Showing papers in "International Journal of Molecular Sciences in 2000"
TL;DR: In this paper, the molecular geometry of complexes of uracil and thymine with 11 water mole-cules was calculated using the density functional theory with the B3LYP functional.
Abstract: Computational Center for Molecular Structure and Interactions, Department of Chemistry, JacksonState University, P.O. Box 17910, 1325 Lynch Street, Jackson, MS 39217, USAE-mail: jerzy@tiger.jsums.edu*Author to whom correspondence should be addressed.Received: 4 January 2000 / Accepted: 30 March 2000 / Published: 4 March 2000Abstract: The molecular geometry of complexes of uracil and thymine with 11 water mole-cules was calculated using the density functional theory with the B3LYP functional. Thestandard 6-31G(d) basis set has been employed. It was found that the arrangement of watermolecules forming a locked chain around the nucleobases significantly differs for uracil andthymine. The presence of a methyl group in thymine results in strong non-planarity of thehydrated shell. The existence of C-H...O hydrogen bonds between the water molecules andthe hydrophobic part of the nucleobases is established. Interactions with water moleculescause some changes in the geometry of uracil and thymine which can be explained by thecontribution of a zwitter-ionic dihydroxy resonance form into the total structure of themolecules.Keywords: Uracil, Thymine, Hydration, Molecular structure, Hydrogen bonds, Densityfunctional theory.IntroductionSince Franklin and Gosling [1] examined the first fibers of DNA it has been known that DNA oc-curs in vivo in the hydrated form. Numerous experimental studies using different methods [2,3] haveled to the conclusion that DNA is heavily hydrated. The hydration layer is known to play a crucial role
58 citations
TL;DR: In this paper, the Microtox Assay was used to investigate the acute toxicity of a significant number of triazines including atrazine, atraton, ametryne, bladex, prometryne and propazine.
Abstract: The Computational Center for Molecular Structure and Interactions Department of Chemistry,Jackson State UniversityP. O. Box 17910, Jackson, Mississippi 39217,E-mail: jerzy@tiger.jsums.eduReceived: 14 February 2000 / Accepted: 3 July 2000 / Published: 13 October 2000Abstract: The triazines are a group of chemically similar herbicides including atrazine,cyanazine, and propazine, primarily used to control broadleaf weeds. About 64 to 80 millionlbs of atrazine alone are used each year in the United States, making it one of the two mostwidely used pesticides in the country. All triazines are somewhat persistent in water andmobile in soil. They are among the most frequently detected pesticides in groundwater.They are considered as possible human carcinogens (Group C) based on an increase inmammary gland tumors in female laboratory animals. In this research, we performed theMicrotox Assay to investigate the acute toxicity of a significant number of triazinesincluding atrazine, atraton, ametryne, bladex, prometryne, and propazine, and some of theirdegradation products including atrazine desethyl, atrazine deisopropyl, and didealkyledtriazine. Tests were carried out as described by Azur Environmental [1]. The proceduremeasured the relative acute toxicity of triazines, producing data for the calculation oftriazine concentrations effecting 50% reduction in bioluminescence (EC
53 citations
TL;DR: Hinchliffe et al. as discussed by the authors reported accurate ab initio studies of the static dipole polarizabilities of anthra-cene and phenanthrene and optimized at the HF/6-311G(3d,2p) level of theory.
Abstract: Departamento de Quemica, Fac. Exp. de Ciencias, La Universidad del Zulia, Grano de Oro ModuloNo. 2, Maracaibo, VenezuelaTel.: (+44 (0) 161 200 4554, Fax: +44 (0) 161 228 7040, E-mail: Alan.Hinchliffe@UMIST.ac.ukURL: http://www.ch.umist.ac.uk/hinchlif.htm* For Part 6, see Reference 17.**Author to whom correspondence should be addressed.Received: 7 February 2000 / Accepted: 7 March 2000 / Published: 28 March 2000Abstract: We report accurate Ab Initio studies of the static dipole polarizabilities of anthra-cene and phenanthrene. Geometries were optimized at the HF/6-311G(3d,2p) level of the-ory. Dipole polarizabilities were calculated at the HF/6-311++G(3d,2p) and BLYP/6-311++G(3d,2p) levels of theory, using HF/6-311G(3d,2p) geometries. The calculated dipolepolarizabilities for anthracene are compared with experiment. Inclusion of electron correla-tion using the BLYP procedure increases the L and M components of the dipole polari-zability, but not the perpendicular (N) component. Examination of corresponding BLYP re-sults for the polyacene series benzene, naphthalene and anthracene shows that the normalcomponent of the dipole polarizability scales linearly with the number of benzene ring units,with an increment of 20.8 au. The medium component also scales linearly with an incrementof 42.8 atomic units. The long component does not scale linearly.Semi-emiprical AM1 calculations are also given for comparison; the normal component ofthe dipole polarizability tensor is poorly represented by such calculations.Keywords: Ab Initio, Anthracene, phenanthrene, dipole polarizability, molecular geometry,density functional theory, AM1.
26 citations
TL;DR: In this paper, the static dipole polarizabilities and first hyperpolarizabilities of the [n,m] fulvalene series of molecules (with n, m = 3,5,7) were investigated at the HF/6-311G(3d,2p) level of theory.
Abstract: Departamento de Quimica, Fac. Exp. de Ciencias, La Universidad del Zulia, Grano de Oro, ModuloNo. 2, Maracaibo, VenezuelaReceived: 2 August 2000 / Accepted: 18 August 2000 / Published: 4 September 2000Abstract: We report accurate Ab Initio Hartree Fock (HF) and Density Functional Theory(DFT) studies of the static dipole polarizabilities and first hyperpolarizabilities of the [n]fulvene and the [n,m] fulvalene series of molecules (with n, m = 3,5,7). Calculations are alsoreported for the parent cycloalkenes: cyclopropene, cyclopentadiene and cycloheptatriene(1-3 respectively). Geometries were optimized at the HF/6-311G(3d,2p) level of theory. Allthe fulvenes (4-6) and the smaller fulvalenes (7, 9 and 10) are found to be planar. Pentahep-tafulvalene (11) is slightly non-planar whilst heptafulvalene (12) has a folded C
15 citations
TL;DR: Martin and Justin D.Brown as discussed by the authors presented a new graphical model for predicting the effect of a proton's position relative to a carbon-carbon double bond on its chemical shift, which was used to predict the long-range shielding effect of the magnetic anisotropy of the carbon-carbondouble bond.
Abstract: Ned H. Martin* and Justin D. Brown*Department of Chemistry, University of North Carolina at Wilmington, Wilmington, NC 28403-3297USA, Phone (910) 962-3453, Fax (910) 962-3013*Author to whom correspondence should be addressed. E-mail: martinn@uncwil.eduWebsite: www.uncwil.edu/chem/nhm.htmReceived: 5 June 2000 / Accepted: 25 August 2000 / Published:14 November 2000Abstract: The long-held “shielding cone” model of the through-space NMR shielding effectof a carbon-carbon double bond predicts only the effect of the magnetic anisotropy of thedouble bond; it ignores other important contributors to the overall shielding. GIAO-SCFandGIAO-MP2calculations have been performed on a simple model system, methane movedsequentially above ethene or 2-methylpropene. These calculations permit the net NMRshielding surface to be mapped. Based on those results, a new and very different graphicalmodel for predicting the effect of a proton’s position relative to a carbon-carbon doublebond on its chemical shift is presented.Keywords: NMR, shielding cone, isotropic shielding, GIAO-SCF, GIAO-MP2, alkenes.IntroductionThe long-held “shielding cone” model used for predicting the through-space magnetic influence ofthe magnetic anisotropy of a carbon-carbon double bond on the chemical shift of a nearby proton,found in most textbooks on NMR spectroscopy [1], is based on the McConnell equation [2]. It wasdesigned to predict the long-range shielding effect of the magnetic anisotropy of the carbon-carbondouble bond. This model has been used improperly in many textbooks to predict the effect on achemical shift of a proton due to its proximity and position relative to the double bond. Recently thismodel has been called into question as the result of ab initioSCF calculations [3-8] and experimentalobservation [9] of protons over carbon-carbon double bonds which report deshielding rather thanshielding for protons above and within 3 A of the plane of a carbon-carbon double bond. Substantial
10 citations
[...]
TL;DR: In this article, the authors discuss the question "What is a molecule?" during the four years when they edited Molecules (http://www.mdpi.org/molecules/) and handled chemical samples at MDPI.
Abstract: During recent four years when I edited the chemistry journal Molecules (www.mdpi.org/molecules/) and handled chemical samples at MDPI (http://www.mdpi.org), an international nonprofit organization for worldwide collection, deposit and exchange of chemical samples, I always had a question in mind: what is a molecule?[...]
3 citations
TL;DR: De Graaf et al. as discussed by the authors applied state-of-the-art molecular quantum chemical techniques to the solid-state compound Li and found that the results showed that Li is stable with respect to Li.
Abstract: 2C. de Graaf*, I. de P. R. Moreira and F. IllasDept. de Quimica Fisica i Centre Especial de Recerca en Quimica Teorica, Universitat de Barcelona,C/ Marti i Franques 1, 08028 Barcelona, SpainTel.: +34-934029021, Fax: +34-934021231, E-mail: c.degraaf@qf.ub.es, f.illas@qf.ub.esReceived: 5 July 2000 / Accepted: 21 August 2000 / Published: 23 August 2000Abstract: State-of-the-art molecular quantum chemical techniques have been applied to thesolid-state compound Li
3 citations
TL;DR: Ferraro et al. as discussed by the authors presented a new method to calculate solid-state effects on NMR chemi-cal shifts using full crystal potentials, this new method (CPPCh) eliminates the need to ar-bitrarily select the point charges that are included in the calculations of the NMR chemicalshieldings to take into account intermolecular effects.
Abstract: Center for High Performance Computing, University of Utah, Salt Lake City, UT 84112, US.*M. B. Ferraro: marta@df.uba.ar**J. C. Facelli: facelli@chpc.utah.eduReceived: 9 April 2000 / Accepted: 10 October 2000 / Published: 13 October 2000Abstract: This paper presents a new method to calculate solid-state effects on NMR chemi-cal shifts. Using full crystal potentials, this new method (CPPCh) eliminates the need to ar-bitrarily select the point charges that are included in the calculations of the NMR chemicalshieldings to take into account intermolecular effects. By eliminating the arbitrary selectionof the point charges, the method provides a mechanism to systematically improve the simu-lation of intermolecular effects on chemical shielding calculations.This new method has been applied to the calculation of the
3 citations
TL;DR: In this paper, the authors compare the capabilities of rapid highly charged projectiles and intense femtosecond lasers to ionize simple metal clusters while leaving as little intrinsic excitation as possible in the residue.
Abstract: We compare the capabilities of rapid highly charged projectiles and intense femtosecond lasers to ionize simple metal clusters while leaving as little intrinsic excitation as possible in the residue. We show that both excitation mechanisms are able to produce highly charged clusters. The deposited excitation energies increase with ionization but with different trends. Cold ionization, corresponding to moderate deposited excitation energy, is better attained with ionic projectiles for low charge states, and with lasers for high charge states.
2 citations
TL;DR: In this paper, a rationalization of the signs and magnitudes of A in a sequence of related molecules has been suggested, consistent with both the high symmetry of the molecules and the available extensive experimental data for TMS.
Abstract: TMS is the commonest standard reference for both protons and 13C NMR spectroscopy. The Magnetic Shielding and its Polarizabilities, plus the static polarizability have been calculated for TMS, tetramethyl ammonium cation and 2,2-dimethylpropane. An investigation of continuum solvation effects on these highly symmetrical molecules, whose first surviving electric moment is the octopole, showed interaction with solvent makes little change to these magnetic properties. This small change is however consistent with both the high symmetry of the molecules and the available extensive experimental data for TMS. A rationalization of the signs and magnitudes of A in a sequence of related molecules has been suggested.
2 citations
TL;DR: MDPI launched Molecules (http://www.mdpi.org/molecules) in 1995, which is the first electronic journal of experimental chemistry in the world.
Abstract: MDPI launched Molecules (http://www.mdpi.org/molecules) in 1995, which is the first electronic journal of experimental chemistry in the world.[...]
TL;DR: The basic theme of the journal is the 'science of molecules', and this broad subject area will allow it to encompass disciplines as wide and diverse as chemistry, molecular biology, molecular physics and chemical physics.
Abstract: is a truly international affair, with the editorial board comprising notable scientists fromcountries all over the world. The basic theme of the journal is the 'science of molecules', and this broadsubject area will allow us to encompass disciplines as wide and diverse as chemistry, molecular biology,molecular physics and chemical physics. We hope that in the coming years we will have the opportunity topublish many high quality papers in all these areas, and that the Journal will build into a valuable repository ofscientific findings.I have personally had quite a bit of experience with both formal internet publications [1, 2] and informalinternet presentations [3], and believe that the