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Relative Energies (relative + energy)

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Chemistry	96%

Distribution within Chemistry

General & Introductory Chemistry	20%
Mass Spectrometry	6%

Selected Abstracts

Relative energies of conformations and sulfinyl oxygen-induced pentacoordination at silicon in 4-bromo- and 4,4-dibromo-4-silathiacyclohexane 1-oxide: A computational study

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005
Fillmore Freeman
Abstract The equilibrium geometries and relative energies of the chair, twist, and boat conformations of cis - and trans -4-bromo-4-silathiacyclohexane 1-oxide and 4,4-dibromo-4-silathiacyclohexane 1-oxide have been calculated at the B3LYP/6-311G(d,p) and MP2/6-311+G(d,p) theoretical levels. The axial (SO) chair conformers of the sulfoxides are of lower energy than the chair conformers of the corresponding equatorial (SO) sulfoxides. The chair conformer of the axial (SO) trans -4-bromo-4-silathiacyclohexane 1-oxide is only 0.10 kcal/mol more stable than the corresponding 1,4-boat conformer which is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The 1,4-boat structure of equatorial (SO) trans -4-bromo-4-silathiacyclohexane 1-oxide is a transition state and is 5.77 kcal/mol higher in energy than the respective chair conformer. The 1,4-boat conformer of axial (SO) 4,4-dibromo-4-silathiacyclohexane 1-oxide is also stabilized by transannular coordination of the sulfinyl oxygen and silicon, but it is 4.31 kcal/mol higher in energy than the corresponding chair conformer. The relatively lower stability of the 1,4-boat conformer of 4,4-dibromo-4-silathiacyclohexane 1-oxide may be due to repulsive interactions of the axial halogen and sulfinyl oxygen atom. The relative energies of the conformers and transition states are discussed in terms of hyperconjugative interactions, orbital interactions, nonbonded interactions, and transannular sulfinyl oxygen-silicon coordination. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source]

Sulfur Dioxide and Water: Structures and Energies of the Hydrated Species SO2·nH2O, [HSO3],·nH2O, [SO3H],·nH2O, and H2SO3·nH2O (n = 0,8)

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 10 2009
Ralf Steudel
Abstract The structures of a large number of hydrates of sulfur dioxide (SO2·nH2O), of the sulfonate ion ([HSO3],·nH2O), of the tautomeric hydrogensulfite anion ([SO3H],·nH2O), and of sulfurous acid (H2SO3·nH2O) with up to eight water molecules attached to these species have been optimized at the B3LYP/6-31G(2df,p) level of theory (DFT). The calculated vibrational frequencies allow the definite assignment of certain characteristic modes, and in this way a convincing interpretation of published spectra of aqueous SO2 as well as of SO2 adsorbed on very cold ice crystals has been achieved for the first time. Single-point calculations at the G3X(MP2) level of theory were used to calculate the binding energies of the water molecules in SO2·nH2O as well as the relative stabilities of the isomeric anionic species [HSO3],·nH2O and [SO3H],·nH2O. Generally, the water molecules tend to stick together forming clusters, whereas the particular sulfur-containing molecule remains at the surface of the water cluster, but it is always strongly hydrogen-bonded. Only when there are more than six water molecules are the anions more or less completely surrounded by water molecules. DFT calculations erroneously predict that the gaseous hydrated sulfonate ions are more stable than the isomeric hydrogensulfite ions, even when hydrated with six water molecules. However, if these hydrated species are calculated as being embedded in a polar continuum simulating the aqueous phase, the hydrogensulfite ions are more stable than the sulfonate ions, in agreement with various spectroscopic observations on aqueous sulfite solutions. On the other hand, at the higher G3X(MP2) level, the gaseous hydrated hydrogensulfite anions are more stable than the corresponding sulfonate ions only if the number of water molecules is larger than four, whereas for the weakly hydrated anions the order of relative energies is reversed. The possible implications of these results for the enzymatic oxidation of "sulfite ions" ([HSO3], and [SO3H],) by sulfite oxidase are discussed. The conversion of SO2·6H2O into its isomer H2SO3·5H2O is predicted to be exothermic (,H°298 = ,56.1 kJ,mol,1) and exergonic (,G°298 = ,22.5 kJ,mol,1). (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]

Synthesis, Protonation and CuII Complexes of Two Novel Isomeric Pentaazacyclophane Ligands: Potentiometric, DFT, Kinetic and AMP Recognition Studies

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 1 2009
Andrés G. Algarra
Abstract The synthesis and coordination chemistry of two novel ligands, 2,6,9,12,16-pentaaza[17]metacyclophane (L1) and 2,6,9,12,16-pentaaza[17]paracyclophane (L2), is described. Potentiometric studies indicate that L1 and L2 form a variety of mononuclear complexes the stability constants of which reveal a change in the denticity of the ligand when moving from L1 to L2, a behaviour that can be qualitatively explained by the inability of the paracyclophanes to simultaneously use both benzylic nitrogen atoms for coordination to a single metal centre. In contrast, the formation of dinuclear hydroxylated complexes is more favoured for the paraL2 ligand. DFT calculations have been carried out to compare the geometries and relative energies of isomeric forms of the [CuL]2+ complexes of L1 and L2 in which the cyclophane acts either as tri- or tetradentate. The results indicate that the energy cost associated with a change in the coordination mode of the cyclophane from tri- to tetradentate is moderate for both ligands so that the actual coordination mode can be determined not only by the characteristics of the first coordination sphere but also by the specific interactions with additional nearby water molecules. The kinetics of the acid promoted decomposition of the mono- and dinuclear CuII complexes of both cyclophanes have also been studied. For both ligands, dinuclear complexes convert rapidly to mononuclear species upon addition of excess acid, the release of the first metal ion occurring within the mixing time of the stopped-flow instrument. Decomposition of the mononuclear [CuL2]2+ and [CuHL2]3+ species occurs with the same kinetics, thus showing that protonation of [CuL2]2+ occurs at an uncoordinated amine group. In contrast, the [CuL1]2+ and [CuHL1]3+ species show different decomposition kinetics indicating the existence of significant structural reorganisation upon protonation of the [CuL1]2+ species. The interaction of AMP with the protonated forms of the cyclophanes and the formation of mixed complexes in the systems Cu,L1 -AMP, Cu,L2 -AMP, and Cu,L3 -AMP, where L3 is the related pyridinophane containing the same polyamine chain and 2,6-dimethylpyridine as a spacer, is also reported. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]

The Reductive Elimination of Methane from ansa -Hydrido(methyl)metallocenes of Molybdenum and Tungsten: Application of Hammond's Postulate to Two-State Reactions

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 15 2005
José-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]

The Additive Nature of Energy Penalties in 10-Vertex nido -(Car)boranes

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 12 2005
Farooq A. Kiani
Abstract A structural increment system, i.e. quantitative rules that govern the relative stabilities of 10-vertex nido -boranes and-carboranes, has been determined. Density functional theory computations at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level with ZPE corrections were carried out for 81 different boron hydride and carborane structures from [B10H12]2, to C3B7H11 to determine their relative stabilities. A set of eleven disfavored geometrical features that destabilize a cluster structure relative to a hypothetical ideal situation were identified and weighted by so-called energy penalties. The latter show good additive behavior and allow us to reproduce the DFT computed relative energies mostly with an accuracy of 6.0 kcal,mol,1. Some unknown 10-vertex nido- carboranes that are thermodynamically more stable than their known isomers are also identified. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]

Relative energies of conformations and sulfinyl oxygen-induced pentacoordination at silicon in 4-bromo- and 4,4-dibromo-4-silathiacyclohexane 1-oxide: A computational study

Predicting the tautomeric equilibrium of acetylacetone in solution.

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010

Abstract This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by ,10 kJ mol,1, whereas the very promising SCS-MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double , basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split-valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low-temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

DFT conformational studies of ,-maltotriose,

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2008
Udo Schnupf
Abstract Recent DFT optimization studies on ,-maltose improved our understanding of the preferred conformations of ,-maltose. The present study extends these studies to ,-maltotriose with three ,- D -glucopyranose residues linked by two ,-[1,4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (,H and ,H) move from the region of conformational space of (,, ,), relative to (0°, 0°), to a new position defined by (+, +). Further, it was found previously that the relative energies of ,-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the ,-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2008
Haydée Valdés
Abstract Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and compare the calculated data with benchmark values (experimental or high-level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT-D) is proposed and shown to provide very good results in both of the above described representative cases. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008 [source]

DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2005
Robert J. Deeth
The ligand field molecular mechanics (LFMM) model, which incorporates the ligand field stabilization energy (LFSE) directly into the potential energy expression of molecular mechanics (MM), has been implemented in the "chemically aware" molecular operating environment (MOE) software package. The new program, christened DommiMOE, is derived from our original in-house code that has been linked to MOE via its applications programming interface and a number of other routines written in MOE's native scientific vector language (SVL). DommiMOE automates the assignment of atom types and their associated parameters and popular force fields available in MOE such as MMFF94, AMBER, and CHARMM can be easily extended to provide a transition metal simulation capability. Some of the unique features of the LFMM are illustrated using MMFF94 and some simple [MCl4]2, and [Ni(NH3)n]2+ species. These studies also demonstrate how density functional theory calculations, especially on experimentally inaccessible systems, provide important data for designing improved LFMM parameters. DommiMOE treats Jahn,Teller distortions automatically, and can compute the relative energies of different spin states for Ni(II) complexes using a single set of LFMM parameters. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 123,130, 2005 [source]

A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane)

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2003
Fillmore Freeman
Abstract Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the CHax and CHeq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon,hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (,G°c-t) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 909,919, 2003 [source]

An improved OPLS,AA force field for carbohydrates

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2002
D. Kony
Abstract This work describes an improved version of the original OPLS,all atom (OPLS,AA) force field for carbohydrates (Damm et al., J Comp Chem 1997, 18, 1955). The improvement is achieved by applying additional scaling factors for the electrostatic interactions between 1,5- and 1,6-interactions. This new model is tested first for improving the conformational energetics of 1,2-ethanediol, the smallest polyol. With a 1,5-scaling factor of 1.25 the force field calculated relative energies are in excellent agreement with the ab initio -derived data. Applying the new 1,5-scaling makes it also necessary to use a 1,6-scaling factor for the interactions between the C4 and C6 atoms in hexopyranoses. After torsional parameter fitting, this improves the conformational energetics in comparison to the OPLS,AA force field. The set of hexopyranoses included in the torsional parameter derivation consists of the two anomers of D -glucose, D -mannose, and D -galactose, as well as of the methyl-pyranosides of D -glucose, D -mannose. Rotational profiles for the rotation of the exocyclic group and of different hydroxyl groups are also compared for the two force fields and at the ab initio level of theory. The new force field reduces the overly high barriers calculated using the OPLS,AA force field. This leads to better sampling, which was shown to produce more realistic conformational behavior for hexopyranoses in liquid simulation. From 10-ns molecular dynamics (MD) simulations of ,- D -glucose and ,- D -galactose the ratios for the three different conformations of the hydroxymethylene group and the average 3JH,H coupling constants are derived and compared to experimental values. The results obtained for OPLS,AA,SEI force field are in good agreement with experiment whereas the properties derived for the OPLS,AA force field suffer from sampling problems. The undertaken investigations show that the newly derived OPLS,AA,SEI force field will allow simulating larger carbohydrates or polysaccharides with improved sampling of the hydroxyl groups. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1416,1429, 2002 [source]

Ab initio crystal structure predictions for flexible hydrogen-bonded molecules.

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2001
Part III.
Abstract In crystal structure predictions possible structures are usually ranked according to static energy. Here, this criterion has been replaced by the free energy at any temperature. The effects of harmonic lattice vibrations were found by standard lattice-dynamical calculations, including a rough estimate of the effects of thermal expansion. The procedure was tested on glycol and glycerol, for which accurate static energies had been obtained previously (Part II of this series). It was found that entropy and zero-point energy give the largest contribution to free energy differences between hypothetical crystal structures, adding up to about 3 kJ/mol for the structures with lowest energy. The temperature-dependent contribution to the energy and the effects of thermal expansion showed less variation among the structures. The overall accuracy in relative energies was estimated to be a few kJ/mol. The experimental crystal structure for glycol corresponded to the global free energy minimum, whereas for glycerol it ranked second at 1 kJ/mol. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 816,826, 2001 [source]

Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycine

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2001
L. F. Pacios
Abstract Ab initio calculations at the MP2/6-311++G** level of theory led recently to the identification of 13 stable conformers of gaseous glycine with relative energies within 11 kcal/mol. The stability of every structure depends on subtle intramolecular effects arising from conformational changes. These intramolecular interactions are examined with the tools provided by the Atoms In Molecules (AIM) theory, which allows obtaining a wealth of quantum mechanics information from the molecular electron density ,(r). The analysis of the topological features of ,(r) on one side and the atomic properties integrated in the basins defined by the gradient vector field of the density on the other side makes possible to explore the different intramolecular effects in every conformer. The existence of intramolecular hydrogen bonds on some conformers is demonstrated, while the presence of other stabilizing interactions arising from favorable conformations is shown to explain the stability of other structures in the potential energy surface of glycine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 702,716, 2001 [source]

Entropy considerations in kinetic method experiments

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 9 2004
Chrys WesdemiotisArticle first published online: 7 SEP 200
Abstract In extended kinetic method experiments, relative binding enthalpies (,affinities') and relative entropies are obtained based on unimolecular dissociation kinetics. A series of ion-bound dimers AXBi is formed, in which the sample (A) and structurally similar reference molecules (Bi) are bridged by a central cation or anion (X). The branching ratios of the AXBi set to AX and BiX are determined at different internal energies, usually by subjecting AXBi to collisionally activated dissociation at various collision energies. The dependence of the natural logarithm of the branching ratios on the corresponding BiX bond enthalpies (X affinities of Bi) is evaluated as a function of internal energy to thereby deduce the AX bond enthalpy (X affinity of A) as well as an apparent relative entropy of the competitive dissociation channels, ,(,Sapp). Experiments with proton- and Na+ -bound dimers show that this approach can yield accurate binding enthalpies. In contrast, the derived ,(,Sapp) values do not correlate with the corresponding thermodynamic entropy differences between the channels leading to AX and BiX, even after scaling. The observed trends are reconciled by the transition state switching model. According to this model, the kinetics of barrierless dissociations, such as those encountered in kinetic method studies, are dominated by a family of tight transition states (,entropy bottlenecks') lying lower in energy than the corresponding dissociation thresholds. In general, the relative energies of these tight transition states approximately match those of the dissociation products, but their relative entropies tend to be much smaller, as observed experimentally. Copyright © 2004 John Wiley & Sons, Ltd. [source]

Fragmentations of (M,H), anions of underivatised peptides.

MASS SPECTROMETRY REVIEWS, Issue 1 2009
Part 2: Characteristic cleavages of Ser, of disulfides, other post-translational modifications, together with some unusual internal processes
Abstract In a previous review (Bowie, Brinkworth, & Dua (2002); Mass Spectrom Rev 21:87,107) we described the characteristic backbone cleavages and side chain fragmentations which occur from (M,H), parent anions of underivatized peptides. This work is briefly summarized in the present review. Cys was not described in the previous review: here we describe the Cys characteristic side chain loss of H2S, together with its , backbone cleavage. These processes are compared with those of the related Ser. All experimental observations are backed up with theoretical studies at the HF/6-31G(d)//AM1 level of theory, a level of theory which we have shown gives good geometries and acceptable relative energies. The negative ion cleavages of a number of post-translational modifications are described. Negative ion mass spectrometry is the method of choice for identification of disulfides in both peptides and proteins. Intramolecular disulfides are identified by the presence of the fragment anion [(M,H),,H2S2], and CID MS2 of this fragment normally identifies the positions of the two Cys residues and often the full sequence of the peptide. An unsymmetrically substituted intermolecular disulfide can give up to eight characteristic fragment anions, and CID MS2 of some, or all of these often provides the full sequence of those peptides which form the initial intermolecular disulfide linkage. Negative ion cleavages of disulfides are the most energetically favored of all peptide negative cleavages studied to date. Negative ion mass spectrometry is also valuable for the identification of pyroglutamates, sulfates and phosphates. Finally, some unusual fragmentations are described which involve cyclization/elimination reactions which require the decomposing (M,H), parent anions to adopt the same helical conformation that these peptides have in solution. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 28:20,34, 2009 [source]

Chlorin,Bacteriochlorin Energy-transfer Dyads as Prototypes for Near-infrared Molecular Imaging Probes: Controlling Charge-transfer and Fluorescence Properties in Polar Media

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2009
Hooi Ling Kee
The photophysical properties of two energy-transfer dyads that are potential candidates for near-infrared (NIR) imaging probes are investigated as a function of solvent polarity. The dyads (FbC-FbB and ZnC-FbB) contain either a free base (Fb) or zinc (Zn) chlorin (C) as the energy donor and a free base bacteriochlorin (B) as the energy acceptor. The dyads were studied in toluene, chlorobenzene, 1,2-dichlorobenzene, acetone, acetonitrile and dimethylsulfoxide (DMSO). In both dyads, energy transfer from the chlorin to bacteriochlorin occurs with a rate constant of ,(5,10 ps),1 and a yield of >99% in nonpolar and polar media. In toluene, the fluorescence yields (,f = 0.19) and singlet excited-state lifetimes (,,5.5 ns) are comparable to those of the benchmark bacteriochlorin. The fluorescence yield and excited-state lifetime decrease as the solvent polarity increases, with quenching by intramolecular electron (or hole) transfer being greater for FbC-FbB than for ZnC-FbB in a given solvent. For example, the ,f and , values for FbC-FbB in acetone are 0.055 and 1.5 ns and in DMSO are 0.019 and 0.28 ns, whereas those for ZnC-FbB in acetone are 0.12 and 4.5 ns and in DMSO are 0.072 and 2.4 ns. The difference in fluorescence properties of the two dyads in a given polar solvent is due to the relative energies of the lowest energy charge-transfer states, as assessed by ground-state redox potentials and supported by molecular-orbital energies derived from density functional theory calculations. Controlling the extent of excited-state quenching in polar media will allow the favorable photophysical properties of the chlorin,bacteriochlorin dyads to be exploited in vivo. These properties include very large Stokes shifts (85 nm for FbC-FbB, 110 nm for ZnC-FbB) between the red-region absorption of the chlorin and the NIR fluorescence of the bacteriochlorin (,f = 760 nm), long bacteriochlorin excited-state lifetime (,5.5 ns), and narrow (,20 nm) absorption and fluorescence bands. The latter will facilitate selective excitation/detection and multiprobe applications using both intensity- and lifetime-imaging techniques. [source]

Diastereochemical differentiation of bicyclic diols using metal complexation and collision-induced dissociation mass spectrometry

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2009
Jaana M. H. Pakarinen
Metal complex formation was investigated for di- exo -, di- endo - and trans -2,3- and 2,5-disubstituted trinorbornanediols, and di- exo - and di- endo - 2,3-disubstituted camphanediols using different divalent transition metals (Co2+, Ni2+, Cu2+) and electrospray ionization quadrupole ion trap mass spectrometry. Many metal-coordinated complex ions were formed for cobalt and nickel: [2M+Met]2+, [3M+Met]2+, [M,H+Met]+, [2M,H+Met]+, [M+MetX]+, [2M+MetX]+ and [3M,H+Co]+, where M is the diol, Met is the metal used and X is the counter ion (acetate, chloride, nitrate). Copper showed the weakest formation of metal complexes with di- exo -2,3-disubstituted trinorbornanediol yielding only the minor singly charged ions [M,H+Cu]+, [2M,H+Cu]+ and [2M+CuX]+. No clear differences were noted for cobalt complex formation, especially for cis -2,3-disubstituted isomers. However, 2,5-disubstituted trinorbornanediols showed moderate diastereomeric differentiation because of the unidentate nature of the sterically more hindered exo -isomer. trans -Isomers gave rise to abundant [3M,H+Co]+ ion products, which may be considered a characteristic ion for bicyclo[221]heptane trans -2,3- and trans -2,5-diols. To differentiate cis -2,3-isomers, the collision-induced dissociation (CID) products for [3M+Co]2+, [M+CoOAc]+, [2M,H+Co]+ and [2M+CoOAc]+ cobalt complexes were investigated. The results of the CID of the monomeric and dimeric metal adduct complexes [M+CoOAc]+ and [2M,H+Co]+ were stereochemically controlled and could be used for stereochemical differentiation of the compounds investigated. In addition, the structures and relative energies of some complex ions were studied using hybrid density functional theory calculations. Copyright © 2009 John Wiley & Sons, Ltd. [source]

Single crystal structure and molecular dynamics analysis of a myo -inositol derivative

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2000
Jan Dillen
The crystal structure of 5- O - tert -butyldimethylsilyl-3,4- O -carbonyl-1,2- O -cyclohexylidene-2-oxo-3-oxa-4-bornanylcarbonyl- d - myo -inositol has been studied by single-crystal X-ray diffraction at both room temperature and 173,K. At room temperature, the tert -butyldimethylsilyl group exhibits dynamical disorder. A molecular dynamics simulation was used to model the disorder and this indicates that the group librates between two stable conformations in the crystal. Approximate relative energies of the different forms and energy barriers for the transition were obtained by empirical force field methods. Calculations of the thermal motion of the atoms are in good qualitative, but fair to poor quantitative agreement with the X-ray data. [source]

Mechanistic Investigation of Chiral Phosphoric Acid Catalyzed Asymmetric Baeyer,Villiger Reaction of 3-Substituted Cyclobutanones with H2O2 as the Oxidant

CHEMISTRY - A EUROPEAN JOURNAL, Issue 10 2010
Senmiao Xu Dr.
Abstract The mechanism of the chiral phosphoric acid catalyzed Baeyer,Villiger (B,V) reaction of cyclobutanones with hydrogen peroxide was investigated by using a combination of experimental and theoretical methods. Of the two pathways that have been proposed for the present reaction, the pathway involving a peroxyphosphate intermediate is not viable. The reaction progress kinetic analysis indicates that the reaction is partially inhibited by the ,-lactone product. Initial rate measurements suggest that the reaction follows Michaelis,Menten-type kinetics consistent with a bifunctional mechanism in which the catalyst is actively involved in both carbonyl addition and the subsequent rearrangement steps through hydrogen-bonding interactions with the reactants or the intermediate. High-level quantum chemical calculations strongly support a two-step concerted mechanism in which the phosphoric acid activates the reactants or the intermediate in a synergistic manner through partial proton transfer. The catalyst simultaneously acts as a general acid, by increasing the electrophilicity of the carbonyl carbon, increases the nucleophilicity of hydrogen peroxide as a Lewis base in the addition step, and facilitates the dissociation of the OH group from the Criegee intermediate in the rearrangement step. The overall reaction is highly exothermic, and the rearrangement of the Criegee intermediate is the rate-determining step. The observed reactivity of this catalytic B,V reaction also results, in part, from the ring strain in cyclobutanones. The sense of chiral induction is rationalized by the analysis of the relative energies of the competing diastereomeric transition states, in which the steric repulsion between the 3-substituent of the cyclobutanone and the 3- and 3,-substituents of the catalyst, as well as the entropy and solvent effects, are found to be critically important. [source]

Polyhedral Structures with Three-, Four-, and Five Fold Symmetry in Metal-Centered Ten-Vertex Germanium Clusters

CHEMISTRY - A EUROPEAN JOURNAL, Issue 15 2008
Bruce King Prof.
Abstract Studies using density functional theory (DFT) at the hybrid B3LYP level indicate that the relative energies of structures with three-fold, four-fold, and five-fold symmetry for centered 10-vertex bare germanium clusters of the general type M@Ge10z depend on the central metal atom M and the skeletal electron count. For M@Ge10 clusters with 20 skeletal electrons the DFT results agree with experimental data on the isoelectronic centered 10-vertex bare metal clusters. Thus the lowest energy structure for Ni@Ge10, isoelectronic with the known Ni@In1010,, is a C3v polyhedron derived from the tetracapped trigonal prism. However, Zn@Ge102+ is isoelectronic with the known cluster Zn@In108,, which has the lowest energy structure, a D4d bicapped square antiprism. For the clusters Ni@Ge102,, Cu@Ge10,, and Zn@Ge10 that have 22 skeletal electrons the lowest energy structures are the D4d bicapped square antiprism predicted by the Wade,Mingos rules. For the clusters Ni@Ge104,, Cu@Ge103,, and Zn@Ge102, that have 24 skeletal electrons the lowest energy structures are C3v polyhedra with 10 triangular faces and 3 quadrilateral faces derived from a tetracapped trigonal prism by extreme lengthening of the edges of the capped triangular face of the underlying trigonal prism. For the clusters Cu@Ge105, and Zn@Ge104, that have 26 skeletal electrons the lowest energy structures are the D5d pentagonal antiprisms predicted by the Wade,Mingos rules and the C3v tetracapped trigonal prism as a somewhat higher energy structure. However, for the isoelectronic Ni@Ge106, the relative energies of these two structure types are reversed so that the C3v tetracapped trigonal prism becomes the global minimum. The effects of electron count on the geometries of the D5d pentagonal prism and D4d bicapped square antiprism centered metal cluster structures are consistent with the bonding/antibonding characteristics of the corresponding HOMO and LUMO frontier molecular orbitals. [source]

QM/MM Modeling of Enantioselective Pybox,Ruthenium- and Box,Copper-Catalyzed Cyclopropanation Reactions: Scope, Performance, and Applications to Ligand Design

CHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2007

Abstract An extensive comparison of full-QM (B3LYP) and QM/MM (B3LYP:UFF) levels of theory has been made for two enantioselective catalytic systems, namely, Pybox,Ru and Box,Cu complexes, in the cyclopropanation of alkenes (ethylene and styrene) with methyl diazoacetate. The geometries of the key reaction intermediates and transition structures calculated at the QM/MM level are generally in satisfactory agreement with full-QM calculated geometries. More importantly, the relative energies calculated at the QM/MM level are in good agreement with those calculated at the full-QM level in all cases. Furthermore, the QM/MM energies are often in better agreement with the stereoselectivity experimentally observed, and this suggests that QM/MM calculations can be superior to full-QM calculations when subtle differences in inter- and intramolecular interactions are important in determining the selectivity, as is the case in enantioselective catalysis. The predictive value of the model presented is validated by the explanation of the unusual enantioselectivity behavior exhibited by a new bis-oxazoline ligand, the stereogenic centers of which are quaternary carbon atoms. [source]

Ring-Closing Olefin Metathesis on Ruthenium Carbene Complexes: Model DFT Study of Stereochemistry

CHEMISTRY - A EUROPEAN JOURNAL, Issue 13 2005
Sergei F. Vyboishchikov Dr.
Abstract Ring-closing metathesis (RCM) is the key step in a recently reported synthesis of salicylihalamide and related model compounds. Experimentally, the stereochemistry of the resulting cycloolefin (cis/trans) depends strongly on the substituents that are present in the diene substrate. To gain insight into the factors that govern the observed stereochemistry, density functional theory (DFT) calculations have been carried out for a simplified dichloro(2-propylidene)(imidazole-2-ylidene)ruthenium catalyst I, as well as for the real catalyst II with two mesityl substituents on the imidazole ring. Four model substrates are considered, which are closely related to the systems studied experimentally, and in each case, two pathways A and B are possible since the RCM reaction can be initiated by coordination of either of the two diene double bonds to the metal center. The first metathesis yields a carbene intermediate, which can then undergo a second metathesis by ring closure, metallacycle formation, and metallacycle cleavage to give the final cycloolefin complex. According to the DFT calculations, the stereochemistry is always determined in the second metathesis reaction, but the rate-determining step may be different for different catalysts, substrates, and pathways. The ancillary N-heterocyclic carbene ligand lies in the Ru-Cl-Cl plane in the simplified catalyst I, but is perpendicular to it in the real catalyst II, and this affects the relative energies of the relevant intermediates and transition states. Likewise, the introduction of methyl substituents in the diene substrates influences these relative energies appreciably. Good agreement with the experimentally observed stereochemistry is only found when using the real catalyst II and the largest model substrates in the DFT calculations. [source]

On the Effect of Tether Composition on cis/trans Selectivity in Intramolecular Diels,Alder Reactions

CHEMISTRY - AN ASIAN JOURNAL, Issue 1 2009
Michael
Abstract Intramolecular Diels,Alder (IMDA) transition structures (TSs) and energies have been computed at the B3LYP/6-31+G(d) and CBS-QB3 levels of theory for a series of 1,3,8-nonatrienes, H2CCHCHCHCH2XZCHCH2 [XZ=CH2CH2 (1); OC(O) (2); CH2C(O) (3); OCH2 (4); NHC(O) (5); SC(O) (6); OC(S) (7); NHC(S) (8); SC(S) (9)]. For each system studied (1,9), cis - and trans -TS isomers, corresponding, respectively, to endo - and exo -positioning of the CXZ tether with respect to the diene, have been located and their relative energies (ErelTS) employed to predict the cis/trans IMDA product ratio. Although the ErelTS values are modest (typically <3,kJ,mol,1), they follow a clear and systematic trend. Specifically, as the electronegativity of the tether group X is reduced (XO,NH or S), the IMDA cis stereoselectivity diminishes. The predicted stereochemical reaction preferences are explained in terms of two opposing effects operating in the cis -TS, namely (1),unfavorable torsional (eclipsing) strain about the C4C5 bond, that is caused by the CXC(Y) group's strong tendency to maintain local planarity; and (2),attractive electrostatic and secondary orbital interactions between the endo -(thio)carbonyl group, CY, and the diene. The former interaction predominates when X is weakly electronegative (XN, S), while the latter is dominant when X is more strongly electronegative (XO), or a methylene group (XCH2) which increases tether flexibility. These predictions hold up to experimental scrutiny, with synthetic IMDA reactions of 1, 2, 3, and 4 (published work) and 5, 6, and 8 (this work) delivering ratios close to those calculated. The reactions of thiolacrylate 5 and thioamide 8 represent the first examples of IMDA reactions with tethers of these types. Our results point to strategies for designing tethers, which lead to improved cis/trans -selectivities in IMDAs that are normally only weakly selective. Experimental verification of the validity of this claim comes in the form of fumaramide 14, which undergoes a more trans -selective IMDA reaction than the corresponding ester tethered precursor 13. [source]

Calculation of conformational energies and optical rotation of the most simple chiral alkane,

CHIRALITY, Issue 9 2008
Stefan Grimme
Abstract Quantum chemical calculations have been performed to investigate the conformer distribution of 4-ethyl-4-methyloctane and its optical rotation. With the reference methods MP2 and SCS-MP2, the energies of seven conformers are found within a range of about 1.5 kcal mol,1. It is demonstrated that the relative energies cannot be reliably predicted with conventional GGA or hybrid density functionals, Hartree-Fock, semiempirical AM1, and classical force field (MM3) calculations. An empirical dispersion correction to GGA (PBE-D), hybrid (B3LYP-D), or double hybrid (B2PLYP-D) functionals corrects these errors and results in very good agreement with the reference energies. Optical rotations have been calculated for all seven conformers at the TDDFT(BHLYP/aTZV2P) level. The computed macroscopic rotation is derived from a classical Boltzmann average. The result (1.9,3.2 deg dm,1 (g/mL),1) is very close to the experimental value of 0.2 deg dm,1 (g/mL),1 for the (R)-enantiomer and has the right sign. Because six conformers are significantly populated at room temperature and the rotations of individual conformers differ in sign and magnitude, the calculated average rotation is rather sensitive to the conformer population used. From the electronic structure point of view, this example emphasizes the effect of long-range dispersion effects for the evaluation of population averaged quantities in large molecules. Computations based on free enthalpies are in worse agreement with experiment that is attributed to artefacts of the harmonic approximation used to compute the vibrational entropy terms. Chirality, 2008. © 2008 Wiley-Liss, Inc. [source]

Beyond the Icosahedron: A Density Functional Theory Study of 14-Atom Germanium Clusters

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 25 2008
R. Bruce King
Abstract Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge14z (z = ,8, ,6, ,4, ,2, 0, +2, +4) starting from seven different initial configurations. An Oh omnicapped cube structure is the most stable for Ge142, followed by a hexagonal antiprism structure with a relative energy of 42.7 kcal/mol. The lowest-energy structure for neutral Ge14 is a triplet omnicapped cube with full Oh symmetry followed by a singlet omnicapped cube compressed to D4h symmetry through Jahn,Teller distortion. The lowest energy Ge142+ structure is also an Oh structure derived from the omnicapped cube through elongation of the 12 edges of the underlying cube to give a rhomboidal dodecahedron with 12 rhombus faces. The lowest-energy Ge124+ structure is a bicapped icosahedron. Some D6h hexagonal wheel structures at higher energies are also found for the hypoelectronic systems Ge14, Ge142+, and Ge144+. The lowest-energy structures for the hyperelectronic Ge144,, Ge146,, and Ge148, are relatively unsymmetrical not readily recognizable open structures typically with some pentagonal or hexagonal faces. The D6d bicapped hexagonal antiprism found in 14-vertex C2B12 carborane and M2C2B10 dimetallacarborane structures is not the lowest-energy structure for any of the Ge14z clusters.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]

Study of conformational and optical rotation for the alaninamide

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2007
Shulei Zhao
Abstract Six stationary points of alaninamide have been located on the potential surface energy (PES) at the B3LYP/6-311++G(2d,2p) level of theory both in the gas phase and in aqueous solution. In the aqueous solution, to take the water solvent effect into account, the polarizable continuum model (PCM) method has been used. Accurate geometric structures and their relative stabilities have been investigated. The results show that the intramolecular hydrogen bond plays a very important role in stabilizing the global minimum of the alaninamide. Moreover, the consistent result in relative energy using high-level computations, including the MP2 and MP3 methods with the same basis set [6-311++G(2d,2p)], indicates that the B3LYP/6-311++G(d,p) level may be applied to the analogue system. More importantly, the optical rotation of the optimized conformers (both in the gas phase and in aqueous solution) of alaninamide have been calculated using the density functional theory (DFT) and Hartree,Fock (HF) method at various basis sets (6-31+G*, 6-311++G(d,p), 6-311++G(2d,2p) and aug-cc-pvdz). The results show that the selection of the computation method and the basis set in calculation has great influence on the results of the optical rotations. The reliability of the HF method is less than that of DFT, and selecting the basis set of 6-311++G(2d,2p) and aug-cc-pvDZ produces relative reliable results. Analysis of the computational results of the structure parameters and the optical rotations yields the conclusion that just the helixes in molecules caused the chiral molecules to be optical active. The Boltzmann equilibrium distributions for the six conformers (both in the gas phase and in the aqueous solution) are also carried out. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

Toward accurate relative energy predictions of the bioactive conformation of drugs

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009
Keith T. Butler
Abstract Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol,1 of a local minimum, with penalties above 2.0kcal mol,1 being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source]

Tuning the Magnetic Moment of [Ru2(DPhF)3(O2CMe)L]+ Complexes (DPhF=N,N, -Diphenylformamidinate): A Theoretical Explanation of the Axial Ligand Influence

CHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2010
Carmen Barral Dr.
Abstract The magnetic behaviour of the compounds containing the [Ru2(DPhF)3(O2CMe)]+ ion (DPhF,=N,N, -diphenylformamidinate) shows a strong dependence on the nature of the ligand bonded to the axial position. The new complexes [Ru2(DPhF)3(O2CMe)(OPMe3)][BF4],0.5,CH2Cl2 (1, 0.5,CH2Cl2) and [Ru2(DPhF)3(O2CMe)(4-pic)][BF4] (2) (4-pic=4-methylpyridine) clearly display this influence. Complex 1,0.5,CH2Cl2 shows a magnetic moment corresponding to a S=3/2 system affected by the common zero-field splitting (ZFS) and a weak antiferromagnetic interaction, whereas complex 2 displays an intermediate behaviour between S=3/2 and S=1/2 systems. The experimental data of complex 1 are fitted with a model that considers the ZFS effect using the Hamiltonian ,D=S,D,S. The weak antiferromagnetic coupling is introduced as a perturbation, using the molecular field approximation. DFT calculations demonstrate that, in the [Ru2(O2CMe)(DPhF)3(L)]+ complexes, the energy level of the metal,metal molecular orbitals is strongly dependent on the nature of the axial ligand (L). This study reveals that the increase in the ,-acceptor character of L leads to a greater split between the ,* and ,* HOMO orbitals. The influence of the axial ligand in the relative energy between the doublet and quartet states in this type of complexes was also analysed. This study was performed on the new complexes 1,0.5,CH2Cl2 and 2. The previously isolated [Ru2(DPhF)3(O2CMe)(OH2)][BF4],0.5,CH2Cl2 (3, 0.5,CH2Cl2) and [Ru2(DPhF)3(O2CMe)(CO)][BF4],CH2Cl2 (4,CH2Cl2) complexes were also included in this study as representative examples of spin-admixed and low-spin configurations, respectively. The [Ru2(DPhF)3(O2CMe)]+ (5) unit was used as a reference compound. These theoretical studies are in accordance with the different magnetic behaviour experimentally observed. [source]