bluuebunny/crossref_metadata_2025_split huggingface dataset:
MNDO study of catenated sulfur: The molecules and ions S3 to S8
Authors: Baird N. Colin 
Published: December 2004

AbstractSemiempirical molecular orbital calculations by the MNDO method are reported for sulfur rings and chains S3 through S8, for the corresponding dications, S through S, and for S. The MNDO method seems quite successful in predicting the geometries of neutral catenated sulfur molecules, even the unusual bond‐length alternation and extent of coplanarity in cyclo‐S7. In contrast to hydrocarbon rings, for which its prediction of strain is erratic, MNDO is consistent in its calculated strain energies in small cyclosulfur rings; unfortunately all the strain energies are overestimated by 70%. As a consequence of this error, the method must be considered unreliable in its predictions of structures for the dications S, since many of these ions could potentially exist as strained bicyclic systems. In addition, MNDO appears to have difficulty handling long, partial SS σ bonds, as are found to occur in S. It may be for this reason that MNDO predicts, apparently incorrectly, that the open‐chain isomers of S are more stable than are any of the cyclic forms, at least for S to S. With respect to neutral Sn molecules, however, the MNDO predictions appear more reliable than ab initio molecular orbital (MO) calculations using small basis sets without polarization functions and without configuration interaction (CI). However, MNDO apparently underestimates by about a factor of two the strength of the three‐electron π bonds present in the terminal links of sulfur diradical chains.
On computationally adjusting the Hill equation of adsorption
Authors: Cortés Joaquin , Puschmann Heinrich , Valencia Eliana 
Published: December 2004

AbstractWe discuss the implementation and computational efficiency of one approach to adjusting the Hill equation of adsorption to a set of empirical data, pointing out some aspects that seem to be valid in the general case. The approach consists basically of minimizing squares of deviations of the adsorbed amounts, which are numerically computed in terms of the empirical pressures and the parameters. Hill's equation is dealt with as a prototype of nonlinear equations seldom used by chemists because none of their variables can be set free.
Molecular mechanics assessment of the configurational statistics of polyoxyethylene
Authors: Baldwin D. Theodore , Mattice Wayne L. , Gandour Richard D. 
Published: December 2004

AbstractPrevious investigators have shown that statistical mechanical averages for configuration‐dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche–trans energy difference for rotation about CC bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2OCH2CH2OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean‐square unperturbed end‐to‐end distance, mean‐square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche–trans energy difference for rotation about CC which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche–trans energy difference for rotation about the CO bond. This energy difference is overestimated by MM2.
A quantum mechanical study of the equilibrium between 1,4‐ and 1,6‐dialkylcyclooctatetraenes
Authors: Tosi Camillo 
Published: December 2004

AbstractThe equilibrium between three pairs of 1,4‐ and 1,6‐dialkylcyclooctatetraenes was investigated with the two quantum mechanical algorithms, IBMOL and PCILO. PCILO computations reproduce the trend of stability within each pair of isomers obtained earlier by Allinger with molecular mechanics calculations, while IBMOL computations do not. These results not only can be explained in the light of, but also are a confirmation of Allinger's conclusions that the conformational stability is governed by the magnitude of the van der Waals' attraction between the two alkyl groups: The dispersion energy, which is essentially an electron correlation effect, is not accounted for by a method like IBMOL that, albeit ab initio, is based on the Hartree–Fock independent particle model, while it is fairly well reproduced by a method like PCILO that, albeit semiempirical, is based on a configuration interaction approach. Simulation of the full configuration interaction (CI) correction through a suitable dispersion term brings IBMOL results to a good agreement with the molecular mechanics ones.
Ground states of molecules. 67.MNDO Calculations for compounds containing iodine
Authors: Dewar Michael J. S. , Healy Eamonn F. , Stewart James J. P. 
Published: December 2004

AbstractMNDO has been parametrized for iodine. Since d atomic orbitals (AOS) are not included, the calculations are restricted to II. Heats of formation, molecular geometries, ionization energies, and dipole moments are reproduced with useful accuracy.
Calculation of energies of excited states using MNDO
Authors: Dewar Michael J. S. , Fox Marye Anne , Campbell Kay A. , Chen Chia‐Chung , Friedheim James E. , Holloway Mary K. , Kim Shi Choon , Liescheski Phillip B. , Pakiari Ali M. , Tien Tze‐Pei , Zoebisch Eve G. 
Published: December 2004

AbstractThe energies of the lowest singlet (S1) and triplet (T1) states of 28 molecules have been calculated by the “half‐electron” (MNDO‐HE) and spin‐unrestricted (UMNDO) versions of MNDO. While most of the calculated values are too negative, because of overestimation of the correlation energy in MNDO‐HE and UMNDO, the errors are systematic and depend in an understandable way on the nature of the molecular orbitals (MOS) involved. When appropriate corrections are applied, the calculated energies agree with experiment almost as well as they do for ground states. This justifies the use of MNDO‐HE or UMNDO for studies of excited state processes.
A study of the biologically active conformers for prodine opiates and their derivatives
Authors: Froimowitz Mark , Kollman Peter 
Published: December 2004

AbstractConformational energy calculations using the empirical MM2 (molecular mechanics II) and semiempirical quantum mechanical PCILO (perturbative configuration interaction using localized orbitals) methods are reported for various prodine derivatives. These include 3‐demethylprodine, α‐prodine, β‐prodine, the α‐2‐methyl derivative, α‐promedol, the γ‐2,3‐dimethyl derivative, and γ‐isopromedol. The results are consistent with all of the compounds activating the opiate receptor in a phenyl equatorial conformation with optimum activity resulting from a particular orientation of the phenyl and propionoxyl groups. In disagreement with previous limited experimental data, α‐promedol is found to prefer a phenyl equatorial conformer. It is confirmed that, of the two mirror image phenyl equatorial conformers that are preferred for 3‐demethylprodine, the more active prodines antipodes consistently prefer the one in which the phenyl orientation is the opposite (mirror image) of that found in morphine and in the preferred conformer of the morphine‐like (+)‐phenylmorphan. This is a possible molecular basis for the nonmorphine‐like effects that occur with the introduction of a phenyl meta hydroxyl into some prodine derivatives. It is also suggested that the less active prodine antipodes, which have a morphine‐like phenyl orientation, may act in a morphine‐like manner at opiate receptors.
On the diatomic vibration–rotation eigenvalue equation: Highly accurate results for high levels
Authors: Dagher Mounzer , Kobeissi Hafez 
Published: December 2004

AbstractAccurate vibration–rotation eigenvalues EvJ are sought for very high levels (up to dissociation) of a diatomic potential. The method used is the recent “eigenvalue equation” method [Kobeissi et al., J. Comput. Chem., 4, 218 (1983)] which dissociates the determination of the eigenvalue from that of the eigenfunction. A new mathematical formulation for any numerical potential is presented, which reduces the problem to the use of a single recurrent formula. A numerical application to the model potential used by Cashion [J. Chem. Phys., 39, 1872 (1963)], up to v = 23, gives results equal to the exact eigenvalues to approximately 10−14 cm−1. Another application to the model potential used by Johnson [J. Chem. Phys., 67, 4086 (1977)], up to v = 60, gives similar results.
Substituent effects in second‐row molecules: Basis set performance in calculations of normal valency phosphorus and sulfur compounds
Authors: Magnusson Eric 
Published: December 2004

AbstractAb inito molecular orbital calculations of the phosphorus‐ and sulfur‐containing series PH2X, PH3X+, SHX, and SH2X+ (X = H, CH3, NH2, OH, F) have been carried out over a range of Gaussian basis sets and the results (optimized geometrical structures, relative energies, and electron distributions) critically compared. As in first‐row molecules there are large discrepancies between substituent interaction energies at different basis set levels, particularly in electron‐rich molecules; use of basis sets lower than the supplemented 6‐31G basis incurs the risk of obtaining substituent stabilizations with large errors, including the wrong sign. Only a small part of the discrepancies is accounted for by structural differences between the optimized geometries. Supplementation of low level basis sets by d functions frequently leads to exaggerated stabilization energies for π‐donor substituents. Poor performance also results from the use of split valence basis sets in which the valence shell electron density is too heavily concentrated in diffuse component of the valence shell functions, again likely to occur in electron‐rich molecules. Isodesmic reaction energies are much less sensitive to basis set variation, but d function supplementation is necessary to achieve reliable results, suggesting a marginal valence role for d functions, not merely polarization of the bonding density. Optimized molecular geometries are relatively insensitive to basis set and electron population analysis data, for better‐than‐minimal bases, are uniform to an unexpected degree.
Polyatomic, anharmonic, vibrational–rotational analysis. Application to accurateab initioresults for formaldehyde
Authors: Harding Lawrence B. , Ermler Walter C. 
Published: December 2004

AbstractA computer programSURVIBis described for calculating vibrational anharmonicity constants for polyatomic molecules. The program requires as input a grid of calculated energies in the vicinity of a stationary point. This grid is fit, in a least squares sense, to a polynomial function of the internal coordinates. This analytic representation of the energy surface is employed in a normal mode analysis, and the energy is reexpanded as a polynominal function of the normal mode coordinates (expressed as vectors in the mass‐weighted atomic Cartesian coordinate space). The resulting coefficients are used in a second‐order perturbation theory analysis to obtain the vibrational anharmonicity constants. Also reported is an application of this program to formaldehyde employingab initio,RHF,MP2,MP3, andRHF‐CIcalculations. The spectroscopic constants obtained for H2CO are in good agreement with experimentally derived values recently reported by Reisner.
Simple method of computing the partition coefficient
Authors: Klopman Gilles , Namboodiri Krishnan , Schochet Melvin 
Published: December 2004

AbstractThe values of log10 P (partition coefficient, in octanol/water) were calculated for about 200 organic molecules of diverse structures and functionalities. The method involves a simple procedure and appears accurate enough for semiquantitative applications. Further, this method of calculating log10 P values was shown to be successful in providing a better quantitative structure activity relationship (QSAR) than the Hansch‐type approach in the study of inhibitory activity of substituted phenols on Bacillus Subtilis spore germination.
Ab initio calculations of intermolecular potentials. The ground state of the ArH2 van der Waals molecule
Authors: Olivares Del Valle F. J. , Tolosa S. , Piñeiro A. Lopez , Requena A. 
Published: December 2004

AbstractHartree–Fock computations of the potential surface of ArH2 have been carried out and supplemented with calculations of the dispersion energy, with use of the counterpoise method to remove the basis set superposition error. The collinear and perpendicular bisector geometries are considered. The resulting potentials agree quite well with the actual experimental data.
Computer generation of matching polynimials of chemical graphs and lattices
Authors: Ramaraj Ramamani , Balasubramanian K. 
Published: December 2004

AbstractA computer program in Pascal is developed for computing the matching polynomials of graphs and lattices. This program is based on the recursive relation for matching polynomials outlined by Hosoya [Bull. Chem. Soc. Jpn., 44, 2332 (1971)], Gutman and Hosoya [Theor. Chim. Acta, 48, 279 (1978)], and others. The graph whose matching polynomial is of interest is reduced recursively until the graph reduces to several trees. The characteristic polynomial of a tree is the same as the matching polynomial. The characteristic polynomials of resulting trees are computed using the computer program based on Frame's method developed by Balasubramanian [Theor. Chim. Acta, 65, 49 (1984)]; J. Comput. Chem., 5, 387 (1984). The resulting polynomials are then assembled to compute the matching polynomial of the initial graph. The program is especially useful in generating the matching polynomials of graphs containing a large number of vertices. The matching polynomials thus generated are potentially useful in several applications such as lattice statistics (dimer covering problem), aromaticity, valence bond methods (enumeration of perfect matchings) in the calculation of grand canonical partition functions, in the computation of thermodynamic properties of saturated hydrocarbons, and in chemical documentation.
Atom equivalents for relating ab initio energies to enthalpies of formation
Authors: Ibrahim Mustafa R. , Von Ragué Schleyer Paul 
Published: December 2004

AbstractSets of atom equivalents have been developed which permit the estimation of heats of formation, ΔH°(g), from ab initio total energies (3‐21G and 6‐31G* basis sets). This extends the isodesmic reaction scheme of Pople and the group equivalents of Wiberg. A variety of small inorganic and organic molecules, including fluorocarbons, free radicals, carbocations, and protonated species give excellent agreement with experiment; average errors are less than 1 kcal/mol with unstrained hydrocarbons (both basis sets), and are on the order of 2 kcal/mol for all molecules considered (6‐31G*; the 3‐21G basis errors, as expected, usually are somewhat higher). The results substantiate Pople's early conclusions that Hartree‐Fock theory provides a generally satisfactory description of classical molecules.
Stereodynamics of triethylamine: Molecular mechanics calculations on the direct rotational racemization of the C3‐symmetric conformers
Authors: Fleischman Stephen H. , Weltin Eugen E. , Hackett Bushweller C. 
Published: December 2004

AbstractThe direct interconversion of the two C3‐symmetric enantiomeric conformations of triethylamine, via CN bond rotation, has been studied by molecular mechanics (MM2) calculations. The MM2 calculations have been used to characterize the minima (equilibrium geometries) and first‐order saddle points (transition states) for this process. For one interconversion, there are five saddle points and six minima. The highest energy saddle point results from the uncoupled rotation of one ethyl group to eclipse the lone pair. Two of the barriers result from coupled rotation of two ethyl groups in close passage.
Relativistic effective potential SCF calculations of AgH and AuH
Authors: Krauss M. , Stevens W. J. , Basch Harold 
Published: December 2004

AbstractRelativistic effective potentials (REP) are now widely used in molecular electronic structure calculations. Tests of these REP are needed to assess their accuracy. This can now be done for AgH and AuH since Lee and McLean have published Dirac‐Fock calculations for these molecules. Comparative SCF calculations have been performed for two types of effective potential. Satisfactory agreement between the effective potential results and Dirac‐Fock values is found for spectroscopic constants and dipole moments, which supports the use of these potentials for heavy atom containing molecules.
Usefulness of modified virtual orbitals in multireference CI procedure illustrated by calculations on lithium clusters
Authors: Fantucci P. , BonačiCć‐Koutecký V. , Koutecký J. 
Published: December 2004

AbstractThe maximization of the exchange interaction between the canonical Hartree–Fock virtual and occupied orbitals leads to a transformed set of virtual orbitals which are well suited as one‐electron functions for CI calculations. The procedure, generally known for a long time is seldom applied, despite its simplicity and very low computational demand. However, it is found to be particularly useful in the case of multireference CI, since an improved energy is obtained with a considerable shortening of the CI expansion. Moreover, in the final CI wave function, several configurations appear with considerable weight, thus allowing an easy choice of additional configurations to be inserted in the definition of a new zero‐order wave function. The efficiency of the computational procedure is discussed for the case of a Li6 cluster of D3h symmetry and for the NaCO and PdCO complexes. Results are reported for the relative stability of four different geometrical arrangements of the Li6 cluster.
Molecular structures and intramolecular interactions in dimethyl cyclohexane isomers
Authors: Klimkowski V. J. , Manning J. P. , Schäfer Lothar 
Published: December 2004

AbstractThe geometries of ten isomers of dimethyl cyclohexane were determined by ab initio gradient geometry refinement with the 4‐21G basis set. It is found that many intramolecular interactions are clearly manifested by correlated structural trends, and that they are consistent with strain energies calculated by employing previously defined ab initio group equivalents. Specifically, non‐bonded interactions are found between two adjacent methyl groups in some of the forms, and between axial methyl groups and adjacent axial CH bonds in others. Unperturbed axial CH and CC bonds are consistently longer than equatorial bonds. In general, CH bonds which are involved in non‐bonded repulsive interactions are shortened, i.e., strengthened, and the corresponding HCC angles are large, compared to non‐interacting parameters.
The effects of vinylic and allylic fluorine substitution in iso‐butylene
Authors: Ritchie James P. 
Published: December 2004

AbstractMolecular orbital calculations using the 3‐21G basis set have been performed for iso‐butylene (IB; 2‐methyl‐1‐propene), difluoro‐iso‐butylene (DFIB; 1,1‐difluoro‐2‐methyl‐1‐propene), hexafluoro‐iso‐butylene (HFIB; 3,3,3‐trifluoro‐2‐(trifluoromethyl)‐1‐propene), and perfluoro‐iso‐butylene (PFIB; 1,1,3,3,3‐pentafluoro‐2‐(trifluoromethyl)‐1‐propene). The effects of fluorine substitution were studied by comparison of several calculated quantities of the fluorinated compounds with those of IB. Through an analysis of the computed electron density distributions, it is suggested that a vinylic fluorine acts as a π acceptor, by electron transfer into the CF bond, and a π repeller, by polarization of the adjacent π electrons. An allylic fluorine acts as a π attractor through electrostatic effects, although in HFIB a minor contribution from hyperconjugation was evident. Finally, electrostatic potentials for the molecules were calculated. These show that fluorine substitution has large effects on the electrostatic potential associated with the π electrons. These effects change the sign of the calculated electrostatic potential in the plane containing the π bond to such an extent that PFIB is quite susceptible to nucleophilic attack.
Spatial geometric arrangements of disulfide‐crosslinked loops in proteins
Authors: Kikuchi Takeshi , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe classification of patterns of the three‐dimensional folding of a covalently crosslinked polypeptide chain can be used to introduce long‐range interactions into the theoretical search for the native conformation of a protein. This classification into Spatial Geometric Arrangements of Loops (SGAL) had been proposed earlier (H. Meirovitch and H. A. Scheraga, Macromolecules 14, 1250, 1981). It is based on the subdivision of the protein molecule into closed loops, defined by covalent crosslinks (such as disulfide bonds). Various SGAL classes correspond to the presence or absence of mutual penetration of loops, called entanglements or thrustings. A systematic and objective method is developed here to enumerate all theoretically possible SGAL's for a protein, based only on its covalent structure, i.e., the pattern of disulfide bonds or other crosslinks, regardless of whether the three‐dimensional structure is known or unknown. This information can be of use in structural predictions of folding patterns. Using a modification of the method, it is also possible to determine the SGAL class to which a protein of known structure belongs. Out of 18 proteins with known three‐dimensional structure and containing more than two disulfide bonds, five have a native structure with at least one entanglement or thrusting. Thus, threaded SGAL's represent a significant structural feature of native proteins. All five involve neighboring loops in the sequences. Their presence in a protein can suggest restrictions on the possible ways of folding the protein.
A force‐field study of the conformational characteristics of the iduronate ring
Authors: Ragazzi Massimo , Ferro Dino R. , Provasoli Augusto 
Published: December 2004

AbstractMethods of molecular mechanics were applied to investigate the conformation of the (methyl 2‐O‐sulfate‐4‐methyl‐α‐L‐idopyranose) uronic acid (DMIS), in order to correlate the peculiar vicinal proton coupling constants observed in polysaccharides containing the iduronate ring to the conformational characteristics of this sugar ring. We found three conformers with comparable energies, namely the two chair forms 1C4 and 4C1 and the skew‐boat form 2S0(L); the latter is separated from each chair form by a barrier of about 9 kcal/mol. Along the pseudorotational path three additional minima (3S1, 1S3, and 1S5) were found, yet at least 4 kcal/mol higher than 2S0. The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS. However, the conformational properties of the idopyranosidic ring in DMIS (and in related compounds) should still be interpreted in terms of equilibrium among these three conformers only.