Analytical potential energy function and spectroscopic parameters for the ground and excited states of NaH

set of energies at different internuclear distances for the ground electronic state and two excited electronic states of NaH molecule have been calculated using valence internally contracted multireference configuration interaction(MRCI) including Davidson correction and three basis sets. Then, a potential energy curve (PEC) for each state was determined by extrapolating MRCI energies to the complete basis sets limit. Based on the PECs, accurate vibrational energy levels and rotational constants were determined. The computational PECs are were fitted to analytical potential energy functions using the Murrell-Sorbie potential function. Then, accurate spectroscopic parameters were calculated. Compared with experimental results, values obtained with the basis set extrapolation yield a potential energy curve that gives accurate vibrational energy levels, rotational constants and spectroscopic parameters for the NaH molecule. (C) 2004 Elsevier B.V. All rights reserved.

Theoretical study on analytical potential function and spectroscopic parameters for CaF molecule

The equilibrium properties and potential energy curves of the ground electronic state of CaF have been calculated using the Brueckner Doubles calculation with a triples contribution added [BD(T)] and the gradient-corrected density functional theory with three-parameter exact exchange mixing (B3LY-P) method, with 6-311 + G*,6-311 + G(2df,2pd) and 6-311 + G(3df,3pd) basis sets. All the computational PECs are fitted to analytical potential energy functions using Murrell-Sorbie, Huxley and Tang-Toennies potentials. Based on this, the spectroscopic parameters are calculated, and then compared with some other theoretical and experimental data. (C) 2004 Elsevier B.V. All rights reserved.

Parameterizing a Simple Potential Energy Function Appropriate for Vibrational Frequencies Using Molecular Dynamics

A Maple scheme for quickly parameterizing vibrational potential energy functions is presented. As an example, the potential energy function's parameters for the vibrational motions in H_2O_2 are obtained assuming the simplest potential energy function. This paper was originally written as a research paper, but rejected by the referees. It is therefore being edited into an ``educational'' paper for student usage.

Recent improvements in prediction of protein structure by global optimization of a potential energy function

Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

Analytical potentials for triatomic molecules IX. The prediction of anharmonic force constants from potential energy surfaces based on harmonic force fields and dissociation energies for SO2 and O3

Analytical potential energy functions which are valid at all dissociation limits have been derived for the ground states of SO2 and O3. The procedure involves minimizing the errors between the observed vibrational spectra and spectra calculated by a variational procedure. Good agreement is obtained between the observed and calculated spectra for both molecules. Comparisons are made between anharmonic force fields, previously determined from the spectral data, and the force fields obtained by differentiating the derived analytical functions at the equilibrium configurations.

A potential energy surface for the ground state of acetylene, C2H2

A potential energy function has been derived for the ground state surface of C2H2 as a many-body expansion. The 2- and 3-body terms have been obtained by preliminary investigation of the ground state surfaces of CH2( 3B1) and C2H( 2Σ+). A 4-body term has been derived which reproduces the energy, geometry and harmonic force field of C2H2. The potential has a secondary minimum corresponding to the vinylidene structure and the geometry and energy of this are in close agreement with predictions from ab initio calculations. The saddle point for the HCCH-H2CC rearrangement is predicted to lie 2•530 eV above the acetylene minimum.

A potential energy surface for the ground state of formaldehyde, H2CO(1A1)

A model potential energy function for the ground state of H2CO has been derived which covers the whole space of the six internal coordinates. This potential reproduces the experimental energy, geometry and quadratic force field of formaldehyde, and dissociates correctly to all possible atom, diatom and triatom fragments. Thus there are good reasons for believing it to be close to the true potential energy surface except in regions where both hydrogen atoms are close to the oxygen. It leads to the prediction that there should be a metastable singlet hydroxycarbene HCOH which has a planar trans structure and an energy of 2•31 eV above that of equilibrium formaldehyde. The reaction path for dissociation into H2 + CO is predicted to pass through a low symmetry transition state with an activation energy of 4•8 eV. Both of these predictions are in good agreement with recently published ab initio calculations.

Accurate ground-state potential energy surfaces of the C2H2–Kr and C2H2–Xe van der Waals complexes

Accurate ab initio intermolecular potential energy surfaces (IPES) have been obtained for the first time for the ground electronic state of the C 2H2-Kr and C2H2-Xe van der Waals complexes. Extensive tests, including complete basis set and all-electron scalar relativistic results, support their calculation at the CCSD(T) level of theory, using small-core relativistic pseudopotentials for the rare-gas atoms and aug-cc-pVQZ basis sets extended with a set of 3s3p2d1f1g mid-bond functions. All results are corrected for the basis set superposition error. The importance of the scalar relativistic and rare-gas outer-core (n.1)d correlation effects is investigated. The calculated IPES, adjusted to analytical functions, are characterized by global minima corresponding to skew T-shaped geometries, in which the Jacobi vector positioning the rare-gas atom with respect to the center of mass of the C2H2 moiety corresponds to distances of 4.064 and 4.229Å, and angles of 65.22° and 68.67° for C 2H2-Kr and C2H2-Xe, respectively. The interaction energy of both complexes is estimated to be -151.88 (1.817 kJ mol-1) and -182.76 cm-1 (2.186 kJ mol-1), respectively. The evolution of the topology of the IPES as a function of the rare-gas atom, from He to Xe, is also discussed. © 2012 Taylor and Francis.

Analytical potentials for triatomic molecules from spectroscopic data VI. On choosing internal coordinates to describe triatomic potential energy surfaces with more than one minimum

Orthogonal internal coordinates are defined which have useful properties for constructing the potential energy functions of triatomic molecules with two or three minima on the surface. The coordinates are used to obtain ground state potentials of ClOO and HOF, both of which have three minima.

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.

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.

The Dynamics of a Small Model Glass Former as Viewed from Its Potential Energy Landscape

Despite intensive research during the last decades, thetheoreticalunderstanding of supercooled liquids and the glasstransition is stillfar from being complete. Besides analytical investigations,theso-called energy-landscape approach has turned out to beveryfruitful. In the literature, many numerical studies havedemonstratedthat, at sufficiently low temperatures, all thermodynamicquantities can be predicted with the help of the propertiesof localminima in the potential-energy-landscape (PEL). The main purpose of this thesis is to strive for anunderstanding ofdynamics in terms of the potential energy landscape. Incontrast to the study of static quantities, this requirestheknowledge of barriers separating the minima.Up to now, it has been the general viewpoint that thermallyactivatedprocesses ('hopping') determine the dynamics only belowTc(the critical temperature of mode-coupling theory), in thesense that relaxation rates follow from local energybarriers.As we show here, this viewpoint should be revisedsince the temperature dependence of dynamics is governed byhoppingprocesses already below 1.5Tc.At the example of a binary mixture of Lennard-Jonesparticles (BMLJ),we establish a quantitative link from the diffusioncoefficient,D(T), to the PEL topology. This is achieved in three steps:First, we show that it is essential to consider wholesuperstructuresof many PEL minima, called metabasins, rather than singleminima. Thisis a consequence of strong correlations within groups of PELminima.Second, we show that D(T) is inversely proportional to theaverageresidence time in these metabasins. Third, the temperaturedependenceof the residence times is related to the depths of themetabasins, asgiven by the surrounding energy barriers. We further discuss that the study of small (but not toosmall) systemsis essential, in that one deals with a less complex energylandscapethan in large systems. In a detailed analysis of differentsystemsizes, we show that the small BMLJ system consideredthroughout thethesis is free of major finite-size-related artifacts.

Raman and infrared spectra of dimethyl ether 13C-isotopologue (CH3O13CH3) from a CCSD(T) potential energy surface

So far, no experimental data of the infrared and Raman spectra of 13C isotopologue of dimethyl ether are available. With the aim of providing some clues of its low-lying vibrational bands and with the hope of contributing in a next spectral analysis, a number of vibrational transition frequencies below 300 cm−1 of the infrared spectrum and around 400 cm−1 of the Raman spectrum have been predicted and their assignments were proposed. Calculations were carried out through an ab initio three dimensional potential energy surface based on a previously reported one for the most abundant dimethyl ether isotopologue (M. Villa et al., J. Phys. Chem. A 115 (2011) 13573). The potential function was vibrationally corrected and computed with a highly correlated CCSD(T) method involving the COC bending angle and the two large amplitude CH3 internal rotation degrees of freedom. Also, the Hamiltonian parameters could represent a support for the spectral characterization of this species. Although the computed vibrational term values are expected to be very accurate, an empirical adjustment of the Hamiltonian has been performed with the purpose of anticipating some workable corrections to any possible divergence of the vibrational frequencies. Also, the symmetry breaking derived from the isotopic substitution of 13C in the dimethyl ether was taken into account when the symmetrization procedure was applied.

A mass spectrometry study of XCO+, X = Si, Ge : Is SiCO+ a main group carbonyl? Comments on the bonding in ground state SiCO and the Si,C,O (+) potential energy surface

The cation\[Si,C,O](+) has been generated by 1) the electron ionisation (EI) of tetramethoxysilane and 2) chemical ionisation (CI) of a mixture of silane and carbon monoxide. Collisional activation (CA) experiments performed for mass-selected \[Si,C,O](+), generated by using both methods, indicate that the structure is not inserted OSiC+; however, a definitive structural assignment as Si+-CO, Si+-OC or some cyclic variant is impossible based on these results alone. Neutralisation-reionisation (+NR+) experiments for EI-generated \[Si,C,O](+) reveal a small peak corresponding to SiC+, but no detectable SiO+ signal, and thus establishes the existence of the Si+-CO isomer. CCSD(T)//B3LYP calculations employing a triple-zeta basis set have been used to explore the doublet and quartet potential-energy surfaces of the cation, as well as some important neutral states The results suggest that both Si+-CO and Si+ - OC isomers are feasible; however, the global minimum is (2)Pi SiCO+. Isomeric (2)Pi SiOC+ is 12.1 kcal mol(-1) less stable than (2)Pi SiCO+, and all quartet isomers are much higher in energy. The corresponding neutrals Si-CO and Si-OC are also feasible, but the lowest energy Si - OC isomer ((3)A") is bound by only 1.5 kcal mol(-1). We attribute most, if nor all, of the recovery signal in the +NR' experiment to SiCO+ survivor ions. The nature of the bonding in the lowest energy isomers of Si+ -(CO,OC) is interpreted with the aid of natural bond order analyses, and the ground stale bonding of SiCO+ is discussed in relation to classical analogues such as metal carbonyls and ketenes.