Rotational Energy Barriers Research Articles

Molecular Dynamics Simulation and Experimental Studies on the Thermomechanical Properties of Epoxy Resin with Different Anhydride Curing Agents.

An investigation of the relationship between the microstructure parameters and thermomechanical properties of epoxy resin can provide a scientific basis for the optimization of epoxy systems. In this paper, the thermomechanical properties of diglycidyl ether of bisphenol A (DGEBA)/methyl tetrahydrophthalic anhydride (MTHPA) and DGEBA/nadic anhydride (NA) were calculated and tested by the method of molecular dynamics (MD) simulation combined with experimental verification. The effects of anhydride curing agents on the thermomechanical properties of epoxy resin were investigated. The results of the simulation and experiment showed that the thermomechanical parameters (glass transition temperature (Tg) and Young’s modulus) of the DGEBA/NA system were higher than those of the DGEBA/MTHPA system. The simulation results had a good agreement with the experimental data, which verified the accuracy of the crosslinking model of epoxy resin cured with anhydride curing agents. The microstructure parameters of the anhydride-epoxy system were analyzed by MD simulation, including bond-length distribution, synergy rotational energy barrier, cohesive energy density (CED) and fraction free volume (FFV). The results indicated that the bond-length distribution of the MTHPA and NA was the same except for C–C bonds. Compared with the DGEBA/MTHPA system, the DGEBA/NA system had a higher synergy rotational energy barrier and CED, and lower FFV. It can be seen that the slight change of curing agent structure has a significant effect on the synergy rotational energy barrier, CED and FFV, thus affecting the Tg and modulus of the system.

Halogen bonding as a supramolecular dynamics catalyst

Dynamic processes have many implications in functional molecules, including catalysts, enzymes, host-guest complexes, and molecular machines. Here, we demonstrate via deuterium NMR relaxation experiments how halogen bonding directly impacts the dynamics in solid 2,3,5,6-tetramethylpyrazine cocrystals, catalyzing the methyl group rotation. On average, we observe a reduction of 56% in the rotational activation energy of the methyl groups in the halogen bonded cocrystals, contrasting the reduction of 36% in the hydrogen bonded cocrystals, with respect to pure 2,3,5,6-tetramethylpyrazine. Density functional theory calculations attribute this superior catalytic ability of the halogen bond to the simultaneous destabilization of the staggered conformation and stabilization of the gauche conformation, overall reducing the rotational energy barrier. Furthermore, the calculations suggest that the catalytic ability of the halogen bond may be tuneable, with stronger halogen bond donors acting as superior dynamics catalysts. Thus, halogen bonding may play a role in both assembly and promoting dynamical processes.

Energetics, kinetics and dynamics of self-interstitial clusters in bcc tungsten

ABSTRACTThe configuration, slipping and rotation of self-interstitial atoms cluster along <111> crystal orientation with different sizes in a tungsten are investigated systematically with molecular dynamics. It is found that (I) the SIA clusters with high symmetry are always favoured; (II) the SIA clusters can undergo one-dimensional fast migration along <111> direction, and their migration barriers are no more than 0.07 eV, which is expected due to the strong interaction in the SIA clusters; (III) the rotation energy barriers of the SIA clusters are rather high and they are basically positively correlated with the size of the cluster. For example, the reorientation barrier is 0.66 eV for 1 SIA, 1.2–1.8 eV for SIAn (2 ≤ n ≤ 5) clusters and over 2.7 eV for SIAn (6 ≤ n ≤ 7) clusters. Compared with slipping of SIA clusters, is an infrequent event, especially for larger SIAs cluster, the vast majority SIAs cluster would have already recombination with vacancies or annihilates at surface and grain boundary through slipping before rotation, which explained that there are very low density of SIAs cluster found in the experiment.

Structure, stability and conversions of tautomers and rotamers of azulene-based uracil analogue

In this work, ab initio CBS-QB3 procedures were used to study structure and stability of possible tautomers and rotamers of azulene-based uracil analogue (AZU) in the gas phase and in water. Similar to uracil (U), the di–keto form of the new system is the most stable structure relative to keto–enol and di-enol forms. The calculated barrier heights for proton transfer reactions are in the range of 26.1–41.9 kcal/mol, while the OH rotational energy barriers are less than 12 kcal/mol. The rotomerization process in azulene-based system is more difficult than in uracil. However, tautomerization illustrates the opposite trend. Zwitterion tautomers of AZU were also investigated. Calculations in water cause some reordering of the relative stability of azulene-based tautomers and affect the energy barriers of tautomerization.

Rotational dynamics of the organic bridging linkers in metal–organic frameworks and their substituent effects on the rotational energy barrier

Organic bridging linkers or ligands play an important role in gas and fuel storage, CO2 capture, and controlling the radical polymerization reactions in metal–organic frameworks (MOFs) nanochannels. The rotation of the linkers causes the expansion of the pore size and pore volume in MOFs. To understand the rotational behavior of organic linkers in MOFs and the substituent effects of the linkers, we investigated the equilibrium structure, stability, potential energy curves (PECs), and rotational energy barriers of the organic bridging linkers of a series of MOF model systems imposing three constrained imaginary planes. Both the dispersion-uncorrected and dispersion-corrected density functional theory (DFT and DFT-D i.e. B3LYP and B3LYP-D3) methods with the correlation consistent double-ζ quality basis sets have been applied to study the model MOF systems [Cu4(X)(Y)6(NH3)4] (where X = organic bridging linker, and Y = HCO2). The present study found that the structural parameters and rotational energy barrier of the model MOF containing 1,4-benzendicarboxylate (BDC) linker are in accord with previous experiments. This study reveals that rotational barriers significantly differ depending on the substituents of organic linkers, and the linker dynamical rotation provides information about the framework flexibility with various potential applications in porous materials science. Changing the linkers in the MOFs could be helpful for designing various new kinds of flexible MOFs which will have many important applications in gas storage and separation, catalysis, polymerization, sensing, etc.

Electrical and mechanical properties of polyimide films treated by plasma formed in water and isopropanol

Fluorinated aromatic polyimide films were treated by pulse electrical discharges formed in water or isopropanol. The relative permittivity, measured in large domains of frequencies and temperatures by broadband dielectric spectroscopy, slightly decreased after plasma discharge in both types of liquids. The dipolar relaxation calculated by Arrhenius equation showed that the liquid plasma treatment decreases the rotational potential energy barrier for non-cooperative motions of dipoles, as a consequence of an increased free volume of plasma exposed films. Higher values of hardness, Young's modulus, and an improved elongation were also measured for the plasma treated samples, indicating molecular rearrangements that occur after plasma treatment.

Bond Rotations and Heteroatom Effects in Donor-Acceptor-Donor Molecules: Implications for Thermally Activated Delayed Fluorescence and Room Temperature Phosphorescence.

The synthesis of 1-methylphenoxazine via CO2-directed lithiation chemistry is reported. This electron donor was coupled with 2,8-dibromodibenzothiophene- S, S-dioxide with Buchwald-Hartwig chemistry to give a new donor-acceptor-donor charge-transfer fluorescent molecule 1b. X-ray crystal structures and calculations show that the phenoxazinyl groups are coplanar and equatorial (eq) to the acceptor plane in nonmethylated 1a but are pyramidal and axial (ax) in 1b. The bond rotation energy barriers between donor and acceptor groups for 1a and 1b are only 0.13 and 0.19 eV, respectively, from hybrid-DFT computations at the CAM-B3LYP/6-31G(d) level. Many possible conformers are present in solutions and in zeonex. In zeonex, the methyl groups in 1b shift the emission band 0.13 eV higher in energy compared to 1a. Excited state eq-eq and ax-ax geometries were identified with DFT calculations with charge transfer (CT) emission assigned as 1CT(eq) and 1CT(ax) dominating. The lower energy 1CT(eq) contributes to thermally activated delayed fluorescence, whereas the higher energy 1CT(ax) does not. Phenothiazine analogues 2a and 2b also have major fluorescence emissions assigned as 1CT(eq) and 1CT(ax), respectively. 2a and 2b have substantial room temperature phosphorescence (RTP), whereas 1a and 1b do not, highlighting the importance of the sulfur atom in 2a and 2b to obtain RTP emission.

H2S dimer forms hydrogen bonds

Hydrogen bonds are one reason for water’s unique boiling and freezing behavior and other properties. But scientists have debated for decades whether dimers of hydrogen sulfide, water’s smelly triatomic cousin, also sport hydrogen bonds. Now, Elangannan Arunan of the Indian Institute of Science and colleagues report they have found experimental evidence that hydrogen bonds do indeed hold H2S dimers together (Angew. Chem. Int. Ed. 2018, DOI: 10.1002/anie.201808162). Water’s four hydrogen bonds (via two H atoms and two lone electron pairs) are evident in ice’s tetrahedral structure, but in solid H2S, each molecule is surrounded instead by a shell of 12 others. That suggested to some that H2S does not hydrogen bond. Using microwave spectroscopy, Arunan’s group detected rotational energy barriers in the dimer below about 60 °C that they say indicate the presence of hydrogen bonds. Computational chemists have reached the same conclusion. Arunan explains that at higher temperatures, those

Atomistic Origins of Temperature-Dependent Shear Strength in 2D Materials

We present a model that predicts the macroscale temperature-dependent interfacial shear strength of 2D materials like MoS2 based on atomistic mechanisms and energetic barriers to sliding. Atomistic simulations were used to systematically determine the lamellar size-dependent rotation and translation energy barriers, that were used to accurately predict a broad range of experimental data. This framework provides insight about the origins of characteristic shear strengths of 2D materials.

Electronic Effect on the Molecular Motion of Aromatic Amides: Combined Studies Using VT-NMR and Quantum Calculations.

Rotational barrier energy studies to date have focused on the amide bond of aromatic compounds from a kinetic perspective using quantum calculations and nuclear magnetic resonance (NMR). These studies provide valuable information, not only regarding the basic conformational properties of amide bonds but also the molecular gear system, which has recently gained interest. Thus, we investigate the precise motion of the amide bonds of two aromatic compounds using an experimental rotational barrier energy estimation by NMR experiments and a theoretical evaluation of the density functional theory calculation. The theoretical potential energy surface scan method combined with the quadratic synchronous transit 3 method and consideration of additional functional group rotation with optimization and frequency calculations support the results of the variable temperature 1H NMR, with deviations of less than 1 kcal/mol. This detailed experimental and theoretical research strongly supports molecular gear motion in the aromatic amide system, and the difference in kinetic energy indicates that the electronic effect from the aromatic structure has a key role in conformational movements at different temperatures. Our study provides an enhanced basis for future amide structural dynamics research.

Intramolecular Torque Study of a Molecular Rotation Stimulated by Electron Injection and Extraction.

Rotation-inducing torque based on interatomic forces is a true indicator of internal molecular rotations. We use the induced intramolecular torque to study the underlying rotational mechanism stimulated by an electron injection or extraction for the rotor molecule 9-(2,4,7-trimethyl-2,3-dihydro-1 H-inden-1-ylidene)-9 H-fluorene, which consists of a "rotator" fragment and a "stator" fragment. The results show that the charged molecule in a quartet spin state can rotate internally, while that in the doublet state cannot. The torque on the rotator in the quartet state always maintains unidirectional rotation. In addition, the attachment/extraction of an electron leads to the reduction of the rotational energy barrier by about 18 kcal/mol, facilitating a more favorable molecular rotation than in the neutral singlet state. Our finding provides a molecular-level understanding of various transformation pathways for experimental designs and further demonstrates the effectiveness of the torque approach.

DFT study of [BH4]− rotation in pressure-driven phase transition of MBH4

The pressure-induced phase transitions of MBH4 (M = Na, K) have been studied using first-principles calculations. The optimized results indicate that their high-pressure phases are space group P42/nmc, which have the same symmetry as the C-substructure of their low-pressure phases. The result of [BH4]− rotational barrier shows that rotational barrier will increase with the increase of external pressure. The rotational energy barrier of KBH4 is larger than that of NaBH4 at same pressure due to larger radius of potassium atom, which can explain why potassium borohydride has a lower phase transition pressure. The theoretical rotation barrier obtained with Tkatchenko-Scheffler correction is higher and is more sensitive to change under different pressures than that without vdW correction.

First-Principles Calculations of the Rotational Motion and Hydrogen Bond Capability of Large Organic Cations in Hybrid Perovskites

The organic cation dynamics in organic–inorganic hybrid perovskites affect the unique physical properties of these materials. To date, the rotational dynamics of methylammonium (CH3NH3+) and formamidinium (CH(NH2)2+) have been studied both experimentally and from first-principles calculations. Recently, a novel hybrid perovskite with large organic cation guanidinium (C(NH2)3+, GA), which exhibited extraordinarily long carrier lifetimes, was reported. In order to analyze physical properties of GA, we examined the detailed rotational potential energy surfaces and rotational energy barriers of GA in cubic-phase GASnI3 and alternative perovskites using first-principles calculations. The analysis revealed that the principal rotations of GA involve six hydrogen bonds between the organic cation and the inorganic framework in the crystals. Our results suggest that GA can effectively passivate under-coordinated iodine ions using its high hydrogen bond capability, which is consistent with the experimental speculati...

Fluctuating Carbonaceous Networks with a Persistent Molecular Shape: A Saddle‐Shaped Geodesic Framework of 1,3,5‐Trisubstituted Benzene (Phenine)

AbstractA saddle‐shaped macromolecule has been synthesized. The molecule was designed as a geodesic saddle with 1,3,5‐trisubstituted benzene (named phenine) as the fundamental unit. The phenines were woven into a polygonal framework that was composed of 168 sp2‐hybridized carbon atoms. The saddle‐shaped structure with unique symmetry showed atypical conformational changes. The biaryl linkages in this molecule had a small energy barrier for rotation, and these structural fluctuations resulted in seven 1H NMR resonances representing 84 aromatic hydrogen atoms. Nevertheless, the overall saddle shape of the molecule was persistent, and the “up” and “down” orientations of phenine moieties circulated to give average 1H resonances. The structural characteristics of this molecule, including the anomalous entropy‐driven dimerization, may deepen our understanding of defect‐rich graphitic sheets.

Fluctuating Carbonaceous Networks with a Persistent Molecular Shape: A Saddle-Shaped Geodesic Framework of 1,3,5-Trisubstituted Benzene (Phenine).

A saddle-shaped macromolecule has been synthesized. The molecule was designed as a geodesic saddle with 1,3,5-trisubstituted benzene (named phenine) as the fundamental unit. The phenines were woven into a polygonal framework that was composed of 168 sp2 -hybridized carbon atoms. The saddle-shaped structure with unique symmetry showed atypical conformational changes. The biaryl linkages in this molecule had a small energy barrier for rotation, and these structural fluctuations resulted in seven 1 H NMR resonances representing 84 aromatic hydrogen atoms. Nevertheless, the overall saddle shape of the molecule was persistent, and the "up" and "down" orientations of phenine moieties circulated to give average 1 H resonances. The structural characteristics of this molecule, including the anomalous entropy-driven dimerization, may deepen our understanding of defect-rich graphitic sheets.

Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields.

An approach is presented to directly simulate the dynamics of methyl groups in protein side-chains, as accessible via NMR spin relaxation measurements, by all-atom MD simulations. The method, which does not rely on NMR information or any system-specific adjustable parameters, is based on calculating the time-correlation functions (TCFs) of the C-H bonds in methyl groups and explicitly takes the truncation of the TCFs due to overall tumbling of the molecule into account. Using ubiquitin as a model protein, we show (i) that an accurate description of the methyl dynamics requires reparametrization of the potential energy barriers of methyl group rotation in the AMBER ff99SB*-ILDN force field (and related parameter sets), which was done with CCSD(T) coupled cluster calculations of isolated dipeptides as reference, and (ii) that the TIP4P/2005 solvation model yields overall tumbling correlation times that are in close agreement with experimental data. The methyl axis squared order parameters Saxis2 and associated correlation times τf, obtained within the Lipari-Szabo formalism, are in good agreement with the values derived from NMR deuterium relaxation experiments. Importantly, the relaxation rates and spectral densities derived from MD and NMR agree as well, enabling a direct comparison without assumptions inherent to simplified motional models.

Thermally Induced Transformation of Nonhexagonal Carbon Rings in Graphene-like Nanoribbons

Exploring the structural transformation of nonhexagonal rings is of fundamental importance for understanding the thermal stability of nonhexagonal rings and revealing the structure–property relationships. Here, we report on the thermally induced transformation from the fused tetragon-hexagon (4–6) carbon rings to a pair of pentagon (5–5) rings in the graphene-like nanoribbons periodically embedded with tetragon and octagon (4–8–4) carbon rings. A distinct contrast among tetragon, pentagon, hexagon, and octagon carbon rings is provided by noncontact atomic force microscopy with atomic resolution. The thermally activated bond rotation with the dissociation of the shared carbon dimer between the 4–6 carbon rings is the key step for the 4–6 to 5–5 transformation. The energy barrier of the bond rotation, which results in the formation of an irregular octagon ring in the transition state, is calculated to be 1.13 eV. The 5–5 defects markedly change the electronic local density of states of the graphene-like nan...

Tetrasubstituted bisadamantylidenes—Highly twisted alkenes

AbstractA number of 1,3,1′,3′‐tetrasubstituted bisadamantylidenes are examined with 4 different density functional methods (BP86‐D3, ωB97X‐D, B3LYP, and B3LYP‐D3) and the 6‐311G(d) basis set. With increasing steric bulk, these substituted bisadamantylidenes become ever more twisted about the central carbon‐carbon double bond. This manifests in significantly reduced singlet‐triplet gaps from that of typical alkenes, with the tetra‐t‐butylbisadamantylidene 17, twisted to almost 90°, having a gap of only 2.2 kcal mol−1. While its large strain energy may preclude the synthesis of 17, other less‐strained tetrasubstituted analogues are more feasible synthetic targets and still possess small singlet‐triplet gaps, which should be testable by variable temperature NMR and EPR spectroscopy. The twisted alkenes also result in a low rotational energy barrier, and 4 examples with a low barrier to cis‐trans isomerization are presented. These too should be testable by experiment.

High-Pressure Limit Rate Rules for α-H Isomerization of Hydroperoxyalkylperoxy Radicals.

Hydroperoxyalkylperoxy (OOQOOH) radical isomerization is an important low-temperature chain branching reaction within the mechanism of hydrocarbon oxidation. This isomerization may proceed via the migration of the α-hydrogen to the hydroperoxide group. In this work, a combination of high level composite methods-CBS-QB3, G3, and G4-is used to determine the high-pressure-limit rate parameters for the title reaction. Rate rules for H-migration reactions proceeding through 5-, 6-, 7-, and 8-membered ring transitions states are determined. Migrations from primary, secondary and tertiary carbon sites to the peroxy group are considered. Chirality is also investigated by considering two diastereomers for reactants and transition states with two chiral centers. This is important since chirality may influence the energy barrier of the reaction as well as the rotational energy barriers of hindered rotors in chemical species and transition states. The effect of chirality and hydrogen bonding interactions in the investigated energies and rate constants is studied. The results show that while the energy difference between two diastereomers ranges from 0.1-3.2 kcal/mol, chirality hardly affects the kinetics, except at low temperatures (atmospheric conditions) or when two chiral centers are present in the reactant. Regarding the effect of the H-migration ring size, it is found that in most cases, the 1,5 and 1,6 H-migration reactions have similar rates at low temperatures (below ∼830 K) since the 1,6 H-migration proceeds via a cyclohexane-like transition state similar to that of the 1,5 H-migration.

NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins

Molecular dynamics (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation experiments have become increasingly powerful to study protein dynamics at atomic resolution due to steady improvements in physical models and computation power. Good agreement between generalized Lipari-Szabo (S2NH) order parameters derived from experiment and simulation is now observed for the backbone dynamics of a number of proteins. Unfortunately, the agreement for side chains, as e.g. probed by S2CH3 for methyl-containing side chains, is much poorer. In this work we discuss several issues with methyl side chains that need to be addressed to close the gap between NMR and MD. Accounting for protein tumbling is one very important factor to obtain a good agreement. In our hands, the application of improved water force fields with an appropriate way of including anisotropic overall protein tumbling improves the prediction of experimentally measured dynamic observables by MD simulations. We demonstrate these aspects for T4 lysozyme as a representative example. Our results guide the way for extracting from the NMR relaxation data the most accurate parameters that describe protein side chain dynamics and report on conformational entropy. Additionally, we reparametrized side chain dihedral angle energy barriers for methyl rotation in the Amber99SB∗-ILDN force field. We demonstrate that this leads to a much more realistic dynamics of methyl groups and is another important feature to close the gap between spectral densities from NMR relaxation and MD simulation.