bluuebunny/crossref_metadata_2025_split huggingface dataset:
An empirical potential for interactions of large molecules: Application to binding of dipeptides to DNA
Authors: Hobza P. , Havlas Z. 
Published: January 2005

AbstractAn empirical potential is introduced that is suitable for calculation of the interaction enegies of biomolecules with thousands of atoms. The potential consists of electrostatic, repulsion, and dispersion energy terms. The approach used for parametrization of the potential is entirely different from that used with other existing potentials. Namely, all the terms were parametrized independently to retain their physical significance. The sum of the electrostatic and repulsion terms mimic the SCF interaction energy calculated using Huzinaga's minimal basis set MINI‐1. The dispersion energy is very important and is usually predominant for the interactions of large (polar) molecules in the gas phase as well as in the liquid phase.
Theoretical study of carbonic anhydrase‐catalyzed hydration of co2: A brief review
Authors: Liang Jiin‐Yun , Lipscomb William N. 
Published: January 2005

AbstractQuantum mechanical calculations have been used to study the reaction mechanism of human carbonic anhydrase‐catalyzed hydration of CO2. This reaction is responsible for fast metabolism of CO2 in the human body. For each of the reaction steps, possible catalytic effects of active site residues are examined. The pertinent results are as follows. (1) For CO2 binding, the experimentally observed 2.5 cm−1 frequency shift of the asymmetic stretching frequency between measurements taken in the aqueous solution and in the enzyme is reproduced in our theoretical calculations. Our results suggest that CO2 binds to the zinc ion within the hydrophobic pocket. (2) No energy barrier is found for the nucleophilic attack from Zn2+−bound OH− to C of CO2 to form Zn2+−bound HCO3−. (3) For the internal proton transfer within zinc‐bound HCO3−, the barrier of 35.6 kcal/mol for the direct internal proton transfer is reduced to 3.5 and 1.4 kcal/mol, respectively, when one or two water molecules are included for proton relay. (4) Displacement of Zn2+−bound HCO3− by H2O is facilitated by the presence of the negatively charged Glu 106‐Thr 199 chain and by the association and the subsequent ionization of a fifth water ligand. (5) For the intramolecular proton transfer between Zn2+‐bound H2O and His 64, the Zn2+ ion lowers the pKa of Zn2+−bound water and repels the proton. His 64, or a similar proton receptor with a larger proton affinity than H2O, functions as proton receiver; and the active site water molecules visualized by x‐ray crystallography are important for the proton relay function. In summary, it is demonstrated that in order to achieve effective catalysis, a sequence of precisely coordinated catalytic events among all participating catalytic elements in the enzyme's active site is essential.
Proton transfer and solitonic excitations in model one‐dimensional hydrogen‐bonded systems
Authors: Misiak P. , Chojnacki H. 
Published: January 2005

AbstractThe solitonic models of proton transfer in a molecular hydrogen‐bonded chain have been examined with respect to the shape of protonic interaction potential. The kink‐like excitations with quadratic, quartic, Morse, and Toda interactions are reported and analyzed.
Localization measure and maximum delocalization in molecular systems
Authors: Pipek János 
Published: January 2005

AbstractA mathematically well‐defined measure of localization is presented based on Mulliken's orbital populations. It is shown that this quantity equals 1 for core‐ and lone‐pair orbitals, 2 for two‐atomic bonds, 6 for benzene rings, etc., and it is applicable for delocalized canonical HF orbitals as well. The definition of this quantity is general in the sense that ab initio MOS with overlapping AO expansion, and semiempirical wave functions using the ZDO approximation as well, can be treated. The localization quantity is essentially “intrinsic,” i.e., no subdivision of the molecule is required. For N‐electron wave functions, mean delocalization can be defined. This measure is not invariant to unitary transformations of the one‐electron orbitals, characterizing in this way the localized or extended representation of the N‐electron wave function. It can be proven, however, that for unitary transformed wave functions a maximum delocalization exists which depends only on the physical (N‐electron) properties of the molecule. It is shown that inhomogeneous charge distribution can cause strong electron localization in molecular systems. The delocalization of the canonical Hartree–Fock orbitals, the Parr–Chen circulant orbitals, and the optimum delocalized orbitals is studied by numerical calculations in extended systems.
Surface states in deformed and perturbed diatomic crystals
Authors: Andrade L. , Sánchez M. 
Published: January 2005

AbstractThe electronic properties of a one‐dimensional diatomic crystal have been analyzed by using the MO‐LCAO method in the tight binding approximation, with mathematical techniques involved in setting up and solving difference equations. The approach gives the exact sets of analytic solutions for both localized and nonlocalized states. The theory of surface states is developed as a characteristic value problem. To illustrate the method the surface states for a semiinfinite crystal which contains a local imperfection at the surface were examined. It appears that this method has advantages over previous methods developed to solve surface problems in crystalline lattices.
Ab initio SCF study of the interaction between L‐serine phosphate and ammonia
Authors: Nakamura Y. , Lunell S. 
Published: January 2005

AbstractThe possible conformational changes of L‐serine phosphate due to the interaction with ammonia are investigated by means of ab initio MO‐LCAO‐SCF calculations, using a supermolecule approach and an STO‐3G basis set. The most favorable conformation of a four‐hydrated L‐serine phosphate anion is found to be changed by the binding of an ammonium ion. Cointeraction of ammonia and NH suggests another conformational change through the displacement of the bridging water molecule of the polyhydrated L‐serine phosphate anion.
Quantal approach to study the structure of triatomic I2 ⃛ X (X = He, Ne) VDW clusters
Authors: García‐Vela A. , Villarreal P. , Delgado‐Barrio G. 
Published: January 2005

AbstractEnergy levels of I2 ⃛ X van der Waals (VDW) molecules, where X is a rare gas atom (X = He, Ne) are obtained in an approximate way by using cofocal elliptic coordinates and taking the I2 internuclear axis as a quantization axis. This is the starting point to study vibrational predissociation (VP) of larger I2 ⃛ Xn (n ⩾ 2) clusters, where a good energetic description may provide accurate initial conditions from which trajectory calculations can be carried out.
Generalized graphs and the Sinanoğlu graphical rules
Authors: Shen Mingzuo 
Published: January 2005

AbstractA comparison of Sinanoğlu's VIF (Ref. 1) and generalized graph is presented. Generalized graphs have vertex and edge weights. An abridged history of generalized graphs in theoretical chemistry is given. VIF's are generalized graphs and therefore have adjacency matrices. The “graphical” rules of Sinanoǧlu can be represented by congruent transformations on the adjacency matrix. Thus the method of Sinanoǧlu is incorporated into the broad scheme of graph spectral theory. If the signature of a graph is defined as the collection of the number of positive, zero, and negative eigenvalues of the graph's adjacency matrix, then it is identical to the all‐important {n+, n0, n−}, the {number of positive, zero, and negative loops of a reduced graph} or the {number of bonding, nonbonding, and antibonding MOs}. A special case of the Sinanoğlu rules is the “multiplication of a vertex” by (−1). In matrix language, this multiplication is an orthogonal transformation of the adjacency matrix. Thus, one can multiply any vertex of a generalized graph by −1 without changing its eigenvalues.
A comparative analysis of the electrostatic potentials of some structural analogues of 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin and of related aromatic systems
Authors: Murray Jane S. , Evans Patricia , Politzer Peter 
Published: January 2005

AbstractWe have carried out an ab initio STO‐5G computational analysis of the electrostatic potentials of four structural analogues of the highly toxic 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin (TCDD) and four related aromatic systems benzo[a]pyrene, benz[a]anthracene, and two isomeric benzoflavones. These systems, to varying degrees, induce aryl hydrocarbon hydroxylase activity and are believed to interact with the same cytosolic receptor in initiating their biochemical responses. Our present results for the TCDD analogues support and have allowed us to further qualify our early observations regarding factors which are linked to high biological activities in the dibenzo‐p‐dioxins and structurally similar systems. We find that a high degree of activity appears to require nonoverlapping negative potentials above all or most of the lateral regions, with an observed optimum range of magnitudes. In systems with central oxygens, it is required that the negative oxygen potentials be small and weak; however, oxygen negative regions in the molecule are not necessary for high activity. The observed differences between the potential patterns of the four aromatic systems and those of TCDD and its active analogues may reflect an inherent dissimilarity in the nature of their interactions with the cytosolic receptor. That the carbonyl oxygen negative potential of 7,8‐benzoflavone is significantly more negative than its isomer's supports earlier speculation concerning the former's more effective inhibiting effects on metabolic oxidation.
On the connection between semiempirical molecular orbital theories and effective hamiltonians: A constrained variational point of view
Authors: Khan P. , Das K. K. , Bhattacharyya S. P. 
Published: January 2005

AbstractThe idea of interpreting the semiempirical MO theories from a constrained variational point of view is explored. A density‐based approach is developed for calibrating the parameters of useful semiempirical Hamiltonians of molecular electronic structure theory. Results of some numerical experiments with model Hamiltonians of constrained variational origin are reported.
Two colorful applications of the PPP method
Authors: Balasubramanian K. 
Published: January 2005

AbstractTwo different color‐related applications of the Pariser‐Parr‐Pople method are described. The first one deals with an explanation of the UV‐visible absorption spectrum of the curcumin pigment in turmeric and the color change of curcumin upon addition of OH−. The other application deals with blue and red shifts in poly‐diacetylene to polybutatriene transformation. The applications of the FEMO and PPP methods to curcumin facilitate assignment of the two observed bands of curcumin (UV and visible) to the π → π* (UV) and n → π* (visible) transitions, respectively. A graph‐theoretical formulation of the PPP method is also considered.
Studies on large electronic systems with PPP: Testimony of PPP's activity
Authors: I'Haya Y. J. 
Published: January 2005

AbstractIt is nearly 40 years since the PPP method was proposed, and we demonstrate here that the method is still active in studying the electronic structures of very large conjugated systems and/or periodic systems. The kink (solition) problems in polyacetylene are solved with the UHF‐PPP Hamiltonian, demonstrating that there appear several new features which have not been obtained without considering the interelectronic interactions of the PPP type. Next, the electron correlation effect in polyacetylene is discussed through the crystal orbital‐PPP CI calculations. Finally, three‐dimensional crystal orbital‐CNDO calculations on graphite and black phosphorus are reported.
Peel, a modified PPP method, applied on the spectra of some nucleic acid bases
Authors: Fischer‐Hjalmars Inga , Henriksson‐Enflo Anita 
Published: January 2005

AbstractA comparison between some different modifications of PPP methods is made. It is noticed that each modification may have its advantages but that some may be more suitable for interpretation of electronic spectra than others. It is also pointed out that PPP methods may allow more accurate descriptions of π properties than all‐valence methods, such as CNDO/S.The Peel method, a PPP method especially adapted to reproduce the lowest π → π* transitions of a few reference molecules, has been applied to studies of the pyrimidine bases cytosine, uracil, and thymine. The obtained frequencies and oscillator strengths compare favorably with experimental evidence. The calculated polarization directions are in general agrreement with measurements. In case of cytosine a reinterpretation of measurements is suggested.
Nonlinear phase excitations in the PPP model of polyacetylene
Authors: Sasai Masaki 
Published: January 2005

AbstractThe Pariser‐Parr‐Pople (PPP) method has revealed rich effects of the π electron Coulomb interaction in (CH)x. We discuss results obtained by the PPP model with the unrestricted Hartree‐Fock (UHF) approximation and we show that concepts introduced by the PPP‐UHF model give a new insight on Franck‐Condon‐type electronically excited states in (CH)x. In the first part of this paper, a brief review of the PPP‐UHF model is given. We introduce phase and amplitude variables and show that solitons in the PPP‐UHF model are phase excitations. In the second part of this paper, the effective Hamiltonian describing phase excitations is derived. We show that the phase Hamiltonian derived by the time‐dependent Hartree‐Fock approximation is the classical limit of the Hamiltonian derived by the bosonization method of Tomonaga, Luther, and others. The phase Hamiltonian has a family of new soliton solutions. These solitons are pure electronic excitations and correspond to the exciton and the magnon in (CH)x.
A computational analysis of the electrostatic potentials and relative bond strengths of hydrazine and some of its 1,1‐dimethyl derivatives
Authors: Murray Jane S. , Sukumar Nagamani , Ranganathan Shoba , Politzer Peter 
Published: January 2005

AbstractWe have carried out a computational study of hydrazine and five of its 1,1‐dimethyl derivatives, focusing on their electrostatic potentials and relative bond strengths. Our approach has involved the calculation of ab initio self‐consistent‐field molecular orbital wave functions and molecular properties using the GAUSSIAN 82 system of programs. The electrostatic potentials of the hydrazines possess negative regions of varying sizes and strengths associated with the nitrogens of the α‐diamino linkages. Through an analysis of the positions of the most negative potentials of these regions, we have obtained directly the dihedral angles between the nitrogen lone pairs in these systems. Our use of the electrostatic potential to obtain these angles is a direct and general approach, in contrast to indirect procedures used in the past. We find this dihedral angle to be close to 90° in hydrazine, with variations in the substituted hydrazines that depend on the nature of the substituents. A highly polar structure is found for 1‐chloromethyl‐1‐methylhydrazine, which involves a delocalization of electronic charge from the substituted nitrogen towards the CH2Cl group. We find that substituents able to withdraw significant amounts of electronic density from the central nitrogen lone pair regions, either through resonance or by induction, have a slight bond strengthening effect on the central N‐N bond. This is attributed to a decrease in the repulsion between the weakened nitrogen lone pair regions. The difficulties encountered in seeking the controlled oxidation of hydrazine to nitro derivatives may be due, in part, to the fact that two factors which would favor this, highly negative nitrogen potentials and strong N‐N bonds, are opposing in nature.
Potential surfaces and nonadiabatic couplings in ionic systems: A study of the (O2H)+ interactions
Authors: Gianturco F. A. , Palma A. , Schneider F. 
Published: January 2005

AbstractThe adiabatic potential energy surfaces (PES) which are most likely to be involved in the elementary mechanism presiding over charge‐exchange and direct inelastic collisions between O2 molecules and collimated beams of protons are discussed. The general behavior of Diatomics‐in‐molecule (DIM) model interactions is analyzed in great detail as a function of the molecular vibrational coordinate and of the other internal nuclear coordinates. The general features of the lower two PES are discussed, and the corresponding nonadiabatic coupling terms between these surfaces are also computed and analyzed. These model results turn out to provide very useful indications on the specific dynamical features that are to be considered responsible for the inelastic, vibronic transitions observed in the target molecule during collisional experiments.
Roothaan's open shell theory from the viewpoint of an orthogonal group
Authors: Klimko G. T. , Mestechkin M. M. 
Published: January 2005

AbstractExplicit equations for the constantsaandbof the energy as the average expectation value for the minimal domain of states giving the Roothaan energy functional are derived in terms of the total spin value and the “seniority” quantum number. The state with off‐diagonal long‐range order can appear in the framework of the Roothaan scheme for the quasidegenerate system as an alternative to the Hund rule. Admissible many‐electron states are established for all configurations of the icosahedral symmetry group systems, and correspondingaandbcoefficients are calculated.
The symmetrized basis function method for SU(2) and its application to the total spin states of many‐electron systems
Authors: Ding Peizhu , Wang Yi , Mu Yingkui 
Published: January 2005

AbstractIn this paper, the symmetrized basis function method is extended and used for the classification of the total spin states of many‐electron systems. The reduction matrix, which is expressed as a series of products and direct products of matrices is derived. It is very advantageous that the method can be completed by computer. As an example, the reduction matrix for a 5‐electron system calculated by IBM PC computer and the classification of the total spin states is presented.
Theoretical investigation of the hydration properties for the trans and gauche rotamers of succinonitrile
Authors: Walker G. A. , Bhatia S. C. , Hall J. H. 
Published: January 2005

AbstractAb initio SCF were performed on the trans and gauche rotamers of succinonitrile (SN) and on the monohydrated rotamers to determine the most probable hydration site(s) of water with SN and the relative strengths of these interactions and to examine the effect of one water molecule on the relative stability of the rotamers. MOPAC was used to determine the location of water on the rotamers of SN; the geometries of the hydrated rotamers were then optimized at the HF/4–31G level followed by single‐point calculations at the HF/6–31G and HF/6–31G* levels. The results show that trans SN is more stable than is gauche SN by 1.2 kcal/mol (at the HF/4–31G level with zero‐point energy corrections) and 0.8 kcal/mol (at the HF/6–31G* level, excluding zero‐point energy corrections). The hydrogen bond formed between the methylene hydrogen of trans SN and the oxygen of water is more stable than is the hydrogen bond formed between the nitrogen of SNt and the hydrogen of water by 0.63 kcal/mol. The most stable hydrogen‐bonding interaction for the gauche rotamer occurs for the methylene—OH2 hydrogen‐bonding interaction, which also has the largest hydration energy (ΔE = −4.39 kcal/mol), but it is less stable than is the most stable trans hydrogen‐bonding interaction (SNt—OH2) by 0.63 kcal/mol. Our results suggest that the trans rotamer of SN should associate with more water molecules than should the gauche. The relative rotamer stability between the trans and gauche rotamers of SN decreases by 0.2 kcal/mol (at the HF/6–31G* level) when water is hydrogen bonded to the methylene group of SN. A mechanism is also proposed to explain the phase‐separation behavior of this system.
Applications of the MBPT in the localized representation
Authors: Kapuy Ede , Bartha Ferenc , Bogár Ferenc , Csépes Zoltán , Kozmutza Cornelia 
Published: January 2005

AbstractDiagrammatic formulation of the MBPT is applied when the occupied and the virtual canonical orbitals are separately localized by unitary transformations. In this localized representation, due to the off‐diagonal Fock matrix elements, the perturbation operator contains extra terms generating the so‐called localization corrections. These corrections enter the perturbation energy in third and higher orders. Their magnitude depends on the type of localization, but they represent only a small fraction of the canonical corrections. The calculation of the localization corrections, however, does not need a significant amount of extra computer time. It is shown that by introducing an “order of neighborhood” local and nonlocal effects of the electron correlation can be separated and the contribution of the nonlocal effects can be neglected to a good approximation. Ab initio calculations have been carried out for the normal saturated hydrocarbons: C2n+1H4n+4 and for the all‐trans conjugated polyenes C2n+2H2n+4. As to the ratio of the local and nonlocal corrections, it is shown that there is only a quantitative difference for these two kinds of systems (strongly or weakly localizable). Neglecting nonlocal effects, considerable amount of computer time can be saved.
Spectroscopic studies on the protonation of Schiff bases
Authors: Bicca Alencastro R. De , Badilescu S. , Lussier L. S. , Sandorfy C. , Thanh H. Le , Vocelle D. 
Published: January 2005

AbstractThis short review concerns the protonation of Schiff bases by halogenic or carboxylic acids with a bias toward the chromophore of visual and bacterial rhodopsins. It is pointed out that the weak acids available in these pigments could not protonate the retinyl Schiff base 100% and that a supporting mechanism is needed to achieve full protonation. Our Fourier transform infrared studies both at room and low temperatures relating to this problem are summarized, and the propable role of water is emphasized.
Intermolecular interactions with the direct reaction field method
Authors: Van Duijnen P. Th. , Rullmann J. A. C. 
Published: January 2005

AbstractThe direct reaction field (DRF) method, developed to incorporate the effects of a (large) semiclassical environment into the Hamiltonian of a quantum mechanical system, is briefly reviewed. It is shown that the DRF method behaves—at least—like a supermolecule SCF calculation. With the water dimer as an example, the similarity with the SCF procedure is demonstrated, and an application to the interaction between the active site of papain and the remaining 3000 or so atoms of this protein shows the inadequacy of dielectric constant models and the necessity of including atomic polarizabilities in model force fields.
Nonlinear coupling in the quantum statistical theory of proton transfer dynamics
Authors: Baňacký P. , Zajac A. 
Published: January 2005

AbstractThe possible role of the nonlinear coupling on the character of the dynamics of particle transfer process is investigated. The analysis and solutions of the kinetic equation indicate that nonlinear coupling causes symmetry breaking of particle transfer potential and determines possible equilibrium structure of the system. Dissipative coupling characterizes the rate of the system to reach thermodynamic equilibrium and along with nonlinear coupling and parameters of the system determines in a unique way the resulting equilibrium structure of the system.