Guanine Crystals: A First Principles Study

Directed exciton transport highways in organic semiconductors

Exciton bandwidths and exciton transport are difficult to control by material design. We showcase the intriguing excitonic properties in an organic semiconductor material with specifically tailored functional groups, in which extremely broad exciton bands in the near-infrared-visible part of the electromagnetic spectrum are observed by electron energy loss spectroscopy and theoretically explained by a close contact between tightly packing molecules and by their strong interactions. This is induced by the donor-acceptor type molecular structure and its resulting crystal packing, which induces a remarkable anisotropy that should lead to a strongly directed transport of excitons. The observations and detailed understanding of the results yield blueprints for the design of molecular structures in which similar molecular features might be used to further explore the tunability of excitonic bands and pave a way for organic materials with strongly enhanced transport and built-in control of the propagation direction.

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol–gel silicate material for understanding DNA photodamage

A sol–gel silicate matrix containing entrapped guanine was prepared. The SiO₂ matrix provides UVA protection by reducing the light penetration to the entrapped guanine molecules.

A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors

We employ quantum biochemistry methods based on the Density Functional Theory (DFT) approach to unveil detailed binding energy features of willardiines co-crystallized with the AMPA receptor.

L-Asparagine crystals with wide gap semiconductor features: optical absorption measurements and density functional theory computations

Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the absorption and complex dielectric function, with more structured curves for incident light polarized along the 100 and 101 directions.

Light reflection control in biogenic micro-mirror by diamagnetic orientation

As has become known, most materials, such as proteins and DNA, show orientation under strong magnetic fields. However, the critical threshold for the magnetic field of the magnetomechanical phenomena is still unknown. We demonstrate that a thin micro-mirror from a fish scale with high reflectivity exhibits a distinct magnetic response at 100 mT. A dramatic event under a magnetic field is the decrease of light scattering from guanine crystals as well as rapid rotation against the applied magnetic field. Enhancement of light scattering intensity is also observed when the three vectors of light incidence, magnetic field, and observation are orthogonally directed. The results indicate that biogenic guanine crystals have a large diamagnetic anisotropy along the surface parallel and normal directions. The micrometer to submicrometer scale of thin biogenic plates can act as a noninvasively, magnetically controlled micro-mirror for light irradiation control in the micrometer-scale region.

MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH?

Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical ground — can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within the density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed.

Explaining statin inhibition effectiveness of HMG-CoA reductase by quantum biochemistry computations

By taking advantage of the crystallographic data of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) complexed with statins, a quantum biochemistry study based on the density functional theory is performed to estimate the interaction energy for each statin when one considers binding pockets of different sizes. Assuming a correlation between statin potency and the strength of the total HMGR-statin binding energy, clinical data as well as IC(50) values of these cholesterol-lowering drugs are successfully explained only after stabilization of the calculated total binding energy for a larger size of the ligand-interacting HGMR region, one with a radius of at least 12.0 Å. Actually, the binding pocket radius suggested by classic works, which was based solely on the interpretation of crystallographic data of the HMGR-statin complex, is smaller than that necessary to achieve total binding energy convergence in our simulations. Atorvastatin and rosuvastatin are shown to be the most strongly bound HMGR inhibitors, while simvastatin and fluvastatin are the weakest ones. A binding site, interaction energy between residues and statin atoms, and residues domain (BIRD) panel is constructed, indicating clear quantum biochemistry-based routes for the development of new statin derivatives.

Characteristics of small- and large-polaron motion in organic crystals

Based on a generalized theory of charge transport in organic crystals we investigate the motion of polarons of arbitrary size. Within this theory, we analyze the influence of characteristic electronic, vibronic, and thermal energies and their role for the transport regimes. The polaron bandwidth is identified as the central temperature-dependent quantity. The size of the dressed charge carriers is used to analyze the correlation between the polaron size and transport mechanism. In addition, we propose that the band and hopping transport can be distinguished by investigating the mobility anisotropy. To do this only electronic structure parameters are necessary for comparison.

Encapsulation of ruthenium nitrosylnitrate and DNA purines in nanostructured sol-gel silica matrices

The interactions between DNA purines (guanine and adenine) and the ruthenium complex Ru(NO)(NO(3))(3) were studied within nanostructured silica matrices prepared by a two-step sol-gel process. By infrared analysis in diffuse reflectance mode, it was proved that encapsulation induces a profound modification on the complex, whereas guanine and adenine preserve their structural integrity. The complex undergoes nitrate ligand exchange and co-condenses with the silica oligomers, but the nitrosyl groups remain stable, which is an unusual behavior in Ru nitrosyl complexes. In turn, the doping molecules affect the sol-gel reactions and eventually the silica structure as it forms: the complex yields a microporous structure, and the purine bases are responsible for the creation of macropores due to hydrogen bonding with the silanol groups of the matrix. In a confined environment, the interactions are much stronger for the coencapsulated pair guanine complex. While adenine only establishes hydrogen bonds or van der Waals interactions with the complex, guanine bonds covalently to Ru by one N atom of the imidazole ring, which becomes strongly perturbed, resulting in a deformation of the complex geometry.