Non-adiabatic Couplings in Surface Hopping with Tight Binding Density Functional Theory: The Case of Molecular Motors.

Nonadiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the Born-Oppenheimer approximation, and the accuracy of the results heavily depends on the electronic structure theory employed. Sophisticated electronic methods, however, make these techniques computationally expensive, even for medium size systems.

THz to far-infrared spectra of the known crystal polymorphs of phenylalanine.

There is renewed interest in the structure of the essential amino acid phenylalanine in the solid state. Three new polymorphs were found in the years 2012 to 2014. Here, we investigate the structure, stability, and energetical ordering of these phases using first-principles simulations at the level of density functional theory incorporating van der Waals interactions.

A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle.

A prevalent side-reaction of succinate dehydrogenase oxidizes malate to enol-oxaloacetate (OAA), a metabolically inactive form of OAA that is a strong inhibitor of succinate dehydrogenase. We purified from cow heart mitochondria an enzyme (OAT1) with OAA tautomerase (OAT) activity that converts enol-OAA to the physiological keto-OAA form, and determined that it belongs to the highly conserved and previously uncharacterized Fumarylacetoacetate_hydrolase_domain-containing protein family. From all three domains of life, heterologously expressed proteins were shown to have strong OAT activity, and ablating the OAT1 homolog caused significant growth defects.

Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis.

Methanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H as an electron donor to reduce CO to CH, but in the absence of H many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for the reduction of coenzyme F or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis.

Full thermoelectric characterization of a single molecule.

Molecules are predicted to be chemically tunable towards high thermoelectric efficiencies and they could outperform existing materials in the field of energy conversion. However, their capabilities at the more technologically relevant temperature of 300 K are yet to be demonstrated. A possible reason could be the lack of a comprehensive technique able to measure the thermal and (thermo)electrical properties, including the role of phonon conduction.

Exact non-adiabatic coupling vectors for the time-dependent density functional based tight-binding method.

We report on non-adiabatic coupling vectors between electronic excited states for the time-dependent-density functional theory based tight-binding (TD-DFTB) method. The implementation includes orbital relaxation effects that have been previously neglected and covers also the case of range-separated exchange-correlation functionals. Benchmark calculations with respect to first principles TD-DFT highlight the large dependence of non-adiabatic couplings on the functional.

Systems and strategies for plant protein expression.

At least a quarter of the protein-encoding genes in plant genomes are predicted to encode enzymes for which no physiological function is known. Determining functions for these uncharacterized enzymes is key to understanding plant metabolism. Functional characterization typically requires expression and purification of recombinant enzymes to be used in enzyme assays and/or for protein structure elucidation studies.

Identification of a S-(2-succino)cysteine breakdown pathway that uses a novel S-(2-succino) lyase.

Succination is the spontaneous reaction between the respiratory intermediate fumarate and cellular thiols that forms stable S-(2-succino)-adducts such as S-(2-succino)cysteine (2SC). 2SC is a biomarker for conditions associated with elevated fumarate levels, including diabetes, obesity, and certain cancers, and succination likely contributes to disease progression. Bacillus subtilis has a yxe operon-encoded breakdown pathway for 2SC that involves three distinct enzymatic conversions.

Genome Sequences of Two Pseudomonas Isolates That Can Use Metformin as the Sole Nitrogen Source.

Metformin is a major water pollutant globally. We report the complete genome sequences of two pseudomonads, Pseudomonas sp. strain KHPS1 and Pseudomonas hydrolytica strain KHPS2, isolated from wastewater treatment plant sludge, which can grow on metformin as the nitrogen source.

PioABC-Dependent Fe(II) Oxidation during Photoheterotrophic Growth on an Oxidized Carbon Substrate Increases Growth Yield.

Microorganisms that carry out Fe(II) oxidation play a major role in biogeochemical cycling of iron in environments with low oxygen. Fe(II) oxidation has been largely studied in the context of autotrophy. Here, we show that the anoxygenic phototroph, Rhodopseudomonas palustris CGA010, carries out Fe(II) oxidation during photoheterotrophic growth with an oxidized carbon source, malate, leading to an increase in cell yield and allowing more carbon to be directed to cell biomass.

Molecular electronic refrigeration against parallel phonon heat leakage channels.

Due to their structured density of states, molecular junctions provide rich resources to filter and control the flow of electrons and phonons. Here we compute the out of equilibrium current-voltage characteristics and dissipated heat of some recently synthesized oligophenylenes (OPE3) using the Density Functional based Tight-Binding (DFTB) method within Non-Equilibrium Green's Function Theory (NEGF). We analyze the Peltier cooling power for these molecular junctions as function of a bias voltage and investigate the parameters that lead to optimal cooling performance.

Pathways to fluorescence restriction of intramolecular motion in substituted tetraphenylethylenes.

The design of materials with enhanced luminescence properties is a fast-developing field due to the potential applicability of these materials as light-emitting diodes or for bioimaging. A transparent way to enhance the emission properties of interesting molecular candidates is blocking competing and unproductive non-radiative relaxation pathways by the restriction of intramolecular motions. Rationalized functionalization is an important possibility to achieve such restrictions.

Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions.

Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products.

P∩N Bridged Cu(I) Dimers Featuring Both TADF and Phosphorescence. From Overview towards Detailed Case Study of the Excited Singlet and Triplet States.

We present an overview over eight brightly luminescent Cu(I) dimers of the type CuX(P∩N) with X = Cl, Br, I and P∩N = 2-diphenylphosphino-pyridine (PhPpy), 2-diphenylphosphino-pyrimidine (PhPpym), 1-diphenylphosphino-isoquinoline (PhPiqn) including three new crystal structures (CuBr(PhPpy) , CuI(PhPpym)  and CuI(PhPiqn) ). However, we mainly focus on their photo-luminescence properties. All compounds exhibit combined thermally activated delayed fluorescence (TADF) and phosphorescence at ambient temperature.

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence.

Multicolor carbon dots (CDs) have been developed recently and demonstrate great potential in bio-imaging, sensing, and LEDs. However, the fluorescence mechanism of their tunable colors is still under debate, and efficient separation methods are still challenging. Herein, we synthesized multicolor polymeric CDs through solvothermal treatment of citric acid and urea in formamide.

Analytical Time-Dependent Long-Range Corrected Density Functional Tight Binding (TD-LC-DFTB) Gradients in DFTB+: Implementation and Benchmark for Excited-State Geometries and Transition Energies.

The absorption and emission of light is a ubiquitous process in chemical and biological processes, making a theoretical description inevitable for understanding and predicting such properties. Although and DFT methods are capable of describing excited states with good accuracy in many cases, the investigation of dynamical processes and the need to sample the phase space in complex systems often requires methods with reduced computational costs but still sufficient accuracy. In the present work, we report the derivation and implementation of analytical nuclear gradients for time-dependent long-range corrected density functional tight binding (TD-LC-DFTB) in the DFTB+ program.

Correction: Electronic conductance and thermopower of single-molecule junctions of oligo(phenyleneethynylene) derivatives.

Correction for 'Electronic conductance and thermopower of single-molecule junctions of oligo(phenyleneethynylene) derivatives' by Hervé Dekkiche et al., Nanoscale, 2020, 12, 18908-18917, DOI: 10.1039/D0NR04413J.

Excitonic and charge transfer interactions in tetracene stacked and T-shaped dimers.

Extended quantum chemical calculations were performed for the tetracene dimer to provide benchmark results, analyze the excimer survival process, and explore the possibility of using long-range-corrected (LC) time-dependent second-order density functional tight-biding (DFTB2) for this system. Ground- and first-excited-state optimized geometries, vertical excitations at relevant minima, and intermonomer displacement potential energy curves (PECs) were calculated for these purposes. Ground-state geometries were optimized with the scaled-opposite-spin (SOS) second-order Møller-Plesset perturbation (MP2) theory and LC-DFT (density functional theory) and LC-DFTB2 levels.

Electronic conductance and thermopower of single-molecule junctions of oligo(phenyleneethynylene) derivatives.

We report the synthesis and the single-molecule transport properties of three new oligo(phenyleneethynylene) (OPE3) derivatives possessing terminal dihydrobenzo[b]thiophene (DHBT) anchoring groups and various core substituents (phenylene, 2,5-dimethoxyphenylene and 9,10-anthracenyl). Their electronic conductance and their Seebeck coefficient have been determined using scanning tunneling microscopy-based break junction (STM-BJ) experiments between gold electrodes. The transport properties of the molecular junctions have been modelled using DFT-based computational methods which reveal a specific binding of the sulfur atom of the DHBT anchor to the electrodes.

Liquid-Solid Slip on Charged Walls: The Dramatic Impact of Charge Distribution.

Nanofluidic systems show great promise for applications in energy conversion, where their performance can be enhanced by nanoscale liquid-solid slip. However, efficiency is also controlled by surface charge, which is known to reduce slip. Combining molecular dynamics simulations and analytical developments, we show the dramatic impact of surface charge distribution on the slip-charge coupling.

Simulation of Structural Evolution Using Time-Dependent Density-Functional Based Tight-Binding Method.

A faster and more efficient quantum mechanical simulation method for application to complicated issues of real systems beyond model cases has long been sought after. The density-functional based tight-binding (DFTB) method has successfully explained the atomistic and electronic properties of semiconductors, surfaces, and nanostructures. In addition, the time-dependent formalism implemented in DFTB showed high efficiency in terms of computational cost.

Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle.

Promiscuous enzymes and spontaneous chemical reactions can convert normal cellular metabolites into noncanonical or damaged metabolites. These damaged metabolites can be a useless drain on metabolism and may be inhibitory and/or reactive, sometimes leading to toxicity. Thus, mechanisms to prevent metabolite damage from occurring (metabolite damage preemption) or to convert damaged metabolites back to physiological forms (metabolite repair) are essential for sustained operation of metabolic networks.

Towards a simplified description of thermoelectric materials: accuracy of approximate density functional theory for phonon dispersions.

We calculate the phonon-dispersion relations of several two-dimensional materials and diamond using the density-functional based tight-binding approach (DFTB). Our goal is to verify if this numerically efficient method provides sufficiently accurate phonon frequencies and group velocities to compute reliable thermoelectric properties. To this end, the results are compared to available DFT results and experimental data.