribution.

Notes: Possibilities of improving individual contributions to the statistical interaction energy (kinetic and exchange) are examined. A new method of calculating statistical interaction energies is proposed. The exchange term is calculated using a suitably modified second-order gradient correction. For the kinetic contribution the accurate formula corresponding to the first-order perturbation theory is applied. The calculations have been carried out for several pairs of noble gas atoms.

Notes: The CASSCF method has been applied to some excited states of the BO molecule. Only portions of the full potential curves could be obtained with the help of the usual two-step procedure. It was possible to complete the curves and to consider other excited states by using an averaged field technique. In this approach the energies were computed with orbitals that were self-consistently determined with first- and second-order density matrices averaged over several states.

Notes: The symmetry-adapted-cluster (SAC) and SAC-CI theories reported previously have been applied to the study of electron correlations in ground state, singlet and triplet excited states, ionized state, and electron attached state. Formulas for calculations of one-electron properties and transition properties from the SAC and SAC-CI wave functions are given. Calculations were carried out for the ground and Rydberg excited states of water and its positive and negative ions, with the use of the simpler computational scheme than the previous one. The results compare well with experiments.

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 well-known Hausdorff similarity transformation is used to derive a number of identities for exponential operators. The method does not give new results, but is shown to be a simple alternative to Feynman disentangling, parameter differentiation-differential equation, coherent states, and Lie-algebraic-matrix techniques.

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: 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.

Notes: Using the newly developed discrete variant of the k · p perturbation theory for linear chains an expression is derived for the dispersion interaction between two infinite chains valid for both insulating and metallic polymers. It is shown that the formally divergent dispersion energy is also finite for metallic systems, but it may be considerably enhanced in polymers with partly filled bands as compared with insulting ones. The accuracy of the proposed k · p expansion is investigated on model chains through comparisons with direct ab initio Hartree-Fock crystal orbital calculations. Applying second order perturbation theory an explicit formula in terms of band parameters is given for the numerical calculation of the dispersion energy.

Notes: Calculations of Kato's equations have been carried out as a function of the coordinates of the system using a number of approximate wave functions in order to determine the effects of the energy, electron density, constraints, and the functional form of the wave functions on how well Kato's equations are obeyed. It is shown that by putting constraints on the functional form of some wave functions, the wave functions will give the exact value of Kato's equations.

Notes: The ground state wave function of a model potential consisting of a zero-range square well joined to a Coulomb tail is used in a two equivalent centre problem to evaluate the overlap integral (S) and the resonance integral (β). It is shown that an extended Linderberg relation of the form β = K/R (dS/dR) is generally well obeyed. The extended relation has been used within a LCAO framework to obtain dissociation energies of the homonuclear diatomic molecules of the alkali atoms.

Notes: MSW-SCF-Xα calculations have been carried out to obtain ionization potentials (via Slater's transition state concept) and charge distributions for HNSi. The results are interpreted and compared with previous ab initio and CNDO/2 studies.

Notes: The Silverstone-Stuebing variational principle for the discontinuous wave functions of one-electron systems is generalized for many-electron systems. The variational functional of energy takes real or complex value. The condition that it is real is given. Using the generalized variational principle, a multiconfiguration SCF theory for the composite molecular wave function is formulated. According to the theory, we may divide the whole space into space-filling cells, solve the SCF equations in each cell and build up the wave functions of the system by gathering the wave functions obtained in the cells. For use in the basis-set expansion method, the SCF equations are rewritten as matrix forms in which only one- and two-center integrals appear if an expansion center is located in each cell.

Notes: The molecular electrostatic potentials for several small molecules were investigated using PCILO wave functions at different stages of the perturbation expansion. The utility of the localized picture within the PCILO framework can be shown, even at zeroth order only. For simplicity the approximation of fixed standard bond polarities could be introduced in order to reproduce shape and values of the potential with a sufficient degree of accuracy.

Notes: Theoretical aspects of the MS Xα method are analyzed. It is shown that real field self-consistency is not achieved in an MS Xα calculation and some consequences of this fact are discussed. The approximations involved in the use of the transition-state procedure to evaluate ionization and excitation energies from a MS Xα calculation are presented in some detail and commented.

Notes: For arbitrary k, the separation of spin variables is performed in the reduced density matrix of the kth order (RDM-k) on the basis of the Fock coordinate function method. The independent spatial components of RDM-k are analyzed. For RDM-k of the total spin eigenstate, their number is proved never to exceed its spin multiplicity 2s + 1. Integral and other nontrivial interrelations between spatial components are established which turn out to be the necessary and sufficient conditions of spin purity of a wavefunction corresponding to a given RDM-k. It is shown that the r-rank k-particle spin distribution matrix Fkr, defined as a spatial coefficient at the spin-tensorial operator of rank r in the RDM-k expansion, can be obtained by reduction of the (k + r)-particle charge density matrix Fk+r0. In particular, all spatial components of RDM-2 are explicitly expressed in terms of the four-electron charge density matrix only. This allows us to purpose some approximative formulas for the McWeeny-Mizuno spin-orbit and spin-spin coupling functions in the case of the weak spin contamination.

Notes: Following an interpretive formalism presented earlier, chemical binding in the H2+ molecule has been studied in terms of the variations, with respect to R, of electrostatic field and stress components at five selected points on the interuclear axis. At three points phenomena analogous to those recorded earlier for H2 have been observed. In particular, the existence of extremal relationships for the difference density field and the total field, as well as for the corresponding stresses, at R ≃ Req for certain specific points on the internuclear axis has been confirmed. As in the case of H2, chemical binding in H2+ occurs due to local variations of electrostatic pressure from point to point in such a manner as to cause the vanishing of either the total electrostatic force density or the difference force density at certain points on the internuclear axis.

Notes: (5s, 2p) and (7s, 4p) Gaussian basis sets are presented and evaluated for first- and second-row atoms, respectively, appearing in biologically active molecules. The exponents of the valence shell primitives are taken from larger bases, where the valence shell is better represented, in order to avoid the overemphasis on the core, which occurs in small bases when all exponents are optimized. Contraction coefficients are given for constructing double zeta and minimum molecular basis sets. The basis sets are evaluated by applying them to 19 molecules containing first- or second-row atoms. The results indicate that they are competitive with larger bases for the calculation of properties mainly dependent on the valence shell electrons. In particular, proton affinities seem to be quite reliably reproduced so that they can be used for investigations involving reaction or interaction with proton donors.

Notes: Specific electronic properties related to the metabolic transformation and adduct formation with DNA were calculated for a series of five aflatoxins, AFB1, AFG1, AFP1, AFM1, and aflatoxicol (AFL), as well as for two precursors of AFB1, versicolorin A and sterigmatocystin. The aim of this study was to investigate to what extent such electronic parameters determine relative apparent mutagenic and carcinogenic activities of these compounds. Using two semiempirical all-valence electron methods, IEHT and INDO, the results obtained indicated that for all these compounds the 2,3-vinyl ether double bond is highly susceptible to epoxidation, and this susceptibility is independent of the remaining ring structure and substituents. Further, the epoxides in turn readily form highly electrophilic carbocations whose stability and reactivity are not significantly influenced by chemical structure changes among the seven analogs studied. The results also suggest that major detoxification pathways mitigated by cytochrome P450 metabolism are not likely. Thus differences in potencies do not appear to be caused by differences in electronic properties related to the metabolic transformation and adduct formation, and could be the result of other properties such as lipophilicity and steric effects on enzyme activity.

Notes: Molecular electrostatic potentials are calculated for a single phospholipid molecule (1,2-dilauroyl-phosphatidylethanolamine) and for its model monolayer. For the single molecule the magnitudes of the positive and negative potentials associated with the amino and phosphate groups of the polar head are comparable. For the monolayer a dominantly positive surface potential is obtained.

Notes: The protonation energies (pE) of histamine and methyl histamines were calculated by using the CNDO/II method. After correction for hydration energies, the variation of the pE values has the same trend as that of the pKa1, values determined in aqueous solution. However, there is no apparent relation between the calculated pE and the biological activities for the above-mentioned compounds. On the other hand, it was found that the relative stability of the two tautomers did reflect the H2-receptor agonist activities. The smaller the energy of the N(1) - H tautomer, the greater its H2-receptor activity.

Notes: The imidazole C-2 proton NMR signals of six of the 14 histidine residues per subunit of pyruvate kinase (Mr = 237,000) are detected at 250 MHz using 16-bit analog-to-digital conversion, and their pK′ values have been determined. One of these residues [his (3)] is very near the binding site of the divalent cation activator as indicated by a Mg2+-induced decrease in its pK′ in the presence of K+ and P-enolpyruvate, and by the selective paramagnetic effects of the activator Ni2+ or the substrate β,γ-bidentate CrATP on the relaxation rates of the his (3) signal. Another histidine residue [his (2)] is near the adenine portion of the nucleotide substrate binding site as indicated by paramagnetic broadening by CrATP of the his (2) signal, a nuclear Overhauser effect (NOE) on the adenine H-2 proton of enzyme-bound MgATP upon irradiation of the his (2) signal, and the loss of ATP binding detected kinetically, after selective chemical modification of his (2) as detected by NMR. Intermolecular NOE studies of enzyme-bound MgATP indicate the distance between the adenine H-8 proton and the ribose protons of the substrate to increase in the order H2′ = H3′ ≤ H5′ 〈 H1′ 〈 H4′. These findings are in good agreement with the conformation of enzyme-bound ATP previously and independently determined by distances from Mn2+ at the active site to the protons of ATP.

Notes: The problem of viscous damping of vibrating DNA polymer in aqueous solution is solved in the low-amplitude limit for all acoustic branches of the spectrum. The acoustic spectrum covers the microwave region of frequencies. The viscious damping is found to be a strong function of frequency, singular both at very low and very high frequencies. All acoustic modes are overdamped, implying that the observation of well-defined resonances in DNA requires highly structured water or very dry material.

Notes: The nucleotide building blocks of nucleic acids show a preference for two major conformational motifs mainly determined by the sugar puckering and the concerted changes in the glycosyl sugar-base torsion angle: 3E-low anti (χ) and 2E-high anti (χ). The backbone C4′—C5′ bond torsion prefers the gauche1 range while the C5′—O5′ torsion displays a somewhat broader trans range. Thus the two preferred sugar-base-backbone relationships are: 3E-anti-gauche+ and 2Eanti- gauche+. In 5′-nucleotides there is an extreme reluctance for the syn base. Guanine is notoriously peculiar and has a tendency for syn. When the base is syn, the steric conflict with the phosphate is relieved by a concerted rotation around the C4′—C5′ bond to the trans (or gauche-) states, leading to three additional nucleotide motifs: 3E-syn-trans and 3E-syn-trans (or gauche-). The gauche- state is highly destabilized for the 3E., Superhigh χ's are known to drive the backbone into left-handed structures, as exemplified by the unnatural Ikehara polymers [M. Sundaralingam and N. Yathindra, Int. J. Quantum Biol. QB4, 285-303 (1977)].In the recently discovered left-handed Z helices of the alternating deoxy-CG tetra- and hexanucleotides it may be regarded that the C residues assume the preferred “right-handed” conformational combination 2E-anti-gauche+, while the G residues assume the less favored “left-handed” combination 2E-syn-trans., In the latter, steric interactions between the syn base and the 5′-phosphate drive the C4′—C5′ torsion into the trans range, and the electrostatic interactions between the syn base and the 3′-phosphate now drive the sugar into 2E (a variant of 3E). The departure from the preferred nucleotide conformations leads to correlated changes in the ester P′O bonds of the internucleotide phosphodiester groups, which alternatively adopt (in Z-DNA) the “left-handed” double gauche (gauche+, gauche+) and the “right-handed” (gauche′, trans) conformations.The pseudorotational mobility of the furanose ring provides a simple and elegant way of understanding conformational fluctuations and flexibility of nucleic acids. Thermal fluctuations capitalize on the pseudorotation property of the furanose ring. Because the furanose ring is linked to the base and the phosphate, these fluctuations are correlated to the rotational mobility of the base and the phosphate and lead to phenomena such as premelting changes, breathing modes, or opening of base pairs. Such motions are instrumental in the polymorphic transitions of nucleic acid helices (e.g. A ⇄ B, B ⇄ C, B ⇄ Z, …) or in functional processes, such as unwinding and fork formation. It is also proposed that concerted changes in the sugar-phosphate backbone torsion angles, akin to a crankshaft motion, can bring about the B ⇄ Z transition without necessarily disrupting the hydrogen bonds.

Notes: The significance of the gramicidin channel, its structural elements, and the importance of the peptide libration mechanism are reviewed. Elemental ionic processes of the single-channel currents are considered, which indicate the possibility of two- and three-site models. Data are presented which demonstrate the absence of interactions required for the three-site model, and the resulting free-energy profile for the two-site model is given for the most probable conducting state. The need to extend analyses to include an understanding of multiple conformational states is outlined, and results from approximate conformational energy calculations are presented showing that there are numerous low-energy conformations for the side chains of gramicidin. Specifically the interactions between L·Trp9 and L·Trp15 side chains and between D·Leu4…D·Leu10 are analyzed to show the existence of several energy minima separated by appreciable barriers. These findings provide the basis for understanding facilitated entry of the second ion into the channel and the occurrence of lipid-dependent dispersion of conductance states. Finally perspectives of the molecular mechanism of anesthetics are discussed relevant to the gramicidin channel mean lifetime and single-channel currents.

Notes: A field-theoretic treatment of biological evolution is presented. This treatment (evolutionary field theory) leads to the decomposition of biological evolution, at the molecular level, into permutational and substitutional evolution. The mathematical distinction between these latter two types of evolution is investigated and a nonlinear/linear classification results.

Notes: Theoretical and quantum chemical prediction of toxicity and toxicology is even more challenging than prediction of pharmacology, which is usually a one-stage event at a target site. For toxicity and toxicology, the concept of the “toxic triggering event” was developed which then leads to the cascade of subsequent physiological events. The strategy for computer-generated predictions in this area includes as the major components chemical automated substructure and “toxicophore” identification by powerful chemical substructure searching techniques developed in Europe, geometry optimizations (desirably by ab-initio intramolecular atom class-atom class pair-pair and three-body potentials), quantum chemical calculations (desirably ab-initio, incorporating optimal strategies for such computations on large molecules) on both the toxicant and its metabolites (the structures of which were generated by computer-assisted tracing of metabolic pathways), generation of the three-dimensional electrostatic molecular potential contour maps around the toxicants and their metabolites and matching of these by reverse image holography for new compounds whose toxicity has not yet been tested experimentally against those with a known toxic mechanism, matching of intermolecular interaction maps of untested compounds with known toxicants combined with matching observed physiologic signs and symptoms with “toxic triggering events” and specific pathologies, and using the concepts of systems analysis and control theory and catastrophe theory to track both the dynamic balance of endogenous biomolecules and interactions with these biomolecules. The necessary program modules are described, and the necessary data bases (both theoretical and physiological) are identified along with the form in which they may be used most expeditiously.

Notes: The possibility of applying the half-projected Hartree-Fock method together with the Coulomb hole model to obtain cofrelated potential-energy curves is investigated. Here we report calculations performed on the LiH molecule. The results show that this combined technique can provide potential curves very near to the experimental ones with a similar effort to that involved in the Hartree-Fock calculations.

Notes: Information theory can be used to evaluate the quality of a wave function by considering its ability to give values for some observables as close as possible to the experimental ones. A new method for improving the quality of a wave function is proposed. This paper deals exclusively with the HF (X 1∑+) molecule.

Notes: Classically every physical thing has some geometry or other, but in the quantum theory the notions of spatial structure, shape, and size seem to become hazy if not outright inapplicable. In particular, elementary entities are by definition structureless and seem to have no size or shape other than those imposed by their environmént - as represented, e.g., by the boundary conditions. However, this does not entail that systems of interacting components, such as molecules, lack a geometry as well, as has been argued in recent times. The purpose of this paper is to investigate this claim. Since the solution to the problem whether a quantum-mechanical system possesses a geometry depends critically upon the definition of the latter, we elucidate the notions of extension, shape, and spatial configuration of a system. We do so first classically in terms of the energy density, then quantum mechanically in terms of a suitably constructed position distribution function that depends upon the spatial coordinates (and is thus a field quantity) rather than on the particle coordinates. In this way we construct both classical and quantal concepts of the geometry of a system. We also define the notions of spatial structure and chemical structure of a quantal system. Our quantum-mechanical concepts are quite general and constitute smooth extensions of the corresponding classical concepts. The upshot of this investigation is that a quantal system does have a geometry, albeit not as clearcut a one as a classical system, that is primarily determined by the interactions among its components. (Thus, physics determines geometry of physical systems, not the other way around.) This conclusion is obtained within nonrelativistic quantum mechanics without adding any extra assumptions. Our result vindicates the ball-and-spoke models of molecules and thus shows once again that quantum chemistry, although different from classical chemistry, stays close to the chemist's work bench.

Notes: A perturbation configuration interaction method is formulated for a system in an external oscillating field (PCILOSC). It is closely connected with the static PCILO method and can be used for the conformational analysis of molecules and molecular crystals with localized bonds in external fields.

Notes: In a previous paper, denoted I [C. Duprez and J. Tillieu, Int. J. Quantum Chem. 17, 155 (1980)], a global tensor, invariant in an origin change, has been introduced for all optical phenomena. The results obtained have been applied to two particular cases: refraction and the Faraday effect, in Paper II [C. Duprez, Int. J. Quantum Chem. 17, 169 (1980)]. In this paper, we study the various methods suitable for the calculation of these tensors. Then, we compare the results obtained in II with those previously obtained by other authors who, when studying the two particular cases mentioned above, omitted some terms necessary to obtain the invariance.

Notes: A numerical fit to computed ab initio points of the HF-HF potential energy surface is here employed in its simplest spherical form to solve the corresponding close-coupling equations that yield vibrationally inelastic collision cross sections for the V/T process in the gas phase. The existence of a deep potential well in the interaction is examined here for its effect on near-threshold cross section behavior and evidence is found, through the present calculations, for the relative importance of several (orbiting) shape resonances that contribute to the Q1←0 cross sections at low collision energies (≤0.4 eV). The bearing of such lengthened interaction times on the corresponding low temperature relaxation times is shown in the ensuing calculation of pτ in the T range between 300 and 4000 K. In spite of the simplicity of the present model, quite good agreement is in fact found with experiments in the low- T region, while the lack of V, R/T coupling explains the departure of the computed pτ, above 1000 K, from the experimental findings.

Notes: The mapping between the local one-body potential and the ground state density is discussed. The role of degenerate ground states, which form a set of measure zero in potential space, is shown to be amplified by the unitary transformation between degenerate densities, forming a space filling set in density space. A numerical experiment demonstrating these features is carried out. No indication of non-V representable densities is encountered.

Notes: The kernel of the distorted-wave Born approximation (DWBA) transition amplitude will be explored with attention to the atom-diatomic molecule reactive scattering process of A + BC → AB + C. Our study of the kernel reveals valuable intrinsic properties regarding the state-to-state reactive scattering process. In particular, such a study will help us to better understand (i) the favored geometric configuration during collision, (ii) the spatial domain of contribution to the differential and total cross sections, and (iii) the structural dependence of the kernel distribution on the mass ratio of the reactant molecule BC and the departing atom C, particularly in the case of colinear rearrangement collisions. In this study we choose the FH2 system as an illustration.

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.