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.

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.

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.

Band gap control via tuning of inversion degree in CdIn2S4 spinel

Based on theoretical arguments we propose a possible route for controlling the band-gap in the promising photovoltaic material CdIn2S4. Our ab initio calculations show that the experimental degree of inversion in this spinel (fraction of tetrahedral sites occupied by In) corresponds approximately to the equilibrium value given by the minimum of the theoretical inversion free energy at a typical synthesis temperature. Modification of this temperature, or of the cooling rate after synthesis, is then expected to change the inversion degree, which in turn sensitively tunes the electronic band-gap of the solid, as shown here by Heyd-Scuseria-Ernzerhof screened hybrid functional calculations.

Engineering the electronic bandgaps and band edge positions in carbon-substituted 2D boron nitride: a first-principles investigation

Modification of graphene to open a robust gap in its electronic spectrum is essential for its use in field effect transistors and photochemistry applications. Inspired by recent experimental success in the preparation of homogeneous alloys of graphene and boron nitride (BN), we consider here engineering the electronic structure and bandgap of C2xB1−xN1−x alloys via both compositional and configurational modification. We start from the BN end-member, which already has a large bandgap, and then show that (a) the bandgap can in principle be reduced to about 2 eV with moderate substitution of C (x < 0.25); and (b) the electronic structure of C2xB1−xN1−x can be further tuned not only with composition x, but also with the configuration adopted by C substituents in the BN matrix. Our analysis, based on accurate screened hybrid functional calculations, provides a clear understanding of the correlation found between the bandgap and the level of aggregation of C atoms: the bandgap decreases most when the C atoms are maximally isolated, and increases with aggregation of C atoms due to the formation of bonding and anti-bonding bands associated with hybridization of occupied and empty defect states. We determine the location of valence and conduction band edges relative to vacuum and discuss the implications on the potential use of 2D C2xB1−xN1−x alloys in photocatalytic applications. Finally, we assess the thermodynamic limitations on the formation of these alloys using a cluster expansion model derived from first-principles.

Harmonic force fields from scaled SCF calculations: Program ASYM40

We report an extended version of our normal coordinate program ASYM40, which may be used to transform Cartesian force constants from ab initio calculations to a force field in nonredundant internal (symmetry) coordinates. When experimental data are available, scale factors for the theoretical force field may then be optimized by least-squares refinement. The alternative of refining an empirical force field to fit a wide variety of data, as with the previous version ASYM20, has been retained. We compare the results of least-squares refinement of the full harmonic force field with least-squares refinement of only the scale factors for an SCF calculated force field and conclude that the latter approach may be useful for large molecules where more sophisticated calculations are impractical. The refinement of scale factors for a theoretical force field is also useful when there are only limited spectroscopic data. The program will accept ab initio calculated force fields from any program that presents Cartesian force constants as output. The program is available through Quantum Chemistry Program Exchange.

Vibrational energy levels of water

Several quartic force fields and a full sextic anharmonic force field for H,O have been determined from high-quality ab initio calculations, the highest at the aug-cc-pVQZ CCSD(T) level of theory. These force fields have been used to determine vibrational excited state band origins up to 15 000 cm - ’ above the zero-point level, using both a perturbation-resonancea pproach and a variational approach. An optimisedq uartic force field hasb eeno btained by least squares refinement of our best ab initio results to fit the observed overtone levels of 5 symmetrically substituted isotopomers of water (Hi60, Hi70, HisO, D,O, and T,O) with an rms error of less than 10 cm-‘, using the perturbation-resonancem odel for the vibrational calculation. Predicatel east squaresr efinement was usedt o provide a loose constraint of the refined force field to the ab initio results. The results obtained prove the viability of the perturbation-resonancem odel for usei n larger molecular systemsa nd also highlight someo f its weaknesse

Analytical potentials for triatomic molecules from spectroscopic data V. Application to HOX (X=F, Cl, Br, I)

Analytical potential energy functions are reported for HOX (X=F, Cl, Br, I). The surface for HOF predicts two metastable minima as well as the equilibrium configuration. These correspond to HFO (bent) and OHF (linear). Ab initio calculations performed for the HOF surface confirm these predictions. Comparisons are drawn between the two sets of results, and a vibrational analysis is undertaken for the hydrogen bonded OHF species. For HOCl, one further minimum is predicted, corresponding to HClO (bent), the parameters for which compare favourably with those reported from ab initio studies. In contrast, only the equilibrium configurations are predicted to be stable for HOBr and HOI.

A refined quartic forcefield for acetylene: accurate calculation of the vibrational spectrum

It is now possible to calculate the nine-dimensional rovibrational wavefunctions of sequentially bonded four-atom molecules variationally without dynamical approximation. In the case of HCCH, the simplest such molecule, many hundreds of rovibrational (J = 0, 1, 2) levels can be converged to better than 1.5 cm −1. Variational calculations of this kind are used here systematically to refine the well-known quartic valence-coordinate forcefleld of Strey and Mills [J.Mol. Spectrosc.59, 103-115 (1976)] against experimental term values up to three C-H stretch quanta for the principal and two deuterated isotopomers, yielding a new surface that reproduces the energies of all the known Σ, Π, and Δ states of these species up to the energy of two C-H stretch quanta with an rms error of 3 cm−1 . The refined forcefield is used to study the resonances associated with the accidental degeneracies (ν2 + ν4 + ν5, ν3) and (ν2 + 2ν5, ν1) in the principal isotopomer, leading to a clarification of the assignment of she experimentally detected states in the 2ν3 and 3ν3, polyads, and to the finding that vibrational Coriolis (kinetic energy) terms, rather than quartic anharmonicities in the potential, are the primary cause of the resonant interactions. Using a new cubic ab initio electric dipole field to calculate IR absorption coefficients, 24 undetected Σ and Π states of 1H12C12C1H and 5 undetected Σ states of D12C12CD are identified as candidates for experimental study, and their calculated energies and assignments are given.

Nitrous acid: vibrational frequency shifts due to 15N substitution, and the harmonic force field

Vibration rotation spectra of HO15 NO and DO15 NO have been measured at a resolution of 0•04 cm-1 to determine the isotopic shifts in the vibrational band origins. These have been used together with recently determined data on the vibrational band origins, Coriolis constants, and centrifugal distorition constants, to determine the harmonic force field of both cis and trans nitrous acid in least squares refinement calculations. The results are discussed in relation to recent ab initio calculations, the inertia defects, and the torsional potential function.

Calculated rotational and rovibrational spectra of D2S and HDS

Rovibrational energy levels, transition frequencies, and linestrengths are computed variationally for the sulfur hydrides D2S and HDS, using ab initio potential energy and dipole surfaces. Wave-numbers for the pure rotational transitions agree to within 0.2 cm−1 of the experimental lines. For the fundamental vibrational transitions, the band origins for D2S are 860.4, 1900.6, and 1912.0 cm−1 for ν2, ν1, and ν3, respectively, compared with the corresponding experimental values of 855.4, 1896.4, and 1910.2 cm−1. For HDS, we compute ν2 to be 1039.4 cm−1, compared with the experimental value of 1032.7 cm−1. The relative merits of local and normal mode descriptions for the overtone stretching band origins are discussed. Our results confirm the local mode nature of the H2S, D2S, and HDS system.

Analytical potentials for triatomic molecules VIII. A two valued surface for the lowest 1A¢ surfaces of H2O

Ab initio calculations of the energy have been made at approximately 150 points on the two lowest singlet A' potential energy surfaces of the water molecule, 1A' and 1A', covering structures having D∞h, C∞v, C2v and Cs symmetries. The object was to obtain an ab initio surface of uniform accuracy over the whole three-dimensional coordinate space. Molecular orbitals were constructed from a double zeta plus Rydberg basis, and correlation was introduced by single and double excitations from multiconfiguration states which gave the correct dissociation behaviour. A two-valued analytical potential function has been constructed to fit these ab initio energy calculations. The adiabatic energies are given in our analytical function as the eigenvalues of a 2 2 matrix, whose diagonal elements define two diabatic surfaces. The off-diagonal element goes to zero for those configurations corresponding to surface intersections, so that our adiabatic surface exhibits the correct Σ/II conical intersections for linear configurations, and singlet/triplet intersections of the O + H2 dissociation fragments. The agreement between our analytical surface and experiment has been improved by using empirical diatomic potential curves in place of those derived from ab initio calculations.

Potential energy functions for ground state surfaces of HCO and HNO

Analytical potential functions are reported for the ground state surfaces of HCO and HNO, the functions being derived from spectroscopic and ab initio data. Harmonized force fields have been deduced for the stable configurations of both molecules and vibration frequencies predicted for the metastable species COH and NOH.

Molecular structures of trimethylchlorogermane, (CH3)(3)GeCl, and trimethylbromogermane, (CH3)(3)GeBr, obtained by gas-phase electron diffraction and theoretical calculations

The structures of trimethylchlorogermane ((CH3)(3)GeCl) and trimethylbromogermane ((CH3)(3)GeBr) have been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing second-order Moller-Plesset (MP2) level of theory and the 6-311+G(d) basis set. All the electrons were included in the correlation calculation. The results from the ab initio calculations indicated that these molecules have C-3v symmetry, and models with this symmetry were used in the electron diffraction analysis. The results for the principal distances (r(g)) and angles (angle(alpha)) from the combined GED/ab initio study of trimethylchlorogermane (with estimated 2sigma uncertainties) are: r(Ge-C) = 1.950(4) Angstrom, r(Ge-Cl) = 2.173(4) Angstrom, r(C-H) = 1.090(9) Angstrom, angleCGeC = 112.7(7)degrees, angleCGeCl = 106.0(8)degrees, angleGeCH = 107.8(12)degrees. The results for the principal distances (r(g)) and angles (angle(alpha)) from the combined GED/ab initio study of trimethylbromogermane (with estimated 2sigma uncertainties) are: r(Ge-C) = 1.952(7) Angstrom, r(Ge-Br) = 2.325(4) Angstrom, r(C-H) = 1. 140(28) Angstrom, angleCGeC = 114.2(11)degrees, angleCGeBr = 104.2(13)degrees, angleGeCH 106.9(43)degrees. Local C-3v symmetry and staggered conformation were assumed for the methyl groups.

An investigation of the germylene addition reaction, GeH2+C2H2: Time-resolved gas-phase kinetic studies and quantum chemical calculations of the reaction energy surface

Time resolved studies of germylene, GeH2, generated by laser flash photolysis of 3,4-dimethylgermacyclopentene-3, have been carried out to obtain rate constants for its bimolecular reaction with acetylene, C2H2. The reaction was studied in the gas-phase over the pressure range 1-100 Tort, with SF6 as bath gas, at 5 temperatures in the range 297-553 K. The reaction showed a very slight pressure dependence at higher temperatures. The high pressure rate constants (obtained by extrapolation at the three higher temperatures) gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) (-10.94 +/- 0.05) + (6.10 +/- 0.36 kJ mol(-1))/RTln10. These Arrhenius parameters are consistent with a fast reaction occurring at approximately 30% of the collision rate at 298 K. Quantum chemical calculations (both DFT and ab initio G2//B3LYP and G2//QCISD) of the GeC2H4 potential energy surface (PES), show that GeH2 + C2H2 react initially to form germirene which can isomerise to vinylgermylene with a relatively low barrier. RRKM modelling, based on a loose association transition state, but assuming vinylgermylene is the end product (used in combination with a weak collisional deactivation model) predicts a strong pressure dependence using the calculated energies, in conflict with the experimental evidence. The detailed GeC2H4 PES shows considerable complexity with ten other accessible stable minima (B3LYP level), the three most stable of which are all germylenes. Routes through this complex surface were examined in detail. The only product combination which appears capable of satisfying the (P-3) + C2H4.C2H4 was confirmed as a product by GC observed lack of a strong pressure dependence is Ge(P-3) + C2H4. C2H4 was confirmed as a product by GC analysis. Although the formation of these products are shown to be possible by singlet-triplet curve crossing during dissociation of 1-germiranylidene (1-germacyclopropylidene), it seems more likely (on thermochernical grounds) that the triplet biradical, (GeCH2CH2.)-Ge-., is the immediate product precursor. Comparisons are made with the reaction of SiH2 with C2H2.