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1.
J Chem Theory Comput ; 2020 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-32320232

RESUMO

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.

2.
J Am Chem Soc ; 142(19): 8662-8671, 2020 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-32306725

RESUMO

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.

3.
J Phys Chem Lett ; 10(8): 2008-2016, 2019 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-30946585

RESUMO

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.

4.
Langmuir ; 35(16): 5608-5616, 2019 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-30916976

RESUMO

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.

5.
J Chem Theory Comput ; 15(1): 265-275, 2019 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-30462497

RESUMO

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.

6.
J Phys Chem A ; 122(37): 7482-7490, 2018 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-30157633

RESUMO

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.

7.
J Chem Phys ; 148(23): 231103, 2018 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-29935517

RESUMO

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.

8.
Phys Chem Chem Phys ; 20(2): 898-904, 2018 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-29184919

RESUMO

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.


Assuntos
Ligação de Hidrogênio , Pregnenolona/química , Progesterona/química , Cristalização , Cristalografia , Desenho de Fármacos , Elétrons , Termodinâmica
9.
Nat Commun ; 6: 8318, 2015 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-26370179

RESUMO

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 m while the stabilization energy due to this charge transfer is ∼15 kJ mol(-1). 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.

10.
J Chem Phys ; 141(22): 22D528, 2014 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-25494799

RESUMO

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.

11.
J Am Chem Soc ; 136(9): 3395-9, 2014 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-24521433

RESUMO

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.

12.
Phys Chem Chem Phys ; 15(38): 15746-66, 2013 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-23928575

RESUMO

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.

13.
Nat Commun ; 4: 1450, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23385594

RESUMO

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.

14.
J Chem Theory Comput ; 9(10): 4421-7, 2013 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-26589159

RESUMO

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.

15.
Phys Rev Lett ; 108(11): 115701, 2012 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-22540486

RESUMO

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.

16.
Nat Mater ; 10(9): 693-7, 2011 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-21785417

RESUMO

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.

18.
J Chem Phys ; 128(18): 184112, 2008 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-18532804

RESUMO

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.

19.
Inorg Chem ; 47(10): 4032-44, 2008 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-18422312

RESUMO

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 [M=Cr, Mo, V(-), Mn(+); Arene = C6H5X (X=H, F, Cl, OCH3, NH2, CH3, CF3) or C6H3Y2X (Y=COOH, X=CF3, Cl; L=CO; n=1-3]}. 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.

20.
J Phys Chem B ; 111(37): 10992-8, 2007 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-17722913

RESUMO

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) [tetrakis(pentafluorophenyl)]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.

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