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Advances in computational chemistry create an ongoing need for larger and higher-quality datasets that characterize noncovalent molecular interactions. We present three benchmark collections of quantum mechanical data, covering approximately 3,700 distinct types of interacting molecule pairs. The first collection, which we refer to as DES370K, contains interaction energies for more than 370,000 dimer geometries. These were computed using the coupled-cluster method with single, double, and perturbative triple excitations [CCSD(T)], which is widely regarded as the gold-standard method in electronic structure theory. Our second benchmark collection, a core representative subset of DES370K called DES15K, is intended for more computationally demanding applications of the data. Finally, DES5M, our third collection, comprises interaction energies for nearly 5,000,000 dimer geometries; these were calculated using SNS-MP2, a machine learning approach that provides results with accuracy comparable to that of our coupled-cluster training data. These datasets may prove useful in the development of density functionals, empirically corrected wavefunction-based approaches, semi-empirical methods, force fields, and models trained using machine learning methods., Measurement(s) Molecular Interaction Process • interaction energy • energy Technology Type(s) ab initio quantum chemistry computational method Factor Type(s) molecular entity Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13521638

AZD9291 (Osimertinib) is highly effective in treating EGFR-mutated non-small-cell lung cancers (NSCLCs) with T790M-mediated drug resistance. Despite the remarkable success of AZD9291, its binding pose with EGFR T790M remains unclear. Here, we report unbiased, atomic-level molecular dynamics (MD) simulations in which spontaneous association of AZD9291 with EGFR kinases having WT and T790M mutant gatekeepers was observed. Simulation-generated structural models suggest that the binding pose of AZD9291 with T790M differs from its binding pose with the WT, and that AZD9291 interacts extensively with the gatekeeper residue (Met 790) in T790M but not with Thr 790 in the WT, which explains why AZD9291 binds T790M with higher affinity. The MD simulation-generated models were confirmed by experimentally determined EGFR/T790M complex crystal structures. This work may facilitate the rational design of drugs that can overcome resistance mutations to AZD9291, and more generally it suggests the potential of using unbiased MD simulation to elucidate small-molecule binding poses.

Diffusion coefficient measurements are important for many biological and material investigations, such as studies of particle dynamics and kinetics, and size determinations. Among current measurement methods, single particle tracking (SPT) offers the unique ability to simultaneously obtain location and diffusion information about a molecule while using only femtomoles of sample. However, the temporal resolution of SPT is limited to seconds for single-color-labeled samples. By directly imaging three-dimensional diffusing fluorescent proteins and studying the widths of their intensity profiles, we were able to determine the proteins' diffusion coefficients using single protein images of submillisecond exposure times. This simple method improves the temporal resolution of diffusion coefficient measurements to submilliseconds, and can be readily applied to a range of particle sizes in SPT investigations and applications in which diffusion coefficient measurements are needed, such as reaction kinetics and particle size determinations.

A detailed analysis of the thermal expansion mechanism of graphite oxide to produce functionalized graphene sheets is provided. Exfoliation takes place when the decomposition rate of the epoxy and hydroxyl sites of graphite oxide exceeds the diffusion rate of the evolved gases, thus yielding pressures that exceed the van der Waals forces holding the graphene sheets together. A comparison of the Arrhenius dependence of the reaction rate against the calculated diffusion coefficient based on Knudsen diffusion suggests a critical temperature of 550 °C which must be exceeded for exfoliation to occur. As a result of their wrinkled nature, the functionalized and defective graphene sheets do not collapse back to graphite oxide but are highly agglomerated. After dispersion by ultrasonication in appropriate solvents, statistical analysis by atomic force microscopy shows that 80% of the observed flakes are single sheets.

We employ fully quantum-mechanical molecular dynamics simulations to evaluate the force between two methanes dissolved in water, as a model for hydrophobic association. A stable configuration is found near the methane–methane contact separation, while a shallow second potential minimum occurs for the solvent-separated configuration. The strength and shape of the potential of mean force are in conflict with earlier classical force-field simulations but agree well with a simple hydrophobic burial model which is based on solubility experiments. Examination of solvent dynamics reveals stable water cages at several specific methane–methane separations.

Orientational order of surfactant micelles and proteins on crystalline templates has been observed but, given that the template unit cell is significantly smaller than the characteristic size of the adsorbate, this order cannot be attributed to lattice epitaxy. We interpret the template-directed orientation of rodlike molecular assemblies as arising from anisotropic van der Waals interactions between the assembly and crystalline surfaces where the anisotropic van der Waals interaction is calculated using the Lifshitz methodology. Provided the assembly is sufficiently large, substrate anisotropy provides a torque that overcomes rotational Brownian motion near the surface. The probability of a particular orientation is computed by solving a Smoluchowski equation that describes the balance between van der Waals and Brownian torques. Torque aligns both micelles and protein fibrils; the interaction energy is minimized when the assembly lies perpendicular to a symmetry axis of a crystalline substrate. Theoretical predictions agree with experiments for both hemi-cylindrical micelles and protein fibrils adsorbed on graphite.

We present quantum mechanical calculations using density functional theory and semiempirical methods, and molecular mechanics (MM) calculations with a Tersoff–Brenner potential that explore the role of vacancy defects in the fracture of carbon nanotubes under axial tension. These methods show reasonable agreement, although the MM scheme systematically underestimates fracture strengths. One- and two-atom vacancy defects are observed to reduce failure stresses by as much as 26% and markedly reduce failure strains. Large holes – such as might be introduced via oxidative purification processes – greatly reduce strength, and this provides an explanation for the extant theoretical–experimental discrepancies. 2004 Published by Elsevier B.V.

We have developed a new single-molecule fluorescence imaging analysis method, SIMA, that improves the temporal resolution of single-molecule localization and tracking studies to millisecond timescales without compromising the nanometer range spatial resolution [1,2,3,4]. In this method, the width of the fluorescence intensity profile of a static or a mobile molecule, imaged using submillisecond to milliseconds exposure time, is used for localization and dynamics analyses. We apply this method to three single-molecule investigations: (1) axial localization precision measurements, (2) subdiffraction molecular separation measurements, and (3) protein diffusion coefficient measurements in free solution.

DNA-binding proteins' alternating diffusion kinetics on and off nonspecific DNA (also called sliding and hopping respectively) are important for quantifying their target binding mechanisms. Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulation results suggest the following: (1) In each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of ms; (2) sliding dominates the root mean square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (3) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins. Experimental investigations of sliding proteins on DNA using SIMA [1] measurements on the timescale of milliseconds will be presented.[1]. DeCenzo, S. H., M. C. DeSantis, and Y. M. Wang. 2010 Optics Express 18(16):16628-39.

We probe the bending characteristics of functionalized graphene sheets with the tip of an atomic force microscope. Individual sheets are transformed from a flat into a folded configuration. Sheets can be reversibly folded and unfolded multiple times, and the folding always occurs at the same location. This observation suggests that the folding and bending behavior of the sheets is dominated by pre-existing kink (or even fault) lines consisting of defects and/or functional groups.

A process is described to produce single sheets of functionalized graphene through thermal exfoliation of graphite oxide. The process yields a wrinkled sheet structure resulting from reaction sites involved in oxidation and reduction processes. The topological features of single sheets, as measured by atomic force microscopy, closely match predictions of first-principles atomistic modeling. Although graphite oxide is an insulator, functionalized graphene produced by this method is electrically conducting.

Optical microscope images of graphite oxide (GO) reveal the occurrence of fault lines resulting from the oxidative processes. The fault lines and cracks of GO are also responsible for their much smaller size compared with the starting graphite materials. We propose an unzipping mechanism to explain the formation of cracks on GO and cutting of carbon nanotubes in an oxidizing acid. GO unzipping is initiated by the strain generated by the cooperative alignment of epoxy groups on a carbon lattice. We employ two small GO platelets to show that through the binding of a new epoxy group or the hopping of a nearby existing epoxy group, the unzipping process can be continued during the oxidative process of graphite. The same epoxy group binding pattern is also likely to be present in an oxidized carbon nanotube and cause its breakup.

Surfactant micelles form oriented arrays on crystalline substrates although registration is unexpected since the template unit cell is small compared to the size of a rodlike micelle. Interaction energy calculations based on molecular simulations reveal that orientational energy differences on a molecular scale are too small to explain matters. With atomic force microscopy, we show that orientational ordering is a dynamic, multimolecule process. Treating the cooperative processes as a balance between van der Waals torque on a large, rodlike micellar assembly and Brownian motion shows that orientation is favored.

The modern theory of dispersion forces uses macroscopic dielectric functions $ϵ(\ensuremath{\omega})$ as a central ingredient. We reexamined the formalism and found that at separation distance $l2\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$ the full dielectric function $ϵ(\ensuremath{\omega},\mathbf{k})$ is needed. The use of $ϵ(\ensuremath{\omega},\mathbf{k})$ results in as much as 30% reduction of the calculated Hamaker constants reported in the current literature. At larger distances, the theory reduces to the traditional method, which uses dielectric functions in the long-wavelength limit. We illustrate the formalism using the example of interaction between two graphite slabs. This example is of importance for intercalation and exfoliation of graphite and for the use of exfoliated graphite in composite materials. The formalism can also be extended to study anisotropic van der Waals interactions.

We present a first-principles study of the quasiparticle excitations spectrum of NiO. The calculations are performed using the spin-polarized GW approximation in a plane-wave basis set with ab initio pseudopotentials. We find a feature in the band structure which can explain both an absorption edge of 3.1 eV in optical measurements and an energy gap of 4.3 eV found in XPS/BIS measurements. The calculated quasiparticle density of states shows that the oxygen 2p peaks overlap with the satellite structure at similar to 8 eV below the Fermi level. Finally, we discuss the difference between this work and two previous quasiparticle energy calculations.

Different stacking arrangements of ${\mathrm{BC}}_{3}$ layered crystals are studied with the use of the ab initio pseudopotential density-functional method. The total energies, lattice constants, electron energy band structures and density of states, as well as phonon frequencies are calculated for the possible bulk ${\mathrm{BC}}_{3}$ structures obtained by full relaxations starting from different initial atomic configurations of ABAB (or ABCABC)\ensuremath{\cdot}\ensuremath{\cdot}\ensuremath{\cdot} layer stacking. Two stable ${\mathrm{BC}}_{3}$ structures, one semiconductor and the other metal, are obtained, which have lower total energies comparing with those of the structures proposed previously. Our calculations show that except for these two ${\mathrm{BC}}_{3}$ structures, all the structures we studied, including the ${\mathrm{BC}}_{3}$ structures proposed previously, have imaginary phonon frequencies corresponding to the relative, parallel motion of the adjacent ${\mathrm{BC}}_{3}$ layers, indicating the instability of the layer stacking in these structures.

We study the metal-insulator transition in a model Mott system, a bcc hydrogen solid, by performing ab initio quasiparticle band-structure calculations within the GW approximation for a wide range of lattice constants. The value of the critical electron density n(c) is consistent with Mott's original criterion. For smaller lattice constants, our spin-polarized GW results agree well with previous variational quantum Monte Carlo calculations. For large lattice constants, the computed quasiparticle band gap corresponds to the difference between the ionization energy and electron affinity of an isolated hydrogen atom. Near the metal-insulator transition, we investigate the quality of the quasiparticle wave functions obtained from different starting approximations in density-functional theory. Finally, we gain new insight into the GW method and its applicability to spin-polarized systems, for which several refinements are introduced.

In the past decade, cilia/flagella have come to be known as essential sensory organelles for cells. They perform their sensory duties via signaling pathways comprised of transmembrane signaling proteins (TSP) and intraflagellar transport (IFT) machineries that are responsible for translocating TSPs within the flagellum. While IFT average speed, IFT train frequency, and IFT train size have already been studied, little is known about IFT dynamics at the flagellar tip region where anterograde IFT trains deposit their cargo and rearrange for retrograde transport to the cell body. To address this issue, we use single-molecule fluorescence imaging methods to study the motion of GFP-tagged BBS4, an IFT-associated protein that is part of the BBSome complex, at the flagellar tip in Chlamydomonas reinhardtii. These investigations have yielded the following results: (i) In the tip region, BBSomes remain attached to their cargo TSPs and diffuse along the flagellar membrane with a diffusion coefficient of 1130 nm2/s. This result contrasts with the current understanding that the BBSome either remains bound to IFT train on the microtubule or diffuses in the flagellar lumen. (ii) On average, BBSomes remain at the flagellar tip for 2.6 seconds before undergoing retrograde IFT. (iii) Our BBS4-GFP image-size investigation has helped further uncover the nature of the BBSome's oligomerization on IFT trains both during active transport along the flagellum and during the turn-around period at the flagellar tip.

Surfactant micelles (cetyltrimethylammonium chloride) adsorbed on Au(111) exhibit orientational order dictated by the gold crystal axes. To explain this phenomenon, we take into account the ionic contribution to the dielectric response of the metal. Since the motion of an ion inside the metallic lattice is restricted by its neighbors in an anisotropic way, the total dielectric response of the metal acquires directional dependence. A crystalline substrate is thus able to generate both torque and attraction on geometrically asymmetric objects. Numerical calculations show that the resulting anisotropic van der Waals force is indeed capable of orienting rod-like dielectric micelles on a Au(111) surface.