Click the image to the left to access the full text.
Click article titles to access the journal page.
For statistics, visit the Google profile of Rustam Khaliullin.
Publications
© 2024 · www.khaliullin.com
Click the image to the left to access the full text.
Click article titles to access the journal page.
For statistics, visit the Google profile of Rustam Khaliullin.
Lithium-stuffed garnets based on Li7La3Zr2O12 (LLZO) have attracted a lot of attention as candidate electrolytes for all-solid lithium batteries. Doping studies have shown that substitutions will induce lithium vacancies and convert the structure from tetragonal to cubic and greatly increase ionic conductivity. However, the impacts of structure and composition have not been fully decoupled. Herein, we systematically study over 700 samples from the Li-La-Zr-O composition space to produce phase stabilities over the entire pseudoternary for the first time. The results obtained for samples made at 900°C show that the pyrochlore phase La2Zr2O7, previously only known to exist at its formal composition in the Li-La-Zr-O system, is in fact part of a large lithium containing solid solution region extending well into the pseudoternary. Furthermore, the LLZO phase of highest interest is also a solid solution with the cubic phase representing a very small region on the lithium-deficient side of Li7La3Zr2O12 such that it is nearly impossible to synthesize the cubic phase in the Li-La-Zr-O system without the presence of the detrimental pyrochlore phase. We also show that the cubic phase here has only marginally higher bulk conductivity than the tetragonal phase, indicating that the structural change to cubic, though necessary, is not sufficient to yield the large improvements in conductivity seen in doping studies in the literature. We also demonstrate that secondary phases can help improve the grain boundary conductivity, as we reported previously in perovskite La-Li-Ti-O materials.
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.
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 (>140oC) 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.
The on-surface Ullmann coupling of aromatic molecules has emerged as the most successful approach to synthesize atomically precise carbon nanostructures with unique electronic properties including molecular wires, graphene nanoribbons and two-dimensional conjugated polymers. Despite substantial progress in determining the mechanism of this reaction, the most fundamental question of whether the coupling is catalyzed directly by surface atoms or adatoms remains unanswered. In this work, the feasibility of the adatom creation and adatom-catalyzed Ullmann coupling of iodo-, bromo- and chlorobenzene on Cu(111), Ag(111) and Au(111) surfaces is examined using density functional theory modeling. Analysis of competing pathways reveals that two phenyl intermediates extract a silver atom from Ag(111) surface faster (energy barrier 0.43 eV) than they form the carbon-carbon bond (0.62 eV). However, on Cu(111) and Au(111), the extraction process is slower (0.71 eV Cu, 0.36 eV Au) than the C-C formation (0.49 eV Cu, 0.14 eV Au). The adatom creation is greatly facilitated by the strengthening of phenyl-metal bonds upon the extraction. However, if these bonds are too strong they create an insurmountable barrier for the subsequent adatom-catalyzed C-C coupling, as on Cu(111) and Ag(111) (1.78 eV Cu, 1.52 eV Ag). In contrast, Au adatoms that do not bind phenyl groups strongly can catalyze the C-C bond formation almost as efficiently (0.20 eV) as surface atoms (0.14 eV). Our results explain why adatoms are difficult to observe during surface-confined reactions and how their presence can lead to defects in the assembled nanostructures. The revealed trends can facilitate design of efficient on-surface reactions.
Cyclodextrin-derived metal-organic frameworks (MOFs) are remarkable not only because of their ability to absorb carbon dioxide strongly and reversibly but also because they can be readily obtained from inexpensive, renewable, and environmentally benign components. Despite the wealth of data on the carbon dioxide intake by CD-MOF-2, a representative of these MOFs, the nature and structural characteristics of its diverse adsorption sites, capable of binding carbon dioxide in the irreversible and reversible regimes, remains unclear. A comprehensive analysis of the results of the density functional theory modeling performed in this work in conjunction with experimental data shows that the hydroxyl counterions in CD-MOF-2 pull the protons away from the cyclodextrin alcohol groups, increasing their nucleophilic strength and turning them into strongly binding alkoxide chemisorption sites. At the same time, the diverse hydrogen bonding environments of the alkoxide sites reduce their nucleophilic character to a different extent, tuning their carbon dioxide binding to be irreversible, strong reversible or weak. By linking the acid-base proton equilibrium and hydrogen bonding - two chemical concepts widely used for liquids - to the strength of the carbon dioxide binding in CD-MOF-2, this work suggests new strategies for advancing design of tunable solid materials for carbon dioxide capture or detection.
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.
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.
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.
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.
Although the development of C−H functionalization methods has enlightened many reactivities in chemistry, the direct functionalization of unactivated C−H bonds, which are particularly common in petroleum compounds, is still faced with great difficulty. Herein, we describe a photocatalytic approach that allows direct methylation of unactivated sp3 and sp2 C−H bonds using methanol as the methylation reagent, with gallium nitride as a powerful yet robust catalyst. Mechanistic studies suggested that the methanol is dehydrated into methyl carbene intermediate via a bimolecular mechanism.
Stereocontrolled multilayer growth of supramolecular porous networks at the interface between graphite and a solution was investigated. For this study, we designed a chiral dehydrobenzoannulene (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.
The potassium salt of polyheptazine imide (K–PHI) is a promising photocatalyst for various chemical reactions. From powder X–ray diffraction data an idealized structural model of K–PHI has been derived. Using atomic coordinates of this model we defined an energetically optimized K–PHI structure, in which the K ions are present in the pore and between the PHI–planes. The distance between the anion framework and K+ resembles a frustrated Lewis pair-like structure, which we denote as frustrated Coulomb pair that results in an interesting adsorption environment for otherwise non-adsorbing, non-polar gas molecules. We demonstrate that even helium (He) gas molecules, which are known to have the lowest boiling point and the lowest intermolecular interactions, can be adsorbed in this polarized environment with an adsorption energy of −4.6 kJ mol-1 per He atom. The interaction between He atoms and K–PHI is partially originating from charge transfer, as disclosed by our energy decomposition analysis based on absolutely localized molecular orbitals. Due to very small charge transfer interactions, He gas adsorption saturates at 8 at%, which however can be subject to further improvement by cation variation.
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.
Water confined in nanomaterials demonstrates anomalous behavior. Recent experiments and simulations have established that room-temperature water inside carbon nanotubes and between graphene layers behaves as solid ice: its molecules form four hydrogen bonds in a highly organized network with long-range order and exhibit low mobility. Here, we applied a first-principle energy decomposition analysis to reveal that the strength and patterns of donor−acceptor interactions between molecules in these low-dimensional ice structures resemble those in bulk liquid water rather than those in hexagonal ice. A correlation analysis shows that this phenomenon originates from a variety of hydrogen-bond distortions, different in 1D and 2D ice, from the tetrahedral configuration due to constraints imposed by nanomaterials. We discuss the implications of the reported interplay between the electronic and geometric structure of hydrogen bonds in “room-temperature ice” for computer modeling of confined water using traditional force fields.
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.
Efficient carbon–carbon bond formation is of great importance in modern organic synthetic chemistry. The pinacol coupling discovered over a century ago is still one of the most efficient coupling reactions to build the C–C bond in one step. However, traditional pinacol coupling often requires over-stoichiometric amounts of active metals as reductants, causing long-lasting metal waste issues and sustainability concerns. A great scientific challenge is to design a metal-free approach to the pinacol coupling reaction. Herein, we describe a light-driven pinacol coupling protocol without use of any metals, but with N2H4, used as a clean non-metallic hydrogen-atom-transfer (HAT) reductant. In this transformation, only traceless non-toxic N2 and H2 gases were produced as by-products with a relatively broad aromatic ketone scope and good functional group tolerance. A combined experimental and computational investigation of the mechanism suggests that this novel pinacol coupling reaction proceeds via a HAT process between photo-excited ketone and N2H4, instead of the common single-electron-transfer (SET) process for metal reductants.
The energy decomposition analysis based on block localized wave functions (BLW-EDA) allows one to gain physical insight into the nature of chemical bonding, decomposing the interaction energy in (1) a “frozen” term, accounting for the attraction due to electrostatic and dispersion interactions, modulated by Pauli repulsion, (2) the variationally assessed polarization energy, and (3) the charge transfer. This method has so far been applied to gas- and condensed-phase molecular systems. However, its standard version is not compatible with fractionally occupied orbitals (i.e., electronic smearing) and, as a consequence, cannot be applied to metallic surfaces. In this work, we propose a simple and practical extension of BLW-EDA to fractionally occupied orbitals, termed Ensemble BLW-EDA. As illustrative examples, we have applied the developed method to analyze the nature of the interaction of various adsorbates on Pt(111), ranging from physisorbed water to strongly chemisorbed ethylene. Our results show that polarization and charge transfer both contribute significantly at the adsorption minimum for all studied systems. The energy decomposition analysis provides details with respect to competing adsorption sites (e.g., CO on atop vs hollow sites) and elucidates the respective importance of polarization and charge transfer for the increased adsorption energy of H2S compared to H2O. Our development will enable a deeper understanding of the impact of charge transfer on catalytic processes in general.
Locality of compact one-electron orbitals expanded strictly in terms of local subsets of basis functions can be exploited in density functional theory (DFT) to achieve linear growth of computation time with systems size, crucial in large-scale simulations. However, despite advantages of compact orbitals the development of practical orbital-based linear-scaling DFT methods has long been hindered because a compact representation of the electronic ground state is difficult to find in a variational optimization procedure. In this work, we showed that the slow and unstable optimization of compact orbitals originates from nearly-invariant mixing of occupied orbitals with the states that are mostly but not fully localized within the local vector subspace. We proposed a simple and practical method for identifying and removing the problematic nearly-invariant modes using an approximate Hessian and, as a result, developed a robust linear-scaling optimization procedure with a low computational overhead. We demonstrated the new method is highly efficient yet accurate in fixed-nuclei calculations and molecular dynamics simulations for a variety of systems ranging from semiconductors to insulators.
Today, ab initio molecular dynamics (AIMD) relies on the locality of one-electron density matrices to achieve linear growth of computation time with systems 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 to extend first-principle studies of molecular systems to completely new physical phenomena on previously inaccessible length scales.
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.
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.
The concept of covalency is widely used to describe the nature of intermolecular bonds, to explain their spectroscopic features and to rationalize their chemical behaviour. Unfortunately, the degree of covalency of an intermolecular bond cannot be directly measured in an experiment. Here we established a simple quantitative relationship between the calculated covalency of hydrogen bonds in liquid water and the anisotropy of the proton magnetic shielding tensor that can be measured experimentally. This relationship enabled us to quantify the degree of covalency of hydrogen bonds in liquid water using the experimentally measured anisotropy. We estimated that the amount of electron density transferred between molecules is on the order of ~10 me while the stabilization energy due to this charge transfer is ~15 kJ/mol. The physical insight into the fundamental nature of hydrogen bonding provided in this work will facilitate new studies of intermolecular bonding in a variety of molecular systems.
A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.
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.
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.
Ab-initio-Molekulardynamik bietet neue Einblicke in die Struktur von flüssigem Wasser.
Despite recent progress in linear scaling (LS) density function theory (DFT), the computational cost of the existing LS methods remains too high for a widespread adoption at present. In this work, we exploit nonorthogonal localized molecular orbitals to develop a series of LS methods for molecular systems with a low computational overhead. High efficiency of the proposed methods is achieved with a new robust two-stage variational procedure or by replacing the optimization altogether with an accurate nonself-consistent approach. We demonstrate that, even for challenging condensed-phase systems, the implemented LS methods are capable of extending the range of accurate DFT simulations to molecular systems that are an order of magnitude larger than those previously treated.
The O-H stretching vibrational modes of water molecules are sensitive to their local environments. Here, we applied effective normal-mode analysis to isolate contributions of each of the two hydrogen atoms to the vibrational modes ν1 and ν3 of water molecules in the liquid phase. We demonstrate that the decoupling of the two contributions fd and the frequency splitting of the vibrational modes Δω13 are inextricably related to the symmetry of the hydrogen bonding environment. We show that ambient liquid water modeled at the density functional level of theory exhibits the characteristics of an asymmetric environment with an average decoupling of 0.82 and a splitting of 137 inverse centimeters. Such large value of decoupling and splitting would account for the inhomogeneous broadening as observed in the vibrational spectra of liquid water. The computational protocols and the results of this work will facilitate the interpretation of experimental Raman and infrared spectra of interfacial water molecules at hydrophobic, membrane, and protein surface.
Interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the conventional symmetric 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 water obtained using a novel energy-decomposition method. Our simulations reveal that although a water molecule forms, on average, two strong donor and two strong acceptor bonds, there is a significant asymmetry in the energy of these contacts. We demonstrate that this asymmetry is a result of small instantaneous distortions of hydrogen bonds, which appear as fluctuations on a time scale of hundreds of femtoseconds around the average symmetric structure. Furthermore, we show that the distinct features of the X-ray absorption spectra originate from molecules with high instantaneous asymmetry. Our findings have important implications as they help reconcile the symmetric and asymmetric views on the structure of water.
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.
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.
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 potential13, 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.
An interatomic potential for high-pressure high-temperature (HPHT) crystalline and liquid phases of sodium is created using a neural-network (NN) representation of the ab initio potential-energy surface. It is demonstrated that the NN potential provides an ab initio quality description of multiple properties of liquid sodium and bcc, fcc, and cI16 crystal phases in the P-T region up to 120 GPa and 1200 K. The unique combination of computational efficiency of the NN potential and its ability to reproduce quantitatively experimental properties of sodium in the wide P-T range enables molecular-dynamics simulations of physicochemical processes in HPHT sodium of unprecedented quality.
An interatomic potential for the diamond and graphite phases of carbon has been created using a neural-network (NN) representation of the ab initio potential energy surface. The NN potential combines the accuracy of a first-principles description of both phases with the efficiency of empirical force fields and allows one to perform a molecular-dynamics study, of ab initio quality, of the thermodynamics of graphite-diamond coexistence. Good agreement between the experimental and calculated coexistence curves is achieved if nuclear quantum effects are included in the simulation.
Decomposition analysis, based on absolutely localized molecular orbitals, provides an alternative and somewhat unconventional view of hydrogen bonding in the water dimer. A new description of the electron-donating orbital is uncovered: unlike sp3 lone pairs, a single donor–acceptor orbital pair forms, in which the donating orbital changes its orientation according to the relative positions of the two molecules.
A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.
Molecular hydrogen is known to form stable, “nonclassical” sigma complexes with transition metal centers that are stabilized by donor–acceptor interactions and electrostatics. In this computational study, we establish that strong H2 sorption sites can be obtained in metal-organic frameworks by incorporating open transition metal sites on the organic linkers. Using density functional theory and energy decomposition analysis, we investigate the nature and characteristics of the H2 interaction with models of exposed open metal binding sites {half-sandwich piano-stool shaped complexes of the form (Arene)ML(3-n)(H2)n }. The metal−H2 bond dissociation energy of the studied complexes is calculated to be between 48 and 84 kJ/mol, based on the introduction of arene substituents, changes to the metal core, and of charge-balancing ligands. Thus, design of the binding site controls the H2 binding affinity and could be potentially used to control the magnitude of the H2 interaction energy to achieve reversible sorption characteristics at ambient conditions. Energy decomposition analysis illuminates both the possibilities and present challenges associated with rational materials design.
A quasichemical method that combines ab initio treatment of explicit solvent with dielectric continuum models has been used to study the origin of a strong effect of methanol on the extent of iron(III) porphyrin chloride dissociation in acetonitrile−methanol solutions. It is shown that the dissociation is energetically more favorable in methanol than in acetonitrile primarily because of the strong specific interactions between the chloride anion and the solvent methanol molecules in its first solvation shell. These interactions are weaker in acetonitrile. The final estimate for the difference in the dissociation free energies in methanol and acetonitrile is -23 kJ/mol, in a good agreement with the experimental value of -21 kJ/mol. Energy decomposition analysis of chloride-solvent interactions suggests that stronger chloride-methanol binding is a result of the contribution of charge delocalization effects to the chloride-methanol interactions.
Metal-alkane binding energies have been calculated for (alkane) and (alkane), where M = Re or Mn. Calculated binding energies were found to increase with the number of metal-alkane interaction sites. In all cases examined, the manganese-alkane binding energies were predicted to be significantly lower than those for the analogous rhenium-alkane complexes. The metal (Mn or Re)-alkane interaction was predicted to be primarily one of charge transfer, both from the alkane to the metal complex (70-80% of total charge transfer) and from the metal complex to the alkane (20-30% of the total charge transfer).
An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.
Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
Faster computation of the Pulay error vector for the direct inversion in the iterative subspace acceleration scheme is achieved by expanding the density matrix in terms of the occupied molecular orbitals and by performing matrix multiplications in an optimal order. The predicted speed-up over the usual implementation is N/O, where N is the size of the atomic orbital basis set, and O is number of occupied molecular orbitals, which is confirmed by test calculations.
An efficient method for removing the self-consistent field (SCF) diagonalization bottleneck is proposed for systems of weakly interacting components. The method is based on the equations of the locally projected SCF for molecular interactions (SCF MI) which utilize absolutely localized nonorthogonal molecular orbitals expanded in local subsets of the atomic basis set. A generalization of direct inversion in the iterative subspace for nonorthogonal molecular orbitals is formulated to increase the rate of convergence of the SCF MI equations. Single Roothaan step perturbative corrections are developed to improve the accuracy of the SCF MI energies. The resulting energies closely reproduce the conventional SCF energy. Extensive test calculations are performed on water clusters up to several hundred molecules. Compared to conventional SCF, speedups of the order of (N/O)2 have been achieved for the diagonalization step, where N is the size of the atomic orbital basis, and O is the number of occupied molecular orbitals.
Experimental studies by Shul'pin and co-workers have shown that vanadate anions in combination with pyrazine-2-carboxylic acid (PCA ≡ pcaH) produce an exceptionally active complex that promotes the oxidation of alkanes and other organic molecules. Reaction of this complex with H2O2 releases HOO• free radicals and generates V(IV) species, which are capable of generating HO• radicals by reaction with additional H2O2. The oxidation of alkanes is initiated by reaction with the HO• radicals. The mechanism of hydrocarbon oxidation with vanadate/PCA/H2O2 catalyst has been studied using density functional theory. The proposed model reproduces the major experimental observations. It is found that a vanadium complex with one pca (PCA ≡ pcaH) and one H2O2 ligand is the precursor to the species responsible for HOO• generation. It is also found that species containing two pca ligands and an H2O2 molecule do not exist in the solution, in contradiction to previous interpretations of experimental observations. Calculated dependences of the oxidation rate on initial concentrations of PCA and H2O2 have characteristic maxima, the shapes of which are determined by the equilibrium concentration of the active species. Conversion of the precursors requires hydrogen transfer from H2O2 to a vanadyl group. Our calculations show that direct transfer has a higher barrier than pca-assisted indirect transfer. Indirect transfer occurs by migration of hydrogen from coordinated H2O2 to the oxygen of a pca ligand connected to the vanadium atom. The proposed mechanism demonstrates the important role of the cocatalyst in the reaction and explains why H2O2 complexes without pca are less active. Our work shows that the generation of HOO• radicals cannot occur via cleavage of a V-OOH bond in the complex formed directly from the precursors, as proposed before. The activation barrier for this process is too high. Instead, HOO• radicals are formed via a sequence of additional steps involving lower activation barriers. The new mechanism for free radical generation underestimates the observed rate of hexane oxidation by less than an order of magnitude; however, the calculated activation energy (67-81 kJ/mol) agrees well with that determined experimentally (63-80 kJ/mol).
Density functional theory was used to investigate the mechanism and kinetics of methanol oxidation to formaldehyde over vanadia supported on silica, titania, and zirconia. The catalytically active site was modeled as an isolated VO4 unit attached to the support. The calculated geometry and vibrational frequencies of the active site are in good agreement with experimental measurements both for model compounds and oxide-supported vanadia. Methanol adsorption is found to occur preferentially with the rupture of a V−O-M bond (M = Si, Ti, Zr) and with preferential attachment of a methoxy group to V. The vibrational frequencies of the methoxy group are in good agreement with those observed experimentally as are the calculated isobars. The formation of formaldehyde is assumed to occur via the transfer of an H atom of a methoxy group to the O atom of the VO group. The activation energy for this process is found to be in the range of 199-214 kJ/mol, and apparent activation energies for the overall oxidation of methanol to formaldehyde are predicted to lie in the range of 112-123 kJ/mol, which is significantly higher than that found experimentally. Moreover, the predicted turnover frequency (TOF) for methanol oxidation is found to be essentially independent of support composition, whereas experiments show that the TOF is 103 greater for titania- and zirconia-supported vanadia than for silica-supported vanadia. On the basis of these findings, it is proposed that the formation of formaldehyde from methoxy groups may require pairs of adjacent VO4 groups or V2O7 dimer structures.
The interactions of methane with Brønsted acid sites in H-ZSM-5 were investigated both experimentally and theoretically. Diffuse reflectance infrared spectroscopy was used to acquire spectra for methane adsorbed on H-ZSM-5 at room temperature and at 77 K. Upon adsorption, the ν1 and ν3 vibrational bands of methane shift by -15 and -23 cm-1, respectively, and the vibrational band for OH groups associated with Brønsted acid sites shifts by -93 cm-1. Quantum chemical calculations conducted at the DFT level of theory with a 6-31g**++ basis set show that the observed shifts for methane are attributable to the effects of the electrostatic field created by the atoms of the zeolite. To represent the influence of the zeolite on the adsorbed methane correctly, it is essential to take into account the effects of the Madelung field, as well as the local effects of the acid center. The calculated shift in the vibrational frequency of the bridging OH group lies within the range observed experimentally. However, the quantitative agreement of the calculated and observed shift is not as good as that seen for the bands of CH4.
A series of mixed porphyrins with different numbers of metallocenyl (ferrocenyl and cymantrenyl) and aryl (Ph and C6F5) groups at themeso-positions was obtained and characterized by 1H NMR, electronic absorption, and mass spectra. The downfield shift of NH signals as well as the bathochromic shift of Q-bands can be attributed to a distortion of the porphyrin macrocycle upon the introduction of bulky meso-substituents.
© 2024 · www.khaliullin.com