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H Bernhard Schlegel

Publications and source records attributed to H Bernhard Schlegel.

At least 19 recordsLinked to original sources
PubMed2006

Experimental and theoretical study of the coordination of 1,2,4-triazolato, tetrazolato, and pentazolato ligands to the [K(18-crown-6)]+ fragment.

Treatment of 3,5-diisopropyltriazole, 3,5-diphenyltriazole, 3,5-di-3-pyridyltriazole, phenyltetrazole, pyrrolidinyltetrazole, or tert-butyltetrazole with equimolar quantities of potassium hydride and 18-crown-6 in tetrahydrofuran at ambient temperature led to slow hydrogen evolution and formation of (3,5-diisopropyl-1,2,4-triazolato)(18-crown-6)potassium (88%), (3,5-diphenyl-1,2,4-triazolato)(tetrahydrofuran)(18-crown-6)potassium (87%), (3,5-di-3-pyridyl-1,2,4-triazolato)(18-crown-6)potassium (81%), (phenyltetrazolato)(18-crown-6)potassium (94%), (pyrrolidinyltetrazolato)(18-crown-6)potassium (90%), and (tert-butyltetrazolato)(18-crown-6)potassium (94%) as colorless crystalline solids. (1,2,4-Triazolato)(18-crown-6)potassium was isolated as a hemi-hydrate in 81% yield upon treatment of 1,2,4-triazole with potassium metal in tetrahydrofuran. The X-ray crystal structures of these new complexes were determined, and the solid-state structures consist of the nitrogen heterocycles bonded to the (18-crown-6)potassium cationic fragments with eta2-bonding interactions. In addition, (3,5-diphenyl-1,2,4-triazolato)(tetrahydrofuran)(18-crown-6)potassium has one coordinated tetrahydrofuran ligand on the same face as the 3,5-diphenyl-1,2,4-triazolato ligand, while (3,5-di-3-pyridyl-1,2,4-triazolato)(18-crown-6)potassium forms a polymeric solid through coordination of the distal 3-pyridyl nitrogen atoms to the potassium ion on the face opposite the 1,2,4-triazolato ligand. The solid-state structures of the new complexes show variable asymmetry in the potassium-nitrogen distances within the eta2-interactions and also show variable bending of the heterocyclic C2N3 and CN4 cores toward the best plane of the 18-crown-6 ligand oxygen atoms. Molecular orbital and natural bond order calculations were carried out at the B3LYP/6-311G(d,p) level of theory on the model complex, (phenyltetrazolato)(18-crown-6)potassium, and demonstrate that the asymmetric potassium-nitrogen distances and bending of the CN4 core toward the 18-crown-6 ligand are due to hydrogen bond-like interactions between filled nitrogen-based orbitals and carbon-hydrogen sigma orbitals on the 18-crown-6 ligands. Calculations carried out on the model pentazolato complex (pentazolato)(18-crown-6)potassium predict a structure in which the pentazolato ligand N5 core is bent by 45 degrees toward the best plane of the 18-crown-6 oxygen atoms. Such bending is induced by the formation of intramolecular nitrogen-hydrogen-carbon hydrogen bonds. Examination of the solid-state structures of the new complexes reveals many intramolecular and intermolecular nitrogen-hydrogen distances of < or =3.0 A which support the presence of nitrogen-hydrogen-carbon hydrogen bonds.

Journal Article↗
PubMed2006

Structural, spectroscopic, and electrochemical behavior of trans-phenolato cobalt(III) complexes of asymmetric NN'O ligands as archetypes for metallomesogens.

In order to understand and predict structural, redox, magnetic, and optical properties of more complex and potentially mesogenic electroactive compounds such as [Co(III)(L(t-BuLC))2]ClO4 (1), five archetypical complexes of general formula [Co(III)(L(RA))2]ClO4, where R = H (2), tert-butyl (3), methoxy (4), nitro (5), and chloro (6), were obtained and studied by means of several spectrometric, spectroscopic, and electrochemical methods. The complexes 2, 4, and 6 were characterized by single-crystal X-ray diffraction, and show the metal center in an approximate D2h symmetry. Experimental results support the fact that the electron donating or withdrawing nature of the phenolate-appended substituents changes dramatically the redox and spectroscopic properties of these compounds. The 3d6 electronic configuration of the metal ion dominates the overall geometry adopted by these compounds with the phenolate rings occupying trans positions to one another. Formation of phenoxyl radicals has been observed for 1, 3, and 6, but irreversible ligand oxidation takes place upon bulk electrolysis. These data were compared to detailed B3LYP/6-31G (d)-level computational calculations and have been used to account for the results observed. A comparison between compound 1 and archetype 3, validates the approach of using archetypical models to study metal-containing soft materials.

Journal Article↗
PubMed2006

A single transition state serves two mechanisms. The branching ratio for CH2O*- + CH3Cl on improved potential energy surfaces.

The reaction of formaldehyde radical anion with methyl chloride, CH2O*- + CH3Cl, is an example in which a single transition state leads to two products: substitution at carbon (Sub(C), CH3CH2O* + Cl-) and electron transfer (ET, CH2O + CH3* + Cl-). The branching ratio for this reaction has been studied by ab initio molecular dynamics (AIMD). The energies of transition states and intermediates were computed at a variety of levels of theory and compared to accurate energetics calculated by the G3 and CBS-QB3 methods. A bond additivity correction has been constructed to improve the Hartree-Fock potential energy surface (BAC-UHF). A satisfactory balance between good energetics and affordable AIMD calculations can be achieved with BH&HLYP/6-31G(d) and BAC-UHF/6-31G(d) calculations. Approximately 200 ab initio classical trajectories were calculated for each level of theory with initial conditions sampled from a thermal distribution at 298 K at the transition state. Three types of trajectories were distinguished: trajectories that go directly to ET product, trajectories that go to Sub(C) product, and trajectories that initially go into the Sub(C) valley and then dissociate to ET products. The BH&HLYP/6-31G(d) calculations overestimate the number of nonreactive and direct ET trajectories because the transition state is too early. For the BH&HLYP and BAC-UHF methods, about one-third of the trajectories that initially go into the Sub(C) valley dissociate to ET products, compared to just over half with UHF/6-31G(d) in the earlier study. This difference can be attributed to a better value for the calculated energy release from the initial transition state and to an improved Sub(C) --> ET barrier height with the BH&HLYP and BAC-UHF methods.

Journal Article↗
PubMed2006

A computational exploration of some transnitrosation and thiolation reactions involving CH3SNO, CH3ONO and CH3NHNO.

Nitric oxide (NO) is a biologically active species and its carrier molecules RXNO (X = S, O, NH) have drawn significant attention recently. In the present work, the CBS-QB3 level of theory was used to study the transnitrosation and thiolation reaction between MeXNO (X = S, O, and NH) molecules and three reactive forms of the methanethiol: the neutral molecule, MeSH, the anion, MeS-, and the radical, MeS . The transnitrosation and thiolation reactions between MeXNO and MeSH have the highest barriers, both with and without a molecule of water assisting. Reactions with MeS- proceed with much lower barriers, while reactions with radical MeS have the lowest barriers. Comparing the reactions of MeXNO (X = S, O, NH), both transnitrosation and thiolation are more favorable for X = S than X = O or NH.

Hydrogen Bonding↗
PubMed2006

Chemical failure modes of AlQ3-based OLEDs: AlQ3 hydrolysis.

Tris(8-hydroxyquinoline)aluminum(III), AlQ3, is used in organic light-emitting diodes (OLEDs) as an electron-transport material and emitting layer. The reaction of AlQ3 with trace H2O has been implicated as a major failure pathway for AlQ3-based OLEDs. Hybrid density functional calculations have been carried out to characterize the hydrolysis of AlQ3. The thermochemical and atomistic details for this important reaction are reported for both the neutral and oxidized AlQ3/AlQ3+ systems. In support of experimental conclusions, the neutral hydrolysis reaction pathway is found to be a thermally activated process, having a classical barrier height of 24.2 kcal mol(-1). First-principles infrared and electronic absorption spectra are compared to further characterize AlQ3 and the hydrolysis pathway product, AlQ2OH. The activation energy for the cationic AlQ3 hydrolysis pathway is found to be 8.5 kcal mol(-1) lower than for the neutral reaction, which is significant since it suggests a role for charge imbalance in promoting chemical failure modes in OLED devices.

Aluminum↗
PubMed2006

Structural and electronic behavior of unprecedented five-coordinate iron(III) and gallium(III) complexes with a new phenol-rich electroactive ligand.

A new asymmetric pentadentate ligand was designed to impose low symmetry to trivalent ions. Five-coordinate Fe3+ and Ga3+ complexes were investigated by crystallographic, electrochemical, and electron paramagnetic resonance methods showing enhanced redox reversibility. Calculations were performed to account for the observed trends.

Crystallography, X-Ray↗
PubMed2006

Optical excitations in carbon architectures based on dodecadehydrotribenzo[18]annulene.

The origin of excitations in multi-chromophore carbon network substructures based on dodecadehydrotribenzo[18]annulene has been investigated by steady-state and photon echo spectroscopy, configuration interaction (CIS and CIS(D)), and time-dependent density functional theory (TD-DFT). 1,4-diphenylbutadiyne, the simplest structural subunit within the annulene, was used in modeling the spectroscopic studies to explain the origin of excitations in the macrocycles. The optical excitations in longer linear systems were found to be similar to its diphenylacetylene analogue. However, the results from dodecadehydrotribenzo[18]annulene and other multichromophore networks systems illustrate the possibility of strong intramolecular interactions and the formation of delocalized excited states. Calculations were carried out to explain the basic similarities and differences in excitations of the model compounds such as diphenylbutadiyne and the macrocycles. The fundamental excitation in these systems can be primarily described as a pi --> pi* transition. Two low-energy resonances were observed from experiment for the annulene systems, and possible explanations for these low-energy resonances in the macrocycles are explored. The significant difference found in the calculated oscillator strength of the two low-energy bands for the macrocycles as well as the dynamics of solvent interactions was further investigated by three-pulse photon echo measurements. A simple exciton model was developed to discuss the excitations in the larger macrocycles. The results from this model were found to be in good agreement with the TD-DFT calculations.

Journal Article↗
PubMed2005

Dissociation of benzene dication [C6H6]2+: exploring the potential energy surface.

The singlet potential energy surface for the dissociation of benzene dication has been explored, and its three major dissociation channels have been studied: C6H6(2+) --> C3H3(+) + C3H3(+), C4H3(+) + C2H3(+), and C5H3(+) + CH3(+). The calculated energetics suggest that the products will be formed with considerable translational energy because of the Coulomb repulsion between the charged fragments. The calculated energy release in the three channels shows a qualitative agreement with the experimentally observed kinetic energy release. The formation of certain intermediates is found to be common to the three dissociation channels.

Journal Article↗
PubMed2005

Numerical simulation of nonadiabatic electron excitation in the strong field regime. 2. Linear polyene cations.

Time-dependent Hartree-Fock theory has been used to study the electronic optical response of a series of linear polyene cations (+1 and +2) in strong laser fields. The interaction of ethylene, butadiene, and hexatriene, with pulsed and CW fields corresponding to 8.75 x 10(13) W/cm(2) and 760 nm, have been calculated using the 6-31G(d,p) basis set. Nonadiabatic processes including nonlinear response of the dipole moment to the field and non-resonant energy deposition into excited states were more pronounced for the monocations in comparison with dications. For a given charge state and geometry, the nonadiabatic effects in the charge distribution and instantaneous dipole increased with the length of the polyene. For pulsed fields, the instantaneous dipole continued to oscillate after the field returned to zero and corresponded to a non-resonant electronic excitation involving primarily the lowest electronic transition. For a given molecule and fixed charge state, the degree of nonadiabatic coupling and excitation was greater for geometries with lower excitation energies.

Journal Article↗
PubMed2005

Ab initio QM/MM study of class A beta-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70.

Beta-lactamase acquisition is the most prevalent basis for Gram-negative bacteria resistance to the beta-lactam antibiotics. The mechanism used by the most common class A Gram-negative beta-lactamases is serine acylation followed by hydrolytic deacylation, destroying the beta-lactam. The ab initio quantum mechanical/molecular mechanical (QM/MM) calculations, augmented by extensive molecular dynamics simulations reported herein, describe the serine acylation mechanism for the class A TEM-1 beta-lactamase with penicillanic acid as substrate. Potential energy surfaces (based on approximately 350 MP2/6-31+G calculations) reveal the proton movements that govern Ser70 tetrahedral formation and then collapse to the acyl-enzyme. A remarkable duality of mechanism for tetrahedral formation is implicated. Following substrate binding, the pathway initiates by a low energy barrier (5 kcal mol(-1)) and an energetically favorable transfer of a proton from Lys73 to Glu166, through the catalytic water molecule and Ser70. This gives unprotonated Lys73 and protonated Glu166. Tetrahedral formation ensues in a concerted general base process, with Lys73 promoting Ser70 addition to the beta-lactam carbonyl. Moreover, the three-dimensional potential energy surface also shows that the previously proposed pathway, involving Glu166 as the general base promoting Ser70 through a conserved water molecule, exists in competition with the Lys73 process. The existence of two routes to the tetrahedral species is fully consistent with experimental data for mutant variants of the TEM beta-lactamase.

Acylation↗
PubMed2005

Lysine carboxylation in proteins: OXA-10 beta-lactamase.

An increasing number of proteins are being shown to have an N(zeta)-carboxylated lysine in their structures, a posttranslational modification of proteins that proceeds without the intervention of a specific enzyme. The role of the carboxylated lysine in these proteins is typically structural (hydrogen bonding or metal coordination). However, carboxylated lysines in the active sites of OXA-10 and OXA-1 beta-lactamases and the sensor domain of BlaR signal-transducer protein serve in proton transfer events required for the functions of these proteins. These examples demonstrate the utility of this unusual amino acid in acid-base chemistry, in expansion of function beyond those of the 20 standard amino acids. In this study, the ONIOM quantum-mechanical/molecular-mechanical (QM/MM) method is used to study the carboxylation of lysine in the OXA-10 beta-lactamase. Lys-70 and the active site of the OXA-10 beta-lactamase were treated with B3LYP/6-31G(d,p) density functional calculations and the remainder of the enzyme with the AMBER molecular mechanics force field. The barriers for unassisted carboxylation of neutral lysine by carbon dioxide or bicarbonate are high. However, when the reaction with CO2 is catalyzed by a molecule of water in the active site, it is exothermic by about 13 kcal/mol, with a barrier of approximately 14 kcal/mol. The calculations show that the carboxylation and decarboxylation of Lys-70 are likely to be accompanied by deprotonation and protonation of the carbamate, respectively. The analysis may also be relevant for other proteins with carboxylated lysines, a feature that may be more common in nature than previously appreciated.

Computational Biology↗
PubMed2005

Influence of ligand rigidity and ring substitution on the structural and electronic behavior of trivalent iron and gallium complexes with asymmetric tridentate ligands.

Species 1-6 are [M(III)(L)2]ClO4 complexes formed with the PhO--CH=N-CH2-Py imines, (L(I))- and (L(tBuI))-, and PhO--CH2-NH-CH2-Py amines, (L(A))- and (L(tBuA))-, in which PhO- is a phenolate ring and Py is a pyridine ring and the prefix tBu indicates the presence of tertiary butyl groups occupying the positions 4 and 6 of the phenol ring. Monometallic species with d5 high-spin iron (1, 2, 3, 4) and d10 gallium (5, 6) were synthesized and characterized to assess the influence of the ligand rigidity and the presence of tertiary butyl-substituted phenol rings on their steric, electronic, and redox behavior. Characterization by elemental analysis, mass spectrometry, IR, UV-visible, and EPR spectroscopies, and electrochemistry has been performed, and complexes [FeIII(L(tBuI))2]ClO4 (2), [FeIII(L(tBuA))2]ClO4 (4), and [Ga(III)(L(tBuI))2]ClO4 (5) have been characterized by X-ray crystallography. The crystal structures show the imine ligands meridionally coordinated to the metal centers, whereas the amine ligands are coordinate in a facial mode. Cyclic voltammetry shows that the complexes with the ligands (L(tBuI))- and (L(tBuA))- were able to generate ligand-based phenoxyl radicals, whereas unsubstituted ligands displayed ill-defined redox processes. EPR spectroscopy supports high-spin configurations for the iron complexes. UV-visible spectra are dominated by charge-transfer phenomena, and imine compounds exhibit dramatic hyperchromism when compared to equivalent amines. The tertiary butyl groups on the phenolate ring enhance this trend. Detailed B3LYP/6-31G(d)-level calculations have been used to account for the results observed.

Journal Article↗
PubMed2005

Theoretical investigation of uranyl dihydroxide: oxo ligand exchange, water catalysis, and vibrational spectra.

Density functional theory is employed to investigate uranyl dihydroxide, UO2(OH)2, isomerization reaction energy barriers, including those occurring via proton shuttles. The ground-state structure of a uranyl dihydroxide complex containing a uranyl moiety with a near 90 degrees O=U=O bond angle is reported for the first time. Furthermore, we predict the vibrational spectra of these compounds. Scalar-relativistic effects for uranium are treated by employing a relativistic effective core potential.

Journal Article↗
PubMed2005

Ab initio Ehrenfest dynamics.

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation.

Journal Article↗
PubMed2005

Weak carbon-hydrogen-nitrogen interactions affect the heterocyclic ligand bonding modes in barium complexes containing eta2-tetrazolato and eta2-pentazolato ligands.

Treatment of Ba[N(SiMe3)2]2(THF)2 with 2 equiv of dimethylaminotetrazole or diisopropylaminotetrazole and 1 equiv of 18-crown-6 afforded Ba[CN4(NMe2)]2(18-crown-6) (87%) and Ba[CN4(NiPr2)]2(18-crown-6) (79%) as colorless crystalline solids. Ba[CN4(NMe2)]2(18-crown-6) contains two 1,2-eta2-tetrazolato ligands and one eta6-18-crown-6 ligand. The molecular structure of Ba[CN4(NiPr2)]2(18-crown-6) is similar to that of Ba[CN4(NMe2)]2(18-crown-6), except that the tetrazolato ligands exhibit the isomeric 2,3-eta2-coordination mode and the tetrazolato ligand CN4 cores are bent significantly toward the 18-crown-6 ligands. Molecular orbital calculations were carried out on the model complexes Ba(azolate)2(18-crown-6) (azolate = 1,2-eta2-CHN4, 2,3-eta2-CHN4, and eta2-N5) and demonstrate that the ligand coordination modes are influenced by intramolecular interactions between filled nitrogen orbitals on the azolato ligands and empty C-H sigma* orbitals on the 18-crown-6 ligands.

Journal Article↗
PubMed2005

A numerical simulation of nonadiabatic electron excitation in the strong field regime: Linear polyenes.

Time-dependent Hartree-Fock theory has been used to study of the electronic optical response of a series of linear polyenes in strong laser fields. Ethylene, butadiene, and hexatriene have been calculated with 6-31G(d,p) in the presence of a field corresponding to 8.75 x 10(13) W/cm2 and 760 nm. Time evolution of the electron population indicates not only the pi electrons, but also lower lying valence electrons are involved in electronic response. When the field is aligned with the long axis of the molecule, Löwdin population analysis shows large charges at each end of the molecule. For ethylene, the instantaneous dipole moment followed the field adiabatically, but for hexatriene, nonadiabatic effects were very pronounced. For constant intensity, the nonadiabatic effects in the charge distribution, instantaneous dipole, and orbital populations increased nonlinearly with the length of the polyene. These calculations elucidate the mechanism of the strong field nonadiabatic electron excitation of polyatomic molecules leading to their eventual ionization and fragmentation. The described computational methods are a viable tool for studying the complex processes in multielectron atomic and molecular systems in strong laser fields.

Journal Article↗
PubMed2005

Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A.

Zinc proteases are ubiquitous and the zinc ion plays a central function in the catalytic mechanism of these enzymes. A novel class of mechanism-based inhibitors takes advantage of the zinc ion chemistry in carboxypeptidase A (CPA) to promote covalent attachment of an inhibitor to the carboxylate of Glu-270, resulting in irreversible inhibition of the enzyme. The effect of the active site zinc ion on irreversible inactivation of CPA was probed by molecular orbital (MO) calculations on a series of active site models and the Cl(-) + CH(3)Cl S(N)2 reaction fragment. Point charge models representing the active site reproduced energetics from full MO calculations at 12.0 A separation between the zinc and the central carbon of the S(N)2 reaction, but at 5.0 A polarization played an important role in moderating barrier suppression. ONIOM MO/MO calculations that included the residues within 10 A of the active site zinc suggest that about 75% of the barrier suppression arises from the zinc ion and its ligands. A model of the pre-reactive complex of the 2-benzyl-3-iodopropanoate inactivator with CPA was constructed from the X-ray structure of l-phenyl lactate bound in the active site of the enzyme. The model was fully solvated and minimized by using the AMBER force field to generate the starting structure for the ONIOM QM/MM calculations. Optimization of this structure led to the barrierless S(N)2 displacement of the iodide of the inhibitor by Glu-270, assisted by interaction of the zinc ion with the leaving group. The resulting product is in good agreement with the X-ray structure of the covalently modified enzyme obtained by irreversible inhibition of CPA by 2-benzyl-3-iodopropanoate.

Carboxypeptidases A↗