Influence of Ligand Complexity on the Spectroscopic Properties of Type 1 Copper Sites: A Theoretical Study.

Multi-copper oxidases (MCOs) are enzymes of significant interest in biotechnology due to their efficient catalysis of oxygen reduction to water, making them valuable in sustainable energy production and bio-electrochemical applications. This study employs time-dependent density functional theory (TDDFT) to investigate the electronic structure and spectroscopic properties of the Type 1 (T1) copper site in Azurin, which serves as a model for similar sites in MCOs. Four model complexes of varying complexity were derived from the T1 site, including 3 three-coordinate models and 1 four-coordinate model with axial methionine ligation, to explore the impact of molecular branches and axial coordination.

Modeling adsorption reactions of ammonium perchlorate on rutile and anatase surfaces.

In this work, the effects of two TiO polymorphs on the decomposition of ammonium perchlorate (NHClO) were studied experimentally and theoretically. The interactions between AP and various surfaces of TiO were modeled using density functional theory (DFT) calculations. Specifically, the adsorption of AP on three rutile surfaces (1 1 0), (1 0 0), and (0 0 1), as well as two anatase surfaces (1 0 1), and (0 0 1) were modeled using cluster models, along with the decomposition of adsorbed AP into small molecules.

The effect of water on gold supported chiral graphene nanoribbons: rupture of conjugation by an alternating hydrogenation pattern.

In the last few years we have observed a breakpoint in the development of graphene-derived technologies, such as liquid phase filtering and their application to electronics. In most of these cases, they imply exposure of the material to solvents and ambient moisture, either in the fabrication of the material or the final device. The present study demonstrates the sensitivity of graphene nanoribbon (GNR) zigzag edges to water, even in extremely low concentrations.

Polyradical character assessment using multireference calculations and comparison with density-functional derived fractional occupation number weighted density analysis.

The biradicaloid character of different types of polycyclic aromatic hydrocarbons (PAHs) based on small band gaps is an important descriptor to assess their opto-electronic properties. In this work, the unpaired electron densities and numbers of unpaired electrons ( values) calculated at the high-level multireference averaged quadratic coupled-cluster (MR-AQCC) method are used to develop a test set to assess the capabilities of different biradical descriptors based on density functional theory. A benchmark collection of 29 different compounds has been selected.

High-Level Multireference Investigations on the Electronic States in Single-Vacancy (SV) Graphene Defects Using a Pyrene-SV Model.

The nonplanar character of graphene with a single carbon vacancy (SV) defect is investigated utilizing a pyrene-SV model system by way of complete-active-space self-consistent field theory (CASSCF) and multireference configuration interaction singles and doubles (MR-CISD) calculations. Planar structures were optimized with both methods, showing the B state to be the ground state with three energetically close states within an energy range of 1 eV. These planar structures constitute saddle points.

A comprehensive analysis of charge transfer effects on donor-pyrene (bridge)-acceptor systems using different substituents.

The alternant polycyclic aromatic hydrocarbon pyrene has photophysical properties that can be tuned with different donor and acceptor substituents. Recently, a D (donor)-Pyrene (bridge)-A (acceptor) system, DPA, with the electron donor N,N-dimethylaniline (DMA), and the electron acceptor trifluoromethylphenyl (TFM), was investigated by means of time-resolved spectroscopic measurements (J. Phys.

Resonance Raman spectra and excited state properties of methyl viologen and its radical cation from time-dependent density functional theory.

Time-dependent density functional theory (TDDFT) was applied to gain insights into the electronic and vibrational spectroscopic properties of an important electron transport mediator, methyl viologen (MV ). An organic dication, MV has numerous applications in electrochemistry that include energy conversion and storage, environmental remediation, and chemical sensing and electrosynthesis. MV is easily reduced by a single electron transfer to form a radical cation species (MV ), which has an intense UV-visible absorption near 600 nm.

Quantum Dynamical Investigation of Dihydrogen-Hydride Exchange in a Transition-Metal Polyhydride Complex.

The ongoing shift toward clean, sustainable energy is a primary driving force behind hydrogen fuel research. Safe and effective storage of hydrogen is a major challenge (particularly for mobile applications) and requires a detailed understanding of the atomic level interactions of hydrogen with its host materials. The light mass of hydrogen, however, implies that quantum effects are important, so a quantum dynamical treatment is required to properly account for these effects in computational simulations.

Informing air-carbon ablation modeling with theoretical calculations of atomic oxygen and nitrogen interacting with carbon surfaces.

To understand the gas-surface chemistry above the thermal protection system of a hypersonic vehicle, it is necessary to map out the kinetics of key elementary reaction steps. In this work, extensive periodic density functional theory (DFT) calculations are performed to elucidate the interaction of atomic oxygen and nitrogen with both the basal plane and edge sites of highly oriented pyrolytic graphite (HOPG). Reaction energies and barriers are determined for adsorption, desorption, diffusion, recombination, and several reactions.

Spin-dependent reactivity and spin-flipping dynamics in oxygen atom scattering from graphite.

The formation of two-electron chemical bonds requires the alignment of spins. Hence, it is well established for gas-phase reactions that changing a molecule's electronic spin state can dramatically alter its reactivity. For reactions occurring at surfaces, which are of great interest during, among other processes, heterogeneous catalysis, there is an absence of definitive state-to-state experiments capable of observing spin conservation and therefore the role of electronic spin in surface chemistry remains controversial.

Reaction mechanism for fluorination reactions with hydroxylated alumina sites: Pathways promoting aluminum combustion.

Density functional theory calculations were used to reveal the mechanism for the fluorination reaction of active Lewis acid sites on alumina structures, which is important in understanding the pyrophoric processes involving Al particles. In this reaction, hydroxyl groups of active sites are replaced by fluorine anions. Alumina structures were represented by three aluminum aqua hydroxo clusters (labeled AlOOH), in which the Al atom had different coordination spheres, particularly four, five, or six.

Insights into adsorption, diffusion, and reactions of atomic nitrogen on a highly oriented pyrolytic graphite surface.

To gain insight into the nitrogen-related gas-surface reaction dynamics on carbon-based thermal protection systems of hypersonic vehicles, we have investigated the adsorption, diffusion, and reactions of atomic nitrogen, N(S), on the (0001) face of graphite using periodic density functional theory with a dispersion corrected functional. The atomic nitrogen is found to bind with pristine graphite at a bridge site, with a barrier of 0.88 eV for diffusing to an adjacent bridge site.

Exploration of Graphene Defect Reactivity toward a Hydrogen Radical Utilizing a Preactivated Circumcoronene Model.

A preexisting chemisorbed defect is well-known to increase the reactivity of graphene which is normally chemically inert. Specifically, the presence of chemisorbed hydrogen atoms forming an sp-hybridized C-H bond is known to increase the reactivity of neighboring carbon atoms toward additional hydrogenation with wide-ranging applications from materials science to astrochemistry. In this work, static DFT and DFT-based direct dynamics simulations are used to characterize the reactivity of a graphene sheet around an existing C-H bond defect.

A General New Method for Calculating the Molecular Nonpolar Surface for Analysis of LC-MS Data.

The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatograph/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models.

Exploring reactivity and product formation in N(S) collisions with pristine and defected graphene with direct dynamics simulations.

Atomic nitrogen is formed in the high-temperature shock layer of hypersonic vehicles and contributes to the ablation of their thermal protection systems (TPSs). To gain atomic-level understanding of the ablation of carbon-based TPS, collisions of hyperthermal atomic nitrogen on representative carbon surfaces have recently be investigated using molecular beams. In this work, we report direct dynamics simulations of atomic-nitrogen [N(S)] collisions with pristine, defected, and oxidized graphene.

Diradical Organic One-Dimensional Polymers Synthesized on a Metallic Surface.

We report on the synthesis and characterization of atomically precise one-dimensional diradical peripentacene polymers on a Au(111) surface. By means of high-resolution scanning probe microscopy complemented by theoretical simulations, we provide evidence of their magnetic properties, which arise from the presence of two unpaired spins at their termini. Additionally, we probe a transition of their magnetic properties related to the length of the polymer.

The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry.

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g.

Benchmark ab initio calculations on intermolecular structures and the exciton character of poly(p-phenylenevinylene) dimers.

Benchmark ab initio calculations have been performed for poly(p-phenylenevinylene) (PPV) dimers, a paradigmatic material for studying excitation energy transfer mechanisms. Second-order Møller-Plesset perturbation theory was utilized with the scaled opposite spin approach (SOS-MP2) and correlation consistent basis sets to determine the geometric properties and interaction energies in the ground state. Vertical excitations and optimized structures for the S state were computed using the SOS second-order algebraic diagrammatic construction method.

Interplay of Biradicaloid Character and Singlet/Triplet Energy Splitting for -/-Diindenoacenes and Related Benzothiophene-Capped Oligomers as Revealed by Extended Multireference Calculations.

The biradicaloid character of different types of polycyclic aromatic hydrocarbons is an important quality that guides the development of new materials with interesting magneto-optical properties. Diindenoacene-based systems represent such a class of promising compounds. In this work, the three types -diindenoacenes, -diindenoacenes, and -dicyclopentaacenobis(benzothiophenes) have been studied by means of advanced ab initio methods.

Characterization of glycan isomers using magnetic carbon nanoparticles as a MALDI co-matrix.

Matrix-assisted laser desorption ionization-in source decay (MALDI-ISD) analysis is a useful technique in the structural analysis of glycans. Our recent publication demonstrated that magnetic carbon nanoparticles (MCNPs), used as a MALDI co-matrix, significantly enhanced ISD efficiency for glycomic analysis by MALDI-TOF. In this study, MCNPs were used for the structural study of isomeric glycans.

Photoacidity of the 7-Hydroxyflavylium Cation.

Theoretical descriptions of excited state proton transfer (ESPT) have had various degrees of success. This work presents a theoretical description of the photodissociation of the 7-hydroxyflavylium cation (7-HF), the fundamental chromophoric moiety of anthocyanin natural plant pigments. ESPT of 7-HF is promoted by a significant shift of charge away from the OH group in the first singlet excited state, leading smoothly to the excited conjugate base and a protonated water cluster.

A Multireference Ab Initio Study of the Diradical Isomers of Pyrazine.

Three diradical pyrazine isomers were characterized using highly correlated, multireference methods. The lowest lying singlet and triplet state geometries of 2,3-didehydropyrazine ( ortho), 2,5-didehydropyrazine ( para), and 2,6-didehydropyrazine ( meta) were determined. Two active reference spaces were utilized.

The crucial role of a spacer material on the efficiency of charge transfer processes in organic donor-acceptor junction solar cells.

Organic photovoltaic donor-acceptor junction devices composed of π-conjugated polymer electron donors (D) and fullerene electron acceptors (A) show greatly increased performance when a spacer material is inserted between the two layers (W. Y. Nie, G.

Structure and electronic states of a graphene double vacancy with an embedded Si dopant.

Silicon represents a common intrinsic impurity in graphene, bonding to either three or four carbon neighbors, respectively, in a single or double carbon vacancy. We investigate the effect of the latter defect (Si-C) on the structural and electronic properties of graphene using density functional theory. Calculations based both on molecular models and with periodic boundary conditions have been performed.

Intermolecular interactions and charge transfer transitions in aromatic hydrocarbon-tetracyanoethylene complexes.

A comprehensive theoretical study of the electronically excited states in complexes between tetracyanoethylene (TCNE) and three aromatic electron donors, benzene, naphthalene and anthracene, was performed with a focus on charge transfer (CT) transitions. The results show that the algebraic diagrammatic construction method to second order (ADC(2)) provides excellent possibilities for reliable calculations of CT states. Significant improvements in the accuracy of the computed transition energies are obtained by using the scaled opposite-spin (SOS) variant of ADC(2).