Spectra Of Polyatomic Molecules Research Articles

Efficient simulation of time- and frequency-resolved four-wave-mixing signals with a multiconfigurational Ehrenfest approach.

We have extended the multiconfigurational Ehrenfest approach to the simulation of four-wave-mixing signals of systems involving multiple electronic and vibrational degrees of freedom. As an illustration, we calculate signals of three widely used spectroscopic techniques, time- and frequency-resolved fluorescence spectroscopy, transient absorption spectroscopy, and two-dimensional (2D) electronic spectroscopy, for a two-electronic-state, twenty-four vibrational-mode conical intersection model. It has been shown that all these three spectroscopic signals characterize fast population transfer from the higher excited electronic state to the lower excited electronic state. While the time- and frequency-resolved spectrum maps the wave packet propagation exclusively on the electronically excited states, the transient absorption and 2D electronic spectra reflect the wave packet dynamics on both electronically excited states and the electronic ground state. Combining trajectory-guided Gaussian basis functions and the nonlinear response function formalism, the present approach provides a promising general technique for the applications of various Gaussian basis methods to the calculations of four-wave-mixing spectra of polyatomic molecules.

SENSING COOPERATIVE ELECTRON-GAMMA-NUCLEAR EFFECT IN MULTIATOMIC MOLECULES AND ITS APPLICATION

One of the promising areas of sensor electronics, molecular spectroscopy and physics is the creation of molecular sensors for the detection of various compounds or phenomena, and, as a rule, the principle of operation of a molecular sensor is based on certain physical or chemical properties or effects. Nowadays, the cooperative spectral effects for polyatomic molecules in the external field of laser radiation are of great interest. When a nucleus in a molecule absorbs or emits a photon, then it is possible changing the electron, vibrational and rotational energy of the molecule, and then the so-called cooperative electron-vibrational-rotational-nuclear transitions take place. The spectrum of a molecule contains a set of electron-vibrational-rotational-nuclear satellites, the appearance of which is caused by a change in the state of a molecular system interacting with a photon. This paper presents the first quantitative data on the probability of vibrational -nuclear transitions in the case of the radiation spectrum and absorption of the 186Re nucleus (E = 186.7 keV) in the ReO4 molecule. It seems that the cooperative electron-gamma-nuclear effect in the spectra of polyatomic molecules can be used as a basis for the creation of new techniques and practical implementations of molecular sensors.

A Simple Mathematical Model of Optical Spectra of Polyatomic Molecules

A mathematical model which is logically very simple and convenient for programming is proposed for describing and studying the optical spectra of polyatomic molecules from the IR to the UV, including the Rydberg region, with computer simulations. For a specified molecular geometry, the only variable parameters are the elements of the force constant matrices for the ground and electronically excited states and the well depths. The functions for the electrons are specified by sets of principal quantum numbers for the radial components in a hydrogen-like atom. The model can be used to solve both direct and inverse problems.

Raman spectral calculation by vibrational coupled-cluster method in bosonic representation

ABSTRACTWe present a method to calculate the Raman spectra of poly-atomic molecules using the vibrational coupled-cluster method in bosonic representation. The effective operator-based approach with Arponen's extended coupled-cluster ansatz is used to calculate the transition matrix elements associated with the polarisability surface to calculate the Raman intensities. A test calculation is made on furan and the resultant spectrum is compared with the experimental spectrum. The agreement between the theoretical anharmonic spectrum and experimental spectrum is quite good. An observation made from these calculations is that the transitions in the 3000–3200 cm−1 range (CH stretch) is dominated by several transitions to final states that are dominated by multiple quantum states and hardly to any single fundamental state. We used both dynamic and static polarisabilities and found that the spectra generated from these two polarisability tensors are practically identical, implying that the polarisability tensor is insensitive to the incident frequency.

On algorithms for calculating the SVL-fluorescence spectra of polyatomic molecules

A software package for modeling the fluorescence spectra from a single vibrational level (SVL) of excited electron states under resonance laser excitation, in the adiabatic approximation with allowance for the “confusion” of normal coordinates under electron excitation, i.e., the Dushinsky effect, is presented. To algorithmize the calculation of the intensities in resonance fluorescence spectra, thirteen modules for the calculating Franck–Condon integrals are created. To optimize the calculation process, some simpler expressions are derived for the common terms of nested sums in the formulas for calculating Franck–Condon integrals from tone and overtone levels. To accelerate calculations, some constraints in the form of inequalities are additionally imposed on the range of vibrational quantum numbers in the ground electron state. The proposed algorithm for the modeling of SVL-fluorescence spectra of polyatomic molecules is based on quantum models of molecules in the ground and excited electron states calculated within the framework of contemporary ab initio quantum-mechanical methods and methods based on density functional theory.

Stretching Vibrational IR Active Spectra of Carbon Fullerenes

Molecular vibration spectra are of great significance in the study of molecular structures and characters. Here, an analytical method of Lie algebraic approach is imported into the domain of micro-scaled molecular spectra. The vibrational modes of fullerenes C50, C70 and C80 are calculated considering the C-C bond interactions. The algebraic Hamiltonian describing vibrational spectra of polyatomic molecules has been derived by using the dynamical U(2) Lie algebra. The calculations are performed within the framework of the vibron model with fewer numbers of algebraic parameters. The calculations show a reasonable agreement with previously published calculated and experimental results.

Unified analytical treatment for calculation of the two-dimensional Franck-Condon factors using the duschinsky transformation

Including binomial expansion theorems, we present an analytical formula for calculating Franck–Condon (FC) factors of two-dimensional (2D) harmonic oscillators including the Duschinsky effect. The FC principle has various practical applications in quantum modeling of electronic spectra of polyatomic molecules. The 2D FC factors are expressed through the binomial coefficients. Use of the memory of the computer for the calculation of binomial coefficients may extend the limits to large arguments for users and result in speeder calculation, should such limits be required in practice. Accurate numerical results are provided to validate the proposed algorithm. © 2012 Wiley Periodicals, Inc.

Toward substantiation of a problem in the general quantum theory of spectra of polyatomic molecules

Certain basic principles of substantiation of the quantum problem in the theory of spectra of complex molecules are considered. A Schroninger equation is introduced that corresponds to the notion of the molecule as a geometric figure. The equation always reflects an inextricable link between electronic and nuclear motions with the separation of variables being retained. A method of formation of the energy matrix, which ensures the most complete description of the molecule as an inextricable electronic-nuclear system, is proposed. The nature of a factor that combines the electronic-nuclear interactions and of the corresponding term in the general electronic-nuclear Hamiltonian and in the expression for the matrix element of the optical transition is analyzed. Attention is drawn to the manifestation of the requirement of complementarity in the most consistent substantiation of the entire problem. Parameters that have a simple meaning and that simultaneously affect both vibrational and electronic components of the general wave function and vibronic energy levels are introduced. This makes it possible to pose and solve corresponding inverse spectral problems.

On the stability of parameters of molecular models in the parametric method of the theory of vibronic spectra

We have studied the stability of the system of parameters used in the parametric method of the theory of vibronic spectra of polyatomic molecules with respect to whether the initial structural-dynamic model of the ground state of a molecule is formed either by the fragmentary method or by direct quantum-chemical calculation. Modeling of excited states and spectra of the stilbene-h12 and stilbene-d12 molecules showed that, although the initial models of the ground states are significantly different, calculated changes in the geometry that occur upon excitation and electronic-vibrational spectra of the models are close and quantitatively agree with experiment. This indicates that the parameters of the method are stable and are applicable for performing predictive calculations of vibronic spectra based on models of the ground states created by different methods. We show that the fragmentary method has a considerable advantage, since models created by this method take into account the continuity of the structure in series of related compounds and calculations can be easily performed for molecules of arbitrarily high complexity. We show that direct quantum-chemical calculations are important in the case of molecules with unknown structural-dynamic models of fragments in the ground states.

Evaluation of Ecological Function of Mangrove Soil on Absorbing Heavy Metals: A Case Study from the Dongzhaigang Mangrove in China

ABSTRACT: Mangroves are special plant communities that live along intertidal zones in tropical and subtropical areas. They are regarded as one of the most important types of natural ecosystem in the world because of the many ecosystem functions that they perform, of which water purification is the most complex. Mangrove ecosystems are conducive to the deposition and retention of heavy metals. So it is important to understand the impact of heavy metals on mangrove ecosystems, and especially on soil subsystems. We examined the levels of heavy metals in the soil of mangroves in the Dongzhaigang Mangrove National Nature Reserve. Dongzhaigang, the first mangrove nature reserve established in China, is located south of Haikou in Hainan Island and encompasses 33.37 km 2 , of which mangroves comprise 20.56 km 2 . To assess the impact of human activities, we collected a large number of soil samples in four sampling areas (the protection station, the harbor, a tour area, and Yeboluo island) in the study area. We measured the concentrations of Cu, Pb, Zn and Cd in the soil samples using the spectra of polyatomic molecules. The average concentrations of Cu, Pb, Zn and Cd were 5.04 μg/g, 10.36 μg/g, 20.06 μg/g and 0.06 μg/g, respectively, and the heavy metal concentrations were lowest in the protected area, highest in the harbor, and intermediate in Yeboluo Island and the tour area. The heavy metal concentrations in the soil collected from different sample plots are related not only to the physical and chemical properties of the soil, but also to the heavy metal emitted by nearby pollution sources. Our analysis indicates that tourist boats are the main pollution sources in the study area. Key words: ecological function, heavy metal, mangrove soil

Interpretation of the vibrational spectra of polycrystalline adenine

The infrared and Raman spectra of the tetramer of the adenine N9H are calculated and analyzed. The vibrational spectra of polycrystalline adenine are interpreted. It is demonstrated that the method for calculating the vibrational spectra of molecular complexes formed by hydrogen bonds can be used for interpreting the vibrational spectra of polyatomic molecules in the solid state.

Quantum-mechanical calculation of the intensity distribution in resonance Raman spectra of guanine-cytosine pair

The method of quantum-mechanical calculation of the relative line intensities in the resonance Raman (RR) spectra of polyatomic molecules, which was previously applied to the analysis of the spectra of individual cyclic molecules and makes it possible to take into account the Herzberg-Teller and Duschinsky effects, as well as the frequency effect, is applied for the first time to the calculation of the spectra of a pair guanine-cytosine. Satisfactory agreement between the calculated results and the available experimental data is obtained. The particular features of the intensity distribution in the RR spectra of the guanine-cytosine pair excited by laser radiation at 266, 240, 218, and 200 nm are analyzed. The RR spectra of the guanine-cytosine pair are compared with the spectra of the individual guanine and cytosine molecules excited by the laser radiation at the same wavelengths.

Quantum-mechanical calculation of the relative line intensities in resonance Raman spectra of adenine-thymine and adenine-uracil molecular base pairs

A quantum-mechanical method of calculation of the relative line intensities in the resonance Raman spectra of polyatomic molecules in the Herzberg-Teller approximation is applied for the first time to the description of the spectra of adenine-thymine and adenine-uracil molecular base pairs. The intensity distribution in the resonance Raman (RR) spectra of these pairs excited by laser radiation at 266, 240, 218, and 200 nm is calculated. Satisfactory agreement with the available experimental data is obtained. The basic features of the intensity distribution are discussed and are theoretically substantiated.

Method for assigning absorption bands in IR spectra of polyatomic molecules with respect to internal vibrational coordinates

A method is proposed for assigning absorption bands in IR spectra of polyatomic molecules. An algorithm is developed and a Fortran program is written based on this method. The method is illustrated for the example of the toluene molecule.

Simple model for the description of anharmonic vibrations of polyatomic molecules

We propose a simple, in respect to computations, model and the calculation method for energy levels and intensities in IR spectra of polyatomic molecules in the anharmonic approximation for sufficiently high values of vibrational quantum numbers but with a restriction of possible motions of nuclei within the region not reaching yet the dissociation limit.

Molecular physics: theoretical principles and experimental methods

Preface. 1. Introduction. 2. Molecules Electronic States. 3. Rotation, Vibration, and Potential Curves of Diatomic Molecules. 4. Spectra of Diatomic Molecules. 5. Molecule Symmetries and Group Theory. 6. Rotation and Vibrations of Polyatomic Molecules. 7. Electronic States of Polyatomic Molecules. 8. Spectra of Polyatomic Molecules. 9. Breakdown of the Born-Oppenheimer-Approximation, Perturbations in Molecular Spectra. 10. Molecules in External Fields. 11. Van der Waals Molecules and Clusters. 12. Experimental Techniques in Molecular Physics. Appendix: Charcter Tables of Some Point Groups. Bibliography. Index.

Standardless spectrochemical analysis and direct simulations of time-resolved vibronic spectra of polyatomic molecules, isomers and mixtures

The efficient method for calculation of dynamical time-resolved vibronic spectra of polyatomic molecules is proposed. It allows to perform direct real-time computer simulations of such spectra for models of complex compounds, isomers and multicomponent mixtures with quantum beats and non-radiative vibrational relaxation taken into account. The examples of calculated spectra show the ways of how to search and select optimal experimental conditions and retrieve the most informative data for solution of inverse spectral problems in different situations. The new method of standardless analysis based on time-resolved vibronic spectroscopy has been developed and its main ideas are presented here. This method is able to solve quantitative and qualitative spectrochemical problems for individual substances and multicomponent mixtures (even for species with similar optical properties) with the use of experimentally measured relative intensities of dynamical spectra only. The algorithms of how to perform analysis in various experimental conditions are proposed.

Wave packet propagation for constrained molecular systems: spectroscopic applications to triatomic molecules

A new numerical method for the calculation of parts of the vibrational spectra of polyatomic molecules is presented. In particular, this method accounts for the high-lying floppy states in which the molecule may be delocalized over several isomeric forms. For testing the validity of the method, i.e. for allowing comparisons with reliable results previously obtained, the method is applied to triatomic molecules, namely the molecules isoelectronic to HCN/CNH (HCP, HSiN and HSiP). But the method is obviously designed for larger systems. The potential energy surfaces of the four molecules studied are topologically strongly different, i.e. the repartitions of the minima and the transition states are changing significantly from one another, thus producing different spectral profiles.

Luminescence and absorption spectra of polyatomic molecules subjected to conformational transitions

A general approach and results of specific calculations of conjugated vibronic absorption and fluorescence spectra of “soft” molecules subjected to conformational transitions are presented. The vibronic spectra of these molecules exhibit significant anomalies such as a large energy gap between the fluorescence and absorption spectra, a strong deviation from the mirror symmetry, etc., which cannot be explained within the framework of the theory of vibronic spectra based on single-well adiabatic potentials.

Improvement of the parametric method of the theory of vibronic spectra of polyatomic molecules: Absorption spectra and the structure of butadiene, hexatriene, and octatetraene in the excited state

The structure of the excited states and absorption spectra of butadiene, hexatriene, and octatetraene are calculated by the parametric method of the theory of vibronic spectra using models of the first-and second-order approximations. It is shown that these molecular models adequately reflect the molecular structure and allow one to predict quantitatively the shape and fine vibrational structure of the absorption spectra. When passing to the second-order approximation, only two additional (angular) parameters are used. These parameters are transferable in the series of polyenes. Compared to the first-order approximation model, the second-order approximation model more accurately takes into account the angular deformations of polyenes upon their excitation and describes the intensity distribution in the vibrational spectrum, including weak lines. In addition, the calculations also quantitatively predict spectral variations in the molecular series. The parametric method is more efficient for modeling polyatomic molecules in the excited states and their vibrational spectra compared to other semiempirical and ab initio methods.