Structure Of Molecular Systems Research Articles

Emerging quantum computing algorithms for quantum chemistry

AbstractDigital quantum computers provide a computational framework for solving the Schrödinger equation for a variety of many‐particle systems. Quantum computing algorithms for the quantum simulation of these systems have recently witnessed remarkable growth, notwithstanding the limitations of existing quantum hardware, especially as a tool for electronic structure computations in molecules. In this review, we provide a self‐contained introduction to emerging algorithms for the simulation of Hamiltonian dynamics and eigenstates, with emphasis on their applications to the electronic structure in molecular systems. Theoretical foundations and implementation details of the method are discussed, and their strengths, limitations, and recent advances are presented.This article is categorized under: Quantum Computing > Algorithms Electronic Structure Theory > Ab Initio Electronic Structure Methods Quantum Computing > Theory Development

Temperature and size-dependent modeling for predicting mechanical properties of carbon nanotubes

In this paper, a temperature and size-dependent molecular model is proposed to calculate the mechanical properties of carbon nanotubes. The cross section of carbon nanotubes is regarded as a hexagonal ring structure, and the covalent bond between carbon atoms is regarded as a beam of nonlinear spring structure, that is, the molecular structure system is regarded as a "beam-helical spring" structure. For considering the wall thickness of carbon nanotube, the influence of force constant on the molecular structure model is analyzed. On this basis, according to the principle of molecular mechanics, the expressions of calculating surface Young's modulus, Poisson's ratio, shear modulus and bulk modulus are obtained. It is found that due to the wall thickness, the Young's modulus, shear modulus, and bulk modulus of carbon nanotubes decrease with the increase of radius size.

An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture

The Hartree–Fock method in the General Atomic and Molecular Structure System (GAMESS) quantum chemistry package represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals and the building of the Fock matrix. These are the central components of the main self consistent field (SCF) loop, the key hot spot in electronic structure codes. By threading the Message Passing Interface (MPI) ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4× to 6× for large systems) but also achieve a significant ([Formula: see text]×) reduction in the overall memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel® Xeon Phi™ supercomputer. Scaling numbers are reported on up to 7680 cores on Intel Xeon Phi coprocessors.

Simulation of Near-Edge X-ray Absorption Fine Structure with Time-Dependent Equation-of-Motion Coupled-Cluster Theory.

An explicitly time-dependent (TD) approach to equation-of-motion (EOM) coupled-cluster theory with single and double excitations (CCSD) is implemented for simulating near-edge X-ray absorption fine structure in molecular systems. The TD-EOM-CCSD absorption line shape function is given by the Fourier transform of the CCSD dipole autocorrelation function. We represent this transform by its Padé approximant, which provides converged spectra in much shorter simulation times than are required by the Fourier form. The result is a powerful framework for the blackbox simulation of broadband absorption spectra. K-edge X-ray absorption spectra for carbon, nitrogen, and oxygen in several small molecules are obtained from the real part of the absorption line shape function and are compared with experiment. The computed and experimentally obtained spectra are in good agreement; the mean unsigned error in the predicted peak positions is only 1.2 eV. We also explore the spectral signatures of protonation in these molecules.

Thermal rectification of asymmetric double-stranded molecular structure

Using nonequilibrium molecular dynamics simulation, we study the thermal rectification of an asymmetric double-stranded molecular structure system. We investigate the influence of temperature, intra- and inter-chain interaction and the system size on the thermal rectification effect of the asymmetric double- chain system. It is reported that the intra- and the inter-chain interaction have an advantage on the rectification efficiency. The rectification efficiency goes to a stable value at a large system size. This phenomenon is also explained by the power spectra of the inter-particles, which is similar to the situation of the single chain system.

Ultrafast 2D IR Vibrational Echo Spectroscopy

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Ultrafast 2D IR Vibrational Echo Spectroscopy

The experimental technique and applications of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy are presented. Using ultrashort infrared pulses and optical heterodyne detection to provide phase information, unique information can be obtained about the dynamics, interactions, and structures of molecular systems. The form and time evolution of the 2D IR spectrum permits examination of processes that cannot be studied with linear infrared absorption experiments. Three examples are given: organic solute-solvent complex chemical exchange, dynamics of the hydrogen-bond network of water, and assigning peaks in an IR spectrum of a mixture of species.

Quantum interference during high-order harmonic generation from aligned molecules

High-order harmonic generation (HHG) from atoms and molecules offers potential application as a coherent ultrashort radiation source in the extreme ultraviolet and soft X-ray regions1,2,3. In the three-step model4,5,6 of HHG, an electron tunnels out from the atom and may recombine with the parent ion (emitting a high-energy photon) after undergoing laser-driven motion in the continuum. Aligned molecules7,8,9,10,11 can be used to study quantum phenomena in HHG associated with molecular symmetries; in particular, simultaneous observations of both ion yields and harmonic signals under the same conditions serve to disentangle the contributions from the ionization and recombination processes. Here we report evidence for quantum interference of electron de Broglie waves12,13,14 in the recombination process of HHG from aligned CO2 molecules. The interference takes place within a single molecule and within one optical cycle. Characteristic modulation patterns of the harmonic signals measured as a function of the pump–probe delay are explained with simple formulae determined by the valence orbital of the molecules. We propose that simultaneous observations of both ion yields and harmonic signals can serve as a new route to probe the instantaneous structure of molecular systems.

The structure and spin-states of some Fe(III) mimics of nitrile hydratase, studied by DFT and ONIOM(DFT:PM3) calculations

Density functional methods have been successful in studying the electronic structure of molecular systems containing transition metal atoms, such as metalloenzymes. However, the treatment of large systems is still very computationally demanding, and is definitely not practical for many systems of interest, due to their size. In this paper we assess the use of these methods both alone, and when combined with the semi-empirical PM3 method within an ONIOM scheme, for determining the structure and spin-dependent energetics of a series of Fe(III) model complexes that have been synthesized to mimic the active site of nitrile hydratase, a metalloenzyme that catalyses the conversion of a wide variety of nitriles to their corresponding amides. We have found that geometry optimizations employing B3LYP generally give a good description of the structure and spin-states of these complexes and that when combined with PM3 in the framework of ONIOM, the multilevel method also performs well for some of them, suggesting that the ONIOM(B3LYP:PM3) approach offers the possibility for improvement in future calibration studies. We also find that DFT and ONIOM(DFT:PM3) calculations at the experimental geometries using the BP86, PW91PW91 and B3LYP functionals can also describe the spin-state energetics of these model complexes, with DFT performing the best.

Synthesis, characterization and theoretical study of the structure and second-order nonlinear optical properties of two new Monoazo Schiff-base compounds

We describe the syntheses, characterization and theoretical investigation of two new monoazo Schiff-base ligands 5-[(4-methylphenyl)azo]-N-(2′-hydroxyphenyl)salicylaldimine (SB1) and 5-[(4-nitrophenyl)azo]-N-(2′-hydroxyphenyl)salicylaldimine (SB2). AM1 semiempirical calculations were used to study the structures, electronic properties and second-order nonlinearity of these compounds. Theoretical calculations are useful for describing the relationship between the electronic structure of molecular systems and their nonlinear optical (NLO) response. Second-order NLO calculations and comparison of the NLO properties of these ligands with others reveal that the presence of an NO2 group enhances the second-order NLO properties of the ligands.

Approximate Method for Optimization of the Geometric Structure of Polyatomic Systems

A compact method of calculation for solving a fundamental problem in structural chemistry — the problem of optimizing the geometric structure of molecular systems — is proposed. Solution of this problem will allow predicting a number of properties of polymer systems based on the existence of a structure—property correlation. It should be noted that the proposed method allows performing all calculations in analytical form.

Hole structures of polymers and zeolites probed by two-dimensional angular correlation of annihilation radiation

The two-dimensional angular correlation of annihilation radiation (2D-ACAR) technique has been developed to measure the hole structure of stretched and oriented polymers. The determination of polymer hole structure is demonstrated in a stretched semi-crystalline polyaryl-ether-ether-ketone (PEEK) sample. The atomic scale anisotropy is found to be consistent with the macroscopic scale stretch ratio. Applications of the 2D-ACAR method to image the three-dimensional hole, free-volume, and cavity structures of molecular systems are discussed.

Anisotropy of hole structures in polymers probed by two-dimensional angular correlation of annihilation radiation.

Two-dimensional angular correlation of annihilation radiation (2D-ACAR) experiments have been performed in a semicrystalline polymer, polyaryl-ether-ether-ketone. The two-dimensional hole structures of unstretched and stretched polymers, determined from the momentum distributions, are found to be spherical and ellipsoidal, respectively. The average hole radii are determined to be 2.6 \AA{} in the unstretched sample and between 1.9 and 3.6 \AA{} in the stretched sample. Applications of the 2D-ACAR method to image the three-dimensional hole, free-volume, and cavity structures of molecular systems are discussed. \textcopyright{} 1996 The American Physical Society.

Nonadiabatic treatment of molecular systems by the wavepackets method

ABSTRACT = We have already developed the many-electron wavepackets (MEWP) method in order to study the dynamics and electronic structure of molecular systems. We extended the MEWP method to study the nonadiabatic effects and formulated a nonadiabatic molecular theory, where both electron and nucleus are treated equivalently. Then we applied our method to the isotope series of hydrogen molecule i.e., H,, HD, and D,, and calculated the total energy and the average distance between nucleus-nucleus, electron-electron, and nucleus-electron in order to analyze numerically the nonadiabatic effect in the molecule. Finally we calculated the real-time evolution of the polarization by means of Chebyshev scheme; and by Fourier transforming this, we found out the excitation spectrum of the system, which corresponds to the electronic excitation and the nuclear vibrational frequency. 0 1996 John Wiley & Sons, Inc. International Journal of Quantum Chemistry: Quantum Chemistry Symposium 30, 1261 -1270 (1 996) 0 1996 John Wiley & Sons, Inc. CCC 0360-8832 I96 I071 261 -1

Surface Structure of A Liquid Perfluoropolyether Examined by Reactive Ion/Surface Scattering

ABSTRACTThis study shows that reactive ion/surface collisions can provide information on the surface structure of molecular systems. The microscopic structures of perfluorinated polyether (PFPE) liquid surfaces are characterized by ion/surface collision experiments in a mass spectrometer and the results are compared to those obtained with a fluorinated self-assembled monolayer (F-SAM) surface. Low energy (< 100 eV) beams of W+ and W(CO)6+ ions are used for surface-induced dissociation (SID) and ion/surface reactive scattering, while Xe+ and Kr+ beams are used for chemical sputtering experiments. Both the PFPE and F-SAM surfaces show similar SID fragments while reactions with W+ and W(CO)6+ lead to the scattered metal ion with multiple fluorine atoms attached. The main peaks in chemical sputtering spectra are similar for both surfaces as well. Both hydrogen probe beams and chemical sputtering confirm that the liquid PFPE surface is nearly free of impurities. Our results on both surfaces also suggest that the CF3 group of the monomer units is most likely projected outward from the bulk of the liquid surface.

Evolution of molecular structure

Abstract In several areas of chemical physics, a knowledge of the evolution of the electronic structure of molecular systems along some path of nuclear coodinates is of interest. This paper points out the usefulness of a picture of evolution through wavefunction mixing. The degree of mixing can be gauged from the calculation of delayed overlap matrix elements. Taking directional derivatives as guideline, the paper presents some elementary patterns of evolution, involving narrow as well as wider pseudocrossings, conical intersections, overlap effects, polarization and hybridization, charge transfer and asymptotic couplings.

Programs for the semiempirical calculation of the electronic structure of molecular systems with allowance for symmetry by the Mulliken-Ruedenberg and Mulliken-Wolfsberg-Helmholtz methods

The Hartree--Fock--Roothaan matrices in the MR and MWH approximations are constructed directly in the representation of symmetrized atomic orbitals (SAO), and this makes it possible to decrease considerably the calculation time, the volume of operational memory, and the number of quantum-chemical integrals calculated [3]. In these respects the program differs significantly from that previously used [6].

The use of powder diffraction in the study of molecular phase transitions

An outline is given of the experimental techniques available for studying the structure of molecular systems through powder diffraction. A wide range of physical environments is possible with this technique making it appropriate for the study of phase transitions by means of structure. The difficulties encountered in the data analysis are enumerated and the limitations imposed by resolution are discussed. The state of the art is not yet fine enough for us to be able to put a high probability of success on neutron diffraction studies, though this is possible in practice. A new program to help in the search for unknown unit cells is described. The advantages of the fully operational program EDINP for the study of molecular phase transitions through the use of constrained refinements are stressed. A typical example of the type of system which can be studied in this way is presented, namely C6D6.C6F6, where the powder diffraction scans for the two phases are given for comparison.