Home About us Contact
|
Home About us Contact | ||
|
|
||
DFT Methods (dft + methods)
Selected AbstractsToward the Complete Prediction of the 1H and 13C NMR Spectra of Complex Organic Molecules by DFT Methods: Application to Natural SubstancesCHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2006Alessandro Bagno Prof. Abstract The NMR parameters (1H and 13C chemical shifts and coupling constants) for a series of naturally occurring molecules have been calculated mostly with DFT methods, and their spectra compared with available experimental ones. The comparison includes strychnine as a test case, as well as some examples of recently isolated natural products (corianlactone, daphnipaxinin, boletunone B) featuring unusual and/or crowded structures and, in the case of boletunone B, being the subject of a recent revision. Whenever experimental spectra were obtained in polar solvents, the calculation of NMR parameters was also carried out with the Integral Equation-Formalism Polarizable Continuum Model (IEF-PCM) continuum method. The computed results generally show a good agreement with experiment, as judged not only by statistical parameters but also by visual comparison of line spectra. The origin of the remaining discrepancies is attributed to the incomplete modeling of conformational and specific solvent effects. [source] Calculated on 1H and 13C NMR chemical shifts of 2,4-difluorobenzaldehyde isonicotinoylhydrazone and 2,3-dichlorobenzaldehyde isonicotinoylhydrazone with GIAO, IGAIM, and CSGT modelsCONCEPTS IN MAGNETIC RESONANCE, Issue 5 2009N. Günay Abstract The 1H and 13C NMR chemical shifts of the 2,4-difluorobenzaldehyde isonicotinoylhydrazone (I) and 2,3-dichlorobenzaldehyde isonicotinoylhydrazone (II) were determined with the help of full spectral analysis. The geometry and electronic structure of the title compounds were investigated at both the ab initio Hartree-Fock and the B3LYP levels with 6-31+G(d,p) basis set. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. All quantum-chemical calculations, including those of NMR data, were performed by ab initio level HF and DFT methods. Excellent agreement between the theoretical and experimental results was found for the HF level 1H and 13C chemical shifts. The parameters of molecular geometry and 1H and 13C chemical shift values of the title compounds (I, II) in the ground state have been calculated and and compared with corresponding experimental result. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A: 297,304, 2009. [source] The Reductive Elimination of Methane from ansa -Hydrido(methyl)metallocenes of Molybdenum and Tungsten: Application of Hammond's Postulate to Two-State ReactionsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 15 2005José-Luis Carreón-Macedo Abstract The energetic profile of the methane reductive elimination from a selected number of hydrido(methyl)molybdenocene and -tungstenocene derivatives has been calculated by DFT methods. The calculations were carried out for the CH2(C5H4)2M (a -M), SiH2(C5H4)2M (a -H2Si,M), and SiMe2(C5Me4)2M (a -Me2Si,M*) ansa -metallocene systems for M = Mo, W. They include the full optimization of minima [the hydrido(methyl) starting complexes, M(H)(CH3), the intermediate methane complexes, M(CH4), and the metallocene products in the singlet and triplet configurations, (3M and 1M)], transition states (for the methyl hydride reductive elimination, M,TSins, and for the hydrogen exchange, M,TSexch), and the minimum energy crossing point (M,MECP) leading from the singlet methane complexes to the corresponding triplet metallocenes. The results are compared with those previously obtained for the simpler (C5H5)2M (Cp2M) systems (J. C. Green, J. N. Harvey, and R. Poli, J. Chem. Soc., Dalton Trans.2002, 1861). The calculated energy profiles, notably the relative energies of M,TSins and M,MECP, are in agreement with available experimental observations for the a -Me2Si,M* systems. The comparison of the energies and geometries of the rate-determining M,TSins and M,MECP structures with those of the thermodynamically relevant minima for the various systems show the applicability of Hammond's postulate to two-state reactions. However, one notable exception serves to show that the principle is only quantitatively reliable when all the potential energy surfaces for the set of analogous reactions have similar shapes. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] A New Spherical Metallacryptate Compound [Na{Cu6(Thr)8(H2O)2(ClO4)4}]·ClO4·5,H2O: Magnetic Properties and DFT CalculationsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 13 2005Sheng-Chang Xiang Abstract The hexanuclear copper(II) complex with threoninato acid has been synthesized. Its structure can be described as an octahedron cage with D2h symmetry in which six copper ions are bound by eight threoninato acids with a [3.11223130] coordination mode and one Na+ cation being captured within the center of the cage. In contrast with other hexanuclear copper compounds containing amino acids, the title compound has a prolate Cu6 octahedron with the longest axial distance and a rectangle equatorial plane, as well as special coordinated perchlorate ions. Compared with classic cryptate, hexanuclear copper(II) compounds with amino acids can be regarded as a new topologic type of spherical macrotricyclic metallacryptates [2,2,2,2] whose cages have a high selectivity for sodium ions. The analysis of magnetic susceptibility data shows that the threoninato compound has a ground state with spin S = 3. The computing coupling constant between the equatorial Cu centers and the axial ones is 4.4 cm,1,calculated by using DFT methods for a model compound. This is close to three known experimental values of 1.39, 0.56 or 0.43 cm,1 for complexes with 4-hydroxy- L -prolinato, L -prolinato or L -threoninato acid as ligands, respectively. The dominant ferromagnetic interactions for these complexes can be essentially attributed to the orthogonality between the magnetic orbitals, dxz or dyz orbitals for the equatorial CuII centers and d orbitals for the axial ones. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] (4-Acyl-5-pyrazolonato)titanium Derivatives: Oligomerization, Hydrolysis, Voltammetry, and DFT StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 17 2003Francesco Caruso Abstract Twenty 4-acyl-5-pyrazolonato (Q) titanium derivatives of varied nuclearity have been synthesized from Ti(OR)4 or TiCl4 and characterized with spectroscopic methods (IR, NMR, ESI-MS). While Ti,(,-diketonato) cleavage is not seen in isolated solids, Ti,O(alkoxy) (or Ti,Cl) bonds cleave upon hydrolysis, leading to several structural forms, including oligomers. Ionic Q species with no Ti, i.e., obtained after Ti,Q cleavage, are seen for some Ti,Q derivatives by ESI-MS, which also indicates a varied nuclearity for a given species, e.g., the isolated polynuclear [Q2Ti-,-O]n has several "n" values. Mononuclear Ti complexes are obtained under rigorous anhydrous conditions. The cis structures of the mononuclear species (QT)2Ti(OCH3)2, QT = 3-methyl-4-(neopentylcarbonyl)-1-phenylpyrazol-5-onato have been analyzed with DFT methods. A trans influence is a major driving force that accounts for several sets of Ti,O bonds. One of the cis stereoisomers is 56 kcal/mol higher in energy than the other two. In contrast, all (QT)2TiCl2cis isomers show similar energies. Voltammetry of the mononuclear species (QT)2Ti(OnPr)2 and the antitumor tetranuclear compound [(QB)2Ti-,-O]4, (QB = 4-benzoyl-3-methyl-1-phenylpyrazol-5-onato) indicate that the TiIV is less prone to reduction to TiIII in the latter (Epc for the TiIV/TiIII couple is ,1.71 V and ,1.46 V versus Fc+/Fc, respectively). Potential antitumor compounds having a Ti/Q ratio of 1:1 do not disproportionate, unlike the equivalent acetylacetonato derivatives, and are water-soluble. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] N -Phenyl-1,2,4-triazoline-3,5-dione (PTAD) as a Dienophilic Dinitrogen Equivalent: A Simple Synthesis of 3-Amino-1,2,4-benzotriazines from Arylcarbodiimides,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 4 2010Mateo Alajarin Abstract N -Arylcarbodiimides react with PTAD to provide [1,2,4]triazolo[1,2- a][1,2,4]benzotriazines by a [4+2] cycloaddition reaction. When asymmetrically substituted diarylcarbodiimides are used, the cycloaddition proceeds with total chemoselectivity because only the more electron-rich aryl nucleus is involved. This observation has been rationalized by a computational study using DFT methods that shows that, in the reaction of HTAD with arylcarbodiimides, the magnitude of the energy barriers depend on the electronic features of the substituents at the aryl nucleus; the calculations also indicate that the reaction proceeds through asynchronous states with polar characteristics. The treatment of the final cycloadducts with potassium hydroxide affords 3-aryl(alkyl)amino-1,2,4-benzotriazines. [source] The Mechanism of the Stetter Reaction , A DFT StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 33 2008Kirsty J. Hawkes Abstract On the basis of Breslow's mechanism for benzoin condensation, a model asymmetric Stetter reaction has been investigated using DFT methods. In contrast to the concerted benzoin condensation, after formation of the Breslow intermediate the Stetter reaction is found to be a two-step process in which the rate-determining C,C coupling of the Breslow intermediate and the Michael acceptor precedes final proton transfer. In addition, the enolamine is found to play a significant role in the stereochemistry of the product, with the energy difference between stereoisomers of this intermediate reflected throughout the remainder of the reaction sequence. Consequently, electronic and steric control of the stereochemistry of this intermediate should directly enhance the ee values of the product. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Lewis Acid Induced [2+2] Cycloadditions of Silyl Enol Ethers with ,,,-Unsaturated Esters: A DFT AnalysisEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18 2005Manuel Arnó Abstract The Lewis acid (LA) induced cycloaddition of trimethysilyl vinyl ether with methyl acrylate has been studied by DFT methods at the B3LYP/6-31G* level. In the absence of an LA, a [4+2] cycloaddition between the silyl enol ether and methyl acrylate in the s-cis conformation takes place through an asynchronous, concerted bond-formation process. This cycloaddition presents a large activation enthalpy of 21.1 kcal,mol,1. Coordination of the LA AlCl3 to the carbonyl oxygen atom of methyl acrylate yields a change of molecular mechanism from a concerted to a two-step mechanism and produces a drastic reduction of the activation energy. This stepwise mechanism is initialized by the nucleophilic attack of the enol ether at the ,-position of methyl acrylate in a Michael-type addition. The very low activation energy (7.1 kcal,mol,1)associated with this nucleophilic attack can be related to the increase of the electrophilicity of the LA-coordinated ,,,-unsaturated ester, which favors the cycloaddition through a polar process. The subsequent ring-closure allows the formation of the corresponding [2+2] and [4+2] cycloadducts. While the [4+2] cycloadduct is formed by kinetic control, the [2+2] cycloadducts are formed by thermodynamic control. The energetic results provide an explanation for the conversion of [4+2] cycloadducts into the thermodynamically more stable [2+2] ones. The cis/trans ratio found for the catalytic [2+2] process is in agreement with the experimental outcome. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Theoretical studies on thiabenzene and its fused derivatives: DFT and ab initio computationsHETEROATOM CHEMISTRY, Issue 5 2006M. Z. Kassaee The molecular structures of thiabenzene (1), 1-thianaphthalene (2), 2-thianaphthalene (3), and 9-thiaanthracene (4) are studied using HF and DFT methods with 6-31+G* basis set. The nonplanar boat conformers of 1,4, with 6,-electrons in their heterocyclic ring, appear more stable than the corresponding planar conformers with 8,-electrons in the ring. This study focuses on the stability, the ylide character, the inversion barrier energy of sulfur atoms, and the conformational flexibility of the ring in 1,4. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:376,381, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20214 [source] Theoretical studies on the mechanism and kinetics of the reaction of F atom with NCO radicalINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2003Zheng-Yu Zhou The reaction of a F atom with an NCO radical was studied at 6-311+g* level, using DFT methods. All geometries, vibrational frequencies, and energies of different stationary points were calculated by HF, UMP2, and DFT methods, and the results agreed with the experimental values. The vibrational frequencies and vibrational modes of the reactant, intermediates, transition states, and products were calculated and the changes of these frequencies and modes were analyzed. Simultaneously, the vibrational modes of various species were assigned. The relationship and the change among these confirmed the mechanism of the reaction and the process of electron transfer. The major channel for the reaction was found to be the cis-channel. At the same time the rate constant was estimated. A new method of analyzing reaction mechanism is also presented. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 52,60, 2003 [source] QR-SCMEH-MO calculations on inner-transition metal diatomic molecules having 12 valence electrons-Nd2 and U2INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010Edward A. Boudreaux The QR-SCMEH-MO computational method has been developed and tested on a numerous variety of inorganic systems over some 45-plus years, with surprisingly good success. More recently this method has been applied to the transition metal molecules, Cr2, Mo2, W2, and Sg2 with 12 valence d/s electrons. The results were at least as good as those obtained from the most accurate ab initio and DFT methods currently available. An extension of the method has been made to the diatomic 12 valence electrons, f/s orbital systems, Nd2 and U2, which is the topic of this presentation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Comparative theoretical study of small Rhn nanoparticles (2 , n , 8) using DFT methodsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2010V. Bertin Abstract This work is aimed at identifying some key characteristics (energy, geometry, and spin) concerning Rhn particles (2 = n , 8) to perform further studies on adsorption and coadsorption sites of pollutants (CO and NO). The DFT methods of the Gaussian 03 program with the LANL2DZ basis set and the LANL2 potential are used. With the purpose to obtain a better nanoparticles definition, five different functionals were tested: B3LYP, O3LYP, BPW91, BP86, and HCTH; and the corresponding results are used to determine which of them best describes distances, spin, and gives acceptable highest vibration frequency and binding energy values, by comparing these results with values measured or calculated by many other authors. For the structure optimization process of the particles, the initial geometric shape was taken mainly from the literature, using the Rh,Rh distance: 2.67 Å, known for the bulk; and doing a complete optimization. We also considered flat nanoparticles structures, which most of them display three-dimensional structures after the optimization process. The few flat shapes are mainly higher in energy than those of three-dimensional structure. For some Rhn particles for different n values, the spin of the ground state present degeneration. In some cases, the optimization process changes the initial geometry, but in most cases, there are only minor changes in bonds and geometry. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Internal-rotation and inversion potential energy surfaces for methylamine and methylphosphineINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2008Hae-Won Kim Abstract Using the HF, MP2, and DFT methods with a 6-311G** basis set, we examine the internal-rotation and inversion of the amino and phosphino groups in methylamine and methylphosphine. The resulting energy surfaces are reported as a function of rotation and inversion descriptors. Both surfaces are characterized by several special points: three minimum energy states, three first-order internal-rotation transition states, six first-order inversion transition states, and six second-order inversion transition states. The MP2 method gave better agreement with experiment. For methylamine, the MP2 energy barrier for internal-rotation is 8.73 kJ/mol; for first-order inversion it is 22.80 kJ/mol and for second-order inversion it is 22.41 kJ/mol. For methylphosphine, the MP2 energy barriers are 7.53, 149.88, and 149.65 kJ/mol, respectively. The energy barriers include ZPE correction contributions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Trends of the bonding effect on the performance of DFT methods in electric properties calculations: A pattern recognition and metric space approach on some XY2 (X = O, S and Y = H, O, F, S, Cl) moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010Christos Christodouleas Abstract A test set of 10 molecules (open and ring forms of ozone and sulfur dioxide as well as water and hydrogen sulfide and their respective fluoro- and chloro-substituted analogs) of specific atmospheric interest has been formed as to assess the performance of various density functional theory methods in (hyper)polarizability calculations against well-established ab initio methods. The choice of these molecules was further based on (i) the profound change in the physics between isomeric systems, e.g., open (C2v) and ring (D3h) forms of ozone, (ii) the relation between isomeric forms, e.g., open and ring form of sulfur dioxide (both of C2v symmetry), and (iii) the effect of the substitution, e.g., in fluoro- and chloro-substituted water analogs. The analysis is aided by arguments chosen from the information theory, graph theory, and pattern recognition fields of Mathematics: In brief, a multidimensional space is formed by the methods which are playing the role of vectors with the independent components of the electric properties to act as the coordinates of these vectors, hence the relation between different vectors (e.g., methods) can be quantified by a proximity measure. Results are in agreement with previous studies revealing the acceptable and consistent behavior of the mPW1PW91, B3P86, and PBE0 methods. It is worth noting the remarkable good performance of the double hybrid functionals (namely: B2PLYP and mPW2PLYP) which are for the first time used in calculations of electric response properties. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Can the hybrid meta GGA and DFT-D methods describe the stacking interactions in conjugated polymers?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2009Ahmed Dkhissi Abstract Newly developed hybrid meta density functionals and density functionals augmented by a classical London dispersion term have been systematically applied for the description of stacking energy and intermolecular distance of thiophene dimer and substituted thiophene dimer. The performance of the various approaches is compared with the benchmark ab-initio calculations done with CCSD(T) (Tsuzuki et al., JACS 2002, 124, 12200). Our results indicate that, contrary to the previous DFT methods which are not reliable, the new generation of DFT performs better the stacking interactions. These functionals, and especially those with an empirical correction, are suitable for general application in conducting polymers and, in particular, the modeling of solid state in which the overlap of ,-, interactions between the conjugated chains is important. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Comparison of some representative density functional theory and wave function theory methods for the studies of amino acidsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Wenbo Yu Abstract Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Assessment of theoretical methods for the calculation of methyl cation affinitiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2008Y. Wei Abstract The methyl cation affinity (MCA; 298 K) of a variety of neutral and anionic bases has been examined computationally with a wide variety of theoretical methods. These include high-level composite procedures such as W1, G3, G3B3, and G2, conventional ab initio methods such as CCSD(T) and MP2, as well as a selection of density functional theory (DFT) methods. Experimental results for a variety of small model systems are well reproduced with practically all these methods, and the performance of DFT based methods are far superior in comparison to their MP2 analogs for these small models. For larger model, systems including motifs frequently encountered in organocatalysts, the performance deteriorates somewhat for DFT methods, while it improves significantly for MP2, rendering the former methods unreliable for common organic bases. Thus, MP2 calculations performed in combination with basis sets such as 6-31+G(2d, p) or larger, appear to offer a practical and reliable approach to compute MCAs of organic bases. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Quick scheme for evaluation of atomic charges in arbitrary aluminophosphate sieves on the basis of electron densities calculated with DFT methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2007A. V. Larin Abstract It is demonstrated that unique and simple analytical functions are justified for the atomic charge dependences q of the T (T = Al, P) and O atoms of aluminophosphates (AlPOs) using DFT calculations with several basis sets, starting from STO-3G to 3-21G and 6-21G**. Three internal (bonds, angles, ,) coordinates for the charge dependences of the T atoms and four coordinates for the O are sufficient to reach a precision of 1.8% for the fitted q(Al), 1.0% for q(P), and 2.5% for q(O) relatively to the values calculated at any basis set level. The proposed strategy consists in an iterative scheme starting from charge dependences based on the neighbor's positions only. Electrostatic potential values are computed to illustrate the differences between the calculated and fitted charges in the considered AlPO models. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2007Ross C. Walker Abstract The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 478,490, 2007 [source] Ab initio calculations of intramolecular parameters for a class of arylamide polymersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2006Satyavani Vemparala Abstract Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 693,700, 2006 [source] Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYPJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Jason D. Thompson Abstract We have recently developed a new Class IV charge model for calculating partial atomic charges in molecules. The new model, called Charge Model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree,Fock theory and by hybrid density functional theory (DFT) based on the modified Perdew,Wang density functional with several basis sets. In the present article we extend CM3 to semiempirical molecular orbital theory, in particular Austin Model 1 (AM1) and Parameterized Model 3 (PM3), and to the popular BLYP and B3LYP DFT and hybrid DFT methods, respectively. For the BLYP extension, we consider the 6-31G(d) basis set, and for the B3LYP extension, we consider three basis sets: 6-31G(d), 6-31+G(d), and MIDI!6D. We begin with the previous CM3 strategy, which involves 34 parameters for 30 pairs of elements. We then refine the model to improve the charges in compounds that contain N and O. This modification, involving two new parameters, leads to improved dipole moments for amides, bifunctional H, C, N, O compounds, aldehydes, ketones, esters, and carboxylic acids; the improvement for compounds not containing N results from obtaining more physical parameters for carbonyl groups when the OCN conjugation of amides is addressed in the parameterization. In addition, for the PM3 method, we added an additional parameter to improve dipole moments of compounds that contain bonds between C and N. This additional parameter leads to improved accuracy in the dipole moments of aromatic nitrogen heterocycles with five-membered rings. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1291,1304, 2003 [source] Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNAJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Philippe Arnaud Abstract Cationic porphyrin derivatives such as meso-tetrakis(4- N -methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO5 system was due to an oxidative attack, within the minor groove of B-DNA, at the C5, or C1, carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5,-TCGTCAAACCGC)-d(5,-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5,. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 797,805, 2003 [source] Dispersion interactions in density-functional theoryJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2009Erin R. Johnson Abstract Density-functional theory (DFT) allows for the calculation of many chemical properties with relative ease, thus making it extremely useful for the physical organic chemistry community to understand and focus on various experiments. However, density-functional techniques have their limitations, including the ability to satisfactorily describe dispersion interactions. Given the ubiquitous nature of dispersion in chemical and biological systems, this is not a trivial matter. Recent advances in the development of DFT methods can treat dispersion. These include dispersion-corrected DFT (using explicit, attractive dispersion terms), parameterized functionals, and dispersion-correcting potentials, all of which can dramatically improve performance for dispersion-bound species. In this perspective, we highlight the achievements made in modeling dispersion using DFT. We hope that this will provide valuable insight to both computational chemists and experimentalists, who aim to study physical processes driven by dispersion interactions. Copyright © 2009 John Wiley & Sons, Ltd. [source] Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphateMAGNETIC RESONANCE IN CHEMISTRY, Issue 6 2008Alessandro Bagno Abstract We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters (1H and 13C chemical shifts and 1H1H, 13C1H, 31P13C and 31P1H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the 1H and 13C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems. Copyright © 2008 John Wiley & Sons, Ltd. [source] Indirect nuclear spin,spin coupling constants in 1,2-diboretane-3-ylidene, a homoaromatic system with , and , 3c/2e bonds.MAGNETIC RESONANCE IN CHEMISTRY, Issue 6 2004Comparison of experimental data with calculations using density functional theory (DFT) Abstract The non-classical 1,2-diboretane-3-ylidene 1a was studied by 13C and 29Si NMR spectroscopy in order to obtain coupling constants 1J(13C,11B) and 1J(29Si,13C). The magnitudes of 1J(13C,11B) were deduced from linewidth measurements in low-temperature 13C and 11B NMR spectra. Calculation of the coupling constants for model compounds related to 1a, using DFT methods based on optimized geometries [B3LYP/6,311+G(d,p)], gave data in agreement with the experiments. Furthermore, the calculations predict for the first time a negative sign of 1J(13C,11B) which mirrors the bonding situation in 1 as described by theory. Copyright © 2004 John Wiley & Sons, Ltd. [source] Indazaboles,synthesis and molecular structureAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 5 2010Bernd Wrackmeyer Abstract The reaction of 1-trimethylsilyl-indazole with boranes affords indazaboles accompanied by elimination of trimethysilane. Thus, the two isomers of parent indazabole are formed in a 1:1 ratio using borane in THF (BH3/THF), characterized by NMR spectroscopy in solution (1H, 11B and 13C NMR). In contrast, the analogous reaction with 1,2-bis(tetramethylene)diborane(6) proceeds to give a single isomer of the B-alkylated indazabole via symmetric ring cleavage of the diborane(6), as shown by NMR in solution and X-ray structural analysis in the solid state. The molecular structure is fluxional in solution. In the solid state, the central B2N4 ring adopts a distorted boat conformation. Calculated gas phase geometries of the parent indazaboles and of the B-alkylated indazabole were optimized by DFT methods at the B3LYP/6-311 + G(d,p) level of theory. Copyright © 2010 John Wiley & Sons, Ltd. [source] Boryl-substituted 1-silacyclobutenes.APPLIED ORGANOMETALLIC CHEMISTRY, Issue 1 2007Formation, molecular structure Abstract The 1,2-hydroboration of the chloro(hexyn-1-yl)- (1a) and chloro(phenylethyn-1-yl)diphenylsilanes (1b) with 9-borabicyclo[3.3.1]nonane afforded selectively the alkenylsilanes 2a, b, in which the boryl and the silyl groups are linked to the same olefinic carbon atom. In case of 2a, treatment with phenylethynyl lithium gave a mixture of the alkyn-1-ylborate 3a and the alkenyl(phenylethynyl)diphenylsilanes 4a. In the case of 2b, only the alkyn-1-ylsilane 4b was identified as an intermediate. Both 4a, b slowly rearranged by intramolecular 1,1-vinylboration into the silacyclobutenes 5a, b. The intermediates were characterized by 1H, 11B, 13C and 29Si NMR spectroscopy in solution, and the molecular structure of the 1-silacyclobutene 5a was determined by X-ray analysis. The gas phase geometries of model molecules corresponding to 5a were optimized by MO calculations using DFT methods [B3LYP/6-311 + G(d,p) level of theory], found to be in reasonable agreement with the results of the crystal structure determination, and NMR parameters were calculated at the same level of theory. Copyright © 2006 John Wiley & Sons, Ltd. [source] Bonding and Bending in Zirconium(IV) and Hafnium(IV) HydrazidesCHEMISTRY - A EUROPEAN JOURNAL, Issue 27 2008Heike Herrmann Dr. Abstract Reaction of the dichloro complexes [M(N2TBSNpy)Cl2] (M=Zr: 1, Hf: 2; TBS: tBuMe2Si; py: pyridine) with one molar equivalent of LiNHNPh2 gave mixtures of the two diastereomeric chlorohydrazido(1,) complexes [M(N2TBSNpy)(NHNPh2)Cl] (M=Zr: 3,a,b, Hf: 4,a,b) in which the diphenylhydrazido(1,) ligand adopts a bent ,1 coordination. This mixture of isomers could be cleanly converted into the deep green diphenylhydrazido(2,) complexes [Zr(N2TBSNpy)(NNPh2)(py)] (5) and [Hf(N2TBSNpy)(NNPh2)(py)] (6), respectively, by dehydrohalogenation with lithium hexamethyldisilazide (LiHMDS) in the presence of one molar equivalent of pyridine. Both complexes contain a linearly coordinated hydrazinediide for which a DFT-based frontier orbital analysis established bonding through one , and two , orbitals. A high polarity of the MN bond was found, in accordance with the description of hydrazinediide(2,) acting as a six-electron donor ligand. The pyridine ligand in [M(N2TBSNpy)(NNPh2)(py)] (M=Zr: 5, Hf: 6) is substitutionally labile as established by line-shape analysis of the dynamic spectra (,G,=19,kcal,mol,1). A change in denticity of the hydrazido unit from ,1 to ,2 was studied by DFT methods. Both forms are calculated to be very close in energy and are only separated by shallow activation barriers, which supports the notion of a rapid ,1 to ,2 interconversion. This process is believed to happen early on in the NN scission in the presence of coupling reagents. Frontier orbital and natural population analyses suggest that a primarily charge-controlled nucleophilic attack at N, is unlikely whereas interaction with an electrophile could play an important role. This hypothesis was tested by the reaction of 5 and 6 with one molar equivalent of B(C6F5)3 to give [Zr(N2TBSNpy)(NNPh2){B(C6F5)3}] (7) and [Hf(N2TBSNpy)(NNPh2){B(C6F5)3}] (8). In these products, B(C6F5)3 becomes attached to the N, atom of the side-on bound hydrazinediide and there is an additional interaction of an ortho -F atom of a C6F5 ring with the metal centre. [source] Chiral Fluorous Dialkoxy-Diamino Zirconium Complexes: Synthesis and Use in Stereospecific Polymerization of 1-HexeneCHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2007Evgueni Kirillov Dr. Abstract New catalysts for the isospecific polymerization of 1-hexene based on cationic zirconium complexes incorporating the tetradentate fluorous dialkoxy-diamino ligands [OC(CF3)2CH2N(Me)(CH2)2N(Me)CH2C(CF3)2O]2, [(ON2NO)2,] and [OC(CF3)2CH2N(Me)(1R,2R -C6H10)N(Me)CH2C(CF3)2O]2, [(ONCyNO)2,] have been developed. The chiral fluorous diamino-diol [(ONCyNO)H2, 2] was prepared by ring-opening of the fluorinated oxirane (CF3)2COCH2 with (R,R)- N,N, -dimethyl-1,2-cyclohexanediamine. Proligand 2 reacts cleanly with [Zr(CH2Ph)4] and [Ti(OiPr)4] precursors to give the corresponding dialkoxy complexes [Zr(CH2Ph)2(ONCyNO)] (3) and [Ti(OiPr)2(ONCyNO)] (4), respectively. An X-ray diffraction study revealed that 3 crystallizes as a 1:1 mixture of two diastereomers (,- 3 and ,- 3), both of which adopt a distorted octahedral structure with trans -O, cis -N, and cis -CH2Ph ligands. The two diastereomers ,- 3 and ,- 3 adopt a C2 -symmetric structure in toluene solution, as established by NMR spectroscopy. Cationic complexes [Zr(CH2Ph)(ON2NO)(THF)n]+ (n=0, anion=[B(C6F5)4],, 5; n=1, anion=[PhCH2B(C6F5)3],, 6) and [Zr(CH2Ph)(ONCyNO)(THF)]+[PhCH2B(C6F5)3], (7) were generated from the neutral parent precursors [Zr(CH2Ph)2(ON2NO)] (H) and [Zr(CH2Ph)2(ONCyNO)] (3), and their possible structures were determined on the basis of 1H, 19F, and 13C NMR spectroscopy and DFT methods. The neutral zirconium complexes H and 3 (,- 3/,- 3 mixture), when activated with B(C6F5)3 or [Ph3C]+[B(C6F5)4],, catalyze the polymerization of 1-hexene with overall activities of up to 4500,kg,PH,mol,Zr,1,h,1, to yield isotactic-enriched (up to 74,% mmmm) polymers with low-to-moderate molecular weights (Mw=4800,47,200) and monodisperse molecular-weight distributions (Mw/Mn=1.17,1.79). [source] Interaction of Zinc Oxide Clusters with Molecules Related to the Sulfur Vulcanization of Polyolefins ("Rubber")CHEMISTRY - A EUROPEAN JOURNAL, Issue 33 2006Ralf Steudel Prof. Dr. Abstract The vulcanization of rubber by sulfur is a large-scale industrial process that is only poorly understood, especially the role of zinc oxide, which is added as an activator. We used the highly symmetrical cluster Zn4O4 (Td) as a model species to study the thermodynamics of the initial interaction of various vulcanization-related molecules with ZnO by DFT methods, mostly at the B3LYP/6-31+G* level. The interaction energy of Lewis bases with Zn4O4 increases in the following order: CO
| | ||||||||||||||||||||||||