Global mapping of equilibrium and transition structures on potential energy surfaces by the scaled hypersphere search method: applications to ab initio surfaces of formaldehyde and propyne molecules

Technical details of a new global mapping technique for finding equilibrium (EQ) and transition structures (TS) on potential energy surfaces (PES), the scaled hypersphere search (SHS) method (Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384, 277), are presented. On the basis of a simple principle that reaction pathways are found as anharmonic downward distortions of PES around an EQ point, the reaction pathways can be obtained as energy minima on the scaled hypersphere surface, which would have a constant energy when the potentials are harmonic. Connections of SHS paths between each EQ are very similar to corresponding intrinsic reaction coordinate (IRC) connections. The energy maximum along the SHS path reaches a region in close proximity to the TS of the reaction pathway, and the subsequent geometry optimization from the SHS maximum structure easily converges to the TS. The SHS method, using the one-after-another algorithm connecting EQ and TS, considerably reduces the multidimensional space to be searched to certain limited regions around the pathways connecting each EQ with the neighboring TS. Applications of the SHS method have been made to ab initio surfaces of formaldehyde and propyne molecules to obtain systematically five EQ and nine TS for formaldehyde and seven EQ and 32 TS for propyne.     

Finding important anharmonic terms in the sixth-order potential energy function by the scaled hypersphere search method: an application to vibrational analyses of molecules and clusters

A fitting method of the sixth-order potential energy function is proposed, where ab initio potential energy data for the fitting are sampled in directions containing maximal anharmonic downward distortions detected by the scaled hypersphere search (SHS) method. This technique has been applied to H2O, HCHO, HCOOH, C2H4, CH3OH, CH3CHO, CH3NH2, B2H6, (H2O)2, and (H2O)3, where, without using the symmetry, 176, 904, 1432, 2992, 2520, 2760, 3608, 6232, 768, and 1456 times single-point energy calculations, respectively, were required for obtaining anharmonic terms. Experimental IR peak positions of not only fundamentals but also overtones and combinations in the excitation energy range of 1000-4000 cm(-1) could be reproduced very accurately by the post-vibrational self-consistent field theory employing potential functions obtained by the present SHS based polynomial fitting method.     

Automated exploration of adsorption structures of an organic molecule on RuH2-BINAP by the ONIOM method and the scaled hypersphere search method

Automated exploration of adsorption structures of a molecule (CH3COCH2COOCH3) on an organometallic complex of (R)-RuH2-BINAP (BINAP=2,2'-bis(diphenylphosphino)-1,1'-binaphthyl) has been performed by a combination of the ONIOM method and the scaled hypersphere search (SHS) method. As many as 135 potential minima have been obtained as candidates of adsorption structures. The most stable structure among the 135 is a precursor of the (R)-type product, which is about 30 kJ/mol more stable than the most stable structure among precursors of the (S)-type product. This unbiased search is theoretically showing the power of BINAP to distinguish (R)-type and (S)-type at the adsorption state. This result is in line with very high optical yield of the (R)-type product in the corresponding experiment.     

Theoretical study of the potential energy surface for CH3 and CH4 losses from ethyltoluenes

The decomposition of o-, m-, and p-ethyltoluene has been studied by density functional theory. It was found that monomolecular homolytic methyl loss from ethyl moiety seems to be the most favorable mechanism than other proceeding through ethyl, ring-methyl and hydrogen loss. Two possible channels of methane elimination from o-ethyltoluene were studied at B3LYP/6-311++G(df,p) level of theory.     

Quantum chemistry study of H+(H2O)8: a global search for its isomers by the scaled hypersphere search method, and its thermal behavior

The structures of the protonated water cluster H+(H2O)8 have been globally explored by the scaled hypersphere search method. On the Hartree-Fock potential energy surface 174 isomers were found, among which 168 were computed to be minima at the B3LYP/6-31+G** level, and their energies were further refined at the level of MP2/6-311++G(3df,2p). The global minimum on the potential energy surface computed at the B3LYP/6-31+G** level shows a cagelike structure with the "Eigen" motif, while the lowest-free-energy isomer has a five-membered-ring structure at 170 K and a chain form at 273 K. The present results are well in line with previous experimental findings. In addition, the ADMP (atom-centered density matrix propagation) simulation indicates that the extra proton in the lowest-free-energy isomer (170 K), which has a five-membered ring and the "Zundel" feature, is often in an asymmetrical hydrogen bond.     

A systematic investigation of the ground state potential energy surface of H3+

Based on different ab initio electronic structure calculations (CI-R12 and Gaussian Geminals) of the Born-Oppenheimer electronic energy E(BO) of H(3)(+) from high to highest quality, we build up a potential energy surface which represents a highly reliable form of the topology of the whole potential region, locally and globally. We use the CI-R12 method in order to get within reasonable CPU-time a relatively dense grid of energy points. We demonstrate that CI-R12 is good enough to give an accurate surface, i.e., Gaussian Geminals are not absolutely necessary. For different types of potential energy surface fits, we performed variational calculations of all bound vibrational states, including resonances above the dissociation limit, for total angular momentum J = 0. We clarify the differences between different fits of the energy to various functional forms of the potential surface. Small rms-values (<1 cm(-1)) of the fit do not provide precise information about the interpolatory behaviour of the fit functions.     

"Roaming" dynamics in CH3CHO photodissociation revealed on a global potential energy surface

We present a quasiclassical trajectory study of the photodissociation of CH3CHO to molecular and radical products, CH4 + CO and CH3 + HCO, respectively, using global ab initio-based potentials energy surfaces. The molecular products have a well-defined potential barrier transition state (TS) but the dynamics exhibit strong deviations from the TS pathway to these products. The radical products are formed via a variational TS. Calculations are reported at total energies corresponding to photolysis wavelengths of 308, 282, 264, 248 and 233 nm. The results at 308 nm focus on a comparison with experiment [Houston, P. L.; Kable, S. H. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16079] and the elucidation of the nature and extent of non-TS reaction dynamics to form the molecular products, CH4 + CO. At the other wavelengths the focus is the branching ratio of these products and the radical products, CH3 + HCO.     

Ab initio potential energy surface of CH and reaction dynamics of H + CH+

This work presents a new ground state potential energy surface (PES) for CH. The potential is tested using quasi classical trajectory (QCT) and quantum reactive scattering methods for the H + CH(+) reaction. Cross sections and rate coefficients for all reaction channels up to 300 K are calculated. The abstraction rate coefficients follow the expected slightly decreasing behaviour above 90 K, but have a positive gradient with lower temperatures. The inelastic collision and exchange reaction rate constants are increasing monotonically with temperature. The rate coefficients of the exchange reaction differ significantly between QCT and quantum reactive scattering, due to intrinsic shortcomings of the QCT final state distributions.     

Minima hopping: an efficient search method for the global minimum of the potential energy surface of complex molecular systems

A method is presented that can find the global minimum of very complex condensed matter systems. It is based on the simple principle of exploring the configurational space as fast as possible and of avoiding revisiting known parts of this space. Even though it is not a genetic algorithm, it is not based on thermodynamics. The efficiency of the method depends strongly on the type of moves that are used to hop into new local minima. Moves that find low-barrier escape-paths out of the present minimum generally lead into low energy minima.     

Study of the interaction between aniline and CH3CN, CH3Cl and CH3F

A computational study of dimers formed by aniline and one or two CH₃X molecules, X being CN, Cl or F, was carried out to elucidate the main characteristics of the interacting systems. Two different structures were found for each of the dimers, depending on the relative location of the CH₃X molecule with respect to the NH₂ hydrogen atoms. The most stable complex is formed with acetonitrile, with a complexation energy amounting to ?27.0?kJ/mol. Methyl chloride and methyl fluoride form complexes with complexation energies amounting to ?18.1 and ?17.5?kJ/mol, respectively, though the structural arrangement is quite different for both structures. In most complexes, the leading contribution to the stabilization of the complex is dispersion, though the electrostatic contribution is almost as important. Three different minima were obtained for clusters containing two CH₃X molecules depending on the side they occupy with respect to the phenyl ring. The complexation energies for these structures amount to ?58.5, ?38.6 and ?36.3?kJ/mol for acetonitrile, methyl chloride and methyl fluoride, respectively.     

A computational investigation on the potential energy surface of thiosulfeno with O(3P) reaction

The reaction paths of thiosulfeno radical (HS₂) with O(³P) have been investigated at the UB3LYP/aug-cc-pV(T + d)Z and UCCSD(T)/aug-cc-pV(T + d)Z//B3LYP levels. Two stable collision intermediates, HSSO and SS(H)O, have been considered for the HS₂ + O(³P) reaction. Four products of S + HSO, H + SSO, HS + SO, and S₂ + OH are obtained by starting from HSSO and SS(H)O. The calculated results show that the most feasible paths for the formation of S + HSO, H + SSO, and HS + SO products include no transition states in reaction path, while that of S₂ + OH product includes relatively high energy barriers of 23.0 kcal/mol. Therefore, S + HSO, H + SSO, and HS + SO are main products (with the stability other of HS + SO > H + SSO > S + HSO) and S₂ + OH is the second product in HS₂ + O(³P) reaction. Because, all intermediates, transition states, and products involved in the reaction paths lie below the initial reactants, the HS₂ + O(³P) reaction is expected to be rapid even at low temperatures.     

An ab initio based global potential energy surface describing CH5+ --> CH3+ + H2

A full-dimensional, ab initio based potential energy surface (PES) for CH(5)(+), which can describe dissociation is reported. The PES is a precise fit to 36173 coupled-cluster [CCSD(T)] calculations of electronic energies done using an aug-cc-pVTZ basis. The fit uses a polynomial basis that is invariant with respect to permutation of the five H atoms, and thus describes all 120 equivalent minima. The rms fitting error is 78.1 cm(-1) for the entire data set of energies up to 30,000 cm(-1) and a normal-mode analysis of CH(5)(+) also verifies the accuracy of the fit. Two saddle points have been located on the surface as well and compared with previous theoretical work. The PES dissociates correctly to the fragments CH(3)(+) + H(2) and the equilibrium geometry and normal-mode analyses of these fragments are also presented. Diffusion Monte Carlo calculations are done for the zero-point energies of CH(5)(+) (and some isotopologs) as well as for the separated fragments of CH(5)(+), CH(3)(+) + H(2) and those of CH(4)D(+), CH(3)(+) + HD and CH(2)D(+) + H(2). Values of D(0) are reported for these dissociations. A molecular dynamics calculation of CH(4)D(+) dissociation at one total energy is also performed to both validate the applicability of the PES for dynamics studies as well as to test a simple classical statistical prediction of the branching ratio of the dissociation products.     

The formation of the stable radicals .CH2CN, CH3.CHCN and .CH2CH2CN from the anions -CH2CN, CH3-CHCN and -CH2CH2CN in the gas phase. A joint experimental and theoretical study

Franck-Condon one-electron oxidation of the stable anions -CH2CN, CH3-CHCN and -CH2CH2CN (in the collision cell of a reverse-sector mass spectrometer) produce the radicals .CH2CN, CH3.CHCN and .CH2CH2CN, which neither rearrange nor decompose during the microsecond duration of the neutralisation-reionisation experiment. Acetonitrile (CH3CN) and propionitrile (CH3CH2CN) are known interstellar molecules and radical abstraction of these could produce energised .CH2CN and CH3.CHCN, which might react with NH2. (a known interstellar radical) on interstellar dust or ice surfaces to form NH2CH2CN and NH2CH(CH3)CN, precursors of the amino acids glycine and alanine.     

Insight into global reaction mechanism of [C2, H4, O] system from ab initio calculations by the scaled hypersphere search method

A detailed computational study is performed on the singlet potential energy surface (PES) for possible isomerization and dissociation reactions of CH(3)CHO at the DFT (B3LYP/6-311++G(d,p)) and CCSD(T)/cc-pVTZ//B3LYP/6-311++G(d,p) levels. The pathways around the equilibrium structures can be discovered by the scaled hypersphere search (SHS) method, which enables us to make a global analysis of the PES for a given chemical composition. Fourteen isomers inclusive of 11 single-molecules and three "non-stabilized" oxygen-based ylides, 5 energetically favored complexes, and 79 interconversion transition states have been found on the singlet PES. Four lowest lying isomers with thermodynamic stability are also kinetically stable with respect to metastable intermediates. It was revealed that vinyl alcohols, which could be generated by the tautomerization of acetaldehyde, could undergo dissociation to form acetylene and water. In addition, recombination channels between some fragments, such as H(2)CO + (1)CH(2) and (1)CHOH + (1)CH(2), are energetically accessible via collision complex or oxygen-based ylides. Most of available unimolecular decompositions are found to be responsible for favorable hydrogen abstraction processes.     

A semi-empirical calculation of the potential surface for the CH 3 . +CH2=CH2 reaction

A model for the reaction CH ₃ ^. +CH₂=CH₂ is studied including the hybridization change of the reaction center. The interaction energy is devided into two parts. The first is a stabilization energy — the contribution due to the -electron delocalization (including the hybridization effects). It is computed by the PPP method. The second part is an exchange repulsion due to all valence electrons of the three carbon atoms. Correlation corrections are considered. A potential energy surface is constructed, giving a saddle point value close to the experimental activation energy. A discussion is given of the approximations involved. The method suggested is a generalization of the reactivity indices method of the theory of chemical reactivity. It can be regarded as a justification of this more empirical approach.

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Zusammenfassung Ein Modell für die Reaktion CH ₃ ^. +CH₂=CH₂ wird untersucht, einschließlich der Änderung der Hybridisation des Reaktionszentrums. Die Wechselwirkungsenergie wird in zwei Teile zerlegt. Der erste Teil ist eine Stabilisationsenergie — der Beitrag, der der Delokalisierung des -Elektrons (einschließlich Hybridisationseffekte) entspricht. Der zweite Teil ist eine Austauschabstoßung, die von allen Valenzelektronen der drei Kohlenstoffatome herrührt. Korrellationskorrekturen werden berücksichtigt. Eine Fläche der potentiellen Energie wird konstruiert mit einem Sattelpunktswert, der dicht an der experimentellen Aktivierungsenergie liegt. Die verwendeten Näherungsmethoden werden diskutiert. Die vorgeführte Methode ist eine Verallgemeinerung der Methode der Reaktivitätsindices aus der Theorie der chemischen Reaktivität. Sie kann als eine Rechtfertigung dieser mehr empirischen Näherung angesehen werden.

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Résumé Etude d'un modèle pour la réaction CH ₃ ^. +CH₂=CH₂ où l'on tient compte du changement d'hybridation du centre réactif. L'énergie d'interaction est divisée en deux termes. Le premier est une énergie de stabilisation; c'est la contribution dela délocalisation des électrons (effets d'hybridation compris). Il est calculé par la méthode PPP. Le second terme est une répulsion d'échange dûe à tous les électrons de valence des trois atomes de carbone. Les corrections de corrélation sont introduites.Une surface d'énergie potentielle est construite; elle fournit une valeur de l'énergie d'activation proche de celle obtenue expérimentalement. Les approximations utilisées sont discutées. La méthode proposée est une généralisation de celles des indices de réactivité. On peut la considérer comme justifiant cette approche plus empirique.

     

Conformational search by potential energy annealing: Algorithm and application to cyclosporin A

Summary A major problem in modelling (biological) macromolecules is the search for low-energy conformations. The complexity of a conformational search problem increases exponentially with the number of degrees of freedom which means that a systematic search can only be performed for very small structures. Here we introduce a new method (PEACS) which has a far better performance than conventional search methods.To show the advantages of PEACS we applied it to the refinement of Cyclosporin A and compared the results with normal molecular dynamics (MD) refinement. The structures obtained with PEACS were lower in energy and agreed with the NMR parameters much better than those obtained with MD. From the results it is further clear that PEACS samples a much larger part of the available conformational space than MD does.     

Accurate potential energy surface and quantum reaction rate calculations for the H+CH4-->H2+CH3 reaction

Calculations for the cumulative reaction probability N(E) (for J=0) and the thermal rate constant k(T) of the H+CH(4)-->H(2)+CH(3) reaction are presented. Accurate electronic structure calculations and a converged Shepard-interpolation approach are used to construct a potential energy surface which is specifically designed to allow the precise calculation of k(T) and N(E). Accurate quantum dynamics calculations employing flux correlation functions and multiconfigurational time-dependent Hartree wave packet propagation compute N(E) and k(T) based on this potential energy surface. The present work describes in detail the various convergence test performed to investigate the accuracy of the calculations at each step. These tests demonstrate the predictive power of the present calculations. In addition, approximate approaches for reaction rate calculations are discussed. A quite accurate approximation can be obtained from a potential energy surface which includes only interpolation points on the minimum energy path.     

CH_3自由基与C_2H_5CN高温反应机理的理论研究

用G3(MP2)//B3PW91/6-311G(d,p)双级别方法研究了CH_3自由基与C_2H5_CN的反应机理和动力学性质.计算表明反应存在抽氢、加成-消除和取代3种机理7条反应通道.用CVT方法计算了所有反应通道在1 000K~3 000K温度范围内的速率常数,结果表明计算值与实验值符合得很好.     

Microsolvation of hydrogen sulfide: exploration of H2S.(H2O)n and SH-.H3O+.(H2O)n-1 (n = 5-7) cluster structures on ab initio potential energy surfaces by the scaled hypersphere search method

The scaled hypersphere search method was applied to ab initio potential energy surfaces of the H2S.(H2O)n/SH-.H3O+.(H2O)n-1 system with n = 5-7. Local minima databases including 121, 326, and 553 structures for n = 5-7, respectively, were obtained based on calculations at the MP2/6-311++G(3df,2p)//B3LYP/6-31+G** level. In these small cluster sizes, the SH-.H3O+.(H2O)n-1 type is still unstable relative to the H2S.(H2O)n type, and the global minima for H2S.(H2O)n are very similar to those of pure water clusters of (H2O)n+1. Thermodynamic simulations based on the present databases showed a structure transition from the well-mixed (H2O)n+1-like global minimum at low temperatures to unmixed complexes between H2S and (H2O)n at high temperatures.     

Application of the stabilization method to temporary anion states of CH3CN, CH3NC, CH3SCN, and CH3NCS in density functional theory with asymptotically corrected potentials

In this paper, density functional theory (DFT) with asymptotically corrected potentials is used to investigate CH(3)CN, CH(3)NC, CH(3)SCN, and CH(3)NCS molecules. For the energies of σ* and π* temporary anion states, the stabilized Koopmans' theorem (S-KT) using long-range correction functional and stabilized Koopmans-based (S-KB) approximation using local functional, are adopted. The stabilization procedure is accomplished by varying the exponents of appropriate diffuse functions. Results indicate that the calculations based on asymptotically corrected density functionals can yield better energy results of temporary anion states over conventional DFT methods.