Intermolecular potentials of the silane dimer calculated with Hartree-Fock theory, Møller-Plesset perturbation theory, and density functional theory

We have calculated the intermolecular interaction potentials of the silane dimer at the D3d conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order M?ller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with 108 functionals chosen from the combinations of 9 exchange and 12 correlation functionals. Single-point coupled cluster [CCSD(T)] calculations have also been carried out to calibrate the correlation effect. The HF calculations yield unbound potentials largely because of the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater type orbitals fitted with Gaussian functions (STO-nG, n = 3 approximately 6), Pople's medium size basis sets [up to 6-311++G(3df,3pd)], to Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(3d,3p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy ( approximately 0.05 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the expected C6 value from molecular polarizability calculations. We attribute the slow convergence partly to the inefficacy of using the MP2 calculations with Gaussian type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the expected potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energies calculated using the OPTXHCTH147, PBEVP86, PBEP86, PW91TPSS, PW91PBE, and PW91PW91 functionals and the equilibrium bond lengths calculated using the MPWHCTH93, TPSSHCTH, PBEVP86, PBEP86, PW91TPSS, PW91PBE, and PW91PW91 functionals are close to the MP2 results using the 6-311++G(3df,3pd) basis set. A correlation between the calculated DFT potentials and the exchange and correlation enhancement factors at the low-density region has been elucidated. The asymptotic behaviors of the DFT potentials are also analyzed.     

A mathematical approach to chemical equilibrium theory for gaseous systems—I: theory

Equilibrium theory occupies an important position in chemistry and it is traditionally based on thermodynamics. A novel mathematical approach to chemical equilibrium theory for gaseous systems at constant temperature and pressure is developed. Six theorems are presented logically which illustrate the power of mathematics to explain chemical observations and these are combined logically to create a coherent system. This mathematical treatment provides more insight into chemical equilibrium and creates more tools that can be used to investigate complex situations. Although some of the issues covered have previously been given in the literature, new mathematical representations are provided. Compared to traditional treatments, the new approach relies on straightforward mathematics and less on thermodynamics, thus, giving a new and complementary perspective on equilibrium theory. It provides a new theoretical basis for a thorough and deep presentation of traditional chemical equilibrium. This work demonstrates that new research in a traditional field such as equilibrium theory, generally thought to have been completed many years ago, can still offer new insights and that more efficient ways to present the contents can be established. The work presented here can be considered appropriate as part of a mathematical chemistry course at University level.     

Paired-permanent approach to valence bond theory

A new function called paired-permanent is defined and widely discussed, and a practicable procedure for evaluations of paired-permanents is proposed, which is similar to the Laplace method for determinants. Using the concept of paired-permanents, an efficient algorithm is presented for evaluating the Hamiltonian and overlap matrix elements in the spin-free form of valence bond (VB) theory. With the new algorithm, a spin-free wavefunction is simply written as a paired-permanent, and an overlap matrix element may be obtained by evaluating a corresponding paired-permanent. Meanwhile, the Hamiltonian matrix element is expressed in terms of the summation of the products of electronic integrals and the corresponding sub-paired-permanents     

Intermolecular potentials of the methane dimer calculated with Møller-Plesset perturbation theory and density functional theory

We have calculated the intermolecular interaction potentials of the methane dimer at the minimum-energy D(3d) conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order M?ller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with the Perdew-Wang (PW91) functional as the exchange or the correlation part. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions (STO-nG) (n=3-6) [Quantum Theory of Molecular and Solids: The Self-Consistent Field for Molecular and Solids (McGraw-Hill, New York, 1974), Vol. 4], Pople's medium size basis sets of Krishnan et al. [J. Chem. Phys. 72, 650 (1980)] [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets [J. Chem. Phys. 90, 1007 (1989)] (cc-pVXZ and aug-cc-pVXZ) (X=D, T, and Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d,2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (approximately 0.01 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the destined C6 value from molecular polarizability calculations. The slow convergence could indicate the inefficacy of using the MP2 calculations with Gaussian-type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the destined potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energy calculated using the PW91PW91 functional and the equilibrium bond length calculated using the PW91VP86 functional are close to the MP2 results at the basis set limit.     

Introducing the γ function in quantum theory

Through a series of postulates, we define a function γ(x) whose square acts as Dirac's δ(x) and exhibits several unusual properties. Though the square root of δ cannot be defined among distributions, it appears in quantum theory if one wants to associate a wave function to a (quasi)classical particle having charge distribution δ(x) . The newly defined function γ(x) serves to describe quasi-classical particles using part of the quantum formalism (eg, wave functions, operators, expectation values) but exhibiting classical properties. The function γ(x) appears to be useful to define model wave functions for simple (quasi)quantum systems. In a spherical coordinate system, γ(r − r₀) leads to a quasi-classical “bubble” model of the hydrogen atom, where the electron is distributed on the surface of a sphere with radius r₀, and it provides exact quantum mechanical energies of its total symmetric levels. For other simple quantum systems, it provides approximate but meaningful energies. In particular, exact energy differences for harmonic oscillator levels are obtained, with the zero-point energy missing.     

Improved third-order Møller-Plesset perturbation theory

Based on a partitioning of the total correlation energy into contributions from parallel‐ and antiparallel‐spin pairs of electrons, a modified third‐order Møller–Plesset (MP) perturbation theory is developed. The method, termed SCS–MP3 (SCS for spin‐component‐scaled) continues previous work on an improved version of MP2 (S. Grimme, J Chem Phys 2003, 118, 9095). A benchmark set of 32 isogyric reaction energies, 11 atomization energies, and 11 stretched geometries is used to assess to performance of the model in comparison to the standard quantum chemical approaches MP2, MP3, and QCISD(T). It is found, that the new method performs significantly better than usual MP2/MP3 and even outperforms the more costly QCISD method. Opposite to the usual MP series, the SCS third‐order correction uniformly improves the results. Dramatic enhancements are especially observed for the more difficult atomization energies, some of the stretched geometries, and reaction and ionization energies involving transition metal compounds where the method seems to be competitive or even superior to the widely used density functional approaches. Further tests performed for other complex systems (biradicals, C₂₀ isomers, transition states) demonstrate that the SCS–MP3 model yields often results of QCISD(T) accuracy. The uniformity with which the new approach improves for very different correlation problems indicates significant robustness, and suggests it as a valuable quantum chemical method of general use. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1529–1537, 2003     

A theoretical study of CO adsorption on gold by Hückel theory and density functional theory calculations

It is crucial to understand the nature of CO adsorption on gold so as to elucidate the mechanism of low-temperature CO oxidation on nanogold catalysts. We performed theoretical analysis of CO adsorption on gold by using Hückel theory and density functional theory (DFT) calculations. Hückel theory indicates that CO adsorption on gold is dominated by the electron distribution at the Au atom, which is greatly affected by neighboring Au atoms, coadsorbed or doping species. The increase of σ-bonding electrons should weaken the CO adsorption, while the increase of π-electrons should strengthen the adsorption. DFT calculations proved this prediction quantitatively for various systems, including CO adsorption on a Au(100)-hex surface with locally varying subsurface configurations and CO coadsorption with acceptor or donor species.     

A new theory for symmetric orbital and tensor

Ｐｏｉｎｔｇｒｏｕｐｓｙｍｍｅｔｒｉｅｓａｒｅｅｓｓｅｎｔｉａｌｔｏｔｈｅｉｌｌｕｓｔｒａｔｉｏｎｏｆｔｈｅｒｅｌａｔｉｏｎｓｈｉｐｓｂｅｔｗｅｅｎｍｏｌｅｃｕｌａｒｓｔｒｕｃｔｕｒｅｓａｎｄｐｒｏｐｅｒｔｉｅｓ,ｔｈｅｓｔａｔｅｌａｂｅｌｉｎｇａｎｄｓｐｅｃｔｒｏｓｃｏｐｉｃｓｅｌｅｃｔｉｏｎｒｕｌｅｓ,ａｓｗｅｌｌａｓｔｈｅｓｉｍｐｌｉｆｉｃａｔｉｏｎｏｆｔｈｅｏｒｅｔｉｃａｌｃａｌｃｕｌａｔｉｏｎｓｏｆｑｕａｎｔｕｍｃｈｅｍｉｓｔｒｙ.Ｉｎｔｈｅｐｏｉｎｔｇｒｏｕｐｔｈｅｏｒｙ,ｈｏｗｅｖｅｒ…     

Applications of self-consistent field theory in polymer systems

1Introduction Owing to the specificity of the long chain,polymers present complexity and versatility.These molecules in the system can be various in their topological struc-tures,such as linear,star,comb or circle structures;meanwhile they can be polymeri…     

What I like about Hückel theory

We start with some biographical notes on Erich Hückel, in the context of which we also mention the merits of Otto Schmidt, the inventor of the free-electron model. The basic assumptions behind the HMO (Hückel Molecular Orbital) model are discussed, and those aspects of this model are reviewed that make it still a powerful tool in Theoretical Chemistry. We ask whether HMO should be regarded as semiempirical or parameter-free. We present closed solutions for special classes of molecules, review the important concept of alternant hydrocarbons and point out how useful perturbation theory within the HMO model is. We then come to bond alternation and the question whether the pi or the sigma bonds are responsible for bond delocalization in benzene and related molecules. M?bius hydrocarbons and diamagnetic ring currents are other topics. We come to optimistic conclusions as to the further role of the HMO model, not as an approximation for the solution of the Schr?dinger equation, but as a way towards the understanding of some aspects of the Chemical Bond.     

Relating β+ radionuclides’ properties by order theory

We studied 27 β⁺ radionuclides taking into account some of their variants encoding information of their production, such as integral yield, threshold energy and energy of projectiles used to generate them; these radionuclides are of current use in clinical diagnostic imaging by positron emission tomography (PET). The study was conducted based on physical, physico-chemical, nuclear, dosimetric and quantum properties, which characterise the β⁺ radionuclides selected, with the aim of finding meaningful relationships among them. In order to accomplish this objective the mathematical methodology known as formal concept analysis was employed. We obtained a set of logical assertions (rules) classified as implications and associations, for the set of β⁺ radionuclides considered. Some of them show that low mass defect is related to high and medium values of maximum β⁺ energy, and with even parity and low mean lives; all these parameters are associated to the dose received by a patient subjected to a PET analysis.     

Intruder state avoidance multireference Møller-Plesset perturbation theory

A new perturbation approach is proposed that enhances the low‐order, perturbative convergence by modifying the zeroth‐order Hamiltonian in a manner that enlarges any small‐energy denominators that may otherwise appear in the perturbative expansion. This intruder state avoidance (ISA) method can be used in conjunction with any perturbative approach, but is most applicable to cases where small energy denominators arise from orthogonal‐space states—so‐called intruder states—that should, under normal circumstances, make a negligible contribution to the target state of interests. This ISA method is used with multireference Møller–Plesset (MRMP) perturbation theory on potential energy curves that are otherwise plagued by singularities when treated with (conventional) MRMP; calculation are performed on the 1³Σ state of O₂; and the 2¹Δ, 3¹Δ, 2³Δ, and 3³Δ states of AgH. This approach is also applied to other calculations where MRMP is influenced by intruder states; calculations are performed on the ³Π_u state of N₂, the ³Π state of CO, and the 2¹A′ state of formamide. A number of calculations are also performed to illustrate that this approach has little or no effect on MRMP when intruder states are not present in perturbative calculations; vertical excitation energies are computed for the low‐lying states of N₂, C₂, CO, formamide, and benzene; the adiabatic ¹A₁–³B₁ energy separation in CH₂, and the spectroscopic parameters of O₂ are also calculated. Vertical excitation energies are also performed on the Q and B bands states of free‐base, chlorin, and zinc–chlorin porphyrin, where somewhat larger couplings exists, and—as anticipated—a larger deviation is found between MRMP and ISA‐MRMP. © 2002 Wiley Periodicals, Inc. J Comput Chem 10: 957–965, 2002     

Generalized Rayleigh-Schrödinger perturbation theory in matrix form

Thenested summation symbols (NSS) formalism is used as a starting point to formulate a completely general Rayleigh-Schrödinger perturbation theory (RSPT) scheme. In order to make the theoretical framework practical from a computational point of view, the matrix form for the theory is given in every case. As a result, an algorithmic iterative recipe to compute eigenvalue and eigenvector corrections up to any order is described. Degenerate systems are also treated. At the same time the described procedure allows the computation of eigenvalue and eigenvector derivatives with respect to a set of parameters.A contribution of the Grup de Quimica Quàntica de l'Institut d'Estudis Catalans.     

Tensor factorizations of local second-order Møller-Plesset theory

Efficient electronic structure methods can be built around efficient tensor representations of the wavefunction. Here we first describe a general view of tensor factorization for the compact representation of electronic wavefunctions. Next, we use this language to construct a low-complexity representation of the doubles amplitudes in local second-order M?ller-Plesset perturbation theory. We introduce two approximations--the direct orbital-specific virtual approximation and the full orbital-specific virtual approximation. In these approximations, each occupied orbital is associated with a small set of correlating virtual orbitals. Conceptually, the representation lies between the projected atomic orbital representation in Pulay-Saeb? local correlation theories and pair natural orbital correlation theories. We have tested the orbital-specific virtual approximations on a variety of systems and properties including total energies, reaction energies, and potential energy curves. Compared to the Pulay-Saeb? ansatz, we find that these approximations exhibit favorable accuracy and computational times while yielding smooth potential energy curves.     

Is Poisson-Boltzmann theory insufficient for protein folding simulations?

The Poisson-Boltzmann theory has been widely used in the studies of energetics and conformations of biological macromolecules. Recently, introduction of the efficient generalized Born approximation has greatly extended its applicability to areas such as protein folding simulations where highly efficient computation is crucial. However, limitations have been found in the folding simulations of a well-studied beta hairpin with several generalized Born implementations and different force fields. These studies have raised the question whether the underlining Poisson-Boltzmann theory, on which the generalized Born model is calibrated, is adequate in the treatment of polar interactions for the challenging protein folding simulations. To address the question whether the Poisson-Boltzmann theory in the current formalism might be insufficient, we directly tested our efficient numerical Poisson-Boltzmann implementation in the beta-hairpin folding simulation. Good agreement between simulation and experiment was found for the beta-hairpin equilibrium structures when the numerical Poisson-Boltzmann solvent and a recently improved generalized Born solvent were used. In addition simulated thermodynamic properties also agree well with experiment in both solvents. Finally, an overall agreement on the beta-hairpin folding mechanism was found between the current and previous studies. Thus, our simulations indicate that previously observed limitations are most likely due to imperfect calibration in previous generalized Born models but not due to the limitation of the Poisson-Boltzmann theory.