Empirical Force Field Calculations Research Articles

Atomic Structure of Dislocations and Grain Boundaries in Two-Dimensional PtSe2.

Each 2D material has a distinct structure for its grain boundary and dislocation cores, which is dictated by both the crystal lattice geometry and the elements that participate in bonding. For the class of noble metal dichalcogenides, this has yet to be thoroughly investigated at the atomic scale. Here, we examine the atomic structure of the dislocations and grain boundaries (GBs) in two-dimensional PtSe2, using atomic-resolution annular dark field scanning transmission electron microscopy, combined with density functional theory and empirical force field calculations. The PtSe2 we study adopts the 1T phase in large-area polycrystalline films with numerous planar tilt GB distinct dislocations, including 5|7+Se and 4|4|8+Se polygons, in tilt-angle monolayer GBs, with features sharply distinguished from those in 2H-phase TMDs. On the basis of dislocation cores, the GB structures are investigated in terms of pathways of dislocation chain arrangement, dislocation core distributions in different misorientation angles, and 2D strain fields induced. Based on the Frank-Bilby equation, the deduced Burgers vector magnitude is close to the lattice constant of 1T-PtSe2, building the quantitative relationship of dislocation spacings and small GB angles. The 30° GBs are most frequently formed as a stitched interface between the armchair and zigzag lattices, constructed by a string of 5|7+Se dislocations asymmetrically with a small deviation angle. Another special angle GB, mirror twin 60° GB, is also mapped linearly by metal-condensed asymmetric or Se-rich symmetric dislocations. This report gives atomic-level insights into the GBs and dislocations in 1T-phase noble metal TMD PtSe2, which is a promising material to underpin extending properties of 2D materials by local structure engineering.

Interplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption Enthalpies

We present a combined experimental and theoretical study aimed at understanding the behavior of polar probe ethanol on graphene and graphite hydrophobic surfaces. We measured isosteric adsorption enthalpies and entropies by inverse gas chromatography for coverages ranging from 0.1 to 20%. The adsorption enthalpies were found to vary with surface coverage and differed considerably between the materials at low coverage. However, they approached the same adsorption enthalpy value of −12.0 ± 0.4 kcal/mol for T centered at 303–393 K and coverages above 5%. We explained the observed behavior using molecular dynamics simulations by employing empirical force-field and density functional theory calculations on two graphene models: circumcoronene and infinite graphene. The simulations showed that various hydrogen-bonded ethanol clusters formed spontaneously from isolated ethanol molecules on graphene and provided a distribution of cluster sizes. Nonlocal density functional theory was used to calculate adsorption en...

Selective Adsorption/Absorption of Formamide in NaCl Crystals Growing from Solution

NaCl crystals were obtained from water–formamide (H–CO-NH2) solutions, either by slow evaporation at 30 °C or by programmed cooling of solutions saturated at 95 °C, the formamide concentration ranging from 0 to 100% (in weight). Accordingly, the crystal morphology changes from {100} (pure aqueous solution) to {100} + {111} (water-formamide solutions) to {111} (pure formamide solution). X-ray powder diffraction diagrams, carried out on the bulky crystallized population, prove that formamide is not only adsorbed on the {111}NaCl octahedron but is also selectively captured within the {111} growth sectors. The excellent two-dimensional lattice coincidences between the d101 layers of formamide and the NaCl - d111 ones suggest that formamide can be adsorbed in the form of ordered epitaxial layers; further, the striking equivalence between the thickness of the elementary layers d111NaCl and d101formamide indicates that formamide is allowed to be buried (absorption) in the growing crystal. Moreover, empirical force field calculations carried out on reconstructed {111} NaCl surfaces, both Na+ and Cl– terminated, allowed to evaluate the adhesion energy between the formamide epitaxial layers and the underlying {111}NaCl substrate. Hence, one can definitively state that formamide is not only an habit modifier of NaCl crystals, but that “anomalous NaCl/formamide mixed crystals” form, limited to the {111} NaCl growth sectors.

A convenient synthesis of difficult medium-sized cyclic peptides by Staudinger mediated ring-closure

Novel, efficient and mild preparation of 7- and 8-membered cyclic di- and 10-membered cyclic tripeptides containing α-, β- or γ-amino acid residues is effected by a Staudinger-mediated ring closure. Medium-sized cyclic di- and tripeptides--recognized as difficult targets--were obtained in moderate to good yields according to a straightforward sequence. Empirical force-field calculations were undertaken to determine their conformational behaviors and showed high levels of similarity with X-ray results. A computational study at the B3LYP/6-31+G** level of theory afforded information regarding the impact of the sequence, ring-size and substitution on the activation barriers for the cyclization of azido peptide thioesters.

Vibrational fundamentals and natural bond orbitals analysis of some tri-fluorinated benzonitriles in ground state

The theoretical IR and Raman spectra of the 2,3,4-, 2,3,6-, 2,4,5- and 3,4,5-tri-fluorobenzonitrile molecules have been calculated by using the density functional method in the ground state. The rigorous normal coordinate analyses based upon both an empirical force field and quantum chemical calculations have been performed and the detailed vibrational assignment has been made on the basis of the calculated potential energy distributions (PEDs). A comparison of molecular geometries, atomic charges and vibrational fundamentals of these molecules has been reported. The effects of fluorination upon the geometries, atomic charges and vibrational frequencies of benzonitrile have been discussed. Several ambiguities and contradictions in the previously reported vibrational assignments have been clarified. In addition, the variation of Raman intensity with excitation frequency and with temperature has also been studied.

Three-Dimensional Mapping of Microenvironmental Control of Methyl Rotational Barriers

Sterical (van der Waals-induced) rotational barriers of methyl groups are investigated theoretically, using ab initio and empirical force field calculations, for various three-dimensional microenvironmental conditions around the methyl group rotator of a model neopentane molecule. The destabilization (reducing methyl rotational barriers) or stabilization (increasing methyl rotational barriers) of the staggered conformation of the methyl rotator depends on a combination of microenvironmental contributions from (i) the number of atoms around the rotator, (ii) the distance between the rotator and the microenvironmental atoms, and (iii) the dihedral angle between the stator, rotator, and molecular environment around the rotator. These geometrical criteria combine their respective effects in a linearly additive fashion, with no apparent cooperative effects, and their combination in space around a rotator may increase, decrease, or leave the rotator's rotational barrier unmodified. This is exemplified in a geometrical analysis of the alanine dipeptide crystal where microenvironmental effects on methyl rotators' barrier of rotation fit the geometrical mapping described in the neopentane model.

Unique Orientation of Organic Epitaxial Thin Films: The Role of Intermolecular Interactions at the Interface and Surface Symmetry

The investigation of the mechanisms driving the growth of single crystalline organic thin films is a fundamental issue of organic electronics in view of the optimization of transport properties in thin film-based devices. In this paper, a complete azimuthal order of heteroepitaxial domains of α-quaterthiophene grown by organic molecular beam epitaxy on tetracene single crystal substrates is assessed by oblique incidence absorption spectroscopy and fully validated by empirical force field calculations. The effect of the many-body interactions combined with the symmetry of the substrate and deposit surfaces involved in the heterojunction is demonstrated to drive toward this relevant achievement, which unveils new strategies for controlling the growth of single crystalline organic thin films.

Etude Conformationnelle De 2,3,5,6,7,8-Hexahydro-4H-Benzopyranne-4-Ones, A L'Aide De La Mecanique Moleculaire

The conformational study of 2,3,5,6,7,8-hexahydro-4H-benzopyran-4-ones, using molecular mechanics, shows that the more stable conformations contain a half-chair cyclohexenic ring and a half-chair strongly distorted toward a sofa form for the dihydropyran-4-one ring. The interconversion barrier of 3,4-dihydro-2H-pyran-4-one is lower than that for cyclohexene (5 versus 6.1 Kcal/mol). This work is ratified by reasonable correlation between experimental data and empirical force-field calculations.

Organic−Organic Heteroepitaxy of Semiconductor Crystals: α-Quaterthiophene on Rubrene

Organic−organic epitaxy is a successful strategy for growing highly oriented and crystalline heterojunctions of organic semiconductors. Within this class of materials, crystalline rubrene is especially promising because of its outstanding hole mobility. Here, the (200) surface of rubrene single crystals was used as substrate for growing thin films of another organic semiconductor: α-quaterthiophene. The film growth proceeds via a 3D mechanism, with the formation of a few-monolayer-thick crystalline islands oriented along two main directions, as deduced by the optical reflection of the α-quaterthiophene/rubrene heterostructure measured over macroscopic regions. An atomic-scale analysis of the film surface performed with scanning force microscopy revealed a complete textural order achieved through a line-on-line epitaxial relation. With the help of empirical force-field calculations of the heteroepitaxial interface, this orienting propensity is demonstrated to be strictly related to the peculiar corrugation...

Kinetic Phase Selection of Rubrene Heteroepitaxial Domains

The high carrier mobility measured in rubrene single crystals makes its growth in the form of crystalline thin films a challenge of great interest in view of their use as semiconductor layers in integrated organic devices. Here, heteroepitaxial thin films of rubrene are grown by molecular beam epitaxy under different conditions, showing that the film structure can be tuned from disordered to crystalline by the sole control of the deposition rate. Highly oriented crystalline films are demonstrated to grow undergoing a transition characterized by a strong mass transport among different domains, persisting even during the postgrowth stages. This mechanism is rationalized within a thermodynamic model which gives quantitative predictions starting from empirical force field calculations and atomic force microscopy topographical data. By an appropriate setting of the growth parameters, an epitaxial rubrene monolayer is obtained at room temperature. These results, rationalizing the concrete possibility of growing crystalline and oriented rubrene thin films, open new perspectives to organic-based thin film technology and devices.

Novel Bispidine Ligands and Their First-Row Transition Metal Complexes: Trigonal Bipyramidal and Trigonal Prismatic Geometries

Four very rigid second generation bispidine-based ligands (bispidine = 3,7-diazabicyclo[3.3.1]nonane; tetra-, penta- and hexadentate; exclusively tertiary amine donors except for one of the pentadentate ligands, where one of the donors is a pyridyl group) and their Co(II), Ni(II), Cu(II), and Zn(II) complexes are reported. The experimentally determined X-ray crystal structures and computational data, based on empirical force field (MM) and approximate density functional theory (DFT) calculations, indicate that these new ligands, which are based on a modular system and therefore allow for a wide range of donor sets and coordination geometries, have rather large cavities (i.e., lead to a preference for +II over +III oxidation states and induce relatively low ligand fields), enforce trigonal geometries (pentacoordinate systems: preference for trigonal bipyramidal, hexacoordinate complexes: preference for trigonal prismatic), and lead, especially for Cu(II), to very high complex stabilities.

Epitaxially grown sexiphenyl nanocrystals on the organic KAP(0 1 0) surface

Nanocrystals of the organic molecule sexiphenyl are grown on the (0 1 0) cleavage plane of potassium hydrogen phthalate (KAP). The single crystalline organic surface is composed exclusively by phenyl rings and displays two distinct directions of aromatic rows forming surface corrugations. Sexiphenyl crystals grow epitaxially ordered with the ( 2 0 3 ¯ ) plane parallel to KAP(0 1 0) with the long molecular axes of the molecule aligned along one specific surface corrugation; empirical force field calculations confirm the experimentally observed epitaxial alignment of the sexiphenyl crystals. The sexiphenyl crystals grow as elongated islands, which can be shown to be of single crystalline nature.

Simulated non-contact AFM images of an alcohol molecule in an alkanethiol self-assembledmonolayer

Based on all-atom empirical force field calculations, non-contact atomic force microscopy(nc-AFM) images are simulated of a self-assembled monolayer (SAM) of 1-hexanethiol(C6) in which a single4-mercapto-1-butanol (C4OH) molecule is inserted. The tip is modelled by a carbon nanoconeapex and the temperature is assumed to be 0 K. It is found that theC6 molecules can be recognized individually in the topographic, frequencyshift and energy dissipation images. In addition, the position of aH2O molecule, which is adsorbed by forming a hydrogen bond with the hydroxyl head group of theC4OH molecule,is observed more clearly in the energy dissipation image than in the topographic image. Furthermore,this H2O molecule is observed to be higher than the surroundingC6 matrix in the topographic image, although the former is slightly lower than the latter. Thiscan be explained by the enhancement of the normal force by an attractive electrostaticinteraction between the water molecule and the tip apex.

Van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-Sized Rotators: A Theoretical Study

Rotational barriers of methyl-sized molecular rotators are investigated theoretically using ab initio and empirical force field calculations in molecular models simulating various environmental conditions experienced by the molecular rotors. Calculations on neopentane surrounded by methyl groups suggest that the neopentane's methyl rotational potential energy barrier can be reduced by up to an order of magnitude by locating satellite functional groups around the rotator at a geometry that destabilizes the staggered conformation of the rotator through van der Waals repulsive interactions and reduces the staggered/eclipsed relative energy difference. Molecular mechanics and molecular dynamics calculations indicate that this barrier-reducing geometry can also be found in molecular rotators surface mounted on graphite surfaces or carbon nanotube models. In these models, molecular dynamics simulations show that the rotation of methyl-sized functional groups can be catalyzed by van der Waals interactions, thus making very rigid rotators become thermally activated at room temperature. These results are discussed in the context of design of nanostructures and use of methyl groups as markers for microenvironmental conditions.

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.

Structural variation in the copper(II) complexes with a tetradentate bis-6-methylpyridine-substituted bispidine ligand

Abstract Four single crystal X-ray structures of the complex cation [CuII(L)(X)]n+ (L = 3,7-dimethyl-2,4-di-(6-methyl-2-pyridyl)-9-diol-3,7-diazabicyclo[3.3.1]nonane-1,5-dicarboxylate dimethylester, X = NCCH3, OH2, Cl–, NO3–) are discussed together with their spectroscopic properties. The bispidine ligand L enforces a square pyramidal or cis-octahedral coordination geometry with two cis-disposed tertiary amines (N3 and N7), two trans-disposed pyridines which are co-planar and in-plane with the metal center and one of the two amines (N3), and one or two co-ligands trans to the amine donors (N3 or N7). Three structural types have been found: (i) X = NCCH3, square pyramidal, X trans to N3, in-plane with the pyridine donors, elongation of the Cu–N7 bond; (ii) X = Cl–, OH2, square pyramidal, X trans to N7, perpendicular to the pyridine planes, slight elongation of the Cu–N3 bond; (iii) X = NO3–, octahedral, bidentate NO3–, elongation of the Cu–Npyridine bonds. The three isomeric chromophores (Cu(L)-fragments, the three possible minima of the ‘Mexican hat’ Jahn–Teller potential energy surface) are discussed on the basis of the experimental structural data, the steric contributions to the stabilization/destabilization of the three energetically similar minima are discussed on the basis of empirical force field calculations, and the results of DFT model calculations are used for a qualitative interpretation of electronic effects. Solid state and solution electronic spectra and frozen solution EPR spectra are used for a qualitative analysis of the three electronic ground states and a possible equilibration of the three isomeric forms, and this is supported by a preliminary ligand field analysis, based on AOM model calculations. To cite this article: P. Comba et al., C R Chimie 8 (2005).

Computational modeling of azotobactin–goethite/diaspore interactions: applications to molecular force measurements and siderophore–mineral reactivity

Empirical force field and quantum mechanical calculations were completed to investigate the interaction between azotobactin and iron/aluminum oxide surfaces, and to further evaluate force measurements made on the same systems using an atomic force microscope (AFM). The increased force affinity for goethite over diaspore, characteristic of the experimental force signatures, was also observed in the simulated siderophore interaction with these minerals. Ab initio calculations on siderophore fragment analogs confirm previous findings and suggest that the iron affinity can, in part, be attributed to greater electron density associated with the Fe–O bond compared to the Al–O bond. This observation correlates with iron's larger electronegativity compared to aluminum leading to a more covalent Fe goethite–O siderophore bond. Calculations with hydrated fragment analog Al 3+/Fe 3+ complexes suggest the lowered siderophore force affinity observed experimentally for diaspore could also reflect the extra energy required to remove water coordinated to the Al in the surface. In the molecular mechanics simulations, chelating ligand pairs, which consisted of both backbone and amino acid side chain oxygen atoms, coordinated with neighboring iron and aluminum atoms to form a binuclear geometry. Upon retraction of azotobactin from each surface, simulated Fe–O siderophore bonds persisted into a higher force regime than Al–O siderophore bonds, and surface metals were removed from both minerals. Extrapolation of the model to more realistic hydrated conditions using a polarizable continuum model (PCM) (e.g., solvent is modeled as a continuum of uniform dielectric constant) and water coordination shells in quantum mechanical calculations and water clusters in the molecular mechanics model demonstrated that the presence of water energetically favors and enhances metal extraction. In this way, our system may be a good model to understand the forces of the azotobactin–mineral interaction and how they relate to siderophore-mediated dissolution of Fe from goethite in a natural system.

Long range interactions on wires: A reciprocal space based formalism

There are many atomic scale systems in materials, chemistry, and biology that can be effectively modeled as finite in two of the physical spatial dimensions and periodically replicated in the third including nanoscale metallic and semiconducting wires, carbon nanotubes, and DNA. However, it is difficult to design techniques to treat long range forces in these systems without truncation or recourse to slowly convergent supercells or computationally inefficient Poisson solvers. In this paper, a rigorous reciprocal space based formalism which permits long range forces on wires to be evaluated simply and easily via a small modification of existing methods for three dimensional periodicity is derived. The formalism is applied to determine long range interactions both between point particles using an Ewald-like approach and the continuous charge distributions that appear in electronic structure calculations. In this way, both empirical force field calculations and, for example, plane-wave based density functional theory computations on wires can be performed easily. The methodology is tested on model and realistic systems including a lithium doped carbon nanotube.

All-Atom Numerical Studies of Self-Assembly of Zwitterionic Peptide Amphiphiles

We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4 × 4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure ...

Why does spontaneous resolution take place? (empirical force-field calculations)

Empirical force-field calculations were performed on [Ag{Co(aet)(en)2}](NO3)3 (aet = H2NCH2CH2S−) systems to further understand the occurrence of spontaneous resolution [1]. Results of the calculations reveal that the ΛΛΛΛ strand is more stable than the ΛΔΛΔ strand. Furthermore, the spontaneously crystallized system ΛΛΛΛ, with six constitutional repeating units (CRUs), ΛΛΛΛΛΛ, was more stable than the hetero-chiral system, ΔΔΔΔ, with the same six units as above. In addition, the calculations revealed that electrostatic interactions contributed most of the stability to the system.