Molecular Systems Of Interest Research Articles

Quantum HF/DFT-embedding algorithms for electronic structure calculations: Scaling up to complex molecular systems.

In the near future, material and drug design may be aided by quantum computer assisted simulations. These have the potential to target chemical systems intractable by the most powerful classical computers. However, the resources offered by contemporary quantum computers are still limited, restricting the simulations to very simple molecules. In order to rapidly scale up to more interesting molecular systems, we propose the embedding of the quantum electronic structure calculation into a classically computed environment obtained at the Hartree-Fock (HF) or density functional theory (DFT) level of theory. This result is achieved by constructing an effective Hamiltonian that incorporates a mean field potential describing the action of the inactive electrons on a selected Active Space (AS). The ground state of the AS Hamiltonian is then determined by means of the variational quantum eigensolver algorithm. We show that with the proposed HF and DFT embedding schemes, we can obtain significant energy corrections to the reference HF and DFT calculations for a number of simple molecules in their strongly correlated limit (the dissociation regime) as well as for systems of the size of the oxirane molecule.

Interplay between the Gentlest Ascent Dynamics Method and Conjugate Directions to Locate Transition States.

An algorithm to locate transition states on a potential energy surface (PES) is proposed and described. The technique is based on the GAD method where the gradient of the PES is projected into a given direction and also perpendicular to it. In the proposed method, named GAD-CD, the projection is not only applied to the gradient but also to the Hessian matrix. Then, the resulting Hessian matrix is block diagonal. The direction is updated according to the GAD method. Furthermore, to ensure stability and to avoid a high computational cost, a trust region technique is incorporated and the Hessian matrix is updated at each iteration. The performance of the algorithm in comparison with the standard ascent dynamics is discussed for a simple two dimensional model PES. Its efficiency for describing the reaction mechanisms involving small and medium size molecular systems is demonstrated for five molecular systems of interest.

DFT Characterization of Metallole-Decorated Silicon (001) Surface

Multifunctional molecules have been important for being building blocks of interesting molecular systems. A combination of these multifunctional molecules with conventional semiconductor surfaces has been utilized in designing new materials for different electronic and optical applications. Metalloles, as a group of multifunctional molecules, have unique electronic and photophysical properties. In this study, density functional theory calculations were performed to examine the structural and electronic properties of metallole (MC4H6; M = Si, Ge, and Sn)-decorated Si(001)-(2 × 2) surfaces. After determining the structural parameters of single isolated metallole molecules, eight different adsorption configurations on the silicon surface were proposed to find out the most stable binding model for each. The self-dissociation of H atoms in the stannole [4 + 2]-(II) model during these calculations led to three different dissociation models (including M–H and C–H dissociation) to be considered for all M atoms. A...

Conformational preference and cationic structure of 2-methylpyrazine by VUV-MATI spectroscopy and natural bond orbital analysis.

Alkylpyrazines, which are well-known as aromatic substances and traditional medicines, are interesting molecular systems, and their methyl conformations result in unique structural and dynamical properties. We explored the conformational preference of the methyl group and the highest occupied molecular orbitals (HOMOs) of 2-methylpyrazine and its cation by utilizing high-resolution one-photon vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy and natural bond orbital analysis to understand the relevant molecular activities. The measured VUV-MATI spectrum of 2-methylpyrazine revealed its adiabatic ionization energy and the vibrational frequencies of its cation. From the 0-0 band in the MATI spectrum under the zero-field limit, the accurate adiabatic ionization energy was determined as 9.0439 ± 0.0006 eV (72 944 ± 5 cm-1), which is lower than that of pyrazine. The peaks observed in the spectrum were unambiguously assigned based on vibrational frequencies and Franck-Condon factors from quantum chemical calculations for individual totally symmetric transitions between the S0 and D0 states using the simple one-photon dipole selection rules. The most convincing molecular structure of the 2-methylpyrazine cation was determined by Franck-Condon fit spectral simulations. Upon removal of an electron from the non-bonding orbital (HOMO) on the para nitrogen atoms, a significant structural change takes place along the vibrational motion associated with ring distortion by contraction of the N-N distance, resulting in prominent overtones and combination bands. In addition, the methyl substitution of pyrazine lowered the adiabatic ionization energy and the methyl group preferred the anti-configuration with respect to the pyrazine moiety in the D0 state, resulting in a frozen internal rotation regardless of ionization.

New insight into the action of tryptanthrins against Plasmodium falciparum: Pharmacophore identification via a novel submolecular QSAR descriptor

A new submolecular quantitative structure activity relationship (QSAR) descriptor was applied toward elucidating the anti-malarial pharmacophore of tryptanthrins, a class of compounds known for their anti-parasitic activities. The new descriptor is based on experimental and computational measurements of the tunneling barriers of individual lobes of the molecular orbitals. Lobe-by-lobe QSAR correlation plots revealed a single lobe of the LUMO to be strongly associated with tryptanthrin’s anti-malarial activity. The correlation also showed a threshold behavior wherein barriers below a particular value show low IC50 values. Above the threshold, the correlation of IC50 vs the logarithm of the barrier is linear with R2 = 0.999. This barrier threshold may be applied as a design criterion for future tryptanthrin-based anti-malarial lead optimization. The new descriptor may be broadly applicable toward other molecular systems of interest, such as catalysts, pesticides, and herbicides. The authors have named the new descriptor: submolecular tunneling analysis of barriers (STAB).

Magic-Angle Spinning NMR of Cold Samples

Magic-angle-spinning solid-state NMR provides site-resolved structural and chemical information about molecules that complements many other physical techniques. Recent technical advances have made it possible to perform magic-angle-spinning NMR experiments at low temperatures, allowing researchers to trap reaction intermediates and to perform site-resolved studies of low-temperature physical phenomena such as quantum rotations, quantum tunneling, ortho-para conversion between spin isomers, and superconductivity. In examining biological molecules, the improved sensitivity provided by cryogenic NMR facilitates the study of protein assembly or membrane proteins. The combination of low-temperatures with dynamic nuclear polarization has the potential to boost sensitivity even further. Many research groups, including ours, have addressed the technical challenges and developed hardware for magic-angle-spinning of samples cooled down to a few tens of degrees Kelvin. In this Account, we briefly describe these hardware developments and review several recent activities of our group which involve low-temperature magic-angle-spinning NMR. Low-temperature operation allows us to trap intermediates that cannot be studied under ambient conditions by NMR because of their short lifetime. We have used low-temperature NMR to study the electronic structure of bathorhodopsin, the primary photoproduct of the light-sensitive membrane protein, rhodopsin. This project used a custom-built NMR probe that allows low-temperature NMR in the presence of illumination (the image shows the illuminated spinner module). We have also used this technique to study the behavior of molecules within a restricted environment. Small-molecule endofullerenes are interesting molecular systems in which molecular rotors are confined to a well-insulated, well-defined, and highly symmetric environment. We discuss how cryogenic solid state NMR can give information on the dynamics of ortho-water confined in a fullerene cage. Molecular motions are often connected with fundamental chemical properties; therefore, an understanding of molecular dynamics can be important in fields ranging from material science to biochemistry. We present the case of ibuprofen sodium salt which exhibits different degrees of conformational freedom in different parts of the same molecule, leading to a range of line broadening and line narrowing phenomena as a function of temperature.

Assessment of the Performance of B2PLYP-D for Describing Intramolecular π-π and σ-π Interactions

Intramolecular <TEX>${\pi}-{\pi}$</TEX> and <TEX>${\sigma}-{\pi}$</TEX> interactions are omnipresent for numerous energetic and structural phenomena in nature, and the exact description of these nonbonding interactions plays an important role in the accurate prediction of the three-dimensional structures for numerous interesting molecular systems such as protein folding and polymer shaping. We have selected two prototype molecular systems for benchmarking calculations of intramolecular <TEX>${\pi}-{\pi}$</TEX> and <TEX>${\sigma}-{\pi}$</TEX> interactions. Accurately describing conformational energy of such systems requires highly elaborate but very expensive ab initio methods such as coupled cluster singles, doubles, and (triples) (CCSD(T)). Our calculations reveal a double hybrid density functional incorporating dispersion correction (B2PLYP-D) that agrees excellently with the CCSD(T) results, indicating that B2PLYP-D can serve as a practical method of choice.

Extension of high harmonic spectroscopy in molecules by a 1300 nm laser field

The emerging techniques of molecular spectroscopy by high order harmonic generation have hitherto been conducted only with Ti:Sapphire lasers which are restricted to molecules with high ionization potentials. In order to gain information on the molecular structure, a broad enough range of harmonics is required. This implies using high laser intensities which would saturate the ionization of most molecular systems of interest, e.g. organic molecules. Using a laser at 1300 nm, we are able to extend the technique to molecules with relatively low ionization potentials (approximately 11 eV), observing wide harmonic spectra reaching up to 60 eV. This energy range improves spatial resolution of the high harmonic spectroscopy to the point where interference minima in harmonic spectra of N(2)O and C(2)H(2) can be observed.

Single‐Step Electron Transfer on the Nanometer Scale: Ultra‐Fast Charge Shift in Strongly Coupled Zinc Porphyrin–Gold Porphyrin Dyads

The synthesis, electrochemical properties, and photoinduced electron transfer processes of a series of three novel zinc(II)-gold(III) bisporphyrin dyads (ZnP--S--AuP(+)) are described. The systems studied consist of two trisaryl porphyrins connected directly in the meso position via an alkyne unit to tert-(phenylenethynylene) or penta(phenylenethynylene) spacers. In these dyads, the estimated center to center interporphyrin separation distance varies from 32 to 45 A. The absorption, emission, and electrochemical data indicate that there are strong electronic interactions between the linked elements, thanks to the direct attachment of the spacer on the porphyrin ring through the alkyne unit. At room temperature in toluene, light excitation of the zinc porphyrin results in almost quantitative formation of the charge shifted state (.+)ZnP--S--AuP(.), whose lifetime is in the order of hundreds of picoseconds. In this solvent, the charge-separated state decays to the ground state through the intermediate population of the zinc porphyrin triplet excited state. Excitation of the gold porphyrin leads instead to rapid energy transfer to the triplet ZnP. In dichloromethane the charge shift reactions are even faster, with time constants down to 2 ps, and may be induced also by excitation of the gold porphyrin. In this latter solvent, the longest charge-shifted lifetime (tau=2.3 ns) was obtained with the penta-(phenylenethynylene) spacer. The charge shift reactions are discussed in terms of bridge-mediated super-exchange mechanisms as electron or hole transfer. These new bis-porphyrin arrays, with strong electronic coupling, represent interesting molecular systems in which extremely fast and efficient long-range photoinduced charge shift occurs over a long distance. The rate constants are two to three orders of magnitude larger than for corresponding ZnP--AuP(+) dyads linked via meso-phenyl groups to oligo-phenyleneethynylene spacers. This study demonstrates the critical impact of the attachment position of the spacer on the porphyrin on the electron transfer rate, and this strategy can represent a useful approach to develop molecular photonic devices for long-range charge separations.

Viscoelastic Measurements of Single Molecules on a Millisecond Time Scale by Magnetically Driven Oscillation of an Atomic Force Microscope Cantilever

The dynamical nature of biomolecular systems means that knowledge of their viscoelastic behavior is important in fully understanding function. The linear viscoelastic response can be derived from an analysis of Brownian motion. However, this is a slow measurement and technically demanding for many molecular systems of interest. To address this issue, we have developed a simple method for measuring the full linear viscoelastic response of single molecules based on magnetically driven oscillations of an atomic force microscope cantilever. The cantilever oscillation frequency is periodically swept through the system resonance in less than 200 ms allowing the power spectrum to be obtained rapidly and analyzed with a suitable model. The technique has been evaluated using dextran, a polysaccharide commonly used as a test system for single molecule mechanical manipulation experiments. The monomer stiffness and friction constants were compared with those derived from other methods. Excellent agreement is obtained indicating that the new method accurately and, most importantly, rapidly provides the viscoelastic response of a single molecule between the tip and substrate. The method will be a useful tool for studying systems that change their structure and dynamic response on a time scale of 100-200 ms, such as protein folding and unfolding under applied force.

Applications of size-consistent state-specific multi-reference coupled cluster (SS-MRCC)theory to study the potential energy curves of some interesting molecular systems

In this paper we apply the state-specific multi-reference coupled cluster method(SS-MRCC) (Mahapatra et al 1999 J. Chem. Phys. 110 6171) to compute the potential energycurves (PECs) of some interesting diatomic molecular systems. The theory is built oncomplete active space (CAS) reference functions. This formulation relies upon asmall CAS, but is capable of producing energies to a high degree of accuracy. In the SS-MRCC method, depending upon the method of iteration, we maydetermine cluster amplitudes and consequently the effective Hamiltonian either with the frozen (unrelaxed scheme) or with the converged coefficients (relaxedscheme) which are the model space coefficients in the final wavefunction. Thus the energycan be obtained either as an expectation value with respect to the unrelaxed function or bydiagonalizing within the CAS. The SS-MRCC method is rigorously size-extensive and size-consistent.The method bypasses the intruders by focusing on a single state of interest in anatural manner. The method could thus serve as a reliable choice for PEC studiesover a wide range of geometries. We will also compare the relative performancesof the description of ‘unrelaxed’ versus ‘relaxed’ coefficients. We also evaluatecertain spectroscopic constants and compare them with experimental results.