bluuebunny/crossref_metadata_2025 huggingface dataset:
Modified components of RNA. The molecular and crystal structure of 5‐carboxymethylaminomethyl‐2‐thiouridine (S2cmnm5U)
Authors: Wieczorek Michał W. , Bujacz Grzegorz D. , Adamiak Dorota A. , Małkiewicz Andrzej , Nawrot Barbara
Published: January 2005

The structure of the title compound 1 has been determined by X‐ray analysis. The following crystal data were found: orthorhombic, P212121, a = 5.243(2), b = 24.864(4), and c = 37.083(6) Å. Three molecules of the compound with four molecules of water are present in the independent part of the unit cell. The sugar ring puckering is 3E for the molecules A and C and 3T2 for the molecule B. The conformation of the hydroxymethylene group is g+ and g− for B and A, C, respectively. The torsion angles χ for all molecules are in the range of the anti conformation. In the crystal lattice of 1 both the intra‐and intermolecular hydrogen bonding systems occur.
Convenient synthesis of heterocycles by sulfur‐assisted carbonylation at ordinary pressure and temperature
Authors: Mizuno Takumi , Toba Hitoshi , Miyata Toshiyuki , Nishiguchi Ikuzo
Published: January 2005

Heterocyclic compounds, including benzimidazolones, naphthimidazolone, benzoxazolones, benzothiazolone, quinazolinone, benzoxazinone, quinazolinedione, and imidazopyridinone were synthesized in good yields by sulfur‐assisted carbonylation of aromatic amines with carbon monoxide (1 atm) at room temperature, with subsequent oxidation using molecular oxygen (1 atm, RT). The present method is characterized as a simple procedure carried out under quite mild conditions.
An unexpected synthesis of thiophene derivatives by thionation of N‐phenylacetylthiobenzamides
Authors: Lai Long‐Li , Reid David H. , Wang Sue‐Lein , Liao Fen‐Ling
Published: January 2005

Four thiophene derivatives have been obtained unexpectedly from the reaction of N‐phenylacetyithiobenzamides with P4S10 in boiling carbon disulfide. The structure of one of these was established by X‐ray crystallography.
Synthesis of 1‐(8‐phosphonomethoxy‐3,6‐dioxaoctyl)pyrimidines and purines, a novel series of acyclonucleotide analogues
Authors: Charron Marie , Tse H. L. Allan , Mansour Tarek S. , Knight David J. , O'Sullivan Corrine , Coates Jonathan A. V.
Published: January 2005

A convenient synthesis of 1‐(8‐phosphonomethoxy‐3,6‐dioxaoctyl) uracil, cytosine, adenine, and guanine nucleotide analogues 26, 28, 30, and 32 by Mitsunobu coupling of the nucleobases with suitably functionalized alcohol derivative 24 is described. The antiviral activity of this series of compounds against herpes simplex virus (HSV) types 1 and 2 and human cytomegalovirus is reported.
Electrophilic chemistry of the cubic arsaalkyne tetramer (AsCtBu)4: Arsonium ions of ethylation (EtOTf), benzylation (PhCH2OTf), and mono‐ and diprotonation (FSO3H/SO2)
Authors: Laali Kenneth K. , Nixon John F. , Johnson Julian A.
Published: January 2005

The cubic arsaalkyne tetramer 2 reacts at room temperature with ethyl triflate to give the As‐ethylated arsonium salt 4. A similar reaction of 2 with benzyl triflate (generated in situ via PhCH2Cl/AgOTf) gives the As‐benzylated salt 5. Low‐temperature protonation of 2 with FSO3H/SO2 produces a mixture of arsonium ions 6 and 7 resulting from mono‐ and diprotonation. The NMR characteristics of the resulting arsonium ions are discussed and compared with those of the corresponding phosphonium ions derived from the tetraphosphacubane 3. The FAB mass spectrum of 4 and its decomposition products (FAB‐CAD‐MS/MS) are also discussed.
1,3‐Dipolar cycloaddition of diazocompounds to 1‐alkenylboronic esters
Authors: Jazouli Mohammed , Carboni Bertrand , Carrié Robert , Soufiaoui Mohammed , Toupet Loïc
Published: January 2005

A variety of diazo compounds was added to the parent vinylboronic ester derived from pinacol. The reactivity of some substituted 1‐alkenylboronic esters is also briefly examined. The nonisolated primary adducts spontaneously rearrange via a 1,3‐boron migration and lead to 1‐borylated‐2‐pyrazolines. The structure of one of these compounds has been established by X‐ray diffraction analysis.
Methanolysis of 1,3‐oxathiolane‐2‐thione: A stereospecific preparation of episulfides
Authors: Uenishi Jun'ichi , Motoyama Mitsuhiro , Kubo Yuki
Published: January 2005

Potassium carbonate mediated methanolysis of optically active 1,3‐oxathiolane‐2‐thiones (5‐membered cyclic xanthates) took place under very mild conditions to give optically pure 1,2‐episulfides. Also, methanolysis of 4‐[1‐(methanesulfonyloxy)alkyl]‐1,3‐oxathiolane‐2‐thiones and 2,4‐dialkyl substituted 1,3‐oxathiolane‐2‐thione gave 2,3‐episulfides, stereospecifically.
Oxidation of ketene‐S,S‐acetals, thioacetals, and thioketals by dimethyldioxirane: A convenient method for the preparation of bis‐sulfones
Authors: Curi Denise , Pardini Vera L. , Viertler Hans , Baumstark Alfons L. , Harden Donald B.
Published: January 2005

The oxidation of a series of ketene‐S,S‐acetals, 2a–f, and a series of thioacetals and thioketals, 4a–g, with a fourfold or greater excess of dimethyldioxirane, 1, produced the corresponding bis‐sulfones 3a–f and 5a–g in excellent yields. The reaction of the bis‐sulfides with one, two, and three equivalents of 1 yielded monosulfoxides, bis‐sulfoxides, and sulfoxide‐sulfones, respectively, as the major products. The order of addition of the reactants as well as the temperature of the reaction mixture changed the product distributions. The use of low‐temperature, rapid stirring and the addition of the dioxirane solution to the bis‐sulfide maximized the yield of the major product. The results are consistent with an electrophilic oxygen‐atom transfer mechanism in which the rate of sulfide oxidation is much faster than oxidation of sulfoxide to sulfone. However, sulfoxide oxidation is of a sufficient rate such that local concentration effects affect the results.
Synthesis of some new spiro[indoline‐3‐heterocycle]‐2‐one derivatives
Authors: Al‐Thebeiti Marzoog S.
Published: January 2005

Indole‐2,3‐dione was treated with malonic acid in a mixture of ethanol/pyridine to afford 1‐[3‐(2‐oxoindolinylidene)]acetic acid (3), which was then reacted with thionyl chloride to give the corresponding acid chloride (4). The acid chloride 4 reacted with arenes in the presence of AlCl3 to yield substituted 3‐(2‐oxoindolinylidene)acetophenones 5a–c. Compounds 5a–c were alkylated with methyl iodide to afford 6a–c. Compounds 6a–c were treated with hydrazine derivatives, hydroxylamine hydrochloride, urea, and thiourea to yield the complex spiro compounds 7a–i, 8a–c, and 9a–f, respectively.
Oxidation of tetraphosphacubane by bis(trimethylsilyl) peroxide, sulfur, and selenium [1]
Authors: Ma Xiao‐Bo , Birkel Manfred , Wettling Thomas , Regitz Manfred
Published: January 2005

Although the nucleophilicity/basicity at the phosphorus atom of the tetraphosphacubane 2 is reduced, apparently owing to the participation of the lone pairs of electrons in the P/C σ bonds, stepwise oxidation of the phosphorus atoms with bis(trimethylsilyl) peroxide or sulfur (in the presence of triethylamine) can be realized until all four phosphorus atoms have reacted to give products 10–17. When 2 was treated with a large excess of selenium at 110°C, only the triselenide 18 was obtained.
Palladium‐catalyzed hydrosilylation of silyl‐substituted butadienes
Authors: Weng Wu‐Wang , Chen Ruey‐Min , Luh Tien‐Yau
Published: January 2005

Palladium‐catalyzed hydrosilylation of silyl‐substituted butadienes 1 and 2 with MeSiCl2H has been investigated. Both steric effects and the presence of an aryl substituent affect the regiochemistry of the hydrosilylation reaction. Hydrosilylation of siloxanetethered bis‐dienes 9 exhibits high regio‐ and diastereoselectivity.
Trans‐annular interactions in morpholines: A photoelectron spectroscopic study
Authors: Novak Igor , Kovaĉ Branka
Published: January 2005

The He I and He II photoelectron spectra of 4‐methylmorpholine, 4‐morpholinecarbonitrile, and 4‐morpholinepropionitrile have been measured. The electronic structure and heteroatom lone pair interactions, in particular, were analyzed with the aid of HeII/HeI intensity variations, comparison with the spectra of related compounds, and AM1 semiempirical calculations. We present an example of combined inductive and resonance interactions operating in the morpholine ring system.
Preparation, spectral characterization, and single crystal X‐ray structures of cis and trans isomers of 2,4,6‐trifluoroethoxy‐1,3,5‐triethyl‐1,3,5,2λ5, 4λ5, 6λ5‐triazatriphosphorinane‐2,4,6‐trioxide, [ETNP(O)(OCH2CF3)]3
Authors: Murugavel Ramaswamy , Thirupathi Natesan , Krishnamurthy Setharampattu S. , Nethaji Munirathinam
Published: January 2005

Oxidation of the cis isomer of the λ3‐cyclotriphosphazane [EtNP(OCH2CF3)]3 with trimethylamine‐N‐oxide (TMNO) gives the cis isomer of trioxo‐λ5‐cyclotriphosphazane [EtNP(O)(OCH2CF3)]3; the trans isomer of [EtNP(O)(OCH2CF3)]3 is obtained by the treatment of a cis and trans mixture of [EtNP(OCH2CF3)]3 with aqueous H2O2. The two trioxocyclotriphosphazanes have been characterized by elemental analysis, IR, and NMR (1H, 13C, 19F, and 31P) spectroscopy. The solid state structures of both the isomers have been determined by single crystal X‐ray diffraction. The six‐membered P3N3 ring in both the isomers exhibits a twist‐boat conformation; in the cis isomer, the trifluoroethoxy substituents lie on the same side of the ring, whereas, in the trans isomer, two trifluoroethoxy groups are on one side of the ring and the third on the other side of the ring. Crystal data for cis‐[EtNP(O)(OCH2CF3)]3: monoclinic, P21/n, a = 13.593(3), b = 9.721(2), c = 17.539(3) Å, β = 99.49(2)°, V = 2286(1) Å3, Z = 4, and Final R = 0.047. Crystal data for trans‐[EtNP(O)(OCH2CF3)]3: monoclinic, P21/n, a = 11.685(4), b = 15.115(5), c = 13.233(5) Å, ‐ = 102.21(3)°, V = 2284(1) Å3, Z = 4, and Final R = 0.078.
Synthesis and properties of optically active phosphine‐boranes possessing an l‐menthyloxy group
Authors: Imamoto Tsuneo , Yoshizawa Takeshi , Hirose Koutaro , Wada Yoshiyuki , Masuda Hideki , Yamaguchi Kentaro , Seki Hiroko
Published: January 2005

(SP)‐9‐Anthryl(l‐menthyloxy)phenylphosphine‐borane and (SP)‐(1‐l‐menthyloxy)benzo[b]phosphole‐borane were synthesized, and their structures were characterized by X‐ray crystallographic analysis. The latter compound was reduced by lithium naphthalenide at −78°C with cleavage of the PO bond, and the subsequent reaction with electrophiles afforded the corresponding tertiary phosphine‐boranes possessing good to excellent enantiomeric excesses.
A symmetric oxyselenenylation of simple olefins using optically active selenobinaphthyls
Authors: Fujita Ken‐Ichi , Murata Kazuhisa , Iwaoka Michio , Tomoda Shuji
Published: January 2005

Asymmetric trans‐addition reactions of simple olefins have been performed by using optically active 2‐selenobinaphthyls 1,2a–g. Introduction of an amide group at the 2′‐position in the binaphthyl skeleton enhances considerably the diastereomeric excess (de) of the asymmetric methoxyselenenylation. In the case of trans‐olefins, introduction of another chiral center in the amide group further enhances the de due to double stereodifferentiation between the (R)‐binaphthyl skeleton and the chiral amide group introduced at the 2′‐position in the binaphthyl skeleton. The use of chiral nucleophiles is also effective to enhance the de for symmetrical cis‐olefins.
Novel syntheses of pyrrolone and pyrrolopyridine derivatives
Authors: Kandeel Zaghloul E. , Hafez Ebtisam A. , Sleim Maghraby A. , Abdelatif Fawi M. , Elnagdi Mohamed H.
Published: January 2005

4‐Arylmethylene‐2‐phenyl‐2‐oxazolin‐5‐ones 1a,b reacted with some active methylene reagents to afford pyrrolidine‐3,5‐dione, pyrrolo[2,3‐b]pyridine and pyrrolinone derivatives. The cinnamate ester, obtained from 1a and sodium ethoxide, could be converted into a pyrrolidinone derivative having an active methylene group. This compound coupled with diazonium salts to afford the corresponding azo coupling products.
Complexation of poly‐bis‐(3‐silsesquioxanylpropyl)amino‐sulfoxide and‐sulfone with rare‐earth elements
Authors: Vlasova Natalia N. , Zhila Galina Yu. , Kirillov Anatoly I. , Voronkov Mikhail G.
Published: January 2005

Polymers of silsesquioxane structure, poly[bis‐(3‐silsesquioxanyl‐propylamino)]sulfoxide (IV) and ‐sulfone (V) have been prepared and examined as complexation agents toward samarium(III) and thulium(III). Polymer IV was an effective complexation agent toward both of these elements. However, polymer V was an effective complexation agent only toward thulium(III) ions.

The selective complexation of polymer V with thulium is not affected by the presence of excess amounts of lanthanum, cerium, neodymium, or samarium salt. This suggests that polymer V may prove to be useful in rare‐earth element (REE) separation and isolation. The selective complexation of V with thulium(III) is also observed in the presence of nickel(II), copper(II), or lead(II) salt.
Preparation of tetra‐n‐butylammonium peroxydisulfate. Novel tetrahydrofuranylation [1] and tetrahydropyranylation of alcohols
Authors: Choi Hyun Chul , Jung Jae Chul , Cho Kyu Ii , Kim Yong Hae
Published: January 2005

Tetra‐n‐butylammonium peroxydisulfate (Bu4N+ −OS(O2)O–O(O2)SO− +NBu4: (TBA)2S2O8) has been successfully prepared and turned out to be a useful source of the tetra‐n‐butylammonium sulfate radical in organic solvents. Primary, secondary, and tertiary alcohols containing functional groups, such as benzylic, allylic, and sulfide, reacted with tetrahydrofuran or tetrahydropyran in the presence of (TBA)2S2O8 to give the corresponding 2‐tetrahydrofuranyl‐ or 2‐tetrahydropyranyl‐ether in excellent yields under nearly neutral conditions.
1, 2λ5‐azaphosphinines and a new 1λ5, 3λ5‐. Diphosphinine
Authors: Fluck Ekkehard , Rosche Fred , Heckmann Gernot , Weller Frank
Published: January 2005

The 1,2‐azaphosphinine, 9, and the 1,3‐diphosphinine, 10, can be isolated from a mixture resulting from the reaction of 1,1,3,3‐tetrakis(dimethylamino)‐1λ5,3λ5‐diphosphete, 1, and ethyl isothiocyanate. The reaction of 1 with phenyl isothiocyanate yields the 1,2‐azaphosphinine, 16. Mechanisms for the formation of the compounds 9, 10, and 16 are suggested. The properties, the NMR, mass, and IR spectra, and the molecular and crystal structures of 9 and 10 are described and discussed.
The reactions of tetrakis(triphenylphosphine)platinum and ‐palladium with selenium: X‐Ray crystal structure of [Pt(Se2CH2)(PPh3)2]
Authors: Khanna Pawan K. , Morley Christopher P. , Hursthouse Michael B. , Malik K. M. Abdul , Howarth Oliver W.
Published: January 2005

Treatment of tetrakis(triphenylphosphine)platinum with elemental selenium (red or vitreous) in toluene solution under reflux yields an insoluble solid. This dissolves in dichloromethane with reaction, eventually to form a 1 : 1 mixture of [PtCl2(PPh3)2] and the new compound [Pt(Se2CH2)(PPh3)2], which has been characterized by multinuclear NMR spectroscopy and X‐ray crystallography. Under the same conditions, tetrakis(triphenylphosphine)‐palladium yields only decomposition products. © John Wiley & Sons, Inc.
Studies with polyfunctionally substituted heteroaromatics: New routes for the synthesis of polyfunctionally substituted pyridines and 1,2,4‐triazolo[1,5‐a]pyridines
Authors: Al‐Omran Fatima , Khalik Mervat Mohamed Abdel , Elnagdi Mohamed Hilmy
Published: January 2005

The 1‐substituted ethylidenemalononitriles 1a–c condensed with triethyl orthoformate in refluxing acetic anhydride to yield the dienes 2a–c. On the other hand, a mixture of N,N‐dimethylformamide and triethyl orthoformate condensed with 1a–d to yield the N,N‐dimethylaminopentadienonitriles 2d–g. The pentadienonitriles 2d–g were also formed from the reaction of 1a–d with dimethylformamide dimethylacetal in refluxing acetic acid. When compounds 1a–c were treated with dimethylformamide dimethylacetal in refluxing p‐xylene, a mixture of 3,4 and 2e–g was formed.

The reaction of 2a,b with hydrazine hydrate afforded the N‐amino‐2‐iminopyridines 5a,b. These were converted into the triazolo[1,5‐a]pyridines 8a–d on treatment with benzoyl chloride and with dimethylformamide dimethylacetal. On the other hand, the reaction of 2c with hydrazine hydrate afforded the pyrazolo[3,4‐b]pyridine 7c. Treatment of 2a,c or 2e,g with cyanoethanoic hydrazide afforded the N‐(cyanoacetamido)pyridines 9a,b. The dienes 2d,f,g afforded the pyridones 11a–c on treatment with acetic acid and hydrochloric acid mixture. Compounds 11b,c were also formed on treatment of 2b,c with acetic acid hydrochloric acid mixture. The reaction of 2d,g with ethanolic sodium ethoxide gave the ethoxypyridines 13a,b.
The structure and energies of some unsaturated four‐membered ring carbocycles
Authors: Allinger N. L. , Yuh Y. , Sprague J. T.
Published: January 2005

A number of cyclobutane derivatives containing one or more double bonds in endo‐ or exocyclic positions have been studied by the molecular mechanics method within the context of the MM2 force field. Generally speaking, the structures and energies of these compounds are well calculated in cases in which they are known experimentally and are predicted in others. Examples are shown of the use of the moments of inertia of molecules, which are known from microwave studies, in conjunction with molecular mechanics calculations to yield better structures than could be obtained by either method alone. Compounds examined include cyclobutene, methylenecyclobutane, Dewar benzene, and related compounds.
Metal–metal bond energies in Mo2, Mo2Cl, and Mo2(O2CH)4
Authors: Norman Joe G. , Ryan P. Barry
Published: January 2005

Previous attempts to determine the strengths of multiple metal‐metal bonds are reviewed. Estimates of 73 and 97 kcal/mole for the MoMo bond energies in Mo2Cl and Mo2(O2CH)4, respectively, are obtained by combining the known experimental bond energy in Mo2 (96.5 ± 5 kcal/mole) with the results of SCF‐Xα‐SW calculations on Mo2, Mo2Cl, and Mo2(O2CH)4. Possible errors in the estimates are discussed. It is noted that the quadruple bonds in the complexes are predicted stronger per component than the sextuple bond in the diatomic.
A systematic CI procedure with modified virtual orbitals
Authors: Cooper Ian L. , Pounder Christopher N. M.
Published: January 2005

The use of modified virtual orbitals is studied in a systematic conventional CI procedure which offers considerable potential in regard to convergence and extension to larger systems. The method is applied to the HCN molecule by using 37 basis functions, and analysis of energy expectation values, together with the one‐electron density, yields some insight into the physical content of CI wavefunctions.
Atomic Xα calculations based on EHFS(α) = Eexp
Authors: Tseng T. J. , Hong S. H. , Whitehead M. A.
Published: January 2005

The total energies and one‐electron energies for first‐ and second‐row atoms were calculated by using the Hartree–Fock and the Hartree–Fock‐Slater Hamiltonian with Xα orbitals, ui(αexp); α was parametrized from EHFS(αexp) = Eexp. The EHF(αexp) total energies are always higher than the Hartree–Fock energies for the atoms. The relation of the calculated ionization potential to the experimental ionization potential depends on the α used to define ui(α), αexp, or αHF.
Theoretical development of a Gaussian potential function in the description of the radial portion of isotropic bending vibrations
Authors: Lieb S. G. , Perry W. L. , Bevan J. W.
Published: January 2005

Analysis of a Gaussian potential function suitable for modeling degenerate bending vibrations in weakly bound molecular complexes is presented. Approximate eigenvalues and eigenvectors are obtained by application of perturbation theory. Comparison to the “exact” eigenvalues obtained via a numerical solution shows that the first‐ and higher‐order perturbation corrections are consistent with variational principles.
Initial conformations of macrocyclic compounds with rotational symmetry generated from a molecular fragment
Authors: Felder Clifford E. , Shanzer Abraham , Lifson Shneior
Published: January 2005

An algorithm is described for generating atomic Cartesian coordinates of conformations of macrocyclic molecules possessing exact rotational or rotation‐reflection symmetries. A fragment representing the asymmetric unit of the molecule is suitably oriented in space, and then a symmetry operator is applied to generate the initial coordinates of the molecule. An empirical force field of interatomic interactions is used to generate equilibrium conformations. Results of calculations performed on two cyclic polylactones and one crown ether using this approach are given. They reveal that symmetric conformations of these molecules are often preferred. Since the latter conformations are probably responsible for the specialized properties of these molecules, this method should facilitate doing theoretical studies on these kinds of compounds.
Optimized method for the evaluation of the convolutionally distorted decay curves
Authors: Szöke J.
Published: January 2005

A nonlinear least squares procedure based on the Meiron method is described for the evaluation of the convolutionally distorted decay curves consisting of exponentials. Most of the special procedures are well known and the selected ones proved to be the most effective. Some new procedures are introduced to facilitate the evaluation work and literature data are analyzed as an example.
The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization
Authors: Billeter M. , Havel T. F. , Wüthrich K.
Published: January 2005

A new method for constrained nonlinear optimization known as the ellipsoid algorithm is evaluated as a means of determining and refining the conformations of peptides. Advantages of the ellipsoid algorithm over conventional optimization methods include that it avoids many local minima that other methods would be trapped by, and that it is sometimes able to find optimum solutions in which the constraints are satisfied exactly. The dihedral angles about single bonds were used as variables to keep the dimensionality low (the rate of convergence decreases rapidly with increasing dimensionality of the problem). The method is evaluated on problems involving distance constraints, and for minimization of conformational energy functions. In an initial application, conformations consistent with an experimental set of NMR distance constraints were obtained in a problem involving 48 variable dihedral angles.
An objective computer‐oriented method for the calculation of formation constants from the formation function. A weighted least‐squares curve fitting
Authors: Sidrak Yousry L. , Aboul‐Seoud A.
Published: January 2005

A computer program has been developed that calculates, using the weighted least‐squares technique, the overall formation constants, Bi, of mononuclear complexes, the standard deviations of Bi, SDVi, and an estimate of goodness of fit, Goodness‐of‐Fit Parameter (GOFP), given a set of average ligand numbers, VNj, the corresponding free ligand concentrations, VAj, and an error parameter P. The formation function used is ∑(VNj – i) · (Bi) · (VAj)i = 0 where i ranges from O to n with a maximum of 10 and j ranges from O to l with a maximum of 40. The Bi and (Bi – SDVi) must be positive and GOFP must be either unity or as close to unity as possible. An option is available that allows the computation of P, if it is not provided, so that GOFP is equal or very close to unity. The method has been applied to the formation of the complexes Cadmium‐Imidazole, Cobalt(II)‐Bis(2‐Quinaldylphenyl Ketone), Copper‐Ammonia, Silver‐4‐Aminobutan‐1‐ol Nitrate, and Copper(II)‐Bis(2‐Quinaldylphenyl Ketone). The results are quite satisfactory and reliable as compared with other computational techniques. Input data and results for the five complexes mentioned are shown.
Basis sets for molecular interactions. 2. Application to H3NHF, H3NHOH, H2OHF, (NH3)2, and H3CHOH2
Authors: Latajka Zdzislaw , Scheiner Steve
Published: January 2005

Modifications of the standard 6‐31G** basis set as recommended in the accompanying paper are found to markedly lower the basis set superposition error (BSSE) in the title complexes, in contrast to enlargement to a triple‐ζ scheme or by addition of a diffuse sp shell or a second set of d‐functions without prior optimization, all of which lead to BSSE increase. After appropriate correction for correlation and superposition effects, all basis sets (with the exception of the standard 6‐31G** and 6‐311G** with their very large BSSE) predict the cyclic geometry of NH3 dimer to be more stable than the linear arrangement. Correlation and BSSE can shift the equilibrium intermolecular distance in H3CH‐OH2 by up to 0.4 Å. Failure to correct for superposition error leads to a drastic exaggeration of both the SCF and MP2 components of the interaction energy in this complex. Much better estimates are furnished by our recommended basis sets with their smaller superposition errors.
Two approaches to the calculation of molecular resonance states: Solution of scattering equations and matrix diagonalization
Authors: Basilevsky M. V. , Ryaboy V. M.
Published: January 2005

We have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert‐Humblet‐Rosenfeld (SHR) and the second on the Fano‐Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano‐Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas‐phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.
The inverse problem of isomer enumeration
Authors: Hässelbarth Werner
Published: January 2005

The present article addresses the problem of identifying the structure of a parent compound through its chemical fingerprints such as the various numbers of isomeric substitution patterns, along the lines of Kekulé when he arrived at his benzene formula. In a pioneering paper (1929), Lunn and Senior laid out the conceptual framework for the permutation group description of substitution isomerism. It remained, however, for Pólya's celebrated contribution (1937) to initiate the actual mathematical realization of their vision. Pólya supplied the tools for solving the isomer enumeration problem: given a (symmetrical) parent compound, enumerate its spectrum of substitution patterns. The converse problem, though ranked the more interesting one by Lunn & Senior, hardly received any mathematical attention. The present article offers a complete and effective solution.
Ab‐initioMRD–CI calculations on a CNO2 decomposition pathway of nitrobenzene
Authors: Kaufman Joyce J. , Hariharan P. C. , Roszak Szczepan , van Hemert Marc
Published: January 2005

To study molecular decomposition pathways it is necessary to use ab initio multireference determinant–configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD–CI (multireference double excitation–configuration interaction technique of Buenker and Peyerimhoff) calculations on the magnified image decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the magnified image bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of magnified image distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
Characteristics of the Watson‐Crick type hydrogen‐bonded DNA base pairs: An ab initio molecular orbital study
Authors: Aida Misako
Published: January 2005

Characteristics of the Watson‐Crick‐type hydrogen‐bonded base pairs, thymine‐adenine and cytosineguanine, are presented. These were established using an ab initio molecular orbital method. Base–base interactions are revealed to have dominant roles in the structures of nucleic acids and also in their functions. The most stable conformations in Watson‐Crick‐type base pairs are almost in accord with the structure observed in fiber X‐ray diffraction study. Explanations are given of the origin of the sequencedependent local structures which differ from one base pair to the next, as observed in single‐crystal X‐ray analyses. In the case of the thymine‐adenine base pair, it is shown that various geometrical parameters having almost the same stability are available. According to the propeller twist, the instability is not large enough for a base pair to be twisted readily.
Automatic classification of chemical structure databases using a highly parallel array processor
Authors: Rasmussen Edie M. , Downs Geoffrey M. , Willett Peter
Published: January 2005

This article describes the use of the ICL Distributed Array Processor (DAP) for the automatic classification of chemical structure databases using the Jarvis‐Patrick clustering method. This method is based upon the calculation of a table containing the nearest neighbors for each of the molecules in the database which is to be clustered. These nearest neighbors can be identified very efficiently using the DAP since it allows up to 4096 molecules to be compared with a specified molecule in parallel. Experiments with files of 4096 and 8192 structures from the Fine Chemicals Database show that clustering with the DAP is up to 6.7 times as fast as using a highly efficient, inverted file algorithm on an IBM 3083 mainframe.
Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes
Authors: Hammarström Lars‐Gunnar , Liljefors Tommy , Gasteiger Johann
Published: January 2005

The PEOE (partial equalization of orbital electronegativity) procedure has been modified slightly and reparametrized for haloalkanes to calculate partial atomic charges suitable for evaluation of dipole moments and electrostatic energies in conjunction with molecular mechanics (MM2) calculations. Dipole moments of 66 haloalkanes are calculated with an average absolute deviation of 0.14 D from experimental values. The conformational energies of 40 compounds have been calculated and the agreement with experimental data is generally good and compares well with calculations by the IDME (induced dipole moment and energy) method. In addition, carbon and proton charges correlate well with C‐1s core binding energies and 1H‐NMR (nuclear magnetic resonance) shifts for halomethanes. The most striking benefit of treating electrostatics through a set of partial charges compared to the standard MM2 bond dipole approach is demonstrated by calculations on 1,4‐disubstituted cyclohexanes, for which standard MM2 fails to predict the most stable conformation.
An algorithm for the location of branching points on reaction paths
Authors: Baker J. , Gill P. M. W.
Published: January 2005

A branching point is a point on a reaction path leading from reactants to products (via a transition state) at which it is energetically favorable for the system to break symmetry. Such a point can be defined in terms of normal modes along the reaction path and corresponds to zero curvature (a zero Hessian eigenvalue) along a symmetry‐breaking mode. An effective method for the location of such points is presented and realized in an efficient, practical algorithm designed for use in the ab initio program package Gaussian 82.
Barriers to rotation adjacent to double bonds. 4. Effect of basis set on structures, and of electron correlation on relative energies
Authors: Wiberg Kenneth B. , Murcko Mark A.
Published: January 2005

The optimized geometries for the rotamers of propanal, 2‐butanone, isobutyraldehyde, methyl isopropyl ketone, and isobutyric acid obtained using the 3–21G and 6–31G* basis sets are compared, and systematic changes are noted. The relative 6–31G* energies using the 3–21G and 6–31G* geometries are generally the same within 0.1 kcal/mol. The effect of electron correlation on the relative energies is generally small. These and related data show that 6–31G* relative energies obtained using 3–21G geometries are generally satisfactory when studying rotation about CC bonds. However, this is not the case for CO bonds. The calculated relative energies of isomeric compounds are reproduced only with the full MP4 correction for electron correlation.
Hydrogen bonding in MM2
Authors: Allinger Norman L. , Kok Randall A. , Imam Mita R.
Published: January 2005

Hydrogen bonding is qualitatively accounted for in the early versions of the MM2 program, but not quantitatively. Experimentally, the hydrogen bonds are somewhat shorter and stronger than calculated by MM2. This has been corrected now in MM2(87), by reducing the van der Waals radius of the hydrogen involved in hydrogen bonding for that interaction only, and by increasing the van der Waals' attraction between the hydrogen and the various electronegative atoms to which it can hydrogen bond by about 1–3 kcal/mol, depending on the particular atoms involved. It is now possible to reproduce reasonably well ab initio calculations on simple amides and the methanol dimer, and experimental data on compounds in which a hydroxyl hydrogen is hydrogen bonded to an alcohol, an alkyl chloride, or to a carbon–carbon double bond.
Ab initio studies of the ground‐state potential energy surface of formamide
Authors: Wright Gregory M. , Simmonds Richard J. , Parry David E.
Published: January 2005

Ab initio calculations employing a standard double‐zeta basis set augmented with various polarization functions have been used to investigate the lowest energy region of the ground‐state potential energy surface of the formamide molecule. Hartree‐Fock calculations with only d polarization functions on the nonhydrogen atoms located two stable minima, that with geometry distorted from planarity having slightly lower energy; only one stable minimum with planar structure is found when p polarization functions on the hydrogens are included. In contrast optimizations, which account approximately for the correlation energy using second‐order Møller‐Plesset perturbation theory consistently favor a single slightly nonplanar minimum energy geometry.
Treatment of symmetry in MO calculations. II. Numerical projection operators for molecular orbitals
Authors: Jaffé H. H.
Published: January 2005

This article describes the numerical application of projection operators to restore the symmetry of molecular orbitals in self‐consistent field (SCF) calculations when the symmetry is lost because of degeneracy or near degeneracy. The application of projection operators is particularly useful in cases of near degeneracies of three or more molecular orbitals, where it is difficult to find an effective algorithm for restoring the symmetry of molecular orbitals by orthonormal transformations.
Development of a program for MCSCF calculations with large basis sets
Authors: Yamamoto Shigeyoshi , Nagashima Umpei , Aoyama Tomoo , Kashiwagi Hiroshi
Published: January 2005

A new program named JASON2 for ab initio MCSCF calculations with large basis sets has been developed. In this program, the density‐formulated super‐CI CASSCF method proposed by Roos et al. was adopted in order to overcome difficult problems caused by large basis sets. The sparsity of integrals and vectorization on supercomputers were utilized as much as possible. With JASON2, we performed CASSCF calculations on a Fe–porphine complex with 232 CGTFs (contracted Gaussian‐type functions). Our algorithms and timing data of the above calculations are reported.
Comparison of semiempirical MO methods for open‐shell systems
Authors: Higgins Derek , Thomson Colin , Thiel Walter
Published: January 2005

The use of AM1, MNDO, and MNDOC semiempirical MO methods for calculation of heats of formation and ionization potentials of a series of 38 radicals are described. AM1 and MNDO calculations are reported using both half‐electron (HE) and Unrestricted Hartree Fock (UHF) wavefunctions. Results show the MNDOC method to give lowest overall errors, being slightly better than the HE‐AM1 method. In all cases, the AM1 method shows considerable improvement over MNDO.
Representation of the molecular electrostatic potential by atomic multipole and bond dipole models
Authors: Williams Donald E.
Published: January 2005

Ab initio wave functions using the 6‐31G** basis set were calculated for a set of 24 organic molecules which included saturated and unsaturated hydrocarbons, fluoro compounds, hydroxyl and ether compounds, carboxylic acids, esters, amines, carbonyl compounds, amides, and N‐methyl amides. The electric potential on a grid within a van der Waals shell around each molecule was calculated directly from the wavefunctions. The electric potential values were modeled by placing multipoles up to quadrupoles at atomic sites. The electric potential was well fitted by a model which included atomic monopoles, dipoles, and quadrupoles. Also, the electric potential was modeled by placing dipoles at bond centers. This bond dipole was either allowed to point in any direction, or was restricted to the bond direction. In general the values shown for the monopoles and the values and directions for the bond dipoles were as expected from considerations of electronegativity and reactivity. For the general bond dipole model in a number of cases the direction of the bond dipole was not parallel to the bond direction. It is suggested that this is an artifact caused by the effects of lone pair electrons or electron delocalization on the model. The restricted bond dipole model fitted the electric potential about as well as the atomic monopole model. Atomic monopole values (net atomic charges) and bond dipole values for various atoms, functional groups, and bonds are discussed. Since bond‐dipole interaction energy has better long‐range convergence than monopole interaction energy, bond dipoles are a useful alternative to atomic monopoles.
Structure and properties of small silicon and aluminum clusters
Authors: Jug Karl , Schluff Hans‐Peter , Kupka Hans , Iffert Rüdiger
Published: January 2005

Small Sin and Aln clusters (n = 3–10) were studied with the semiempirical molecular orbital method (MO) method SINDO1. For each n, various structures were optimized to determine the most stable structure. To obtain good qualitative agreement with available ab initio calculations d orbitals had to be omitted from the basis set. Both silicon and aluminum tend to build three‐dimensional structures rather than two‐ or one‐dimensional structures, except for n = 3 or 4. The structure growth was studied by approaching various sites of stable structures with one or more atoms. It was found that silicon and aluminum exhibit different structure growth, and consequently, different most‐stable structures. Ionization potentials, HOMO‐LUMO energy differences, binding energies per atom, and average atomic valencies are presented.
Application of the higher order finite‐element method to one‐dimensional Schrödinger equation
Authors: Kimura Toshiyasu , Sato Nobuyuki , Iwata Suehiro
Published: January 2005

The accuracy and applicability of the finite‐element method of the higher order interpolation functions to the one‐dimensional Schrödinger equation were examined. When the fifth‐order Lagrange and Hermite interpolation functions were used as the basis functions, practically exact solutions were obtained for all eigenvalues of several model potential energy functions. It was demonstrated that the appropriate analytical integration over the potential energy function within each element is important in the matrix element evaluation. The accuracy of the method was examined for the potential functions with a double minimum, which has a large classically forbidden region. The method was also applied to evaluate the Franck‐Condon factors of the transitions between the 1 1Σ and 2 1Σ states of Na2; the latter state having a double minimum in its potential energy function.
A modular strategy for generating starting conformations and data structures of polynucleotide helices for potential energy calculations
Authors: Schlick Tamar
Published: January 2005

We describe a simple and rapid algorithm for generating data structures and starting coordinates of polynucleotides for potential energy calculations. The algorithm is tailored to investigations in cartesian coordinate, rather than dihedral angle, space. First, instead of a tree structure for molecular design, we set up a helix from a simple list of bonds for the basic DNA subunits (sugar, phosphate, and bases). Second, instead of using successive transformations to obtain a set of coordinates in one reference frame, we apply a simple “matching” routine to patch DNA subunits. Third, we avoid ring closure and geometry optimization by allowing deviations from equilibrium values only for PO3′ bond lengths and O5′PO3′ bond angles at the residue connection sites. A double‐stranded helix is constructed from duplex building blocks (2 hydrogen‐bonded nucleotides) which are in turn built from the basic structural units. Every building block is constructed from two sets of geometric variables: {α, β, γ, χ, P, τmax}, one for each strand. The building blocks are then assembled into a helix by using the 6 rigid body transformations {Δx, Δy, Δz, ΘROLL, ΘTILT, ΘTWIST}. For cartesian space programs, generating starting coordinates by this procedure is particularly useful as an alternative to using actual crystal structure coordinates. After describing the algorithm in detail, we illustrate how it was used to generate model A, B, and Z DNA helices. We conclude by suggesting how the algorithm can be used to pursue a build‐up technique and to set up a wide range of starting conformations in the goal of locating novel helical structures.
Deorthogonalization of atomic originals in the CNDO approach
Authors: Chung‐Phillips Alice
Published: January 2005

The procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO‐3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO‐3G and 6‐31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.
First and second derivative matrix elements for the stretching, bending, and torsional energy
Authors: Miller Kenneth J. , Hinde Robert J. , Anderson Janet
Published: January 2005

Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out‐of‐plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out‐of‐plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space‐fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L‐1‐ and L(L‐1)/2‐independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space‐fixed molecular coordinate system.
Continuum radial dielectric functions for ion and dipole solution systems
Authors: Ehrenson S.
Published: January 2005

Radial dielectric constant (permittivity) functions for ionic solute, polar solvent systems of the type obtainable from the Lorentz‐Debye continuum field formulations are reexamined. Major interest is focused on the assumptions underlying these formulations and their expression in limiting field behavior. The analysis is extended to dipolar solutes and the importance of two types of corrections are evaluated. The first draws connections with the concept of the reaction field as employed by Onsager. This correction is shown to be significant as regards range of predicted saturation effects and for dipole moment self‐consistency, for the same type molecule serving as solute and solvent. The second type correction involves the phenomenon of electrostriction whose effects appear much more limited both in range and on the intensity of the fields necessary for its observation. Application of the permittivity functions developed to compute modified Born model hydration energies for a variety of ions is illustrated. Excellent asymptotic approximations for all radial permittivity equations of interest are also presented which should enhance their future utility.
Simple alkyldisilanes: MM2 and ab initio studies of their structures and barriers to rotation
Authors: Profeta Salvatore , Unwalla Rayomand J. , Cartledge Frank K.
Published: January 2005

For a series of simple alkyldisilanes, 3‐21G (*) full gradient geometry optimizations have been performed to yield both structural and conformational energy data which was suitable for calibrating the MM2 force field for disilanes. We have examined several model structures which yielded sufficient information about the rotational potential around the Si–Si bond to enable us to revise and augment those reported by Frierson. These parameters were questioned by us in the course of MM2 studies of 1,2‐disilacyclobutanes. We report new Si–Si torsion parameters as well as pertinent structural data from 3‐21G(*) geometry optimizations and relative conformational energies derived from Møller‐Plesset (MP2/MP3) calculations at the 6‐31(*)/3‐21G(*) level. The new parameters were applied to the 1,2‐dimethyl‐1,2‐disilacyclohexane system and those results are also reported.