Semiempirical Tight-binding Calculations Research Articles

CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning

Computational and machine learning approaches to model the conformational landscape of macrocyclic peptides have the potential to enable rational design and optimization. However, accurate, fast, and scalable methods for modeling macrocycle geometries remain elusive. Recent deep learning approaches have significantly accelerated protein structure prediction and the generation of small-molecule conformational ensembles, yet similar progress has not been made for macrocyclic peptides due to their unique properties. Here, we introduce CREMP, a resource generated for the rapid development and evaluation of machine learning models for macrocyclic peptides. CREMP contains 36,198 unique macrocyclic peptides and their high-quality structural ensembles generated using the Conformer-Rotamer Ensemble Sampling Tool (CREST). Altogether, this new dataset contains nearly 31.3 million unique macrocycle geometries, each annotated with energies derived from semi-empirical extended tight-binding (xTB) DFT calculations. Additionally, we include 3,258 macrocycles with reported passive permeability data to couple conformational ensembles to experiment. We anticipate that this dataset will enable the development of machine learning models that can improve peptide design and optimization for novel therapeutics.

The role of chemical functional groups in dewaterability of hydrochar: A molecular simulation study

Hydrothermal carbonization (HTC) is a promising technique for conversion of wet biomass materials to hydrochar, a carbon-rich material with a wide range of applications. A crucial property of hydrochar, particularly that obtained from HTC of sewage sludge, is the dewaterability, which may be controlled by certain chemical functional groups of the hydrochar itself. This paper presents results from our recent study on the role of chemical functional groups in the dewaterability of hydrochar, employing a novel approach that integrates molecular dynamics simulations with extended semi-empirical tight-binding calculations. By examining various hydrochar models with distinct chemical functional groups such as hydroxyl, carboxyl, and ketone, multiple factors affecting the dewaterability were investigated. The results show that removal of specific functional groups led to substantial reductions in hydration energy of hydrochar molecules, from -340 kJ/mol to -61 kJ/mol. Findings from this work not only contribute to better understanding the dewaterability of hydrochar in connection to the functional groups, but also provide valuable knowledge for customizing the design and production of hydrochar with specific chemical functional groups to suit diverse applications.

Electronic and optical properties of SixGe1−x−ySny alloys lattice-matched to Ge

We present a combined experimental and theoretical analysis of the evolution of the near-band gap electronic and optical properties of Si$_{x}$Ge$_{1-x-y}$Sn$_{y}$ alloys lattice-matched to Ge and GaAs substrates. We perform photoreflectance (PR) and photoluminescence (PL) measurements on Si$_{x}$Ge$_{1-x-y}$Sn$_{y}$ epitaxial layers grown via chemical vapour deposition, for Si (Sn) compositions up to $x =$ 9.6% ($y =$ 2.5%). Our measurements indicate the presence of an indirect fundamental band gap, with PL observed $\approx$ 200-250 meV lower in energy than the direct $E_0$ transition identified by PR measurements. The measured PL is Ge-like, suggesting that the alloy conduction band (CB) edge is primarily derived from the Ge L-point CB minimum. Interpretation of the PR and PL measurements is supported by atomistic electronic structure calculations. Effective alloy band structures calculated via density functional theory confirm the presence of an indirect fundamental band gap, and reveal the origin of the observed inhomogeneous broadening of the measured optical spectra as being alloy-induced band hybridisation occurring close in energy to the CB edge. To analyze the evolution of the band gap, semi-empirical tight-binding (TB) calculations are employed to enable calculations for large supercell sizes. TB calculations reveal that the alloy CB edge is hybridized in nature, consisting at low Si and Sn compositions of an admixture of Ge L-, $\Gamma$- and X-point CB edge states, and confirm that the alloy CB edge retains primarily Ge L-point CB edge character. Our experimental measurements and theoretical calculations confirm a direct transition energy close to 1 eV in magnitude for Si and Sn compositions $x =$ 6.8 - 9.6% and $y =$ 1.6 - 2.2%.

The pyrrole-water complex: Multidimensional large amplitude dynamics and rotational spectra of its 13C isotopologues

The rotational spectrum of pyrrole-water was investigated before (Tubergen et al., 1993) In this work, we have applied a recently developed semiempirical tight-binding quantum chemistry program and DFT calculations to identify possible low energy conformers of the pyrrole-water complex which feature σ- and π-type hydrogen-bonding interactions. Using a cavity-based and two chirped pulse Fourier transform microwave spectrometers, we have measured and assigned all monosubstituted 13C isotopologues of pyrrole-water in their natural abundances. The 14N nuclear quadrupole hyperfine splittings and water tunneling doublets of these rarer isotopologues have also been observed and analyzed. Furthermore, we have carried out potential energy surface scans along possible paths of water large amplitude motions and identified all four previously proposed pyrrole-water geometries and correlated them to one global minimum and three transition states. The theoretical investigation together with the additional 13C experimental data allow one to confidently identify the ground state geometry and also estimate the water tunneling barrier.

Anisotropic Hydrolysis Susceptibility in Deformed Polydimethylsiloxanes.

Chemical reactions involving the polydimethylsiloxane (PDMS) backbone can induce significant network rearrangements and ultimately degrade macro-scale mechanical properties of silicone components. Using two levels of quantum chemical theory, we identify a possible electronic driver for chemical susceptibility in strained PDMS chains and explore the complicated interplay between hydrolytic chain scissioning reactions, mechanical deformations of the backbone, water attack vector, and chain mobility. Density functional theory (DFT) calculations reveal that susceptibility to hydrolysis varies significantly with the vector for water attacks on silicon backbone atoms, which matches strain-induced anisotropic changes in the backbone electronic structure. Efficient semiempirical density functional tight binding (DFTB) calculations are shown to reproduce DFT predictions for select reaction pathways and facilitate more exhaustive explorations of configuration space. We show that concerted strains of the backbone must occur over at least a few monomer units to significantly increase hydrolysis susceptibility. In addition, we observe that sustaining tension across multiple monomer lengths by constraining molecular degrees of freedom further enhances hydrolysis susceptibility, leading to barrierless scission reactions for less substantial backbone deformations than otherwise. We then compute chain scission probabilities as functions of the backbone degrees of freedom, revealing complicated configurational interdependencies that impact the likelihood for hydrolytic degradation. The trends identified in our study suggest simple physical descriptions for the synergistic coupling between local mechanical deformation and environmental moisture in hydrolytic degradation of silicones.

Thermoelectric efficiency in three-terminal graphene nano-junctions.

The thermoelectric efficiency of a thermal machine consisting of a triangular graphene nano-junction connected to three electrodes in the linear response regime is studied. Using the Onsager formalism and a combination of semi-empirical tight-binding calculations as well as Green's function theory, the efficiency at maximum output power which can be written in terms of generalized figures of merit is investigated. The results for a set temperature and chemical potential parameters have shown that adding a third terminal improves the efficiency at maximum output power compared to the two-terminal setup.

Studying lowest energy structures of carbon clusters by bond-order empirical potentials

A very recently developed optimization algorithm for carbon clusters (C n s) (Yen and Lai J Chem Phys 142:084313, 2015) is combined separately with different empirical bond-order potentials which were proposed also for carbon materials, and they are applied to calculate the lowest energy structures of C n s studying their structural changes at different size n. Based on predicted structures, we evaluate the practicality of four analytic bond-order empirical potentials, namely the Tersoff, Tersoff–Erhart–Albe, first-generation Brenner and second-generation Brenner (SGB) potentials. Generally, we found that the cluster C n (n = 3–60) obtained by the SGB potential undergoes a series of dramatic structural transitions, i.e., from a linear → a single ring → a multi-ring/quasi-two-dimensional bowl-like → three-dimensional fullerene-like shape; such variability of structural forms was not seen in the other three potentials. On closer examination of the C n s calculated using this potential and further comparing them with those obtained by the semiempirical density functional tight-binding theory calculations, we found that these C n are more realistic than similar works reported in the literature. In this respect, due to its potential applications in the study of chemically complex systems of different atoms especially chemical reactions (Che et al. Theor Chem Acc 102:346, 1999), the SGB potential can, moreover, be used to investigate larger size C n , and calculated structural results by this potential are naturally input configurations for higher-level density functional theory calculations. Another most remarkable finding in the present work is the C n results calculated by Tersoff–Erhart–Albe empirical potential. It predicts a two-dimensional development of graphene structure, exhibiting always a zigzag edge in the optimized clusters. This empirical potential can thus be applied to study graphene-related materials such as that shown in a recent paper (Yoon et al. J Chem Phys 139:204702, 2013).

Topological phase in oxidized zigzag stanene nanoribbons

First-principles and semi-empirical tight binding calculations were performed to understand the adsorption of oxygen on the surface of two dimensional (2D) and zigzag stanene nano-ribbons. The intrinsic spin-orbit interaction is considered in the Kane-Mele tight binding model. The adsorption of an oxygen atom or molecule on the 2D stanene opens an electronic energy band gap. We investigate the helical edge states and topological phase in the pure zigzag stanene nano-ribbons. The adsorption of oxygen atoms on the zigzag stanene nano-ribbons deforms the helical edge states at the Fermi level which causes topological (non-trivial) to trivial phase transition. The structural stability of the systems is checked by performing Γ-point phonon calculations. Specific arrangements of adsorbed oxygen atoms on the surface of zigzag stanene nano-ribbons conserve the topological phase which has potential applications in future nano-electronic devices.

Effect of realistic metal electronic structure on the lower limit of contact resistivity of epitaxial metal-semiconductor contacts

The effect of realistic metal electronic structure on the lower limit of resistivity in [100] oriented n-Si is investigated using full band Density Functional Theory and Semi-Empirical Tight Binding calculations. It is shown that the “ideal metal” assumption may fail in some situations and, consequently, underestimate the lower limit of contact resistivity in n-Si by at least an order of magnitude at high doping concentrations. The mismatch in transverse momentum space in the metal and the semiconductor, the so-called “valley filtering effect,” is shown to be sensitive to the details of the transverse boundary conditions for the unit cells used. The results emphasize the need for explicit inclusion of the metal atomic and electronic structure in the atomistic modeling of transport across metal-semiconductor contacts.

Electronic transport in three-terminal triangular carbon nanopatches

The electronic transport properties of three-terminal graphene-based triangular patches are investigated using a combination of semi-empirical tight-binding calculations and Green’s function-based transport theory within Landauer’s framework. The junctions are composed of a triangular structure based on armchair edged graphene nanoribbons. We show how details of the central region influence the resonant electronic transport across the triangular patches and highlight the unique features of the current flow as a function of geometry. These properties indicate an array of functionalities for the development of carbon-based complex nanocircuits and operational devices at the nanoscale.

Tight-Binding Calculation of Deformation and Band Gap of Single-Walled Carbon Nanotubes under Axial Tension and Radial Compression

Application of carbon nanotubes (CNTs) to nanometer-scale electronic devices of the next generation is being highly expected owing to their prominent electronic properties and mechanical and chemical stability. Controlling local strain is a key issue to design and realize such devices because of the interplay between mechanical and electronic properties in carbon nanotubes. In this study, we performed semi-empirical tight-binding band calculation of single-walled carbon nanotubes (SWCNTs) with various chiral structures to investigate the deformation behavior and its relation to electronic properties. Firstly, we performed simulation of SWCNTs subject to axial tension, which is one of the simplest deformation modes, to investigate their mechanical properties and change in band gap energies. Pristine SWCNTs can hold high tensile strain. SWCNTs show transition between semiconducting and metallic features during tension, and the transition behavior depends on the chirality of the nanotubes. Secondly, we investigated the mechanical and electronic properties of SWCNTs under radial compression, as it is relatively easy to apply such deformation, for example by moving an AFM tip to a nanotube lying on a plate. SWCNTs are robust under large compression showing no bond breaking or rebonding. The mechanism of the peculiar elastic behavior is discussed. CNTs that have finite band gap energies (semiconducting) at unstrained state show transition to metallic state under radial compression

Electronic Properties of Quantum Wells Structures with Gaussian Potential Profiles

The flrst semi-empirical tight-binding calculation of the electronic properties of some quantum wells structures with Gaussian conflning potential is presented. The obtained results demonstrate that this methodology can be useful for realistic calculations of the electronic structure in this kind of systems.

Performance of the semiempirical AM1, PM3, MNDO, and tight-binding methods in comparison with DFT method for the large fullerenes C 116–C 120

Are the semiempirical methods still reliable for large fullerenes? To answer this question, in this paper, the semiempirical AM1, PM3, MNDO, and tight-binding calculations were performed on the candidate isomers selected from the complete sets of isolated-pentagon-rule isomers of C 116–C 120 based on the second generation reactive empirical bond order potential. To assess the reliability of these semiempirical methods and predict the ground-state structures more accurately, the density functional theory calculations at the B3LYP/6-31G(d)//B3LYP/3-21G level of theory were also carried out on the top 20 low-energy candidates from each semiempirical method. It was found that the tight-binding potential gives a good agreement for the prediction of the relative energies when compared with the B3LYP/6-31G ∗ results, while AM1, PM3, and MNDO methods behave badly. Furthermore, we also investigated the structures of the B3LYP/6-31G ∗ low-energy isomers for C 116–C 120 to understand the relationship between the stability and some structural factors.

Binding sites for SiH 2/Si(0 0 1): A combined ab initio, tight-binding, and classical investigation

Binding sites for SiH 2 on Si(0 0 1) are investigated theoretically by using several different methods. Possible local minima are first sampled by classical molecular dynamics simulations of the SiH 2/Si(0 0 1) impact, allowing for a preliminary, fast selection. A further refinement is carried out by geometry optimizations using semiempirical tight-binding and density functional theory calculations, based on both the local density and generalized gradient approximations. In most cases only minor morphological changes are obtained when comparing the ab initio sites with the classical potentials and tight-binding ones. The purely classical treatments here tested, however, overestimate the number of minima and fail in accurately reproducing the relative energy of some of the adsorption sites. Closer agreement is obtained with tight-binding, with the noticeable exception of the lowest ab initio minimum (on-dimer site).

04/00136 Hydrogen storage behavior of C 116 system - AM1 treatment : Türker, L. International Journal of Hydrogen Energy, 2003, 28, (10), 1115–1119.

Are the semiempirical methods still reliable for large fullerenes? To answer this question, in this paper, the semiempirical AM1, PM3, MNDO, and tight-binding calculations were performed on the candidate isomers selected from the complete sets of isolated-pentagon-rule isomers of C116–C120 based on the second generation reactive empirical bond order potential. To assess the reliability of these semiempirical methods and predict the ground-state structures more accurately, the density functional theory calculations at the B3LYP/6-31G(d)//B3LYP/3-21G level of theory were also carried out on the top 20 low-energy candidates from each semiempirical method. It was found that the tight-binding potential gives a good agreement for the prediction of the relative energies when compared with the B3LYP/6-31G∗ results, while AM1, PM3, and MNDO methods behave badly. Furthermore, we also investigated the structures of the B3LYP/6-31G∗ low-energy isomers for C116–C120 to understand the relationship between the stability and some structural factors.

A tight-binding study of surface magnetic anisotropy of the Co (0001) and its perturbation by Cu and CO

Recent experiments show that on rather thick Co films deposition of Cu or adsorption of CO or C can switch the magnetization direction along the surface normal. We present semi-empirical self-consistent tight-binding calculations for a semi-infinite hcp Co(0001) crystal. It appears that the contribution of the magnetic anisotropy-energy from the surface layer favors the in-plane alignment of magnetic moments. Various surface perturbations (Cu deposition or CO adsorption, artificial suppression of surface magnetization), however, reduce this contribution considerably or even change the sign of the electronic part of the magnetic anisotropy energy, thus making conditions for perpendicular magnetization more favourable.

Resonant electron tunneling through defects in ultrathin SiO 2 gate oxides in MOSFETs

To analyze defect-assisted elastic tunneling currents through ultrathin SiO 2 gate oxides in metal-oxide semiconductor field-effect transistors (MOSFETs), we have combined semiempirical microscopic tight-binding calculations with full-band Monte Carlo transport simulations. Two prototypical devices with channel lengths of 50 and 90 nm were considered. We find that defects having an area density larger than 10 11 cm −2 can enhance tunneling currents by several orders of magnitude in both devices. Resonant tunneling effects are predicted to be more pronounced for thicker oxides. For oxides thinner than 2 nm, hot electrons are unlikely to dominate gate leakage currents in the presence of defects.

Influence of defects on elastic gate tunneling currents through ultrathin SiO2gate oxides: predictions from microscopic models

We study theoretically the influence of neutral oxygen vacancies on the magnitude of elastic tunneling currents through the ultrathin (1.3 nm) gate oxide of a prototypical metal-oxide field-effect transistor with a channel length of 50 nm. For the calculation of the gate currents, we have used transmission coefficients obtained from three-dimensional semiempirical tight-binding calculations for a model Si–SiO2–Si junction, and electron distribution functions based on full-band Monte-Carlo transport simulations. The positions of the atoms in the junction were determined by first-principles density-functional calculations. It is found that the gate currents increase significantly (by typically one to three orders of magnitude) in the presence of vacancies having a density around 1012cm−2, provided that the resonant energy levels lie less than 1 eV above the Si conduction band edge.

Origin of optical anisotropies of nonpolar GaN surfaces

We investigate the origin of optical anisotropies of the nonpolar GaN (110) and $(101\ifmmode\bar\else\textasciimacron\fi{}0)$ surfaces. Using semiempirical tight-binding calculations, we analyze in detail the main optical signature of each surface. The origin of the optical spectra is discussed in terms of the main surface electronic states and of the specific surface atomic rearrangement. Results of the surface dielectric function, and reflectance anisotropy spectra, are presented.

Optical second harmonic spectroscopy of boron-reconstructed Si(001)

Optical second harmonic generation (SHG) spectroscopy is used to probe Si(001) following thermal decomposition of diborane at the surface. Incorporation of boron (B) at second layer substitutional sites at H-free Si(001) intensifies and redshifts the E1 SHG spectral peak, while subsequent H termination further intensifies and blueshifts E1, in sharp contrast to the effect of bulk B doping or nonsubstitutional B. Ab initio pseudopotential and semiempirical tight binding calculations independently reproduce these unique trends, and attribute them to the surface electric field associated with charge transfer to electrically active B acceptors, and rehybridization of atomic bonds.