Correlated Local Fluctuations in the Hydrogen Bond Network of Liquid Water.

The hypothesis that liquid water can separate into two phases in the supercooled state has been supported by recent experimental and theoretical studies. However, whether such structural inhomogeneity extends to ambient conditions is under intense debate. Due to the dynamic nature of the hydrogen bond network of liquid water, exploring its structure requires detailed insight into the collective motion of neighboring water molecules, a missing link that has not been examined so far. Here, highly sensitive quantum mechanical calculations detect that the time evolution of nearby hydrogen bonds is strongly correlated, revealing a direct mechanism for the appearance of short-range structural fluctuations in the hydrogen bond network of liquid water for the first time. This correlated dynamics is found to be closely connected to the static structural picture. The distortions from the tetrahedral structure do not occur independently but are correlated due to the preference of nearby donors and acceptors to be in similar environments. The existence of such cooperative fluctuations is further supported by the temperature dependence of the local structural evolution and explained by conventional analysis of localized orbitals. It was found that such correlated structural fluctuations are only observed on a short length scale in simulations at ambient conditions. The correlations of the nearby hydrogen bond pairs of liquid water unveiled here are expected to offer a new insight into connecting the dynamics of individual water molecules and the local structure of the hydrogen bond network.

Stereospecific Epitaxial Growth of Bilayered Porous Molecular Networks.

Stereocontrolled multilayer growth of supramolecular porous networks at the interface between graphite and a solution was investigated. For this study, we designed a chiral dehydrobenzo[12]annulene (DBA) building block bearing alkoxy chains substituted at the 2 position with hydroxy groups, which enable van der Waals stabilization in a layer and potential hydrogen-bonding interactions between the layers. Bias voltage-dependent scanning tunneling microscopy (STM) experiments revealed the diastereospecificity of the bilayer with respect to both the intrinsic chirality of the building blocks and the supramolecular chirality of the self-assembled networks. Top and bottom layers within the same crystalline domain were composed of the same enantiomers but displayed opposite supramolecular chiralities.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Redox-Triggered Disassembly of Nanosized Liposomes Containing Ferrocene-Appended Amphiphiles.

We report a redox-responsive liposomal system capable of oxidatively triggered disassembly. We describe the synthesis, electrochemical characterization, and incorporation into vesicles of an alternative redox lipid with significantly improved synthetic efficiency and scalability compared to a ferrocene-appended phospholipid previously employed by our group in giant vesicles. The redox-triggered disassembly of both redox lipids is examined in nanosized liposomes as well as the influence of cholesterol mole fraction on liposome disassembly and suitability of various chemical oxidants for  in vitro disassembly experiments. Electronic structure density functional theory calculations of membrane-embedded ferrocenes are provided to characterize the role of charge redistribution in the initial stages of the disassembly process.

Why pregnenolone and progesterone, two structurally similar steroids, exhibit remarkably different cocrystallization with aromatic molecules.

Selective binding of steroid molecules is of paramount importance for designing drugs that can target the biological pathways of only individual steroids. From this perspective, it is remarkable that progesterone (PRO) and pregnenolone (PRE), two structurally similar steroids, demonstrate a dramatically different propensity to interact with aromatic molecules. It has been recently reported that, in solid-state cocrystallization, PRO forms cocrystals with a wide variety of aromatic systems whereas PRE cocrystallizes only with a few. In this work, a simple yet effective computational procedure was developed to explain the fundamental origins of this surprising phenomenon. This procedure enables a direct comparison of the strength of intermolecular binding in the structurally similar cocrystals of PRO and PRE by generating experimentally inaccessible meta-stable cocrystals of PRE that closely resemble those observed for PRO. Direct comparative analysis shows that interactions between the α-face of the steroid and the π-electrons of aromatic molecules, the focus of previous studies, are not sufficiently different to explain the cocrystallization behavior of PRO and PRE. Instead, the observed difference is attributed to the different stabilities of the cocrystals relative to their pure components: organic and steroid crystals. It is calculated that the cocrystallization process is thermodynamically favorable in the case of PRO and unfavorable in the case of PRE. Furthermore, strong hydrogen bonds in the pure PRE crystal appear to be the major factor that makes the cocrystallization of PRE energetically unfavorable for a wide range of aromatic molecules. The fundamental analysis performed in this work has important practical implications for designing new steroid-containing crystals, selective biomolecular steroid receptors, and steroid-specific drugs. It suggests that a strategy for the selective binding of steroids should focus primarily on tuning the strength of hydrogen bonding.

Contribution of the Covalent Component of the Hydrogen-Bond Network to the Properties of Liquid Water.

Many remarkable properties of liquid water originate from the ability of its molecules to form hydrogen bonds, each of which emerges as a combination of electrostatic, polarization, dispersion, and donor-acceptor or covalent interactions. In this work, ab initio molecular dynamics was tailored to isolate and switch off the covalent component of interactions between water molecules in simulations. Comparison of simulations with and without covalency shows that a small amount of intermolecular electron density transfer has a profound effect on the structure and dynamics of the hydrogen-bond network and thus on observable properties of room-temperature liquid water.

Communication: Compact orbitals enable low-cost linear-scaling ab initio molecular dynamics for weakly-interacting systems.

Today, ab initio molecular dynamics (AIMD) relies on the locality of one-electron density matrices to achieve linear growth of computation time with the system size, crucial in large-scale simulations. While Kohn-Sham orbitals strictly localized within predefined radii can offer substantial computational advantages over density matrices, such compact orbitals are not used in AIMD because a compact representation of the electronic ground state is difficult to find. Here, a robust method for maintaining compact orbitals close to the ground state is coupled with a modified Langevin integrator to produce stable nuclear dynamics for molecular and ionic systems. This eliminates a density matrix optimization and enables first orbital-only linear-scaling AIMD. An application to liquid water demonstrates that low computational overhead of the new method makes it ideal for routine medium-scale simulations, while its linear-scaling complexity allows us to extend first-principle studies of molecular systems to completely new physical phenomena on previously inaccessible length scales.

Nature of the asymmetry in the hydrogen-bond networks of hexagonal ice and liquid water.

The interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the traditional nearly tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen-bond network in water. Here, we present new insights into the nature of local interactions in ice and liquid water obtained using a first-principle energy decomposition method. A comparative analysis shows that the majority of molecules in liquid water in our simulation exhibit hydrogen-bonding energy patterns similar to those in ice and retain the four-fold coordination with only moderately distorted tetrahedral configurations. Although this result indicates that the traditional description of liquid water is fundamentally correct, our study also demonstrates that for a significant fraction of molecules the hydrogen-bonding environments are highly asymmetric with extremely weak and distorted bonds.

On the role of interfacial hydrogen bonds in "on-water" catalysis.

Numerous experiments have demonstrated that many classes of organic reactions exhibit increased reaction rates when performed in heterogeneous water emulsions. Despite enormous practical importance of the observed "on-water" catalytic effect and several mechanistic studies, its microscopic origins remains unclear. In this work, the second generation Car-Parrinello molecular dynamics method is extended to self-consistent charge density-functional based tight-binding in order to study "on-water" catalysis of the Diels-Alder reaction between dimethyl azodicarboxylate and quadricyclane. We find that the stabilization of the transition state by dangling hydrogen bonds exposed at the aqueous interfaces plays a significantly smaller role in "on-water" catalysis than has been suggested previously.

Prediction of highly stable 2D carbon allotropes based on azulenoid kekulene.

Despite enormous interest in two-dimensional (2D) carbon allotropes, discovering stable 2D carbon structures with practically useful electronic properties presents a significant challenge. Computational modeling in this work shows that fusing azulene-derived macrocycles - azulenoid kekulenes (AK) - into graphene leads to the most stable 2D carbon allotropes reported to date, excluding graphene. Density functional theory predicts that placing the AK units in appropriate relative positions in the graphene lattice opens the 0.54 eV electronic bandgap and leads to the appearance of the remarkable 0.80 eV secondary gap between conduction bands - a feature that is rare in 2D carbon allotropes but is known to enhance light absorption and emission in 3D semiconductors. Among porous AK structures, one material stands out as a stable narrow-multigap (0.36 and 0.56 eV) semiconductor with light charge carriers (me = 0.17 m0, mh = 0.19 m0), whereas its boron nitride analog is a wide-multigap (1.51 and 0.82 eV) semiconductor with light carriers (me = 0.39 m0, mh = 0.32 m0). The multigap engineering strategy proposed here can be applied to other carbon nanostructures creating novel 2D materials for electronic and optoelectronic applications.

Anti-Markovnikov Hydroalkylation of Styrene Derivatives via Hydrazones Catalyzed by Ru-PNP Complex.

A well-defined Ru(II)-PNP complex demonstrated high activity in the anti-Markovnikov hydroalkylation of nonpolarized terminal alkenes via hydrazones. Hydrazone served as a carbanion equivalent to combine with the electrophilic alkene substrate upon activation by the ruthenium catalyst, forming a new C-C bond in a concerted pathway with N2 as the only theoretical byproduct. Experimental and computational studies suggested the existence of a push-pull interaction that activated the alkene for hydrazone addition and then deduced the mechanism.

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

Nucleation mechanism for the direct graphite-to-diamond phase transition.

Graphite and diamond have comparable free energies, yet forming diamond from graphite in the absence of a catalyst requires pressures that are significantly higher than those at equilibrium coexistence. At lower temperatures, the formation of the metastable hexagonal polymorph of diamond is favoured instead of the more stable cubic diamond. These phenomena cannot be explained by the concerted mechanism suggested in previous theoretical studies. Using an ab initio quality neural-network potential, we carried out a large-scale study of the graphite-to-diamond transition assuming that it occurs through nucleation. The nucleation mechanism accounts for the observed phenomenology and reveals its microscopic origins. We demonstrate that the large lattice distortions that accompany the formation of diamond nuclei inhibit the phase transition at low pressure, and direct it towards the hexagonal diamond phase at higher pressure. The proposed nucleation mechanism should improve our understanding of structural transformations in a wide range of carbon-based materials.

Microscopic origins of the anomalous melting behavior of sodium under high pressure.

X-ray diffraction experiments have shown that sodium exhibits a dramatic pressure-induced drop in melting temperature, which extends from 1000 K at ~30 GPa to as low as room temperature at ~120 GPa. Despite significant theoretical effort to understand the anomalous melting, its origins are still debated. In this work, we reconstruct the sodium phase diagram by using an ab initio quality neural-network potential. Furthermore, we demonstrate that the reentrant behavior results from the screening of interionic interactions by conduction electrons, which at high pressure induces a softening in the short-range repulsion.

Light-driven transition-metal-free direct decarbonylation of unstrained diaryl ketones via a dual C-C bond cleavage.

The cleavage and formation of carbon-carbon bonds have emerged as powerful tools for structural modifications in organic synthesis. Although transition-metal-catalyzed decarbonylation of unstrained diaryl ketones provides a viable protocol to construct biaryl structures, the use of expensive catalyst and high temperature (>140 oC) have greatly limited their universal applicability. Moreover, the direct activation of two inert C - C bonds in diaryl ketones without the assistance of metal catalyst has been a great challenge due to the inherent stability of C - C bonds (nonpolar, thermo-dynamically stable, and kinetically inert). Here we report an efficient light-driven transition-metal-free strategy for decarbonylation of unstrained diaryl ketones to construct biaryl compounds through dual inert C - C bonds cleavage. This reaction featured mild reaction conditions, easy-to-handle reactants and reagents, and excellent functional groups tolerance. The mechanistic investigation and DFT calculation suggest that this strategy proceeds through the formation of dioxy radical intermediate via a single-electron-transfer (SET) process between photo-excited diaryl ketone and DBU mediated by DMSO, followed by removal of CO2 to construct biaryl compounds.

Variable-Metric Localization of Occupied and Virtual Orbitals.

The key idea of the variable-metric approach to orbital localization is to allow nonorthogonality between orbitals while, at the same time, preventing them from becoming linearly dependent. The variable-metric localization has been shown to improve the locality of occupied nonorthogonal orbitals relative to their orthogonal counterparts. In this work, numerous localization algorithms are designed and tested to exploit the conceptual simplicity of the variable-metric approach with the goal of creating a straightforward and reliable localization procedure for virtual orbitals. The implemented algorithms include the steepest descent, conjugate gradient (CG), limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS), and hybrid procedures as well as trust-region (TR) methods based on the CG and Cauchy-point subproblem solvers. Comparative analysis shows that the CG-based TR algorithm is the best overall method to obtain nonorthogonal localized molecular orbitals (NLMOs), occupied or virtual. The L-BFGS and CG algorithms can also be used to obtain NLMOs reliably but often at higher computational cost. Extensive tests demonstrate that the implemented methods allow us to obtain well-localized Boys-Foster (i.e., maximally localized Wannier functions) and Pipek-Mezey, orthogonal and nonorthogonal, and occupied and virtual orbitals for a variety of gas-phase molecules and periodic materials. The tests also show that virtual NLMOs, which have not been described before, are, on average, 13% (Boys-Foster) and 18% (Pipek-Mezey) more localized than their orthogonal counterparts.

Adatoms in the Surface-Confined Ullmann Coupling of Phenyl Groups.

Despite the importance of the on-surface Ullmann coupling for synthesis of atomically precise carbon nanostructures, it is still unclear whether this reaction is catalyzed by surface atoms or adatoms. Here, the feasibility of the adatom creation and adatom-catalyzed Ullmann coupling of chloro-, bromo-, and iodobenzene on Cu(111), Ag(111), and Au(111) surfaces is examined using density functional theory modeling. The extraction of a metal atom is found to be greatly facilitated by the formation of strong phenyl-metal bonds, making the extraction energy barrier comparable to, and in the case of Ag(111) even lower than, that for the competing surface-catalyzed phenyl-phenyl bond formation. However, if the phenyl-adatom bonds are too strong, as on Cu(111) and Ag(111), they create an insurmountable barrier for the subsequent adatom-catalyzed C-C coupling. In contrast, Au adatoms do not bind phenyl groups strongly and can catalyze the C-C bond formation almost as efficiently as surface atoms.

Direct deoxygenative borylation of carboxylic acids.

Carboxylic acids are readily available, structurally diverse and shelf-stable; therefore, converting them to the isoelectronic boronic acids, which play pivotal roles in different settings, would be highly enabling. In contrast to the well-recognised decarboxylative borylation, the chemical space of carboxylic-to-boronic acid transformation via deoxygenation remains underexplored due to the thermodynamic and kinetic inertness of carboxylic C-O bonds. Herein, we report a deoxygenative borylation reaction of free carboxylic acids or their sodium salts to synthesise alkylboronates under metal-free conditions. Promoted by a uniquely Lewis acidic and strongly reducing diboron reagent, bis(catecholato)diboron (B2cat2), a library of aromatic carboxylic acids are converted to the benzylboronates. By leveraging the same borylative manifold, a facile triboration process with aliphatic carboxylic acids is also realised, diversifying the pool of available 1,1,2-alkyl(trisboronates) that were otherwise difficult to access. Detailed mechanistic studies reveal a stepwise C-O cleavage profile, which could inspire and encourage future endeavours on more appealing reductive functionalisation of oxygenated feedstocks.

Direct Unconstrained Variable-Metric Localization of One-Electron Orbitals.

Spatially localized one-electron orbitals, orthogonal and non-orthogonal, are widely used in electronic structure theory to describe chemical bonding and speed up calculations. In order to avoid linear dependencies of localized orbitals, the existing localization methods either constrain orbital transformations to be unitary, that is, metric preserving, or, in the case of variable-metric methods, fix the centers of non-orthogonal localized orbitals. Here, we developed a different approach to orbital localization, in which these constraints are replaced with a single restriction that specifies the maximum allowed deviation from the orthogonality for the final set of localized orbitals. This reformulation, which can be viewed as a generalization of existing localization methods, enables one to choose the desired balance between the orthogonality and locality of the orbitals. Furthermore, the approach is conceptually and practically simple as it obviates the necessity in unitary transformations and allows one to determine optimal positions of the centers of non-orthogonal orbitals in an unconstrained and straightforward minimization procedure. It is demonstrated to produce well-localized orthogonal and non-orthogonal orbitals with the Berghold and Pipek--Mezey localization functions for a variety of molecules and periodic materials including large systems with nontrivial bonding.

Empowering alcohols as carbonyl surrogates for Grignard-type reactions.

The Grignard reaction is a fundamental tool for constructing C-C bonds. Although it is widely used in synthetic chemistry, it is normally applied in early stage functionalizations owing to poor functional group tolerance and less availability of carbonyls at late stages of molecular modifications. Herein, we report a Grignard-type reaction with alcohols as carbonyl surrogates by using a ruthenium(II) PNP-pincer complex as catalyst. This transformation proceeds via a carbonyl intermediate generated in situ from the dehydrogenation of alcohols, which is followed by a Grignard-type reaction with a hydrazone carbanion to form a C-C bond. The reaction conditions are mild and can tolerate a broad range of substrates. Moreover, no oxidant is involved during the entire transformation, with only H2 and N2 being generated as byproducts. This reaction opens up a new avenue for Grignard-type reactions by enabling the use of naturally abundant alcohols as starting materials without the need for pre-synthesizing carbonyls.