Tests of MULTIMODE calculations of rovibrational energies of CH4

We report variational calculations of rovibrational energies of CH4 using the code MULTIMODE and an ab initio force field of Schwenke and Partridge. The systematic convergence of the energies with respect to the level of mode coupling is presented. Converged vibrational energies calculated using the five-mode representation of the potential for zero total angular momentum are compared with previous, benchmark calculations based on Radau coordinates using this force field for zero total angular momentum and for J = 1. Very good agreement with the previous benchmark calculations is found. (c) 2006 Elsevier B.V. All rights reserved.

Experimental evidence for a partially dissociated water bilayer on Ru{0001}

Core-level photoelectron spectra, in excellent agreement with ab initio calculations, confirm that the stable wetting layer of water on Ru{0001} contains O-H and H2O in roughly 3:5 proportion, for OHx coverages between 0.25 and 0.7 ML, and T<170 K. Proton disorder explains why the wetting structure looks to low energy electron diffraction (LEED) to be an ordered p(root3xroot3)R30degrees adlayer, even though approximate to3/8 of its molecules are dissociated. Complete dissociation to atomic oxygen starts near 190 K. Low photon flux in the synchrotron experiments ensured that the diagnosis of the nature of the wetting structure quantified by LEED is free of beam-induced damage.

Studying reactive processes with classical dynamics: rebinding dynamics in MbNO

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mu s of total simulation time) for the rebinding of NO to myoglobin. The unbound surface ((FeNO)-N-...) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Potential energy surface and moleculardynamics of MbNO: existence of an unsuspected FeON minimum

Ligands such as CO, O2, or NO are involved in the biological function of myoglobin. Here we investigate the energetics and dynamics of NO interacting with the Fe(II) heme group in native myoglobin using ab initio and molecular dynamics simulations. At the global minimum of the ab initio potential energy surface (PES), the binding energy of 23.4 kcal/mol and the Fe-NO structure compare well with the experimental results. Interestingly, the PES is found to exhibit two minima: There exists a metastable, linear Fe-O-N minimum in addition to the known, bent Fe-N-O global minimum conformation. Moreover, the T-shaped configuration is found to be a saddle point, in contrast to the corresponding minimum for NO interacting with Fe(III). To use the ab initio results for finite temperature molecular dynamics simulations, an analytical function was fitted to represent the Fe-NO interaction. The simulations show that the secondary minimum is dynamically stable up to 250 K and has a lifetime of several hundred picoseconds at 300 K. The difference in the topology of the heme-NO PES from that assumed previously (one deep, single Fe-NO minimum) suggests that it is important to use the full PES for a quantitative understanding of this system. Why the metastable state has not been observed in the many spectroscopic studies of myoglobin interacting with NO is discussed, and possible approaches to finding it are outlined.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Time-resolved gas-phase kinetic, quantum chemical and RRKM studies of reactions of silylene with cyclic ethers

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with oxirane, oxetane, and tetrahydrofuran (THF). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at four or five temperatures in the range 294-605 K. All three reactions showed pressure dependences characteristic of third-body-assisted association reactions with, surprisingly, SiH2 + oxirane showing the least and SiH2 + THF showing the most pressure dependence. The second-order rate constants obtained by extrapolation to the high-pressure limits at each temperature fitted the Arrhenius equations where the error limits are single standard deviations: log(k(oxirane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.03 +/- 0.07) + (5.70 +/- 0.51) kJ mol(-1)/RT In 10 log(k(oxetane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.17 +/- 0.11) + (9.04 +/- 0.78) kJ mol(-1)/RT In 10 log(k(THF)(infinity)/cm(3) molecule(-1) s(-1)) = (-10.59 +/- 0.10) + (5.76 +/- 0.65) kJ mol(-1)/RT In 10 Binding-energy values of 77, 97, and 92 kJ mol(-1) have been obtained for the donor-acceptor complexes of SiH2 with oxirane, oxetane, and THF, respectively, by means of quantum chemical (ab initio) calculations carried Out at the G3 level. The use of these values to model the pressure dependences of these reactions, via RRKM theory, provided a good fit only in the case of SiH2 + THF. The lack of fit in the other two cases is attributed to further reaction pathways for the association complexes of SiH2 with oxirane and oxetane. The finding of ethene as a product of the SiH2 + oxirane reaction supports a pathway leading to H2Si=O + C2H4 predicted by the theoretical calculations of Apeloig and Sklenak.

Infrared absorption spectra, radiative efficiencies, and global warming potentials of perfluorocarbons: Comparison between experiment and theory

Experimentally and theoretically determined infrared spectra are reported for a series of straight-chain perfluorocarbons: C2F6, C3F8, C4F10, C5F12, C6F14, and C8F18. Theoretical spectra were determined using both density functional (DFT) and ab initio methods. Radiative efficiencies (REs) were determined using the method of Pinnock et al. (1995) and combined with atmospheric lifetimes from the literature to determine global warming potentials (GWPs). Theoretically determined absorption cross sections were within 10% of experimentally determined values. Despite being much less computationally expensive, DFT calculations were generally found to perform better than ab initio methods. There is a strong wavenumber dependence of radiative forcing in the region of the fundamental C-F vibration, and small differences in wavelength between band positions determined by theory and experiment have a significant impact on the REs. We apply an empirical correction to the theoretical spectra and then test this correction on a number of branched chain and cyclic perfluoroalkanes. We then compute absorption cross sections, REs, and GWPs for an additional set of perfluoroalkenes.

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations

Time-resolved kinetic studies of the reactions of silylene, SiH2, and dideutero-silylene, SiD2, generated by laser. ash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH3C CCH3. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(-1)/RTln10 log(k(D)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTln10 Additionally, pressure-dependent rate coefficients for the reaction of SiH2 with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC4H8 reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH2C(CH3)=C(CH3)-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH3CH=C(CH3)SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H - D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

Self-assembled molecular complexes and coordination polymers of CdII, hexamine, and monocarboxylates: structural analysis and theoretical studies of supramolecular interactions

Four new cadmium(II) complexes [Cd-2(bz)(4)(H2O)(4)(mu 2-hmt)]center dot Hbz center dot H2O (1), [Cd-3(bz)(6)(H2O)(6)(mu 2-hmt)(2)]center dot 6H(2)O (2), [Cd(pa)(2)(H2O)(mu(2)-hmt)](n) (3), and {[Cd-3(ac)(6)(H2O)(3)(mu(3)-hmt)(2)]center dot 6H(2)O}(n) (4) with hexamine (hmt) and monocarboxylate ions, benzoate (bz), phenylacetate (pa), or acetate (ac) have been synthesized and characterized structurally. Structure determinations reveal that 1 is dinuclear, 2 is trinuclear, 3 is a one-dimensional (1D) infinite chain, and 4 is a two-dimensional (2D) polymer with fused hexagonal rings consisting of Cd-II and hmt. All the Cd-II atoms in the four complexes (except one CdII in 2) possess seven-coordinate pentagonal bipyramidal geometry with the various chelating bidentate carboxylate groups in equatorial sites. One of the CdII ions in 2, a complex that contains two monodentate carboxylates is in a distorted octahedral environment. The bridging mode of hmt is mu 2- in complexes 1-3 but is mu 3- in complex 4. In all complexes, there are significant numbers of H-bonds, C-H/pi, and pi-pi interactions which play crucial roles in forming the supramolecular networks. The importance of the noncovalent interactions in terms of energies and geometries has been analyzed using high level ab initio calculations. The effect of the cadmium coordinated to hmt on the energetic features of the C-H/pi interaction is analyzed. Finally, the interplay between C-H/pi and pi-pi interactions observed in the crystal structure of 3 is also studied.

Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei

Blumeria graminis is an economically important obligate plant-pathogenic fungus, whose entire genome was recently sequenced and manually annotated using ab initio in silico predictions [7]. Employing large scale proteogenomic analysis we are now able to verify independently the existence of proteins predicted by 24% of open reading frame models. We compared the haustoria and sporulating hyphae proteomes and identified 71 proteins exclusively in haustoria, the feeding and effector-delivery organs of the pathogen. These proteins are ‘significantly smaller than the rest of the protein pool and predicted to be secreted. Most do not share any similarities with Swiss–Prot or Trembl entries nor possess any identifiable Pfam domains. We used a novel automated prediction pipeline to model the 3D structures of the proteins, identify putative ligand binding sites and predict regions of intrinsic disorder. This revealed that the protein set found exclusively in haustoria is significantly less disordered than the rest of the identified Blumeria proteins or random (and representative) protein sets generated from the yeast proteome. For most of the haustorial proteins with unknown functions no good templates could be found, from which to generate high quality models. Thus, these unknown proteins present potentially new protein folds that can be specific to the interaction of the pathogen with its host.

Assessment of the consistency of H2O line intensities over the near-infrared using sun-pointing ground-based Fourier transform spectroscopy

We report on the consistency of water vapour line intensities in selected spectral regions between 800–12,000 cm−1 under atmospheric conditions using sun-pointing Fourier transform infrared spectroscopy. Measurements were made across a number of days at both a low and high altitude field site, sampling a relatively moist and relatively dry atmosphere. Our data suggests that across most of the 800–12,000 cm−1 spectral region water vapour line intensities in recent spectral line databases are generally consistent with what was observed. However, we find that HITRAN-2008 water vapour line intensities are systematically lower by up to 20% in the 8000–9200 cm−1 spectral interval relative to other spectral regions. This discrepancy is essentially removed when two new linelists (UCL08, a compilation of linelists and ab-initio calculations, and one based on recent laboratory measurements by Oudot et al. (2010) [10] in the 8000–9200 cm−1 spectral region) are used. This strongly suggests that the H2O line strengths in the HITRAN-2008 database are indeed underestimated in this spectral region and in need of revision. The calculated global-mean clear-sky absorption of solar radiation is increased by about 0.3 W m−2 when using either the UCL08 or Oudot line parameters in the 8000–9200 cm−1 region, instead of HITRAN-2008. We also found that the effect of isotopic fractionation of HDO is evident in the 2500–2900 cm−1 region in the observations.

The molecular structure of propylene sulphide (methylthiirane) by gas-phase electron diffraction and theoretical calculations: a molecule used in MOCVD

Gas-phase electron-diffraction (GED) data together with results from ab initio molecular orbital calculations have been used to determine the structure of propylene sulphide. Values found for the main structural parameters for the molecule are consistent with those obtained from microwave studies and are compared here with those found for similar sulphur containing rings of general formula S(CH2)n (n = 2–5). A high ring strain enthalpy was calculated for propylene sulphide which is consistent with the small C–S–C angle (48.2(6)degrees) and the relatively long C–S bond lengths (ra = 1.831(2) Å). This is thought to account for the ease of ring opening in propylene sulphide observed in MOCVD reactions and the ready polymerisation of the molecule.

π-dimerization of pleiadiene radical cations at low temperatures revealed by UV–vis spectroelectrochemistry and quantum theory

One-electron oxidation of the non-alternant polycyclic aromatic hydrocarbon pleiadiene and related cyclohepta[ c,d]pyrene and cyclohepta[c,d]fluoranthene in THF produces corresponding radical cations detectable in the temperature range of 293–263 K only on the subsecond time scale of cyclic voltammetry. Although the EPR-active red-coloured pleiadiene radical cation is stable according to the literature in concentrated sulfuric acid, spectroelectrochemical measurements reported in this study provide convincing evidence for its facile conversion into the green-coloured, formally closed shell and, hence, EPRsilent π-bound dimer dication stable in THF at 253 K. The unexpected formation of the thermally unstable dimeric product featuring a characteristic intense low-energy absorption band at 673 nm (1.84 eV; logεmax=4.0) is substantiated by ab initio calculations on the parent pleiadiene molecule and the PF6 − salts of the corresponding radical cation and dimer dication. The latter is stabilized with respect to the radical cation by 14.40 kcal mol−1 (DFT B3LYP) [37.64 kcal mol−1 (CASPT2/DFT B3LYP)]. An excellent match has been obtained between the experimental and TDDFT- calculated UV–vis spectra of the PF6 − salt of the pleiadiene dimer dication, considering solvent (THF) effects.

Steric effects on uranyl complexation: synthetic, structural, and theoretical studies of carbamoyl pyrazole compounds of the uranyl(VI) ion

New bifunctional pyrazole based ligands of the type [C3HR2N2CONR'] (where R = H or CH3; R' = CH3, C2H5, or (C3H7)-C-i) were prepared and characterized. The coordination chemistry of these ligands with uranyl nitrate and uranyl bis(dibenzoyl methanate) was studied with infrared (IR), H-1 NMR, electrospray-mass spectrometry (ES-MS), elemental analysis, and single crystal X-ray diffraction methods. The structure of compound [UO2(NO3)(2)(C3H3N2CON{C2H5}(2))] (2) shows that the uranium(VI) ion is surrounded by one nitrogen atom and seven oxygen atoms in a hexagonal bipyramidal geometry with the ligand acting as a bidentate chelating ligand and bonds through both the carbamoyl oxygen and pyrazolyl nitrogen atoms. In the structure of [UO2(NO3)(2)(H2O)(2)(C5H7N2CON {C2H5}(2))(2)], (5) the pyrazole figand acts as a second sphere ligand and hydrogen bonds to the water molecules through carbamoyl oxygen and pyrazolyl nitrogen atoms. The structure of [UO2(DBM)(2)C3H3N2CON{C2H5}(2)] (8) (where DBM = C6H5COCHCOC6H5) shows that the pyrazole ligand acts as a monodentate ligand and bonds through the carbamoyl oxygen to the uranyl group. The ES-MS spectra of 2 and 8 show that the ligand is similarly bonded to the metal ion in solution. Ab initio quantum chemical studies show that the steric effect plays the key role in complexation behavior.