A new "spectroscopic" potential energy surface for formaldehyde in its ground electronic state.

We report a new "spectroscopic" potential energy surface (PES) of formaldehyde (H(2)(12)C(16)O) in its ground electronic state, obtained by refining an ab initio PES in a least-squares fitting to the experimental spectroscopic data for formaldehyde currently available in the literature. The ab initio PES was computed using the CCSD(T)/aug-cc-pVQZ method at 30 840 geometries that cover the energy range up to 44 000 cm(-1) above equilibrium. Ro-vibrational energies of formaldehyde were determined variationally for this ab initio PES by means of the program TROVE [Theoretical ROtation-Vibration Energies; S.

QM/MM nonadiabatic decay dynamics of 9H-adenine in aqueous solution.

The photoinduced nonadiabatic decay dynamics of 9H-adenine (hereafter, adenine) in aqueous solution were investigated by surface-hopping simulations within a quantum mechanical/molecular mechanical (QM/MM) framework. The QM subsystem (adenine) was treated at the semiempirical OM2/MRCI level, whereas the MM solvent (water) was described by the TIP3P force field model. Classical molecular dynamics (MD) simulations were used to generate snapshots with different solvent configurations and geometries.

Acetylene⋅⋅⋅furan trimer formation at 0.37 K as a model for ultracold aggregation of non- and weakly polar molecules.

We have studied the aggregation process of (C(2)H(2))⋅⋅⋅furan trimers at ultracold temperatures (0.37 K) in helium nanodroplets. Computational sampling of the potential energy surface using the multiple-minima-hypersurface (MMH) approach yielded seven possible minimum structures, optimized at the MP2 level of theory with the cc-pVTZ and 6-311++G(d,p) basis sets.

Theoretical study on the mechanism of the oxygen activation process in cysteine dioxygenase enzymes.

Cysteine dioxygenase (CDO) is a vital enzyme for human health involved in the biodegradation of toxic cysteine and thereby regulation of the cysteine concentration in the body. The enzyme belongs to the group of nonheme iron dioxygenases and utilizes molecular oxygen to transfer two oxygen atoms to cysteinate to form cysteine sulfinic acid products. The mechanism for this reaction is currently disputed, with crystallographic studies implicating a persulfenate intermediate in the catalytic cycle.

New hexanuclear group 11 pyrazolate complexes: synthesis and photophysical features.

The treatment of 2,2'-di(1,2-pyrazol-3-yl)-1,1'-binaphthyl with two equivalents of appropriate monovalent group 11 precursors in the presence of a base leads to a complete exchange of the pyrazole NH protons with M(+) cations. Structural characterisation of the copper(I) complex revealed a hexanuclear complex with a pelton-wheel-like arrangement of the binaphthyl unit. As indicated by their spectroscopic data, all three complexes are isostructural.

Water as biocatalyst in cytochrome P450.

According to previous quantum mechanics/molecular mechanics (QM/MM) studies, camphor hydroxylation in cytochrome P450 is catalysed by a single water molecule which lowers the computed B3LYP/CHARMM barrier by about 4 kcal mol(-1). Gas-phase B3LYP model studies for a variety of different substrates show the generality of this effect. Its origin is an electrostatic enhancement of hydrogen bonding in the transition state for hydrogen abstraction.

pB(2) intermediate of the photoactive yellow protein: structure and excitation energies.

pB(2) is the last electronically excited intermediate of the photoactive yellow protein (PYP) before it thermally reverts to the dark state. We investigate the structure of pB(2) by quantum refinement and QM/MM methods and compare our results with a previously published crystal structure ( 1TS6 ). We find differences in the chromophore geometries, mostly with regard to torsion angles, that lead to a somewhat higher degree of planarity than in 1TS6 .

Mild transition-metal-free amination of fluoroarenes catalyzed by fluoride ions.

Trimethylsilyl-protected heterocycles undergo N-C bond formation with a variety of electron-deficient fluoroarenes catalyzed by fluoride ions. This reaction avoids stoichiometric amounts of base and thus makes N-arylheterocycles accessible in a very mild and transition-metal-free way.

Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential.

Long-range electrostatic interactions are important in simulations of enzymatic reactions. They can be divided into the effects due to bulk solvent and those due to the electrostatic potential of the outer macromolecule. We study and quantify the importance of these two effects for two test systems by application of the solvated macromolecule boundary potential (SMBP) [J.

Benchmarks of electronically excited states: basis set effects on CASPT2 results.

Vertical excitation energies and one-electron properties are computed for the valence excited states of 28 medium-sized organic benchmark molecules using multistate multiconfigurational second-order perturbation theory (MS-CASPT2) and the augmented correlation-consistent aug-cc-pVTZ basis set. They are compared with previously reported MS-CASPT2 results obtained with the smaller TZVP basis. The basis set extension from TZVP to aug-cc-pVTZ causes rather minor and systematic shifts in the vertical excitation energies that are normally slightly reduced (on average by 0.

Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1.

Quantum refinement is an improvement upon the molecular mechanics (MM)-based crystallographic refinement. In the latter, X-ray data are supplemented with additional chemical information through MM force fields, whereas quantum refinement describes crucial regions of interest in the macromolecule by quantum mechanics (QM) instead of MM. In this paper, we report the implementation of quantum refinement in the ChemShell QM/MM framework and its application in an investigation of the chromophore structure of the red fluorescent protein DsRed.

A Local Pair Natural Orbital Coupled Cluster Study of Rh Catalyzed Asymmetric Olefin Hydrogenation.

The recently developed local pair natural orbital coupled cluster theory with single and double excitations (LPNO-CCSD) was used to study the rhodium-catalyzed asymmetric hydrogenation of two prochiral enamides. The method was carefully calibrated with respect to its accuracy. According to calculations on a truncated model system, the effects of perturbative triples (T) on the reaction energetics are very limited, the LPNO approximation is accurate, and complete basis set extrapolation (CBS) causes only minor changes in the relative energies computed with a standard basis set (def2-TZVP).

Probing the influence of anomeric effects on the lithium ion affinity in 1,3-diaza systems: a computational study.

Lithium ion affinities of methanediamine (MDA), N,N,N',N'-tetramethylmethanediamine (TMMDA), 1,3-diazacyclohexane (DAC), trans-3,5-diazabicyclo[4.4.0]decane (trans-3,5-DBD), trans-1,3-diazabicyclo[4.

Redox active mesoporous hybrid materials by in situ syntheses with urea-linked triethoxysilylated phenothiazines.

Triethoxysilyl functionalized phenothiazinyl ureas were synthesized and immobilized by in situ synthesis into mesoporous hybrid materials. The designed precursor molecules influence the structure of the final materials and the intermolecular distance of the phenothiazines. XRD and N(2) adsorption measurements indicate the presence of highly ordered two-dimensional hexagonally structured functional materials, while the incorporation of the organic compounds in the solid materials was proved by means of (13)C and (29)Si solid state NMR spectroscopy as well as by FT-IR spectroscopy.

Theoretical rotation-torsion spectra of HSOH.

Rotation-torsion spectra of HSOH, involving the vibrational ground state and the fundamental torsional state, have been simulated at T = 300 K. The simulations are carried out with the variational computer program TROVE in conjunction with recently reported ab initio potential energy and electric dipole moment surfaces. HSOH is a near-prolate-symmetric top at equilibrium and the simulated spectra are of perpendicular-band-type with strong R-branch and Q-branch transitions.

Sources of cumulative continuity in personality: a longitudinal multiple-rater twin study.

This study analyzed the etiology of rank-order stability and change in personality over a time period of 13 years in order to explain cumulative continuity with age. NEO five-factor inventory self- and peer report data from 696 monozygotic and 387 dizygotic twin pairs reared together were analyzed using a combination of multiple-rater twin, latent state-trait, and autoregressive simplex models. Correcting for measurement error, this model disentangled genetic and environmental effects on long- and short-term convergent valid stability, on occasional influences, and on self- and peer report-specific stability.

Benchmark of Electronically Excited States for Semiempirical Methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2.

Semiempirical configuration interaction (CI) calculations with eight different Hamiltonians are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies and one-electron properties are computed using the same geometries as in our previous ab initio benchmark study on electronically excited states. The CI calculations for the standard methods (MNDO, AM1, PM3) and for the orthogonalization-corrected methods (OM1, OM2, OM3) include single, double, triple, and quadruple excitations (CISDTQ) using the graphical unitary group approach (GUGA) as implemented in the MNDO code.

QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed.

The far-red fluorescent protein HcRed was investigated using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three models of HcRed (anionic chromophore) were considered, differing in the protonation states of nearby Glu residues (A: Glu214 and Glu146 both protonated; B: Glu214 protonated and Glu146 deprotonated; C: Glu214 and Glu146 both deprotonated). SCC-DFTB/MM MD simulations of model B yield good agreement with the available crystallographic data at ambient pH.

Magnetically separable nanocatalysts: bridges between homogeneous and heterogeneous catalysis.

Recovery and reuse of expensive catalysts after catalytic reactions are important factors for sustainable process management. The aim of this Review is to highlight the progress in the formation and catalytic applications of magnetic nanoparticles and magnetic nanocomposites. Directed functionalization of the surfaces of nanosized magnetic materials is an elegant way to bridge the gap between heterogeneous and homogeneous catalysis.

Thermal averaging of the indirect nuclear spin-spin coupling constants of ammonia: the importance of the large amplitude inversion mode.

Analytic internal-coordinate representations are reported for two accurate ab initio spin-spin coupling surfaces of the ammonia molecule, (1)J ((15)N,H) and (2)J(H,H). Calculations were carried out at the level of the second-order polarization propagator approximation involving coupled-cluster singles and doubles amplitudes (CCSD) and using a large specialized basis set, for a total of 841 different geometries corresponding to 2523 distinct points on the (1)J ((15)N,H) and (2)J(H,H) surfaces. The results were fitted to power series expansions truncated after the fourth-order terms.

Coupling and uncoupling mechanisms in the methoxythreonine mutant of cytochrome P450cam: a quantum mechanical/molecular mechanical study.

The Thr252 residue plays a vital role in the catalytic cycle of cytochrome P450cam during the formation of the active species (Compound I) from its precursor (Compound 0). We investigate the effect of replacing Thr252 by methoxythreonine (MeO-Thr) on this protonation reaction (coupling) and on the competing formation of the ferric resting state and H2O2 (uncoupling) by combined quantum mechanical/molecular mechanical (QM/MM) methods. For each reaction, two possible mechanisms are studied, and for each of these the residues Asp251 and Glu366 are considered as proton sources.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation.