Force Field Calculations Research Articles

Cyanopyridines – Suitable Heterocycles for Cocrystal Syntheses

Abstract2‐cyanopyridine and 4‐cyanopyridine were investigated for the controlled synthesis of cocrystals by applying the pKa rule. Cocrystals were designed with oxalic, glutaric and adipic acids and analyzed by single crystal X‐ray diffraction. To get a deeper insight into the aggregation behavior of the designed cocrystals, UNI Force Field Calculations were used to compare the intermolecular potentials of the main interactions of the crystal structures.

Structure Conformation, Vibrational Properties, NLO Activity, HOMO-LUMO and Thermodynamic Parameters of Dinicotinic Acid Using Experimental and Theoretical Approach

In the present study, the Dinicotinic acid was characterized by FTIR and FT-Raman spectra in the range of 4000-450 and 4000-50 cm-1. The most stable molecular structure and optimized geometrical parameters are calculated using DFT studies. Normal Co-ordinate Analysis (NCA) was studied out by solving Inverse Vibrational Problem using 74-valence force field calculations using overlay least square technique. It reproduces into 35 fundamental frequencies with an rms error of 9.28 cm-1 in the zero-order calculations. Based on PED, vibrational modes are assigned for this molecule. The energy of HOMO & LUMO, NLO parameters, and thermodynamic parameters were computed.

Computational analysis of optical trapping of transparent and reflecting micron-sized spherical particles

In the ray-optics regime, we calculated the radial and axial force field on a micron-sized spherical particle in an optical levitation trap. The momentum change in the photon-stream path of tightly focused incident laser beam causes the calculated force field in the optical trap. The computational results for the force field are compared with the literature and a good agreement is obtained. Utilizing the benchmarked force field, the optical trapping dynamics of (i) a transparent spherical particle with continuous-wave 〖TEM〗_00 Gaussian beam and (ii) a reflecting spherical particle with continuous-wave 〖TEM〗_01^* Laguerre-Gaussian beam under various conditions are simulated in Matlab.

Object-Oriented Building Contour Optimization Methodology for Image Classification Results via Generalized Gradient Vector Flow Snake Model

Building boundary optimization is an essential post-process step for building extraction (by image classification). However, current boundary optimization methods through smoothing or line fitting principles are unable to optimize complex buildings. In response to this limitation, this paper proposes an object-oriented building contour optimization method via an improved generalized gradient vector flow (GGVF) snake model and based on the initial building contour results obtained by a classification method. First, to reduce interference from the adjacent non-building object, each building object is clipped via their extended minimum bounding rectangles (MBR). Second, an adaptive threshold Canny edge detection is applied to each building image to detect the edges, and the progressive probabilistic Hough transform (PPHT) is applied to the edge result to extract the line segments. For those cases with missing or wrong line segments in some edges, a hierarchical line segments reconstruction method is designed to obtain complete contour constraint segments. Third, accurate contour constraint segments for the GGVF snake model are designed to quickly find the target contour. With the help of the initial contour and constraint edge map for GGVF, a GGVF force field computation is executed, and the related optimization principle can be applied to complex buildings. Experimental results validate the robustness and effectiveness of the proposed method, whose contour optimization has higher accuracy and comprehensive value compared with that of the reference methods. This method can be used for effective post-processing to strengthen the accuracy of building extraction results.

Solvent Induced Helix Folding of Defined Indolenine Squaraine Oligomers.

A protecting group strategy was employed to synthesise a series of indolenine squaraine dye oligomers up to the nonamer. The longer oligomers show a distinct solvent dependence of the absorption spectra, that is, either a strong blue shift or a strong red shift of the lowest energy bands in the near infrared spectral region. This behaviour is explained by exciton coupling theory as being due to H‐ or J‐type coupling of transition moments. The H‐type coupling is a consequence of a helix folding in solvents with a small Hansen dispersity index. DOSY NMR, small angle neutron scattering (SANS), quantum chemical and force field calculations agree upon a helix structure with an unusually large pitch and open voids that are filled with solvent molecules, thereby forming a kind of clathrate. The thermodynamic parameters of the folding process were determined by temperature dependent optical absorption spectra.

Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites.

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding toward a given zeolite framework. Over the last few decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, there is no consensus on the best calculation strategy for high-throughput virtual screening undertakings. In this work, we compare binding affinities from density functional theory (DFT) and Dreiding force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. Enabled by automation software, we show that Dreiding binding energies from the frozen pose method correlate best with DFT energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive than their time-averaged counterparts. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over the frozen pose method despite being orders of magnitude more expensive. The code and benchmark data are open-sourced and provide robust and computationally efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

Environmental-sulfur-controlled surface properties of pyrite: a first principles PBE + U study

The structure and stability of pyrite (100), (210), (110), and (111) surfaces in different sulfur conditions were studied in the framework of GGA(PBE) + U implementations of density functional calculations. The Hubbard U correction was found to be a critical parameter in density functional theory (DFT) calculations to describe pyrite surfaces. With the U correction, the surface energy order for stoichiometric pyrite surfaces is (100) < (210) < (110) < (111), which is different with previous knowledge from conventional DFT and classical force field calculations, but consistent with broken bonds number and shape distribution in natural and synthetic systems in different sulfur conditions. Within the considered surfaces, the stoichiometric (100)-S and non-stoichiometric (111)-3S are the most stable under both S-lean and S-rich conditions, respectively. For relative stable surfaces in different environment, (100)-Fe and (100)-2S reconstruct, but (111)-Fe and (111)-3S show no relaxations while (100)-S, (210)-Fe′, and (210)-2S′ show relaxations to certain degree. Electron transfer from surface Fe to S atom on pyrite during relaxation and reconstruction, forming exemplary surface configuration and chemical composition. These findings reveal the nature of pyrite surfaces in various sulfur conditions, proving fundamental not only for surface-related applications but also for geological indicators of pyrite formation conditions.

Cryogenic Messenger-IR Ion Spectroscopy Study of Phenol & Aniline Molecular Ions and of the common Fragment Ion [C5H6][rad]+ formed by EI-MS

Molecular ions of phenol and aniline as well as the fragment ion at m/z 66 formed by electron ionization are examined with cryogenic messenger-IR ion spectroscopy and theory. According to the recorded IR spectra aromatic ground state molecular ions of phenol and aniline are clearly identified. Similar to earlier reports our new set of spectroscopic and computational results supports the assumption that tautomeric molecular ions of phenol and aniline are only short-lived intermediates in the reaction path to the ultimate CO loss reaction product of phenol as well as the HNC loss product of aniline. Even the present cryogenic messenger-IR ion spectroscopy approach failed to collect spectroscopic evidence of the intermediate presence of these elusive tautomers of phenol and aniline molecular ions. However, our study clearly shows that the electron ionization mass spectrometry dissociation product ion of phenol and aniline at m/z 66 is the cyclopentadiene radical cation [C5H6]+ for the presence of which convincing spectroscopic evidence could be collected proving the structure assignment and identification. All messenger-IR ion spectroscopy experiments were conducted on a cryogenic 22-pole ion trap with the use of neon atoms for tagging. The MS instrument was coupled to a free electron laser delivering wavelength tunable IR radiation for spectroscopy. Harmonic and anharmonic force field calculations complement the experiments and support band assignments of the recorded IR spectra and general data interpretation.

Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations.

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

Elucidation of Molybdenum Trioxide Sulfurization: Mechanistic Insights into Two-Dimensional Molybdenum Disulfide Growth.

Powder vaporization is a common method for the generation of large-area, single-crystal, two-dimensional molybdenum disulfide. While commonly employed as a growth method, the fundamental molecular mechanisms are not well understood. Recent ab initio analyses have shown that molybdenum oxysulfide rings play a key role in the sulfurization of molybdenum trioxide from elemental sulfur. In this study, we utilize molecular dynamics simulations with a reactive force field and ab initio calculations to elucidate the reaction pathway of sulfur with molybdenum trioxide. The molecular dynamics simulations demonstrated that for all sulfur allotropes the reaction pathway could be reduced to that of disulfur, trisulfur, or a combination of the two and that molybdenum trioxide can catalyze the decomposition of larger sulfur allotropes. Ab initio calculations were used to illuminate the intermediates and transition states in the reaction pathways for disulfur and trisulfur. Analysis of the temperature dependence of the transition state energies shows that the maximum reaction rates occur between 1000 and 1100 K, which corresponds with commonly reported experimental growth temperatures for molybdenum disulfide.

ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections.

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP·Mg2+. In aqueous solution, two chelation geometries predominate, distinguished by bidentate and tridentate Mg2+–phosphate coordination. These are approximately isoenergetic but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP·Mg2+ coordination. Applying an enhanced sampling scheme to circumvent prohibitively slow sampling of transitions between coordination modes, we observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favored coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP·Mg2+–protein complex structures to supplement otherwise limited experimental data, we quantified systematic biases for each force field. The force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. We reassessed the applicability of the thus corrected force field descriptions of ATP·Mg2+ for biomolecular simulation and observed that, while the CHARMM parameters display an erroneous preference for overextended triphosphate configurations that will affect many common biomolecular simulation applications involving ATP, the force field energy landscapes broadly agree with experimental measurements of solution geometry and the distribution of ATP·Mg2+ structures found in the Protein Data Bank. Our force field evaluation and correction approach, based on maximizing consistency with the large and heterogeneous collection of structural information encoded in the PDB, should be broadly applicable to many other systems.

Large-Scale Screening of Interface Parameters in the WC/W System Using Classical Force Field and First-Principles Calculations

To understand the observed wear in WC/Co tools during machining of Ti-alloys, it is important to know which interfaces are present in the tool-workpiece contact zone. It has been shown that WC grai...

Magnesium Coordination of ATP - Force Field Evaluation and Structure-Driven Correction

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP.Mg2+. In aqueous solution, two chelation geometries predominate, with Mg contacting either the terminal beta and gamma phosphate groups (bidentate) or all three (tridentate). These subforms are approximately isoenergetic, but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP.Mg2+ coordination. With unbiased molecular dynamics simulation showing prohibitively slow interconversion, we devised an enhanced sampling scheme to calculate free energy differences between different Mg2+-phosphate configurations. We observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favoured coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP.Mg2+-protein complex structures to supplement otherwise limited experimental data, we observed systematic biases for each force field. However, the force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. Reassessing the applicability of the corrected force field descriptions of ATP.Mg2+ for biomolecular simulation, we observe that calculated properties broadly agree with experimental measurements of solution geometry and the distribution of ATP.Mg2+ structures found in the Protein Data Bank. However, while the corrected Amber force field appears to reproduce both bidentate and tridentate configurations, CHARMM displays an erroneous preference triphosphate overextension. This will affect the interpretation of simulations of bidentate ATP.Mg2+, which comprises the majority of PDB structures.

Synthesis and Structure-Property Relationships of Polyimide Covalent Organic Frameworks for Carbon Dioxide Capture and (Aqueous) Sodium-Ion Batteries.

Covalent organic frameworks (COFs) are an emerging material family having several potential applications. Their porous framework and redox-active centers enable gas/ion adsorption, allowing them to function as safe, cheap, and tunable electrode materials in next-generation batteries, as well as CO2 adsorption materials for carbon-capture applications. Herein, we develop four polyimide COFs by combining aromatic triamines with aromatic dianhydrides and provide detailed structural and electrochemical characterization. Through density functional theory (DFT) calculations and powder X-ray diffraction, we achieve a detailed structural characterization, where DFT calculations reveal that the imide bonds prefer to form at an angle with one another, breaking the 2D symmetry, which shrinks the pore width and elongates the pore walls. The eclipsed perpendicular stacking is preferable, while sliding of the COF sheets is energetically accessible in a relatively flat energy landscape with a few metastable regions. We investigate the potential use of these COFs in CO2 adsorption and electrochemical applications. The adsorption and electrochemical properties are related to the structural and chemical characteristics of each COF, giving new insights for advanced material designs. For CO2 adsorption specifically, the two best performing COFs originated from the same triamine building block, which—in combination with force-field calculations—revealed unexpected structure–property relationships. Specific geometries provide a useful framework for Na-ion intercalation with retainable capacities and stable cycle life at a relatively high working potential (>1.5 V vs Na/Na+). Although this capacity is low compared to conventional inorganic Li-ion materials, we show as a proof of principle that these COFs are especially promising for sustainable, safe, and stable Na-aqueous batteries due to the combination of their working potentials and their insoluble nature in water.

Antibiotics functionalization intervened morphological, chemical and electronic modifications in chitosan nanoparticles

Applicability and efficacy of chitosan nanoparticles for drug delivery have been widely studied recently. However, the physicochemical effects of antibiotics functionalization in chitosan nanoparticles have not been comprehensively explored. In the current study chitosan nanoparticles have been prepared through an ionic gelation method and subsequently functionalized with antibiotic molecules, namely, Ampicillin, Dalacin (Clindamycin) and Levofloxacin antibiotics. The small angle X – ray scattering studies on these samples inferred that chitosan nanoparticles exhibited spherical morphology with an average size ≈ 90 nm, while antibiotics functionalization interestingly shows diffusion limited aggregation of chitosan nanoparticles to form fractal structures, retaining primary particle radius of chitosan nanoparticles unchanged. These features were further correlated to surface charge using zeta potential measurements and pH of the samples. The interactions between chitosan nanoparticles and antibiotic molecules were corroborated through the optical spectroscopy and Fourier transform infrared spectroscopy measurements. To get a better insight on the above experimental findings and the possible interactions between chitosan nanoparticles and antibiotic molecule, first principles density of states and force field calculations were performed. The calculations show that chitosan nanoparticles exhibit a porous network which can allow a single antibiotic molecule to get incorporated in the single pore. However, this feature was observed to be a function of an antibiotic type. The antibiotic incorporation alters chitosan’s porous network, thereby correlating observation of fractal structure in antibiotic functionalized chitosan nanoparticles. The calculations further show that molecular orbital energy levels and subsequently dipole moments governed experimental observations. Thus our experimental and theoretical studies proved to be complementary offering a new approach to evaluate physicochemical interactions between antibiotic–nanoparticles carrier system crucial for the effective realization of drug delivery.

Rotational spectroscopy and precise molecular structure of 1,2-dichlorobenzene

Supersonic expansion rotational spectroscopy at 4–18 GHz with rectangular pulse and chirp excitation was used to measure spectra of twelve isotopic species of 1,2-dichlorobenzene at conditions of completely resolved double chlorine hyperfine structure by using a newly constructed slit expansion nozzle. Four species: 37Cl13 and the three singly substituted 13C species have been assigned for the first time. Spectroscopic constants for six isotopic species with single deuterium substitution were considerably improved by using chemically synthesised samples. Hyperfine constants in the field gradient principal axes system were determined and used as a test of self-consistency of the analysis. Additional room-temperature measurements up to 275 GHz allowed assignment of rotational transitions in first excited states of the three lowest normal modes. The determined values of vibrational changes in rotational constants, inertial defects, and quartic and sextic centrifugal distortion constants, allowed calibration of harmonic and anharmonic force field calculations, resulting in determination, among others, of precise semi-experimental equilibrium, reSE, geometry of 1,2-dichlorobenzene. It is found that r(C-C) and ∠(C-C-C) in the phenyl ring of 1,2-dichlorobenzene show very small changes relative to benzene.

High Formability and Fast Lithium Diffusivity in Metastable Spinel Chloride for Rechargeable All‐Solid‐State Lithium‐Ion Batteries

Materials with high formability and Li‐ion diffusivity are desired to realize safe bulk‐type all‐solid‐state Li‐ion batteries with high energy density. Spinel‐type Li2FeCl4, which is expected as a Li‐ion‐conductive electrode, adopts the high‐temperature cubic phase (space group: Fd‐3m) by a mechanochemical synthesis method. The powder‐compressed pellet shows a high relative density of 92% and large neck formation between the particles. An analysis of the distribution of relaxation times from the AC impedance results indicates that the contribution of the grain boundary impedance is almost negligible (≈3%) in the powder‐compressed pellet. Even the Li diffusion coefficient, which is underestimated by the Nernst–Einstein equation, is several orders of magnitude higher than those of conventional oxide and sulfide electrode materials. Analyzing the diffusion pathways using a classical force field calculation suggests that stabilizing the high‐temperature phase at room temperature delocalizes Li ions in the diffusion pathway, thus realizing high Li‐ion diffusivity. The Li2FeCl4 green compact containing 10 wt% carbon as an electron‐conductive additive shows a one‐electron charge reaction with a capacity of 126 mAh g−1, with no large overpotential at a high operating voltage of 3.6 V versus Li/Li+ at 30 °C.

Stochastic simulation of nonequilibrium heat conduction in extended molecular junctions.

Understanding phononic heat transport processes in molecular junctions is a central issue in the developing field of nanoscale heat conduction. Here, we present a Langevin dynamics simulation framework to investigate heat transport processes in molecular junctions at and beyond the linear response regime and apply it to saturated and unsaturated linear hydrocarbon chains connecting two gold substrates. Thermal boundary conditions represented by Markovian noise and damping are filtered through several (up to four) gold layers to provide a realistic and controllable bath spectral density. Classical simulations using the full universal force field are compared with quantum calculations that use only the harmonic part of this field. The close agreement found at about room temperature between these very different calculations suggests that heat transport at such temperatures is dominated by lower frequency vibrations whose dynamics is described well by classical mechanics. The results obtained for alkanedithiol molecules connecting gold substrates agree with previous quantum calculations based on the Landauer formula and match recent experimental measurements [e.g., thermal conductance around 20 pW/K for alkanedithiols in single-molecule junctions (SMJs)]. Heat conductance simulations on polyynes of different lengths illuminate the effects of molecular conjugation on thermal transport. The difference between alkanes and polyynes is not large but correlates with the larger rigidity and stronger mode localization that characterize the polyyne structure. This computational approach has been recently used [R. Chen, I. Sharony, and A. Nitzan, J. Phys. Chem. Lett. 11, 4261-4268 (2020)] to unveil local atomic heat currents and phononic interference effect in aromatic-ring based SMJs.

Differentiated adsorption of thiobenzoic acid and thiobenzamide on silver nanoparticles determined by SERS spectroscopy.

Surface-enhanced Raman scattering of thiobenzoic acid and thiobenzamide have been recorded on three different silver colloids in order to find the chemical species responsible for the spectra and to detect differences in the adsorption with respect to their oxygen counterparts, benzoic acid and benzamide, respectively. Very significant and unexpected shifts of opposite sign between the Raman and SERS wavenumbers have been detected. By comparing the experimental and DFT calculated wavenumbers, it can be concluded that the acid is bonded to the metal as thiobenzoate through the sulfur atom with unidentate coordination. SERS spectra of thiobenzamide can be explained by assuming that it is adsorbed as azanion, like in the case of benzamide, linking to the metal through the sulfur and nitrogen atoms of the ionized thiocarboxamide group. In order to support these conclusions, B3LYP/LanL2DZ force field calculations for different complexes of silver cations with the thiobenzoate anion, the neutral thiobenzamide as well as its azanion have been carried out. Additionally, the 8a;νring mode is the most enhanced band in the SERS of both adsorbates pointing to the participation of a metal-to-molecule resonant charge transfer mechanism.

Molecular structure, electronic properties and drug-likeness of xylazine by quantum methods and qsar analysis

Xylazine is an adrenergic alpha-2 agonist used as a sedative, analgesic and centrally acting muscle relaxant in veterinary medicine. In this study, the anaesthetic compound Xylazine was optimized in the electronic ground state using Density Functional Theory at B3LYP/6–311 + G (d, p) level. This study aims at revealing the various electro physical and chemical properties of Xylazine. This study will be useful for future research on the title compound. The stabilization energies and the electronic transitions were achieved with the aid of Natural Bond Orbital (NBO) analysis. The vibrational pattern of the molecule was characterized by FT-IR and FT-Raman spectra using Scaled Quantum Mechanical Force Field calculations. The presence of strong hydrogen bonding interactions was evidently revealed by the shifting of wavenumbers. NBO analysis reveals the stability of the molecule. Further, the strength of association between adrenergic receptor and Xylazine was predicted using a computer-based analysis of molecular modeling interaction techniques. A detailed molecular picture of this anesthetic compound and its interactions were obtained by modeling analysis, NBO analysis, IR, Raman and UV–Vis spectroscopy.