DFT Predictions Research Articles

A Systematic DFT Approach for Studying Mechanisms of Redox Active Enzymes.

When DFT has been applied to study mechanisms of redox processes a common procedure has been to study the results for many different functionals. For redox reactions involving the first row transition metals, this approach has given very different results for different functionals. The conclusion has been that DFT cannot be used for these reactions. In the meantime, results with strong predictability have been generated, most noteworthy for photosystem II, where all DFT predictions have been verified by experiments performed later. In order to obtain these predictive results using DFT, an alternative, systematic approach has been used, where the key differences between the results for different functionals can be rationalized by using a single parameter, rather than using the very large number of differences in the functionals.

A complete characterization of vibrational IR and Raman spectra of the highly-symmetrical octathia[8]circulene

The highly-symmetrical octathia[8]circulene molecule (8S) was synthesized and well studied 10 years ago in Moscow, including X-ray diffraction, IR and Raman spectra assignment on the ground of molecular DFT calculation. Nevertheless, this comprehensive study could not explain a big number of interesting deviations from the DFT predictions based on the molecular D8h symmetry restriction being specific for a free species in a gas phase. In present work we have performed DFT optimization of the 8S tetramer starting with the X-ray diffraction analysis of a similar crystal structure. DFT calculation of IR and Raman spectra of such a huge system provides a good assignment of the crystal-field splitting and new band occurrence. The force-field distortions, electric charges and polarizability dependence on the tetramer structure are well reproduced by the B3LYP functional with the dispersion correction. Thus, the small shifts of IR and Raman bands, their splitting and intensity redistribution upon weak intermolecular interactions in crystal packing are explained and full assignment of all observed bands is presented.

Elucidation of Relative and Absolute Configurations of Highly Rearranged Diterpenoids and Evidence for a Putative Biosynthetic Intermediate from the Australian Nudibranch Goniobranchus geometricus.

A diterpene (1), previously isolated from a Japanese marine sponge, together with two undescribed (2, 3) diterpenes with highly rearranged carbon skeletons have been characterized from the Australian nudibranch species Goniobranchus geometricus. The structures and relative configuration were determined by spectroscopic analyses informed by detailed molecular modeling, as well as by DFT, DP4, and coupling constant predictions. A 13 R,14 R configuration was determined for secoshahamin (1) by chemical correlation with 12-desacetoxyshahamin C (4) and 12-desacetoxypolyrhaphin A (5); each metabolite (1, 4, and 5) was subjected to saponification and lactonization, yielding the same δ-lactone product (6). Secoshahamin has the same carbon skeleton as a putative precursor that may play a key role in the biosynthesis of highly rearranged diterpenoid scaffolds via C-9/C-11 cleavage of a spongian diterpene precursor.

Facile Separation, Spectroscopic Identification, and Electrochemical Properties of Higher Trifluoromethylated Derivatives of [70]Fullerene.

We survey the structure and electronic properties of the family of higher trifluoromethylated C70 (CF3 )n molecules with n=14, 16, 18, and 20. Twenty-two available compounds, of which thirteen are newly obtained and characterized, demonstrate the broad diversity of π-system topologies, which enabled us to study the interplay between the CF3 addition pattern and the electronic properties. UV/Vis spectroscopic and cyclic voltammetric studies demonstrate the importance of the exact addition pattern rather than the plain number of addends. Of particular interest is the skew pentagonal pyramid (SPP) addition pattern, which enables formation of closed-shell cyclopentadienyl anions C70 (CF3 )n-1- through CF3 detachment upon electron transfer. A detailed study of the process is presented for a SPP-C70 (CF3 )16 where potentiostatic electrolysis at the second reduction potential gives C70 (CF3 )15- oxidizable to a persistent C70 (CF3 )15. radical. Together with the literature data for the lower C70 (CF3 )n compounds with n=2-12, the present results show good correlation between the experimental boundary level positions and the DFT predictions. The compounds turn out to be electron acceptor molecular semiconductors with experimental LUMO energies and HOMO-LUMO gaps within the ranges of -4.3 to -3.7 eV and 1.6 to 3.3 eV, respectively, depending on the shape of the conjugated fragments. The HOMO levels fall within the range of -5.6 to -6.9 eV and show linear correlation with the number of addends.

Synthesis, lipophilicity determination, DFT calculation, antifungal and DPPH radical scavenging activities of tetrahydrothiophen-3-one based thiazoles

Synthesis and investigation of antifungal activity of ten novel thiazoles derived from tetrahydrothiophen-3-one are presented. Among the derivatives, (E/Z)-2-(2-(dihydrothiophen-3(2H)-ylidene)hydrazinyl)thiazoles 3a-3d and 3h had very strong activity against reference strains of Candida albicans and Candida krusei with MIC = 0.24–3.91 μg/ml. Their lipophilicity was determined using reversed-phase high performance liquid chromatography and correlated with antifungal activity. Additionally, their DPPH radical scavenging activities was evaluated by spectrophotometric method. According to our results, compounds 3b, 3h and 3j have very strong antioxidant activities with IC50 values from 3.0 to 9.5 μg/ml. The antioxidant activity of these compounds is 5–17 times higher than butylated hydroxytoluene. The RP HPLC analysis revealed that the products are obtained as E/Z mixture in approximately 60:40 ratio, in good agreement with DFT predictions.

Atomistic modeling of thermo‐mechanical properties of cubic SiC

AbstractSiC is an important multifunctional material with application in electronics and as a structural material. Many investigations of SiC have been done using both classical molecular dynamics and first principles methods. However, they are of limited scope and, in particular, SiC properties at finite temperatures have not been adequately evaluated. The good mechanical, thermal, and chemical properties of SiC such as high stiffness, high hardness, high mechanical strength at high temperature, and high thermal conductivity, make SiC a candidate for various applications in nuclear industries. In this work, we evaluated thermomechanical properties at finite temperatures obtained by LAMMPS code with traditionally used Tersoff potential (TR89 with PRB 41 correction), and the newer GW 2002 (GW02) potential. We compared them with the calculations made using MEAM 1995 (MEAM 95) and with our first principles DFT predictions. It is demonstrated that the thermal expansion and mechanical properties calculated as a function of temperature for classical potentials TR89 and GW02 do not agree well with first principles calculations while better agreement is found for the MEAM95 potential. Classical molecular dynamics calculations made with the use of two earlier potentials under‐predict thermal conductivity by one order of magnitude for the TR89 potential and by more than 30% for the GW02.

Surface modification of TiO2 with copper clusters for band gap narrowing

Surface modification of photocatalytic materials to give better activity and potentially extending the response into the visible spectrum, is an area of active research. In this work, DFT modelling suggests that surface modification of rutile and anatase TiO2 with partially oxidised copper clusters can induce a red shift in the photo-action spectrum. Copper clusters were synthesised and characterised separately before TiO2 nanoparticle surface modification. Characterisation of copper clusters and photocatalysts modified with copper clusters showed that ex-situ synthesis can control the size of surface clusters. Sub-nanometre clusters of copper maintained their size and morphology upon attachment to the photocatalyst surface. The copper clusters were determined to be a mixture of Cu(0) and Cu(I), and no significant change in the oxidation state was observed following surface modification or following photoelectrochemical measurements. Experimental measurements including UV–Vis spectroscopy and valence band XPS showed a small red shift the band gap correlating to the DFT predictions. Photoelectrochemical characterisation showed an enhancement in the UV photocurrent response and a small red shift in the effective band gap for the surface modified TiO2.

Crystallite size-dependent metastable phase formation of TiAlN coatings

It is well known that surface energy differences thermodynamically stabilize nanocrystalline γ-Al2O3 over α-Al2O3. Here, through correlative ab initio calculations and advanced material characterization at the nanometer scale, we demonstrate that the metastable phase formation of nanocrystalline TiAlN, an industrial benchmark coating material, is crystallite size-dependent. By relating calculated surface and volume energy contributions to the total energy, we predict the chemical composition-dependent phase boundary between the two metastable solid solution phases of cubic and wurzite Ti1−xAlxN. This phase boundary is characterized by the critical crystallite size dcritical. Crystallite size-dependent phase stability predictions are in very good agreement with experimental phase formation data where x was varied by utilizing combinatorial vapor phase condensation. The wide range of critical Al solubilities for metastable cubic Ti1−xAlxN from xmax = 0.4 to 0.9 reported in literature and the sobering disagreement thereof with DFT predictions can at least in part be rationalized based on the here identified crystallite size-dependent metastable phase formation. Furthermore, it is evident that predictions of critical Al solubilities in metastable cubic TiAlN are flawed, if the previously overlooked surface energy contribution to the total energy is not considered.

Quantifying confidence in density functional theory predictions of magnetic ground states

The success of descriptor-based material design relies on eliminating bad candidates and keeping good candidates for further investigation. While DFT has been widely successfully for the former, often times good candidates are lost due to the uncertainty associated with the DFT-predicted material properties. Uncertainty associated with DFT predictions has gained prominence and has led to the development of exchange correlation functionals that have built-in error estimation capability. In this work, we demonstrate the use of built-in error estimation capabilities within the BEEF-vdW exchange correlation functional for quantifying the uncertainty associated with the magnetic ground state of solids. We demonstrate this approach by calculating the uncertainty estimate for the energy difference between the different magnetic states of solids and compare them against a range of GGA exchange correlation functionals as is done in many first principles calculations of materials. We show that this estimate reasonably bounds the range of values obtained with the different GGA functionals. The estimate is determined as a post-processing step and thus provides a computationally robust and systematic approach to estimating uncertainty associated with predictions of magnetic ground states. We define a confidence value (c-value) that incorporates all calculated magnetic states in order to quantify the concurrence of the prediction at the GGA level and argue that predictions of magnetic ground states from GGA level DFT is incomplete without an accompanying c-value. We demonstrate the utility of this method using a case study of Li and Na-ion cathode materials and the c-value metric correctly identifies that GGA level DFT will have low predictability for NaFePO$_4$F.

Lower trifluoromethyl[70]fullerene derivatives: novel structural data and an survey of electronic properties

We revisit a series of trifluoromethylated C70(CF3)n compounds with n=2–12 to provide a comprehensive comparative characterization thereof by means of a combination of physico-chemical methods. X-ray diffraction studies, including first structural determinations of the major isomers of C70(CF3)2, C70(CF3)4, and the third most abundant isomer of C70(CF3)8 as co-crystals with octaethylporphyrin Ni(II), produce accurate CF3 group rotation angles and intergroup F⋯F distances that enable more reliable 19F NMR signal assignment based on the through-space JFF spin-spin coupling relation to the F⋯F distances. Cyclic voltammetry measurements were performed in a potential range that covers oxidation on the one end and reduction to tri- or tetraanionic states on the other. It was demonstrated that the CF3 addition patterns have marked effects on the redox potentials. A consistent set of the experimental HOMO energy values of the C70(CF3)n molecules is reported for the first time in complement to the LUMO data, and the both sets of results were found to demonstrate good correlation with quantum-chemical DFT predictions. Most of the compounds exhibit electrochemically reversible one-electron reductions up to trianionic (sometimes even tetraanionic) state, a notable exception being C70(CF3)10 with irreversibility of its very first reduction. Bulk electrolysis of C70(CF3)12 at its 4-th reduction potential identifies CF3 detachment as the most likely cause of the observed irreversible processes yielding C70(CF3)11−anions as was identified by means of MALDI MS.

DFT predictions, synthesis, stoichiometric structures and anti-diabetic activity of Cu (II) and Fe (III) complexes of quercetin, morin, and primuletin

The current study is aimed at the synthesis of Cu (II) and Fe (III) complexes of three flavonoids {morin (mor), quercetin (quer) and primuletin (prim)} and characterization through UV–Vis spectroscopy, cyclic voltammetry, FTIR, and thermal analysis. Structure prediction through DFT calculation was supported by experimental data. Benesi-Hildebrand equation was modified to function for 1:2 Cu-flavonoid and 1:3 Fe-flavonoid complexes. DFT predictions revealed that out of poly chelation sites present in morin and quercetin, 3-OH site was utilized as preferable chelation site while primuletin chelated through 5-OH position. In-vivo trials revealed the complexes to have better anti-diabetic potential than respective flavonoid. Fls/M-Fls proved as antagonistic to Alloxan induced diabetes and also retained anti-diabetic activity even in the presence of (2-hydroxypropyl)-β-cyclodextrin (HPβCD).

Quantifying the Molecular-Scale Aqueous Response to the Mica Surface

Modeling assembly at surfaces requires an understanding of the interactions between solutes, solvents, and surfaces at multiple scales. We investigated the solvent response (water structure and orientation) to a dielectric surface (mica) using density functional theory. A different water structure is engendered by replacing naturally occurring surface ions (K+) with H3O+. We also validate classical models for the mica surface (CLAYFF) against DFT predictions. The detailed microscopic response of water to mica can be used as input into continuum models for the total interactions between two mica surfaces supporting a strong correlation between physicochemical phenomena at different scales.

A first principles investigation of the oxygen adsorption on Zr(0001) surface using cluster expansions

The design of corrosion resistant zircalloys is important for a variety of technological applications ranging from medicine to the nuclear industry. Since corrosion resistance is mainly attributed to the formation of a surface oxide layer, developing a detailed understanding of this process may assist in future corrosion resistance design. In this work, we conduct a systematic multi-scale investigation of the early stages of oxide formation. This was accomplished by first using a database of fully relaxed DFT calculations to build a cluster-expansion description of the potential function. The developed potential was reasonably good at predicting DFT energies as evidenced by the cross-validation score of 4.4meV/site. The effective cluster expansion parameters were indicative of repulsive adsorbate interactions in the adlayer in agreement with the literature. The potential then allowed for a systematic investigation of the oxygen configurations on the Zr(0001) surface via Monte Carlo simulations. The adsorption energy was recorded as a function of coverage and an increasing trend was observed in agreement with DFT predictions and the repulsive nature of interactions in the adlayer. The convex hull diagram was recorded indicating the most stable configuration to occur around a coverage of 0.6ML. The adsorption isotherm was also recorded and contrasted for two temperatures relevant for different applications.

Feasibility of N2 Binding and Reduction to Ammonia on Fe-Deposited MoS2 2D Sheets: A DFT Study.

Based on the structure of the nitrogenase FeMo cofactor (FeMoco), it is reported that Fe deposited on MoS2 2D sheets exhibits high selectivity towards the spontaneous fixation of N2 against chemisorption of CO2 and H2 O. DFT predictions also indicate the ability of this material to convert N2 into NH3 with a maximum energy input of 1.02 eV as an activation barrier for the first proton-electron pair transfer.

Exploration of CoSi-based alloys promising for thermoelectricity

The cobalt silicide CoSi seems a suitable material for thermoelectricity: it is inexpensive and non-toxic, but its thermal conductivity is large. Forming CoSi-based alloys by replacing part of Co or Si with a heteroatom M can change electronic properties and improve thermoelectric performances. The insertion energy of different CoSi-based alloys containing abundant, inexpensive and non-toxic elements was estimated by using DFT calculations. Several alloys were synthesized using arc-melting or powder reaction and then characterized using X-Rays powder Diffraction (XRD) and Electron Micro Probe Analysis (EMPA) to determine the limit of solubility of these heteroatoms within CoSi. DFT predictions of solubility limit were in qualitative agreement with experimental results. Vibrational and thermoelectric properties were measured for alloys containing highly soluble elements (Mn and Cr) but also poorly soluble ones (Ti and V). These new CoSi-based alloys, studied for the first time for thermoelectric applications, do not exhibit a notable improvement of the performances.

Metal–carbon bond strengths under polymerization conditions: 2,1-insertion as a catalyst stress test

Quantitative agreement between experimentally determined M–C bond dissociation energies (BDE) and DFT predictions (M06-2X/TZ//TPSSTPSS/DZ) can be reached by choosing the correct anchor for experimentally derived BDE. For the example of the archetypical metallocene catalyst Cp2TiCl2, it is shown that titanium–carbon bonds are very weak under polymerization conditions and fluctuate; steric strain is introduced after 2,1 insertion and via olefin capture. Thus, homolysis can become competitive with chain propagation. Depending on the catalyst and temperature, 2,1 insertion can be only a temporary inconvenience (dormancy) or a definitive decay event. It is then shown for a set of nine common Ti and Zr polymerization catalysts how ligand variation affects the metal–carbon BDE. Predicted stabilities of the M(IV) oxidation state with respect to homolysis are in nice agreement with the experimentally observed temperature tolerance of the various catalysts: homolysis is easier for Ti than for Zr, and cyclopentadienyl groups in particular facilitate homolysis, especially in bis-cyclopentadienyl systems.

First-Principles Investigation of the Epitaxial Stabilization of Oxide Polymorphs: TiO2 on (Sr,Ba)TiO3.

Metastable polymorphs, many of which have never been fabricated, have been predicted to exhibit interesting and technologically relevant properties. Epitaxial synthesis is a powerful structure-directing method that can produce metastable polymorphs but is typically done in a trial and error fashion. Unfortunately, the relevant thermodynamic terms governing epitaxial synthesis of new materials are unknown. Accurate calculation of the relevant thermodynamic terms and their incorporation into predictive models would accelerate the synthesis of metastable polymorphs by identifying thermodynamically favorable paths. Using density functional theory with three different functionals, we computed several relevant terms for TiO2 anatase (A) and rutile (R) film growth on low-index surfaces of SrTiO3 (STO) and BaTiO3 (BTO) cubic perovskites. After identifying potential coherent epitaxial interfaces based on experimental observations, the volumetric formation, volumetric strain, and areal substrate-film interface energies were calculated for (001)A∥(001)(S/B)TO, (102)A∥(011)(S/B)TO, (100)R∥(111)(S/B)TO, and (112)A∥(111)(S/B)TO coherent interfaces. These terms were integrated into a standard model of epitaxial nucleation, and the results yielded reasonable agreement between experimental observations and DFT predictions of the preferred epitaxial polymorph. Predicted trends in epitaxial stability were essentially independent of the three functionals used in the calculations. These results are discussed in light of their promise that DFT-informed epitaxial film growth can accelerate fabrication of new polymorphs. These results also validate the recently proposed 20 kJ/mol stability window for predicting which polymorphs could be epitaxially stabilized.

Fluorinated Alkoxide-Based Magnesium-Ion Battery Electrolytes that Demonstrate Li-Ion-Battery-Like High Anodic Stability and Solution Conductivity.

Based on DFT predictions, a series of highly soluble fluorinated alkoxide-based electrolytes were prepared, examined electrochemically, and reversibly cycled. The alcohols react with ethylmagnesium chloride to generate a fluoroalkoxy-magnesium chloride intermediate, which subsequently reacts with aluminum chloride to generate the electrolyte. Solutions starting from a 1,1,1,3,3,3-hexafluoro-2-methylpropan-2-ol precursor exhibit high anodic stability, 3.2 V vs Mg(2+/0), and a record 3.5 mS/cm solution conductivity. Excellent galvanostatic cycling and capacity retention (94%) is observed with more than 300 h of cycle time while employing the standard Chevrel phase-Mo6S8 cathode material.

IR and UV-NIR Absorption Spectroscopy of Matrix-Isolated C70+ and C70–

C70+ ions were mass-selectively deposited into a neon or an argon matrix at 5 K. Like in the case of C60+ deposition, soft landing into a rare gas matrix is associated with some charge-exchange processes such that C70+ as well as resulting C70 and C70– can be probed simultaneously. In contrast with a very good coincidence of the experimental and DFT-calculated IR spectra of C60±/2+, DFT predictions for C70± IR absorptions strongly deviate from our measurements. A possible explanation for this could be low-lying electronically excited states of C70± in the vicinity of vibrational energy levels. The corresponding non-Born–Oppenheimer case is likely of significant interest to theory.

Optical band gaps of organic semiconductor materials

UV–Vis can be used as an easy and forthright technique to accurately estimate the band gap energy of organic π-conjugated materials, widely used as thin films/composites in organic and hybrid electronic devices such as OLEDs, OPVs and OFETs. The electronic and optical properties, including HOMO–LUMO energy gaps of π-conjugated systems were evaluated by UV–Vis spectroscopy in CHCl3 solution for a large number of relevant π-conjugated systems: tris-8-hydroxyquinolinatos (Alq3, Gaq3, Inq3, Al(qNO2)3, Al(qCl)3, Al(qBr)3, In(qNO2)3, In(qCl)3 and In(qBr)3); triphenylamine derivatives (DDP, p-TTP, TPB, TPD, TDAB, m-MTDAB, NPB, α-NPD); oligoacenes (naphthalene, anthracene, tetracene and rubrene); oligothiophenes (α-2T, β-2T, α-3T, β-3T, α-4T and α-5T). Additionally, some electronic properties were also explored by quantum chemical calculations. The experimental UV–Vis data are in accordance with the DFT predictions and indicate that the band gap energies of the OSCs dissolved in CHCl3 solution are consistent with the values presented for thin films.