Semi-empirical molecular orbital calculations on some tautomers of cytosine

The stability of a series of cytosine tautomers has been investigated using both all valence electron and -electron SCF methods. The effect of general and selective scaling of the bond lengths was studied in the CNDO/2 calculations. The enol tautomer of cytosine exceeded the keto form in stability in these calculations. -electron SCF CI calculations were performed on the cytosine tautomers using two different parameterization schemes. The calculated transitions obtained for the enol form showed a close proximity to that of the keto and imino structures. Comparison was made with the experimental electronic spectrum in water and acetonitrile. No clear distiction between the keto and enol forms could be made on the basis of these calculations.

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Zusammenfassung Die StabilitÄt einer Reihe von Cytosin-Tautomeren wurde mit einer Allvalenzelektronen- und mit einer -Elektronen-SCF-Methode untersucht. Die Auswirkung einer allgemeinen als auch selektiven Skalierung der BindungslÄngen wurde bei den CNDO2-Berechnungen untersucht. Das Enoltautomere des Cytosins übertrifft nach diesen Rechnungen die Ketoform an StabilitÄt. Bei den -Elektronen-SCF-CI-Rechnungen wurden zwei Methoden der Parametrisierung angewandt. Die für die Enolform berechneten übergÄnge zeigten eine gro\e Ähnlichkeit zu denjenigen der Keto- und Iminostrukturen. Die berechneten Werte wurden mit dem experimentellen Spektrum von Cytosin in Wasser sowie Acetonitril verglichen. Auf Grund der Berechnungen konnte keine klare Unterscheidung zwischen der Keto- und der Enolform getroffen werden.

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Résumé Etude de la stabilité d'une série de tautomères de la cytosine par les méthodes SCF à électrons de valence et à électrons . L'effet d'ajustement global ou selectif des longueurs de liaison a été étudié dans le cadre CNDO/2. Le tautomère énolique de la cytosine s'avère dans ces calculs plus stable que la forme cétonique. Des calculs d'électrons SCF CI ont été effectués sur les tautomères de la cytosine en utilisant deux schémas différents pour la paramétrisation. Les transitions calculées obtenues pour la forme énolique montrent une grande analogie avec celles des structures cétoniques et iminiques. La comparaison a été faite avec le spectre électronique expérimental dans l'eau et l'acétonitrile. Aucune distinction claire entre les formes cétoniques et énoliques n'a pu Être faite à partir de ces calculs.

     

Second row molecular orbital calculations: III. Semi-empirical calculations of geometries

The ability of four semi-empirical methods to predict geometries of molecules containing atoms in the second row of the periodic table is investigated for about 80 molecules. Non-empirical, minimal basis set calculations, with and without optimization of valence orbital exponents, are carried out for a number of diatomic molecules. While none of the methods are capable of predicting geometries with an accuracy comparable to the first row parametrization, the SPD' method of Santry and the related INDO method of Benson and Hudson appear to be the most consistent. The ab initio calculations do not suffer from the drawbacks exhibited by the latter two semi-empirical methods. From this it is concluded that the failure of such methods lies in the parametrization rather than in the use of a minimal basis set.     

Second-row molecular orbital calculations: II. Semi-empirical calculations of dipole moments

The ability of four semi-empirical methods to predict dipole moments of molecules containing atoms in the second row of the periodic table is investigated. None of the methods is capable of consistently reproducing either magnitudes or qualitative trends; however, the CNDO method of Santry gives the best agreement overall. The original CNDO method of Santry and Segal emphasizes the importance of d orbitals to a greater extent than does the Santry method. Comparisons are presented with non-empirical results when possible.     

Semi-empirical molecular orbital calculations for pyridinealdoximes and acetamidopyridines

Tautomerism of pyridinealdoximes and acetamidopyridines is discussed with regard to their electronic absorption spectra. The spectra of both neutral and ionic forms of the molecules are interpreted by means of the Pariser—Parr—Pople type of calculation in a satisfactory way.The stability of 2- and 4-pyridinealdoxime tautomers is investigated using the CNDO/2 method. The lactim are more stable than the lactam forms of the molecules. The molecules having the substituent group of the syn-configuration are more stable than the molecules with other configurations of the substituent.     

Semi-empirical LCAO-SCF molecular orbital calculations for selected homo-substituted benzenes

Methods of parameter compilation, for calculating the excited singlet energy levels of substituted benzenes using the Pariser-Parr-Pople method, are compared for selected cases. A process of optimisation is employed to achieve the best fit to the observed spectra of the mono-substituted benzenes. The optimum parameters are then used to calculate the spectra of the di- and tri-homo-substituted cases. Conclusions as to a best set of data are drawn from comparison of the calculated results with the observed spectra of the di- and tri-substituted cases.

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Zusammenfassung Methoden der Parameterwahl im Rahmen des PPP-Verfahrens werden für den Fall einiger substituierter Benzole verglichen. Die Parameter werden bei den monosubstituierten Verbindungen bezüglich der experimentellen Spektren optimalisiert und zur Berechnung der entsprechenden Daten für die di- und trisubstituierten Analoga verwendet. Aus dem Vergleich dieser Ergebnisse mit dem Experiment lassen sich Rückschlüsse auf die verschiedenen Parameter-Verfahren ziehen.

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Résumé On compare sur des cas choisis les méthodes de détermination des paramètres, pour le calcul des états excités singulets des benzènes substitués, par la méthode de Pariser-Parr-Pople. Un procédé d'optimisation permet d'obtenir le meilleur accord avec les spectres observés des benzènes monosubstitués. Ces paramètres optimum sont alors utilisés pour calculer les spectres des dérivés di et tri homosubstitués. Des conclusions sur un ensemble de données optimum sont tirées de la comparaison des calculs avec les spectres observés des composés di et tri substitués.

     

Semi-empirical calculations of π-electron affinities for some conjugated organic molecules

Energy levels have been calculated for some conjugated systems containing C, N, and O atoms using a semi-empiricalmethod based upon a variableβ-γ modification of the Pariser-Parr-Pople approximation to the Hartree-Pock equation. Koopmans' theorem is used to relate the calculated energy of the lowest vacant molecular orbital, ?_LVMO, to the adiabatic electron affinity of a molecule. The approach is identical to that used previously by Kunii and Kuroda [13]. An excellent correlation is found between electron affinities deduced from recent beam experiments and ?_LVMO. This relationship is used to predict electron affinities for over 100 other organic molecules. In addition, excited state energies for negative ions are calculated, and good agreement is found with the available experimental data. Bound excited states are also predicted for some organics which contain the =C(CN)₂ substructure. The additive contribution of group substitutions to the electron affinity is discussed for the case of CN substitutions to ethylene, benzene, and naphthalene.     

Semi-empirical molecular orbital calculations of the properties of 2:1 hydrogen bonded complexes of water with some ketones and ethers

The properties (molecular geometries and hydrogen bond energies) of a number of 2:1 complexes formed between water and some ketones and ethers have been calculated using both the CNDO/2 and the MINDO/3 semi-empirical molecular orbital methods. The CNDO/2 results have been compared with those obtained using the MINDO/3 method, and have been correlated with the i.r. spectroscopic properties of the complexes. The results for the 2:1 complexes have also been compared with those of 1:1 complexes formed with the same solvents.     

Semi-empirical calculations of dihydropyran conformations

Semi-empirical calculations of dihydropyran conformations have been performed using a Karplus-type equation with the sum of chemical shifts as a correction parameter. A graphical method has been proposed to evaluate the conformational state of the molecules.     

Semi-empirical molecular orbital calculations the electronic structure and the spin-orbit coupling in azabenzenes

Electronic structures of pyridine, pyrazine, pyrimidine and pyridazine are studied by a semiempirical SCF method for valence electron systems previously proposed by the present authors. The charge distributions, transition energies and oscillator strengths of these compounds are calculated. The calculated results show fairly good agreement with the observed ones. Using these results, we have further calculated the oscillator strengths of singlet-triplet transitions and the life times of the triplet states (). In this treatment, we have considered the mixing of various singlets with T ₁ and triplets with S ₀, and the effect of -electrons is studied.

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Zusammenfassung Es werden nach einer von den Autoren dieser Arbeit vorgeschlagenen Methode die Elektronenstrukturen von Pyridin, Pyrazin, Pyrimidin und Pyridazin studiert. Die halbempirische SCF-Methode für Valenzelektronensysteme gestattet die Berechnung der Ladungsverteilungen, Übergangsenergien und Oszillatorstärken, die in recht guter Übereinstimmung mit der Beobachtung stehen. Ferner werden die Oszillatorstärken von Singulett-Triplett-Übergängen und die Lebensdauer von Triplett-Zuständen () berechnet.

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Résumé Les structures électroniques de la pyridine, de la pyrazine, de la pyrimidine et de la pyridazine sont étudiées par une méthode SCF semiempirique pour les électrons de valence proposée précédemment par les auteurs. Les distributions de charge, les énergies de transition et les forces oscillatrices de ces composés sont calculées, donnant des résultats en bon accord avec l'expérience. De plus nous avons calculé les forces oscillatrices des transitions singulet-triplet et les durées de vie des états triplets (). Dans ce calcul nous avons inclus l'interaction de configuration et l'étude de l'effet des électrons .

     

Quantum manifestations of classical trajectories in molecular systems

Quantum chaos, understood as the effect of the underlying classical dynamics on the stationary quantum properties in classically chaotic systems, is examined in two molecular floppy systems. Realistic models of two degrees of freedom for HO₂ and HCN/HNC are considered. The structure of the classical phase space is studied using Poincaré surfaces of section and the dynamical characteristics of the corresponding wave functions analyzed also in phase space with the aid of Husimi functions. Some wave functions show strong localization along periodic orbits. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Simplified ab-initio calculations for molecular systems

A method is described for reducing a large part of the arithmetic of exact ab-initio SCF molecularorbital calculations based on Slater-type-orbitals without noticeable loss of numerical accuracy. The procedure involves the transformation to Löwdin orthogonalized orbitals and then invoking the NDDO approximation. The three- and four-centre two-electron integrals required are estimated by a truncated Ruedenberg expansion. All one-electron integrals are evaluated exactly. No empirical parameters are employed. Numerical tests on CO, OF₂, O₃ and ONF show that the NDDO approximation is very accurate for Löwdin functions and that the Ruedenberg expansion is arithmetically satisfactory for the SCF MO calculations.     

Position of protonation of the cresols: Semi-empirical and ab initio calculations

STO-3G and INDO calculations on the isomeric cresols and the protonated cresols indicated that protonation occurs most readily para to the hydroxy substituent, as is observed commonly in experimental work.     

Semi-empirical all-valence-electron SCF calculations of acidities of cycloalkanes

CNDO/2 calculations of the energy change RHR^–+H⁺ for cycloalkanes give the acidity order: cyclohexane > cyclopentane > cyclobutane > cyclopropane, exactly the reverse of the experimental order. INDO results are similar to CNDO/2. A new method, IRDO, related to NDDO is described. Both of these methods give results differing from the first two but agreement with experiment is still poor.

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Zusammenfassung CNDO/2-Berechnungen der Energieänderung der Reaktion RHR^–+H⁺ für Cycloalkane gibt folgende Reihenfolge für die Acidität: Cyclohexan > Cyclopentan > Cyclobutan > Cyclopropan, was genau der umgekehrten experimentellen Reihenfolge entspricht. INDO Resultate sind den CNDO/2 Resultaten ähnlich. Eine neue Methode, IRDO, die der NDDO verwandt ist, wird vorgeschlagen. Diese Methoden führen zu Resultaten, die sich von denen der beiden ersten unterscheiden, aber die Übereinstimmung mit dem Experiment ist noch immer unbefriedigend.

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Résumé Des calculs CNDO/2 de la variation d'énergie de la réaction RHR^–+H⁺ pour les cycloalkanes donnent l'ordre des acidités à l'inverse de l'ordre experimental: cyclohexane > cyclopentane > cyclobutane > cyclopropane. Les résultats INDO sont semblables à ceux de CNDO/2. Une nouvelle méthode, IRDO, liée à NDDO est décrite. Ces deux méthodes donnent des résultats différents des deux premières, mais l'accord avec l'expérience reste faible.

     

Semi-empirical MO calculations of nuclear spin coupling constants

The results obtained using different semi-empirical approaches, namely EHMO, IEHMO, CNDO/2 and INDO, in the calculation of spin–spin coupling constants within the framework of the one-electron MO approximation are systematically compared in the case of several classes of organic molecules. While, at a semi-empirical level SCF methods normally provide satisfactory wave function, the use of the simple EHMO seems better able to satisfy the problem connected with the calculation of spin–spin coupling constants, expecially when an appropriate set of AO's is chosen, in order to avoid parametrisation of Dirac monocentric integrals. Charge iteration (IEHMO) seems to improve the results slightly only when heteroatoms are present, but the complexity introduced into the calculations and the greatly increased computer time do not justify the slight improvement achieved, particularly as the method is applied to large molecules and organometallic compounds.     

Semi-empirical calculations on difluoro- and trifluoroacetic acid and their fluorides

In order to facilitate the interpretation of microwave spectra of difluoro-acetic acid, trifluoroacetic acid, difluoroacetyl fluoride and trifluoroacetyl fluoride quantumchemical estimates of rotational barriers and dipole moments have been made.For difluoroacetic acid and difluoroacetyl fluoride a relatively high barrier (5 kcal mole^?1) and for trifluoroacetic acid and trifluoroacetyl fluoride a low barrier (0.5 kcal mole^?1) for rotation around the C-C axes is predicted in the CNDO/2 approximation (Complete Neglect of Differential Overlap). Dipole moment components in the principal axis system were obtained. Theoretical results are compared with available experimental data.     

Bulk modulus for some simple molecular fluids

The bulk modulus B of several molecular fluids composed of rigid molecules has been calculated from p-p-T data obtained with a high-pressure vibrating tube densitometer. The data of all the substances studied, including Ar, can be described by a single master curve when plotted versus the reduced density *, in agreement with the predictions of the Gubbins-Gray perturbation theory for fluids with the same reference system. Combination of p-p-T and C_v data with the virial theorem has allowed the calculation of the exponent characterizing the repulsive branch of the intermolecular potential n. The different values of n suggest that different reference systems should be used for each substance, in contradiction with the conclusions obtained from the B versus * curves. This indicates that p-p-T data are less sensitive to the details of the intermolecular potential than their combination with other thermal properties like C_v, internal energy or residual entropy.     

The molecular electrostatic potential of some simple molecules

The calculation of the molecular electrostatic potential from simplified models of the electron density is considered. Results are shown for water, hydrogen fluoride and ammonia. Little loss of accuracy is evident when the density is represented by a linear sum of well-chosen Gaussians. When these are further simplified into sets of point charges the inner parts of the molecule are poorly represented. More elaborate point moments make the representation worse. On the other hand a mixed representation with point charges and one diffuse Gaussian gives all the essential features of the potential of these molecules.     

Approximate molecular relativistic Dirac-Coulomb calculations using a simple Coulombic correction

A simple point-charge model is used to correct molecular four-component Dirac-Coulomb calculations which neglect two-electron integrals over the small components of the wave function. The calculated valence properties show no degeneration relative to the full calculation, while a speed-up factor of 3 is obtained. Received: 28 July 1997 / Accepted: 5 August 1997     

Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection

End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question of how the number of selected frames influences the accuracy of the SIE calculations.