Simulation of the infrared spectra of N-methylformamide and N-methylacetamide by the extended molecular mechanics method

The infrared spectra of the matrix isolated species of N-methylformamide (NMF) and N-methylacetamide (NMA) and their N-deuterated molecules have been simulated by the extended molecular mechanics method using an empirical force field which includes charges and charge fluxes as coulombic potential parameters. The structural parameters and dipole. moments of NMF and NMA have. also been computed in satisfactory agreement with the experiment. Good agreement between experimental and calculated vibrational frequencies and infrared absorption band intensities for NMF and NMA and their deuterated molecules has been obtained. The vibrational assignments of NMF and NMA are-discussed taking also into account the infrared absorption intensities.

Electric Field Directed Growth of Molecular Wires of Charge Transfer Molecules on Prefabricated Metal Electrodes

Molecular wires of charge transfer molecules were formed by co-evaporating the 7 7 8 8-Tetracyanoquinodimethane [TCNQ] (acceptor) and Tetrathiafulvalene [TTF] (donor) molecules across prefabricated metal electrodes. Molecular wires of TTF TCNQ were also formed by evaporating single complex of TTF:TCNQ across prefabricated metal electrodes The prefabricated metal electrodes were made using electron beam lithography on SiO2 and glass cover slip substrates. Even though TTF: TCNQ wires grown from both co-evaporation and evaporation techniques show semiconductor like behavior in temperature dependence of resistance they show different activation energies due the difference in stoichiometry of TTF and TCNQ.

String-like propagation of the 5-coordinated defect state in supercooled water: molecular origin of dynamic and thermodynamic anomalies

We find that at low temperature water, large amplitude (similar to 60 degrees) rotational jumps propagate like a string, with the length of propagation increasing with lowering temperature. The strings are formed by mobile 5-coordinated water molecules which move like a Glarum defect (J. Chem. Phys., 1960, 33, 1371), causing water molecules on the path to change from 4-coordinated to 5-coordinated and again back to 4-coordinated water, and in the process cause the tagged water molecule to jump, by following essentially the Laage-Hynes mechanism (Science, 2006, 311, 832-835). The effects on relaxation of the propagating defect causing large amplitude jumps are manifested most dramatically in the mean square displacement (MSD) and also in the rotational time correlation function of the O-H bond of the molecule that is visited by the defect (transient transition to the 5-coordinated state). The MSD and the decay of rotational time correlation function, both remain quenched in the absence of any visit by the defect, as postulated by Glarum long time ago. We establish a direct connection between these propagating events and the known thermodynamic and dynamic anomalies in supercooled water. These strings are found largely in the regions that surround the relatively rigid domains of 4-coordinated water molecules. The propagating strings give rise to a noticeable dynamical heterogeneity, quantified here by a sharp rise in the peak of the four-point density response function, chi(4)(t). This dynamics heterogeneity is also responsible for the breakdown of the Stokes-Einstein relation.

Size-dependent and strain rate effects in quantum dot nanostructures with molecular dynamic simulations

Size and strain rate effects are among several factors which play an important role in determining the response of nanostructures, such as their deformations, to the mechanical loadings. The mechanical deformations in nanostructure systems at finite temperatures are intrinsically dynamic processes. Most of the recent works in this context have been focused on nanowires [1, 2], but very little attention has been paid to such low dimensional nanostructures as quantum dots (QDs). In this contribution, molecular dynamics (MD) simulations with an embedded atom potential method(EAM) are carried out to analyse the size and strain rate effects in the silicon (Si) QDs, as an example. We consider various geometries of QDs such as spherical, cylindrical and cubic. We choose Si QDs as an example due to their major applications in solar cells and biosensing. The analysis has also been focused on the variation in the deformation mechanisms with the size and strain rate for Si QD embedded in a matrix of SiO2 [3] (other cases include SiN and SiC matrices).It is observed that the mechanical properties are the functions of the QD size, shape and strain rate as it is in the case for nanowires [2]. We also present the comparative study resulted from the application of different EAM potentials in particular, the Stillinger-Weber (SW) potential, the Tersoff potentials and the environment-dependent interatomic potential (EDIP) [1]. Finally, based on the stabilized structural properties we compute electronic bandstructures of our nanostructures using an envelope function approach and its finite element implementation.

Influence of the highest occupied molecular orbital energy level of the donor material on the effectiveness of the anode buffer layer in organic solar cells

Efficiency of organic photovoltaic cells based on organic electron donor/organic electron acceptor junctions can be strongly improved when the transparent conductive Anode is coated with a Buffer Layer (ABL). Here, the effects of a metal (gold) or oxide (molybdenum oxide) ABL are reported, as a function of the Highest Occupied Molecular Orbital (HOMO) of different electron donors. The results indicate that a good matching between the work function of the anode and the highest occupied molecular orbital of the donor material is the major factor limiting the hole transfer efficiency. Indeed, gold is efficient as ABL only when the HOMO of the organic donor is close to its work function Phi(Au). Therefore we show that the MoO(3) oxide has a wider field of application as ABL than gold. (C) 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

On a Novel Geometric Representation of Rotation

This paper presents a novel method of representing rotation and its application to representing the ranges of motion of coupled joints in the human body, using planar maps. The present work focuses on the viability of this representation for situations that relied on maps on a unit sphere. Maps on a unit sphere have been used in diverse applications such as Gauss map, visibility maps, axis-angle and Euler-angle representations of rotation etc. Computations on a spherical surface are difficult and computationally expensive; all the above applications suffer from problems associated with singularities at the poles. There are methods to represent the ranges of motion of such joints using two-dimensional spherical polygons. The present work proposes to use multiple planar domain “cube” instead of a single spherical domain, to achieve the above objective. The parameterization on the planar domains is easy to obtain and convert to spherical coordinates. Further, there is no localized and extreme distortion of the parameter space and it gives robustness to the computations. The representation has been compared with the spherical representation in terms of computational ease and issues related to singularities. Methods have been proposed to represent joint range of motion and coupled degrees of freedom for various joints in digital human models (such as shoulder, wrist and fingers). A novel method has been proposed to represent twist in addition to the existing swing-swivel representation.

An ultra-stable Cu nanowire under thermo-mechanical loading: A molecular dynamic study

We report on the formation of a stable Body-Centered Heptahedral (BCH) crystalline nanobridge structure of diameter ~ 1nm under high strain rate tensile loading to a <100> Cu nanowire. Extensive Molecular Dynamics (MD) simulations are performed. Six different cross-sectional dimensions of Cu nanowires are analyzed, i.e. 0.3615 x 0.3615 nm2, 0.723 x 0.723 nm2, 1.0845 x 1.0845 nm2, 1.446 x 1.446 nm2, 1.8075 x 1.8075 nm2, and 2.169 x 2.169 nm2. The strain rates used in the present simulations are 1 x 109 s-1, 1 x 108 s-1, and 1 x 107 s-1. We have shown that the length of the nanobridge can be characterized by larger plastic strain. A large plastic deformation is an indication that the structure is highly stable. The BCH nanobridge structure also shows enhanced mechanical properties such as higher fracture toughness and higher failure strain. The effect of temperature, strain rate and size of the nanowire on the formation of BCH structure is also explained in details. We also show that the initial orientation of the nanowires play an important role on the formation of BCH crystalline structure. Results indicate that proper tailoring of temperature and strain rate during processing or in the device can lead to very long BCH nanobridge structure of Cu with enhanced mechanical properties, which may find potential application for nano-scale electronic circuits.

Conformational studies of the phosphazenyl side chain in cyclophosphazenes. Part 3. Crystal and molecular structure of N3P3Cl4(NEt2)(NPPh3)

The crystal structure of N3P3Cl4(NEt2)(NPPh3) has been determined. The crystals are orthorhombic, space group Pbca, with a= 8.208(1), b= 21.890(1), c= 31.722(2)Å, Z= 8, and m.p. = 146.5 °C. The structure was solved by direct methods and refined to a final R value of 0.045 for 2 025 independent reflections. The analysis reveals significant variations in the ring P–N bond lengths. The two nitrogenous substituents, NPPh3 and NEt2, reside on the same phosphorus atom. The latter, NEt2, has an almost exact type II conformation (the plane NC2 almost perpendicular to the local NPN plane)(the first observed for a dialkylamino-group in cyclophosphazenes), the former, NPPh3, deviates from type II towards type III (in type III the plane Pring–N–Pexo makes an angle of ca. 45° with the local N–P–N ring plane). The present structure is compared with others of triphenylphosphazenyl-cyclophosphazenes and the conformation of the NPPh3 substituent and its electron supply in the ground and perturbed states are discussed.

Conductance of a photochromic molecular switch with graphene leads

We report a full self-consistent ab initio calculation of the conductance of a diarylethene-based molecular switch with two graphene electrodes. Our results show the contributions of the resonant states of the molecule, of the electrode density of states, and of graphene unique features, such as edge states. The conductivities are found to be significantly different for the two photochromic isomers at zero and finite applied bias. Further we point out the possibility of causing the switching by the application of a large potential difference between the two electrodes.