Frequency dispersed transient absorption spectra of dissolved perylene: A case study using the density matrix version of the MCTDH method

A theoretical scheme is presented to calculate non-linear optical spectra of molecules in solution. Starting with electronic structure calculations of the ground and excited state, a subset of vibrational coordinates exhibiting the largest Huang–Rhys factors is assigned. It is used to set up a model Hamiltonian for density matrix multi configurational time-dependent Hartree (MCTDH) calculations. The expression derived for the dissipative part of the equation of motion goes beyond the earlier used Lindblad-form. In order to calculate the non-linear response the electric field strength is introduced into the density matrix equations used to directly determine the polarization. The whole scheme is applied to perylene as a reference case.     

Solutions of the Klein–Gordon equation with the improved Tietz potential energy model

We present the relativistic rotation–vibrational energy equation of a diatomic molecule which moves under the improved Tietz potential energy model in higher spatial dimensions. The nonrelativistic limits of the bound state solutions of the Klein–Gordon equation are the bound state solutions of the Schrödinger equation with the same potential energy function. Numerical analysis results show that there exists a critical point around which the solution behaviors bifurcate into two extreme cases. Below the critical point, the behavior of the relativistic vibrational energies for the ground electronic state of carbon monoxide in higher dimensions keeps similar to that of the three-dimensional system, while this symmetry phenomenon breaks and the Klein–Gordon equation has no stability solution upon the critical point.     

Variational method for the calculation of the vibrational structure of the electronic spectra of polyatomic molecules. I

A method is proposed to calculate the vibrational structures of the electronic spectra of polyatomic molecules based on the variational solution of the vibrational problem in the excited state with the vibrational wave functions of the ground state as basis set. The electrono-vibrational problem leads to an evaluated and diagonalized variational matrix. The elements of the variational matrix have a simple form which is easily evaluated, has a clear physical meaning and is directly interconnected with observed spectral effects. This allows preliminary estimation of spectral phenomena and correction of the molecular model to take account of experimental results. The use of contemporary methods of diagonalization of the variational matrix, which possesses a characteristic structure, facilitates a tenfold increase in the speed of the method in comparison with traditional methods.K. A. Timiryazev Agricultural Academy. Translated from Zhurnal Strukturnoi Khimii, Vol. 34, No. 1, pp. 141–148, January–February, 1993.     

Determining partial differential cross sections for low-energy electron photodetachment involving conical intersections using the solution of a Lippmann-Schwinger equation constructed with standard electronic structure techniques

A method for obtaining partial differential cross sections for low energy electron photodetachment in which the electronic states of the residual molecule are strongly coupled by conical intersections is reported. The method is based on the iterative solution to a Lippmann-Schwinger equation, using a zeroth order Hamiltonian consisting of the bound nonadiabatically coupled residual molecule and a free electron. The solution to the Lippmann-Schwinger equation involves only standard electronic structure techniques and a standard three-dimensional free particle Green's function quadrature for which fast techniques exist. The transition dipole moment for electron photodetachment, is a sum of matrix elements each involving one nonorthogonal orbital obtained from the solution to the Lippmann-Schwinger equation. An expression for the electron photodetachment transition dipole matrix element in terms of Dyson orbitals, which does not make the usual orthogonality assumptions, is derived.     

Variational method for the calculation of the vibrational structure of the electronic spectra of polyatomic molecules. II

A variational method has been developed to solve the vibrational problem in the excited electronic state and to calculate the vibrational structure of the electronic spectrum of polyatomic molecules. The properties and structural characteristics of the variational matrix have been analyzed and an effective algorithm has been proposed for its approximate diagonalization. The effectiveness of the method and the corresponding suite of programs for the personal computer have been analyzed via the results of model calculations for a number of molecular structures. The method has high precision (errors of about 5% for frequencies and 15% for relative intensities), is an order of magnitude faster than previously used methods, and provides the possibility for the effective solution of the electrono-vibrational problem for polyatomic molecules, including the reverse problem.K. A. Timiryazev Agricultural Academy. Translated from Zhurnal Strukturnoi Khimii, Vol. 34, No. 1, pp. 149–156, January–February, 1993.     

Simulation of vibrational dephasing of I(2) in solid Kr using the semiclassical Liouville method

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.     

Electronic vibrational problem for molecules with inversion motions

A general approach to the solution of the electronic vibrational problem with imposed conditions on possible vibrational nuclear motions in a double-minimum potential well is proposed.     

Note on the role of vibrational modes in molecular electronic transitions

A simple application of a readily available quantum chemistry program (AMPAC) permits an illuminating presentation of the role of vibrational modes in electronic transitions. A direct comparison of modal surfaces for different electronic states of the same molecule can be made by using a perspective plot of the Duschinsky matrix for the transition with mode indices or eigenvalue sequence, as the planar axes. The sum of squares of the off-diagonal elements of the Duschinsky matrix can be used to give a measure of the difference between vibrational modes of the initial and final states. Calculations indicate that, in biacetyl, the triplet state is closer vibrationally to the anion ground state than either the singlet or the neutral ground state, while in glyoxal the ground state neutral has greater vibrational similarity to the anion ground state. The measure also indicates little change in vibrational modes upon intersystem crossing in formaldehyde.     

Theory and mechanism of electron transfer in a condensed medium at high temperatures with allowance for change in vibrational frequencies

An expression for electron transfer rate has been obtained through the solution of a time wave equation by the variational method by defining the wave function as a linear combination of functions corresponding to electron localization on the donor and on the acceptor. A dependence of electron transfer on temperature, on the electronic and vibrational characteristics of the system has been derived. An activation energy temperature-variation effect has been obtained. It has been proved that many-electron transfers are impossible.     

Accurate potential for the ground state of the hydrogen molecule

Starting from the spectroscopic constants, an electronic potential for the ground state hydrogen molecule is presented. Self-consistence is checked by numerical integration of the radial wave equation. The mean eigenvalue deviation is about 1 cm⁻¹. Comparison with the latest theoretical work is considered. New revised spectroscopic constants and vibrational quanta are calculated.     

Cross sections and rate coefficients for electronic excitation of the triplet states of the hydrogen molecule in different vibrational levels

Cross sections for the excitation of the triplet state of H₂ from different vibrational levels of the ground electronic state have been calculated by using the Gryzinski approximation. The results for the ground vibrational level are in satisfactory agreement with the corresponding values obtained by the quantum mechanical close coupling method. The calculated cross sections have been used to generate rate coefficients for the excitation of the triplet states by using a self-consistent electron energy distribution function, obtained by numerical integration of the Boltzmann equation. The results show a strong increase of the different rate coefficients with increasing the vibrational quantum number.     

Computational spectroscopy of ubiquitin: comparison between theory and experiments

Using the constrained molecular dynamics simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, the authors have established computational schemes for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and two-dimensional (2D) IR photon echo spectra of the protein ubiquitin in water. Vibrational characteristic features of these spectra in the amide I vibration region are discussed. From the semiempirical quantum chemistry calculation results on an isolated ubiquitin, amide I local mode frequencies and vibrational coupling constants were fully determined. It turns out that the amide I local mode frequencies of ubiquitin in both gas phase and aqueous solution are highly heterogeneous and site dependent. To directly test the quantitative validity of thus obtained spectroscopic properties, they compared the experimentally measured amide I IR, 2D IR, and electronic circular dichroism spectra with experiments, and found good agreements between theory and experiments. However, the simulated VCD spectrum is just qualitatively similar to the experimentally measured one. This indicates that, due to delicate cancellations between the positive and negative VCD contributions, the prediction of protein VCD spectrum is critically relied on quantitative accuracy of the theoretical model for predicting amide I local mode frequencies. On the basis of the present comparative investigations, they found that the site dependency of amide I local mode frequency, i.e., diagonal heterogeneity of the vibrational Hamiltonian matrix in the amide I local mode basis, is important. It is believed that the present computational methods for simulating various vibrational and electronic spectra of proteins will be of use in further refining classical force fields and in addressing the structure-spectra relationships of proteins in solution.     

Surface Green's function calculations: a nonrecursive scheme with an infinite number of principal layers

A novel computational method for a surface Green's function matrix is introduced for the calculation of electrical current in molecular wires. The proposed nonrecursive approach includes an infinite number of principal layers and yields the second-order matrix equation for the transformed Green's function matrix. The solution is found by the direct diagonalization of the auxiliary matrix without any iteration process. As soon as complex roots of the auxiliary matrix (approximately GS) are calculated, the gaps and the bands in the surface electronic structure are found. It is shown that the solution of a second-order matrix equation determines the spectral density matrix, that is, the density of states for noninteracting electrons. Single and double principal layer models are studied both analytically and numerically. The energy interval for nonvanishing spectral matrices is determined. This method is applicable to matrices of any rank.     

Size-extensive vibrational self-consistent field method

The vibrational self-consistent field (VSCF) method is a mean-field approach to solve the vibrational Schro?dinger equation and serves as a basis of vibrational perturbation and coupled-cluster methods. Together they account for anharmonic effects on vibrational transition frequencies and vibrationally averaged properties. This article reports the definition, programmable equations, and corresponding initial implementation of a diagrammatically size-extensive modification of VSCF, from which numerous terms with nonphysical size dependence in the original VSCF equations have been eliminated. When combined with a quartic force field (QFF), this compact and strictly size-extensive VSCF (XVSCF) method requires only quartic force constants of the ?(4)V/?Q(i)(2)?Q(j)(2) type, where V is the electronic energy and Q(i) is the ith normal coordinate. Consequently, the cost of a XVSCF calculation with a QFF increases only quadratically with the number of modes, while that of a VSCF calculation grows quartically. The effective (mean-field) potential of XVSCF felt by each mode is shown to be harmonic, making the XVSCF equations subject to a self-consistent analytical solution without matrix diagonalization or a basis-set expansion, which are necessary in VSCF. Even when the same set of force constants is used, XVSCF is nearly three orders of magnitude faster than VSCF implemented similarly. Yet, the results of XVSCF and VSCF are shown to approach each other as the molecular size is increased, implicating the inclusion of unnecessary, nonphysical terms in VSCF. The diagrams of the XVSCF energy expression and their evaluation rules are also proposed, underscoring their connected structures.     

Electronic factor in electron self-exchange reaction of hydrated redox ion pairs from thermodynamic data

An accurate scheme for determining the electronic factor of the electron self-exchange reaction in solution is presented in this paper. The used various activation parameters and slopes of potential energy surfaces are obtained in terms of an improved activation model and the accurate potential function determined from the vibrational spectroscopic and thermodynamic data. The coupling matrix elements are determined using numerical integral method over the perturbed double-zeta Slater-type state functions. Theoretical results of electronic factor in this work are found in close agreement with those extracted from experimental rate constant data and to be less than unity. Results indicate that outer-sphere electron transfer reactions in solution involving hydrated transition metal ions are nonadiabatic in nature.     

Quantum equations for vibrational dynamics on metal surfaces

A first principles treatment of the vibrational dynamics of molecular chemisorbates on metal surfaces is presented. It is shown that the mean field quantum evolution of the vibrational position operator is determined by a quantum Langevin equation with an electronic friction. In the mean field limit, the quantum noise and friction are related by the quantum fluctuation-dissipation theorem. The classical limit of this model is shown to agree with previously proposed models. A criterion is presented to describe the validity of the weak-coupling approximation and equations of motion for the dynamics in the presence of strong nonadiabatic coupling to electron-hole pairs are presented.     

Anharmonic problem without the anharmonic potential

Anharmonic effects are shown to be obtained immediately in the statement of a quantum problem as a general electronic vibrational problem in the matrix formulation and without the use of a traditional anharmonic potential. The methods to form the matrix and to calculate all matrix elements are presented.     

Novel methods for calculating the fine vibronic spectra of polyatomic molecules

Novel approximate methods for calculating the vibrational structure of the electronic spectra of polyatomic molecules—a method for the direct calculation of the overlap integrals of vibrational wave functions for the electronic states involved in a transition and a variational method for the solution of the vibrational problem for the excited states—are discussed. The methods are based on the consideration of the displacement and entanglement of normal coordinates, the quasiorthogonality of the Dushinsky transformation, and the classification of the states by total vibrational quantum numbers. Matrix perturbation theory is employed. It is shown that the accuracy of these methods compares well with the accuracy of the available “exact” techniques (the errors are ∼1 cm⁻¹ for frequency and 10% for relative intensity). At the same time, calculations by the new methods are performed more than two orders of magnitude faster than by the previously known methods. K. A. Timiryazev Agricultural Academy, Moscow. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 217–230, March–April, 1995. Translated by I. Izvekova     

Proton relay reaction in green fluorescent protein (GFP): Polarization-resolved ultrafast vibrational spectroscopy of isotopically edited GFP

The complex transient vibrational spectra of wild type (wt) GFP have been assigned through polarization anisotropy measurements on isotopically edited proteins. Protein chromophore interactions modify considerably the vibrational structure, compared to the model chromophore in solution. An excited-state vibrational mode yields information on excited-state electronic structure. The proton relay pathway is characterized in more detail, and the protonation of the remote E222 residue is shown to occur in a concerted step. Modifications to protein vibrational modes are shown to occur following electronic excitation, and the potential for these to act as a trigger to the proton relay reaction is discussed.     

Ab initio vibration and ro-vibrational spectrum of the 1A1 state of He2Si2+

The low-lying ro-vibrational states for the ground electronic state (1A1) of HeSi2+ have been calculated using an ab initio variational solution of the nuclear Schr?dinger equation. A 96 point CCSD(T)/cc-pCVQZ potential energy surface (PES) has been calculated and a Ogilvie-Padé (3,6) potential energy function has been generated. This force field was embedded in the Eckart-Watson Hamiltonian from which the vibrational and ro-vibrational eigenfunctions and eigenenergies have been variationally calculated. A 70 point QCISD/aug-cc-pCVTZ discrete dipole moment surface (DMS) was calculated and a 5th order power series expansion (in terms of the two bond lengths and the included bond angle) has been generated. Absolute line intensities have been calculated and are presented for some of the most intense transitions between the vibrational ground state and the low-lying ro-vibrational states of this ion.