Jing-Jing Zheng

Potential-energy surface for the electronic ground state of NH3 up to 20000cm−1 above equilibrium

Ab initio coupled cluster calculations with single and double substitutions and a perturbative treatment of connected triple excitations [CCSD(T)] with the augmented correlation-consistent polarized valence triple-zeta aug-cc-pVTZ basis at 51 816 geometries provide a six-dimensional potential-energy surface for the electronic ground state of NH3. At 3814 selected geometries, CBS+ energies are obtained by extrapolating the CCSD(T) results for the aug-cc-pVXZ(X=T,Q,5) basis sets to the complete basis set (CBS) limit and adding corrections for core-valence correlation and relativistic effects. CBS** ab initio energies are generated at 51 816 geometries by an empirical extrapolation of the CCSD(T)/aug-cc-pVTZ results to the CBS+ limit. They cover the energy region up to 20000cm−1 above equilibrium. Parametrized analytical functions are fitted through the ab initio points. For these analytical surfaces, vibrational term values and transition moments are calculated by means of a variational program employing a ...

Rotation–vibration motion of pyramidal XY3 molecules described in the Eckart frame: Theory and application to NH3

We present a new model for the rotation-vibration motion of pyramidal XY3 molecules, based on the Hougen–Bunker–Johns approach. Inversion is treated as a large-amplitude motion, while the small-amplitude vibrations are described by linearized stretching and bending coordinates. The rotation–vibration Schrödinger equation is solved variationally. We report three applications of the model to 14NH3 using an analytic potential function derived from high-level ab initio calculations. These applications address the J = 0 vibrational energies up to 6100 cm, the J≤2 energies for the vibrational ground state and the ν2, ν4, and 2ν2 excited vibrational states, and the J≤7 energies for the vibrational state. We demonstrate that also for four-atomic molecules, theoretical calculations of rotation–vibration energies can be helpful in the interpretation and assignment of experimental, high-resolution rotation–vibration spectra. Our approach incorporates an optimum inherent separation of different types of nuclear motion and thus remains applicable for rotation–vibration states with higher J values where alternative variational treatments are no longer feasible.

High resolution vibration-rotation spectrum of the D2O molecule in the region near the 2ν1 + ν2 + ν3 absorption band

The high resolution Fourier transform spectrum of the D20 (ν = ν1 + ν2/2 + ν3 = 3.5) polyad was analysed within the framework of the Hamiltonian model taking into account resonance interactions between the seven states (310), (211), (112), (013), (230), (131) and (032). Transitions belonging to the 2ν1 + ν2 + ν3, 3ν1 +ν2 and 3ν2 + 2ν3 bands were assigned in the experimentally recorded spectrum. This provided the possibility of obtaining spectroscopic parameters of the ‘visible’ states (211), (310) and (032) and of estimating the band centres, and the rotational and resonance interaction parameters of the ‘dark’ states (112) and (131).

Dipole moment and rovibrational intensities in the electronic ground state of NH3: Bridging the gap between ab initio theory and spectroscopic experiment

We report theoretical values for the transition moments of an extensive set of vibrational bands in the electronic ground state of (14)NH(3). For selected bands, we have further made detailed simulations of the rotational structure. The calculations are carried out by means of recently developed computational procedures for describing the nuclear motion and are based on a high-level ab initio potential energy surface, and high-level dipole moment surfaces, for the electronic ground state of NH(3). The reported theoretical intensity values are compared to, and found to agree very well with, corresponding experimental results. It is believed that the computational method, in conjunction with high-quality ab initio potential energy and dipole moment surfaces, can simulate rotation-vibration spectra of XY(3) pyramidal molecules prior to observation with sufficient accuracy to facilitate the observation of these spectra. By degrading the accuracy of selected elements of the calculations, we have also investigated the influence of customary approximations on the computed intensity values.

Common system setup for the entire catalytic cycle of cytochrome P450cam in quantum mechanical/molecular mechanical studies

We describe a system setup that is applicable to all species in the catalytic cycle of cytochrome P450cam. The chosen procedure starts from the X‐ray coordinates of the ferrous dioxygen complex and follows a protocol that includes the careful assignment of protonation states, comparison between different conceivable hydration schemes, and system preparation through a series of classical minimizations and molecular dynamics (MD) simulations. The resulting setup was validated by quantum mechanical/molecular mechanical (QM/MM) calculations on the resting state, the pentacoordinated ferric and ferrous complexes, Compound I, the transition state and hydroxo intermediate of the CH hydroxylation reaction, and the product complex. The present QM/MM results are generally consistent with those obtained previously with individual setups. Concerning hydration, we find that saturating the protein interior with water is detrimental and leads to higher structural flexibility and catalytically inefficient active‐site geometries. The MD simulations favor a low water density around Asp251 that facilitates side chain rotation of protonated Asp251 during the conversion of Compound 0 to Compound I. The QM/MM results for the two preferred hydration schemes (labeled SE‐1 and SE‐4) are similar, indicating that slight differences in the solvation close to the active site are not critical as long as camphor and the crystallographic water molecules preserve their positions in the experimental X‐ray structures.

Quantum and molecular mechanical study of the first proton transfer in the catalytic cycle of cytochrome P450cam and its mutant D251N

In the catalytic cycle of cytochrome P450cam, the hydroperoxo intermediate (Cpd 0) is formed by proton transfer from a reduced oxyheme complex (S5). This process is drastically slowed down when Asp251 is mutated to Asn (D251N). We report quantum mechanical/molecular mechanical (QM/MM) calculations that address this proton delivery in the doublet state through a hydrogen-bond network in the Asp251 channel, both for the wild-type enzyme and the D251N mutant, using four different active-site models. For the wild-type, we find a facile concerted mechanism for proton transfer from protonated Asp251 via Wat901 and Thr252 to the FeOO moiety, with a barrier of about 1 kcal/mol and a high exothermicity of more than 20 kcal/mol. In the D251N mutant with a neutral Asn251 residue, the proton transfer is almost thermoneutral or slightly exothermic in the three models considered. It is still very facile when the Asn251 residue adopts a conformation analogous to Asp251 in the wild-type enzyme, but the barrier increases significantly when the Asn251 side chain flips (as indicated by classical molecular dynamics simulations). This flip disrupts the hydrogen-bond network and hence the proton-transfer pathway, which causes a longer lifetime of S5 in the D251N mutant (consistent with experimental observations). The entry of an additional water molecule into the active site of D251N with flipped Asn251 regenerates the hydrogen-bond network and provides a viable mechanism for proton delivery in the mutant, with a moderate barrier of about 7 kcal/mol.

The stretching vibrational overtone spectra of PH3: Local mode vibrational analysis, dipole moment surfaces from density functional theory and band intensities

The infrared spectra of PH3 molecule were recorded on a Bruker IFS 120HR Fourier transform spectrometer from 4000 to 9500 cm−1. The P–H stretching vibrational frequencies and intensities were derived from the experimental data. The Morse oscillator parameters De and α in the anharmonically coupled anharmonic oscillator local mode model were determined by the least-squares fitting with the observed vibrational band centers. The ab initio three-dimensional P–H stretching dipole moment surfaces were calculated by the density functional theory method. The dipole moment vectors were projected to three kinds of molecule-fixed reference systems. The corresponding dipole moment components were fitted to polynomial functions in terms of the P–H bond length displacements with the molecular symmetry taken into account. The absolute band intensities were obtained and then compared with the experimental data. The results showed that a proposed improved bond dipole model can predict the absolute band intensities within...

Global Analytical Potential Energy Surface for the Electronic Ground State of NH3 from High Level ab Initio Calculations

The analytical, full-dimensional, and global representation of the potential energy surface of NH(3) in the lowest adiabatic electronic state developed previously (Marquardt, R.; et al. J. Phys. Chem. B 2005, 109, 8439–8451) is improved by adjustment of parameters to an enlarged set of electronic energies from ab initio calculations using the coupled cluster method with single and double substitutions and a perturbative treatment of connected triple excitations (CCSD(T)) and the method of multireference configuration interaction (MRCI). CCSD(T) data were obtained from an extrapolation of aug-cc-pVXZ results to the basis set limit (CBS), as described in a previous work (Yurchenko, S.N.; et al. J. Chem. Phys 2005, 123, 134308); they cover the region around the NH3 equilibrium structures up to 20,000 hc cm(–1). MRCI energies were computed using the aug-cc-pVQZ basis to describe both low lying singlet dissociation channels. Adjustment was performed simultaneously to energies obtained from the different ab initio methods using a merging strategy that includes 10,000 geometries at the CCSD(T) level and 500 geometries at the MRCI level. Characteristic features of this improved representation are NH3 equilibrium geometry r(eq)(NH(3)) ≈ 101.28 pm, α(eq)(NH(3)) ≈ 107.03°, the inversion barrier at r(inv)(NH(3)) ≈ 99.88 pm and 1774 hc cm(–1) above the NH(3) minimum, and dissociation channel energies 41,051 hc cm(–1) (for NH(3) → ((2)B(2))NH(2) + ((2)S(1/2))H) and 38,450 hc cm(–1) (for NH(3) → ((3)Σ(–))NH +((1)Σ(g)(+))H(2)); the average agreement between calculated and experimental vibrational line positions is 11 cm(–1) for (14)N(1)H(3) in the spectral region up to 5000 cm(–1). A survey of our current knowledge on the vibrational spectroscopy of ammonia and its isotopomers is also given.

High-resolution spectrum of the , and ν3+ν4(A2) bands of the PH3 molecule: assignments and preliminary analysis

Abstract The high-resolution (0.005 cm −1 ) Fourier transform infrared spectrum of PH3 is recorded in the region between 3280 and 3580 cm −1 where the following bands are located: ν 1 +ν 4 (E), ν 3 +ν 4 (E), ν 3 +ν 4 (A 1 ) , forbidden on symmetry band ν3+ν4(A2), and very weak bands ν 1 +ν 2 (A 1 ), ν 2 +ν 3 (E) . Transitions are assigned to the first four ones. Vibrational analysis of known experimental data is made.

Overtone spectrum and the Fermi resonance of the SiH chromophore in SiHCI3

The Fourier transform and Fourier transform intracavity laser absorption spectra of the gas phase SiHCl3 molecule were recorded from 1000 cm-1 up to 13 000 cm-1. The normal mode analysis is carried out to fit the observed band centres. The reduced Hamiltonian models in terms of normal and curvilinear internal coordinates are used to study the Fermi resonance between the SiH stretching and bending modes and analyse the observed band centres associated with the SiH chromophore. The resonance in the SiH chromophore is found not to be important due to the cancellation of the contributions from the kinetic and the potential coupling terms. Off-diagonal anharmonic constants between the SiH stretching and bending manifold and the molecular frame have been determined. The SiH chromophore vibrational intensities are also reported.