How Accurate Are DFT Treatments of Organic Energies?

Implementing reactivity in molecular dynamics simulations with harmonic force fields

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods.

Big data benchmarking: how do DFT methods across the rungs of Jacob's ladder perform for a dataset of 122k CCSD(T) total atomization energies?

Total atomization energies (TAEs) are a central quantity in density functional theory (DFT) benchmark studies. However, so far TAE databases obtained from experiment or high-level ab initio wavefunction theory included up to hundreds of TAEs. Here, we use the GDB-9 database of 133k CCSD(T) TAEs generated by Curtiss and co-workers [B. Narayanan, P. C. Redfern, R. S. Assary and L. A. Curtiss, Chem. Sci., 2019, 10, 7449] to evaluate the performance of 14 representative DFT methods across the rungs of Jacob's ladder (namely, PBE, BLYP, B97-D, M06-L, τ-HCTH, PBE0, B3LYP, B3PW91, ωB97X-D, τ-HCTHh, PW6B95, M06, M06-2X, and MN15). We first use the A25[PBE] diagnostic for nondynamical correlation to eliminate systems that potentially include significant multireference effects, for which the CCSD(T) TAEs might not be sufficiently reliable. The resulting database (denoted by GDB9-nonMR) includes 122k species. Of the considered functionals, B3LYP attains the best performance relative to the G4(MP2) reference TAEs, with a mean absolute deviation (MAD) of 4.09 kcal mol-1. This first-generation hybrid functional, in which the three mixing coefficients were fitted against a small set of TAEs, is one of the few functionals that are not systematically biased towards overestimating the G4(MP2) TAEs, as demonstrated by a mean-signed deviation (MSD) of 0.45 kcal mol-1. The relatively good performance of B3LYP is followed by the heavily parameterized M06-L meta-GGA functional, which attains a MAD of 6.24 kcal mol-1. The PW6B95, M06, M06-2X, and MN15 functionals tend to systematically overestimate the G4(MP2) TAEs and attain MADs ranging between 18.69 (M06) and 28.54 (MN15) kcal mol-1. However, PW6B95 and M06-2X exhibit particularly narrow error distributions. Thus, scaling their TAEs by an empirical scaling factor reduces their MADs to merely 3.38 (PW6B95) and 2.85 (M06-2X) kcal mol-1. Empirical dispersion corrections (e.g., D3 and D4) are attractive, and therefore, their inclusion worsens the performance of methods that systematically overestimate the TAEs.

Modeling Multi-Step Organic Reactions: Can Density Functional Theory Deliver Misleading Chemistry?

Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree-Fock exchange. These results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.

Phase-Dependence of Molecular Structures Arising from Weak London Dispersion Interactions

ConspectusThe structures of molecules can be different in different phases. Intermolecular forces, even those of weak noncovalent interactions (WNCIs), can lead to a preference for quite different conformations in the solid, the gas, and the liquid phases. WNCIs can cause variations in bond lengths, angles, and torsional angles. Since structure is a fundamental concept in chemistry, the knowledge of structural changes with phase is important to understand the source and effects of distorting contributions from WNCIs but also as a predictive tool for the design and stabilization of new bonding situations.X-ray crystallography is ubiquitous and now mostly straightforward to perform, but facilities for the determination of accurate gas-phase structure determination are rare, and gas-phase work is laborious and time-consuming. There are currently about 1.25 million crystal structures and more than 12 500 experimental gas-phase structures, but the intersection of the two data sets that can tell us about the structural differences of the same molecule in different phases is surprisingly small.In this Account, we describe several cases of WNCI-dominated systems for which accurate experimental structure determinations exist for both the gas phase and the solid state and, in one case, also for solution. The examples include aryl-aryl, aryl-alkyl, and alkyl-alkyl interactions; systems with chalcogen and halogen bonding; and fluorine-based interactions in arylboranes. We work out the role of WNCIs in stabilizing large, strained, or sterically overloaded molecules. We will show how flexible molecules will fold under the action of WNCIs when isolated in the gas and how they fold or unfold when they are embedded in an environment of neighbors in crystals. We will show how they can vary in strength when the substitution patterns in aryl groups are changed by different halogens and how intramolecular WNCIs, such as those forming rings, change when such systems experience additional intermolecular WNCIs.Overall, we hope that this Account will give the reader an idea of the type and magnitude of structural changes that can be expected from a free molecule in the gas phase or a single molecule calculated by quantum chemistry compared with one embedded in a crystal. This should define the limits of comparability and provide some predictive concepts of the distortions and variations to be expected.

Fullerenes Pose a Strain on Hybrid Density Functional Theory

The computational modeling of fullerenes plays a fundamental role in designing low-dimension carbon nanostructures. Nevertheless, the relative energies of fullerenes larger than C20 and C24 have not been comprehensively examined by means of highly accurate ab initio methods, for example, the CCSD(T) method. Here we report such an investigation for a diverse set of 29 C40 isomers. We calculate the energies of the C40 fullerenes using the G4(MP2) composite ab initio method, which approximates the CCSD(T) energy in conjunction with a triple-ζ-quality basis set (CCSD(T)/TZ). The CCSD(T)/TZ isomerization energies span 43.1-763.3 kJ mol-1. We find a linear correlation (R2 = 0.96) between the CCSD(T)/TZ isomerization energies and the fullerene pentagon signatures (P1 index), which reflect the strain associated with fused pentagon-pentagon rings. Using the reference CCSD(T)/TZ isomerization energies, we examine the relationship between the percentage of exact Hartree-Fock (HF) exchange in hybrid density functional theory (DFT) methods and the pentagon-pentagon strain energies. We find that the performance of hybrid DFT methods deteriorates with the pentagon-pentagon strain energy. This deterioration in performance becomes more pronounced with the inclusion of high amounts of HF exchange. For example, for B3LYP (20% HF exchange), the root-mean-square deviation (RMSD) relative to G4(MP2) increases from 8.9 kJ mol-1 for the low-strain isomers (P1 = 11) to 18.0 kJ mol-1 for the high-strain isomers (P1 > 13). However, for BH&HLYP (50% HF exchange) the RMSD increases from 23.0 (P1 = 11) to 113.2 (P1 > 13) kJ mol-1. A similar trend is observed for the M06/M06-2X pair of functionals. Namely, for M06 (27% HF exchange) the RMSD increases from 0.8 (P1 = 11) to 21.0 (P1 > 13) kJ mol-1, whereas for M06-2X (54% HF exchange) the RMSD increases from 16.7 (P1 = 11) to 77.7 (P1 > 13) kJ mol-1. Overall, we find that the strain associated with pentagon adjacency is an inherently challenging problem for hybrid DFT methods involving high amounts of HF exchange and that there is an inverse relationship between the optimal percentage of HF exchange and the pentagon-pentagon strain energy. For example, for BLYP the optimal percentages of HF exchange are 13% (P1 = 11), 10% (P1 = 12), 7.5% (P1 = 13), and 6% (P1 > 13).

Calculating bond dissociation energies of X-H (X=C, N, O, S) bonds of aromatic systems via density functional theory: a detailed comparison of methods

In this study, the performance of 17 different density functional theory functionals was compared for the calculation of the bond dissociation energy (BDE) values of X-H (X=C, N, O, S) bonds of aromatic compounds. The effect of the size of the basis set (expansions of 6-31(G)) was also assessed for the initial geometry and zero-point energy calculations, followed by the single-point BDE calculations with different model chemistries with the 6-311 + (3df,2p) basis set. It was found that the size of the basis set for geometry optimization has a much smaller effect on the accuracy of BDE than the choice of functional for the following single-point calculations. The M06-2X, M05-2X and M08-HX functionals yielded highly accurate BDE values compared to experimental data (with the average mean unsigned error MUE = 1.2-1.5 kcal mol^-1), performing better than any of the other functionals. The results suggest that geometry optimization may be performed with B3LYP functional and a small basis set, whereas the M06-2X, M05-2X and M08-HX density functionals with a suitably large basis set offer the best method for calculating BDEs of ArX-H (X=C, N, O, S) bonds.

Keto-enol tautomerism from the electron delocalization perspective

The equilibrium between keto and enol forms in acetylacetone and its derivatives is studied using electron delocalization indices and delocalization tensor density. We demonstrate how electron delocalization governs the equilibrium between keto and enol forms. The less stable enols have more distinct double and single bond character in the CCC fragment, while electron delocalization in this fragment is more pronounced in more stable enols. Looking for the origin of such behavior, we considered the one-electron potentials entering the Euler equation for the electron density. We found that electron delocalization is mainly governed by the static exchange potential, which depends on the three-dimensional atomic structure. It, however, does not distinguish differences in electron delocalization in more and less stable enols, the effect arising from the kinetic exchange contribution, which reflects spin-dependent effects in the electron motion. The local depletion of kinetic exchange in the conjugated fragment yields the enhanced electron delocalization along the CCC bonds in more stable enols. Thus, a combination of considered descriptors allowed us to reveal the influence of electron delocalization on the equilibrium between keto and enol forms and showed the significant features of this phenomenon.

Pyrolytic activation of cellulose: Energetics and condensed phase effects

Bottom-up design of lignocellulose pyrolysis to optimize the quality and yield of bio-oil is hindered by the limited knowledge of the underlying condensed phase biomass chemistry. The influence of condensed...

Molecular Energies Derived from Deep Learning: Application to the Prediction of Formation Enthalpies Up to High Energy Compounds

Total electronic energies and frequencies predicted using the deep learning models ANI-1x and ANI-1ccx are converted to gas-phase formation enthalpies Δ_f H⁰ using an atom equivalent (AE) scheme for a database of CHNO compounds. As expected from the accuracy of those models in predicting reference DFT frequencies and DLPNO-CCSD(T)/CBS energies, this procedure usually outperforms DFT-based AE schemes. However, for some compounds, including energetic molecules, significant deviations from experiment are observed, larger than obtained using DFT procedures. A close examination of the GDB-11 database from which the training data was drawn reveals that many structures of interest in the energetic materials community are excluded from this extensive compilation primarily focused on drug discovery and designed with stability constraints in mind. This points to the urgent need to set up a comparable database including energetic species of interest for the design of energetic materials such as propellants or explosives.

Evaluation of Computational Chemistry Methods for Predicting Redox Potentials of Quinone-Based Cathodes for Li-Ion Batteries

High-throughput computational screening (HTCS) is an effective tool to accelerate the discovery of active materials for Li-ion batteries. For the evaluation of organic cathode materials, the effectiveness of HTCS depends on the accuracy of the employed chemical descriptors and their computing cost. This work was focused on evaluating the performance of computational chemistry methods, including semi-empirical quantum mechanics (SEQM), density-functional tight-binding (DFTB), and density functional theory (DFT), for the prediction of the redox potentials of quinone-based cathode materials for Li-ion batteries. In addition, we evaluated the accuracy of three energy-related descriptors: (1) the redox reaction energy, (2) the lowest unoccupied molecular orbital (LUMO) energy of reactant molecules, and (3) the highest occupied molecular orbital (HOMO) energy of lithiated product molecules. Among them, the LUMO energy of the reactant compounds, regardless of the level of theory used for its calculation, showed the best performance as a descriptor for the prediction of experimental redox potentials. This finding contrasts with our earlier results on the calculation of quinone redox potentials in aqueous media for redox flow batteries, for which the redox reaction energy was the best descriptor. Furthermore, the combination of geometry optimization using low-level methods (e.g., SEQM or DFTB) followed by energy calculation with DFT yielded accuracy as good as the full optimization of geometry using the DFT calculations. Thus, the proposed calculation scheme is useful for both the optimum use of computational resources and the systematic generation of robust calculation data on quinone-based cathode compounds for the training of data-driven material discovery models.

Comparison of (5 + 2) Cycloadditions Involving Oxidopyrylium and Oxidopyridinium Ions: Relative Reactivities

A variety of (5 + 2) cycloaddition reactions involving oxidopyridinium and oxidopyrylium zwitterions are compared to investigate the effects of nitrogen-for-oxygen substitution on reactivity. Activation barriers for nitrogen-containing systems are predicted to be larger than those for analogous oxygen-containing systems. Correlations between barrier heights and synchronicity of C-C bond formation, changes to aromaticity, reactant distortion, and interaction energies between zwitterions and alkenes were assessed, leading to the conclusion that reactivity depends more on distortion effects (including aromaticity loss) than on interaction effects (such as those associated with highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) interactions).

Efficient hierarchical models for reactivity of organic layers on semiconductor surfaces

Computational modeling of organic interface formation on semiconductors poses a challenge to a density functional theory-based description due to structural and chemical complexity. A hierarchical approach is presented, where parts of the interface are successively removed in order to increase computational efficiency while maintaining the necessary accuracy. First, a benchmark is performed to probe the validity of this approach for three model reactions and five dispersion corrected density functionals. Reaction energies are generally well reproduced by generalized gradient approximation-type functionals but accurate reaction barriers require the use of hybrid functionals. Best performance is found for the model system that does not explicitly consider the substrate but includes its templating effects. Finally, this efficient model is used to provide coverage dependent reaction energies and suggest synthetic principles for the prevention of unwanted growth termination reactions for organic layers on semiconductor surfaces.

Method for the accurate prediction of electron transfer potentials using an effective absolute potential

A protocol for the accurate computation of electron transfer (ET) potentials from ab initio and density functional theory (DFT) calculations is described. The method relies on experimental pKa values, which can be measured accurately, to compute a computational setup dependent effective absolute potential. The effective absolute potentials calculated using this protocol display strong variations between the different computational setups and deviate in several cases significantly from the "generally accepted" value of 4.28 V. The most accurate estimate, obtained from CCSD(T)/aug-ccpvqz, indicates an absolute potential of 4.14 V for the normal hydrogen electrode (nhe) in water. Using the effective absolute potential in combination with CCSD(T) and a moderately sized basis, we are able to predict ET potentials accurately for a test set of small organic molecules (σ = 0.13 V). Similarly we find the effective absolute potential method to perform equally good or better for all considered DFT functionals compared to using one of the literature values for the absolute potential. For, M06-2X, which comprises the most accurate DFT method, standard deviation of 0.18 V is obtained. This improved performance is a result of using the most appropriate effective absolute potential for a given method.

Reproducibility of potential energy surfaces of organic/metal interfaces on the example of PTCDA on Ag(111)

Molecular adsorption at organic/metal interfaces depends on a range of mechanisms: covalent bonds, charge transfer, Pauli repulsion, and van der Waals (vdW) interactions shape the potential energy surface (PES), making it key to understanding organic/metal interfaces. Describing such interfaces with density functional theory requires carefully selecting the exchange correlation (XC) functional and vdW correction scheme. To explore the reproducibility of the PES with respect to the choice of method, we present a benchmark of common local, semi-local, and non-local XC functionals in combination with various vdW corrections. We benchmark these methods using perylene-tetracarboxylic dianhydride on Ag(111), one of the most frequently studied organic/metal interfaces. For each method, we determine the PES using a Gaussian process regression algorithm, which requires only about 50 density functional theory calculations as input. This allows a detailed analysis of the PESs' features, such as the positions and energies of minima and saddle points. Comparing the results from different combinations of XC functionals and vdW corrections enables us to identify trends and differences between the approaches. PESs for different computation methods are in qualitative agreement but also display significant quantitative differences. In particular, the lateral positions of adsorption geometries agree well with experiment, while adsorption heights, energies, and barriers show larger discrepancies.

Structure–Activity relationship studies of two dietary flavonoids and their Nitric Oxide Synthase inhibition activity by spectroscopic and quantum/classical computational techniques

The Nitric Oxide Synthase inhibitory activity of two dietary phytocompounds naringenin and quercetin that belong to the family of flavonoids was studied by spectroscopic and computational methods. The determining role played by the global reactivity parameters that were calculated using spectroscopic and computational methods were correlated with the Nitric Oxide Synthase inhibitory activity by a Quantitative Structure–Activity Relationship (QSAR) study. The inter and intramolecular charge–transfer interactions responsible for the biological activity of naringenin and quercetin were studied using Natural Bond Orbital Analysis. The reactive sites of the title compounds were studied using their molecular electrostatic map. The likelihood of naringenin and quercetin to be a small drug molecule was determined by Lipinski’s rule. The molecular dynamics and docking studies were carried out to test the energetic and structural favorability of the inhibition of Nitric Oxide Synthase by small drug molecules naringenin and quercetin. Experimental cell culture-based in vitro assays were done to test theoretical predictions. A QSAR study revealed that for Nitric Oxide Synthase inhibitory activity to be better, the compounds belonging to the family of flavonoids ought to have a more negative ionization energy and chemical softness while bandgap and electrophilicity index ought to be more positive.

Mechanism of the Oxidation of Heptafulvenes to Tropones Studied by Online Mass Spectrometry and Density Functional Theory Calculations

We have identified the most likely reaction mechanism for oxidizing heptafulvenes to the corresponding tropones by experimental and theoretical investigations. The experimental studies were done by coupling a three-dimensional printed miniaturized reactor with an integrated electrospray ionization needle to a mass spectrometer. Using the experimentally observed ions as a basis, nine alternative reaction pathways were investigated with density functional theory calculations. The lowest energy reaction pathway starts with the formation of an epoxide that is opened upon the addition of a second equivalent of the oxidizing species meta-chloroperoxybenzoic acid. The adduct formed then undergoes a Criegee-like rearrangement to yield a positively charged hemiketal, which on deprotonation dissociates into acetone and tropone. Overall, the reaction mechanism resembles a Hock-like rearrangement.

Gaussian Process-Based Refinement of Dispersion Corrections

We employ Gaussian process (GP) regression to adjust for systematic errors in D3-type dispersion corrections. We refer to the associated, statistically improved model as D3-GP. It is trained on differences between interaction energies obtained from PBE-D3(BJ)/ma-def2-QZVPP and DLPNO-CCSD(T)/CBS calculations. We generated a data set containing interaction energies for 1248 molecular dimers, which resemble the dispersion-dominated systems contained in the S66 data set. Our systems represent not only equilibrium structures but also dimers with various relative orientations and conformations at both shorter and longer distances. A reparametrization of the D3(BJ) model based on 66 of these dimers suggests that two of its three empirical parameters, a₁ and s₈, are zero, whereas a₂ = 5.6841 bohr. For the remaining 1182 dimers, we find that this new set of parameters is superior to all previously published D3(BJ) parameter sets. To train our D3-GP model, we engineered two different vectorial representations of (supra-)molecular systems, both derived from the matrix of atom-pairwise D3(BJ) interaction terms: (a) a distance-resolved interaction energy histogram, histD3(BJ), and (b) eigenvalues of the interaction matrix ordered according to their decreasing absolute value, eigD3(BJ). Hence, the GP learns a mapping from D3(BJ) information only, which renders D3-GP-type dispersion corrections comparable to those obtained with the original D3 approach. They improve systematically if the underlying training set is selected carefully. Here, we harness the prediction variance obtained from GP regression to select optimal training sets in an automated fashion. The larger the variance, the more information the corresponding data point may add to the training set. For a given set of molecular systems, variance-based sampling can approximately determine the smallest subset being subjected to reference calculations such that all dispersion corrections for the remaining systems fall below a predefined accuracy threshold. To render the entire D3-GP workflow as efficient as possible, we present an improvement over our variance-based, sequential active-learning scheme [ J. Chem. Theory Comput. 2018 , 14 , 5238 ]. Our refined learning algorithm selects multiple (instead of single) systems that can be subjected to reference calculations simultaneously. We refer to the underlying selection strategy as batchwise variance-based sampling (BVS). BVS-guided active learning is an essential component of our D3-GP workflow, which is implemented in a black-box fashion. Once provided with reference data for new molecular systems, the underlying GP model automatically learns to adapt to these and similar systems. This approach leads overall to a self-improving model (D3-GP) that predicts system-focused and GP-refined D3-type dispersion corrections for any given system of reference data.

Spectroscopic and quantum/classical mechanics based computational studies to compare the ability of Andrographolide and its derivative to inhibit Nitric Oxide Synthase

The inhibition of the enzyme Nitric Oxide Synthase by a bioactive compounds results in it possessing anti-inflammatory property. The ability of Andrographolide and its derivative Isoandrographolide to inhibit Nitric Oxide Synthase was studied using computational and experimental techniques. A combination of UV Spectroscopic and DFT computational techniques were used to calculate the molecular descriptors of the title compounds which were used to establish relationship with its biological activity. The drug-likeness of the compounds was estimated using Lipinski's rule. Molecular dynamics and docking studies were carried out to test for the structural and energetic favourability of the title compounds(ligand) being bound to Nitric Oxide Synthase(Protein) to induce inhibition. The force constant data obtained from IR spectroscopy was used in aid to parametrize force fields used in molecular dynamics simulation. The DFT method was used to perform NBO analysis that revealed the charge transfer interactions responsible for its biological properties. The Molecular Electrostatic Potential (MEP) plot revealed the regions of electrophilic and nucleophilic reactivity of the title compounds. MTT (3-(4, 5-dimethyl thiazolyl-2)-2, 5-diphenyltetrazolium bromide) assay was carried out which revealed the cytotoxicity at different concentrations of the title compounds by which means the biologically safe concentration was determined and therefore at this biologically safe concentration the ability of the compounds to inhibit Nitric Oxide formation was determined. Quantitative Structure-Activity Studies (QSAR) were used to furnish relationship between molecular descriptors and the Nitric Oxide Synthase inhibition activity resulting in anti-inflammatory property, based on the chosen molecular descriptors suggestions were made for the search of more potent Nitric Oxide Synthase inhibitors in the Andrographolide derivative family of compounds.

Thermochemistry of Guanine Tautomers Re-Examined by Means of High-Level CCSD(T) Composite Ab Initio Methods

We obtained accurate gas-phase tautomerization energies for a set of 14 guanine tautomers by means of high-level thermochemical procedures approximating the CCSD(T) energy at the complete basis set (CBS) limit. For the five low-lying tautomers, we use the computationally demanding W1-F12 composite method for obtaining the tautomerization energies. The relative W1-F12 tautomerization enthalpies at 298K are: 0.00 (1), 2.37 (2), 2.63 (3), 4.03 (3′), and 14.31 (4) kJmol−1. Thus, as many as four tautomers are found within a small energy window of less than 1.0kcalmol−1 (1kcalmol−1=4.184kJmol−1). We use these highly accurate W1-F12 tautomerization energies to evaluate the performance of a wide range of lower-level composite ab initio procedures. The Gn composite procedures (G4, G4(MP2), G4(MP2)-6X, G3, G3B3, G3(MP2), and G3(MP2)B3) predict that the enol tautomer (3) is more stable than the keto tautomer (2) by amounts ranging from 0.36 (G4) to 1.28 (G3(MP2)) kJmol−1. We also find that an approximated CCSD(T)/CBS energy calculated as HF/jul-cc-pV{D,T}Z+CCSD/jul-cc-pVTZ+(T)/jul-cc-pVDZ results in a root-mean-square deviation (RMSD) of merely 0.11kJmol−1 relative to the W1-F12 reference values. We use this approximated CCSD(T)/CBS method to obtain the tautomerization energies of 14 guanine tautomers. The relative tautomerization enthalpies at 298K are: 0.00 (1), 2.20 (2), 2.51 (3), 4.06 (3′), 14.30 (4), 25.65 (5), 43.78 (4′), 53.50 (6′), 61.58 (6), 77.37 (7), 82.52 (8′), 86.02 (9), 100.70 (10), and 121.01 (8) kJmol−1. Using these tautomerization enthalpies, we evaluate the performance of standard and composite methods for the entire set of 14 guanine tautomers. The best-performing procedures emerge as (RMSDs are given in parentheses): G4(MP2)-6X (0.51), CCSD(T)+ΔMP2/CBS (0.52), and G4(MP2) (0.64kJmol−1). The worst performers are CCSD(T)/AVDZ (1.05), CBS-QB3 (1.24), and CBS-APNO (1.38kJmol−1).

Accurate Thermochemistry for Organic Cations via Error Cancellation using Connectivity-Based Hierarchy

Connectivity-Based Hierarchy (CBH) is an effective error-cancellation scheme for the determination of chemically accurate thermochemical properties of a variety of organic and biomolecules. Neutral molecules and open-shell radicals have already been treated successfully by this approach utilizing inexpensive computational methods such as density functional theory. Herein, we present an extension of the method to a new class of molecules, specifically, organic cations. Because of the presence of structural rearrangements involving hydrogen migrations as well as unusual structures such as bridged cations, the application of the standard CBH protocol to a test set of 25 cations leads to significant errors due to ineffective bond-type matching. We propose an adjusted protocol to overcome such limitations to achieve highly effective error cancellation. The modified CBH methods, in conjunction with a wide range of density functionals, reproduce G4 energies for the test set of organic cations accurately within 1-2 kcal/mol at a reduced computational cost.

Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers

The covalent diamantyl (C₂₈H₃₈) and oxadiamantyl (C₂₆H₃₄O₂) dimers are stabilized by London dispersion attractions between the dimer moieties. Their solid-state and gas-phase structures were studied using a multitechnique approach, including single-crystal X-ray diffraction (XRD), gas-phase electron diffraction (GED), a combined GED/microwave (MW) spectroscopy study, and quantum chemical calculations. The inclusion of medium-range electron correlation as well as the London dispersion energy in density functional theory is essential to reproduce the experimental geometries. The conformational dynamics computed for C₂₆H₃₄O₂ agree well with solution NMR data and help in the assignment of the gas-phase MW data to individual diastereomers. Both in the solid state and the gas phase the central C-C bond is of similar length for the diamantyl [XRD, 1.642(2) Å; GED, 1.630(5) Å] and the oxadiamantyl dimers [XRD, 1.643(1) Å; GED, 1.632(9) Å; GED+MW, 1.632(5) Å], despite the presence of two oxygen atoms. Out of a larger series of quantum chemical computations, the best match with the experimental reference data is achieved with the PBEh-3c, PBE0-D3, PBE0, B3PW91-D3, and M06-2X approaches. This is the first gas-phase confirmation that the markedly elongated C-C bond is an intrinsic feature of the molecule and that crystal packing effects have only a minor influence.

The thermochemistry of long chain olefin isomers during hydroformylation

The isomerization of 1-decene at the Rh(BiPhePhos) catalyst is initially controlled by steric demand of the ligand before the distribution of olefin isomers reaches thermodynamic equilibrium.

Study on the inter- and intra-peptide salt-bridge mechanism of Aβ23-28 oligomer interaction with small molecules: QM/MM method

Amyloid β (Aβ) peptides have long been known to be a potential candidate for the onset of Alzheimer's disease (AD). The biophysical properties of Aβ42 peptide aggregates are of significant importance for the amyloid cascade mechanism of AD. It is necessary to design an inhibitor using small molecules to reduce the aggregation process in Aβ42 peptides. Attention has been given to use the natural products as anti-aggregation compounds, directly targeting Aβ peptides. Polyphenols have been extensively studied as a class of amyloid inhibitors. 9,10-Anthraquinone (AQ) is present in abundance in medicinal plants (rhubarb), the Trp-Pro-Tyr (TPT) peptide has been found in the venom of the black mamba snake, and the morin molecule is naturally present in wine and green tea; several other polyphenol derivatives are under clinical trials to develop anti-neurodegenerative drugs. In vitro and in vivo results strongly suggest that AQ and morin molecules are potential inhibitors of Aβ aggregation; however, the detailed understanding of the inhibition mechanism remains largely unknown. The formation of Aβ fibrils and oligomers requires a conformational change from α-helix to β-sheet, which occurs due to the formation of a salt-bridge between Asp(23) and Lys(28) residues. The present study focused on investigating the salt-bridge mechanism in the monomer, dimer and oligomer of the Aβ23-28 peptide during the interaction with TPT, morin and AQ molecules. Interaction energy and natural bond orbital analyses have been carried out using the ONIOM(M05-2X/6-31++G(d,p):UFF) method. The QM/MM studies have been performed to study the mechanism of salt-bridge formation during the inhibition process of amyloid β protein aggregation. The TPT molecule, which binds with the Asp(23) and Lys(28) residues of Aβ, prevents the salt-bridge formation between Asp(23) and Lys(28) residues and consequently the probability of the formation of Aβ fibrils is reduced.

Performance of the major semiempirical, ab initio, and DFT methods for isomerization enthalpies of linear to branched heptanes

The gas phase standard state (298.15 K, 1 atm) isomerization enthalpy (Δ(isom)H°(g)) prediction performance of the major semiempirical, ab initio, and density functional levels of theory for environmentally relevant transformations was investigated using the linear to branched heptanes as a representative case study. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are well suited for investigating the thermodynamic properties of environmentally interesting isomerizations, although the M062X functional may not be appropriate for all systems. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise.

The Use of a Combination of RDC and Chiroptical Spectroscopy for Determination of the Absolute Configuration of Fusariumin A from the Fungus Fusarium sp

A new alkylpyrrole derivative, fusariumin A (1), was isolated from the culture broth of the fungus Fusarium sp. The absolute configuration of fuasiumin A has been established as (2'R,3'R) using a combination of RDC (residual dipolar coupling)-based NMR and DFT-supported chiroptical spectroscopy. It is worth to note that in this study without the aid of the RDC analysis, an unambiguous determination of configuration and conformation was not feasible due to the excessive conformational possibilities of this open-chain compound.