Rotational Energy Profiles Research Articles

Protostellar Disk Formation Regimes: Angular Momentum Conservation versus Magnetic Braking

Protostellar disks around young protostars exhibit diverse properties, with their radii ranging from less than ten to several hundred astronomical units. To investigate the mechanisms shaping this disk radius distribution, we compiled a sample of 27 Class 0 and I single protostars with resolved disks and dynamically determined protostellar masses from the literature. Additionally, we derived the radial profile of the rotational-to-gravitational-energy ratio in dense cores from the observed specific angular momentum profiles in the literature. Using these observed protostellar masses and rotational energy profile, we computed theoretical disk radii from the hydrodynamic and nonideal magnetohydrodynamic (MHD) models in Y.-N. Lee et al. and generated synthetic samples to compare with the observations. In our theoretical model, the disk radii are determined by hydrodynamics when the central protostar+disk mass is low. After the protostars and disks grow and exceed certain masses, the disk radii become regulated by magnetic braking and nonideal MHD effects. The synthetic disk radius distribution from this model matches well with the observations. This result suggests that hydrodynamics and nonideal MHD can be dominant in different mass regimes (or evolutionary stages), depending on the rotational energy and protostar+disk mass. This model naturally explains the rarity of large (>100 au) disks and the presence of very small (<10 au) disks. It also predicts that the majority of protostellar disks have radii of a few tens of astronomical units, as observed.

How External Electric Field Modulates the Rotation Energy Profiles of Dipolar Dopants Inside C70: A Theoretical Interpretation with Electrostatic Shielding Effect Incorporated

AbstractEndohedral fullerenes, which can switch between distinct states with different geometries when triggered by external electric fields (EFs), can be used as logical devices at the molecular scale. However, the movement of electrons around fullerenes exerts an electrostatic shielding effect which alleviates the Coulomb force experienced by endohedral dopants, and thus must be properly evaluated for better elucidating the switching mechanism. Here we introduced new components to the energy decomposition scheme based on the block‐localized wavefunction method (i. e., BLW‐ED), to incorporate the shielding effect explicitly. We analyzed the external EF‐driven rotation of enclosed dipolar molecules inside C70 and evaluated the magnitudes of shielding in terms of the gradients of electrostatic potential and energy. In the absence of external EF, intrinsic rotational barriers are dominated by the Pauli exchange repulsion between enclosed molecules and C70. When an external EF was applied, computations showed that only about 18% of external EFs can penetrate into the cage and interact with dipolar molecules. Thus, the shielding effect dramatically reduces the energy contribution originated from the interaction between endohedral dopants and external EFs. BLW‐ED analyses were further performed to inspect the effect of external EFs on the potential energy surfaces associated with the molecular rotation processes. Indeed, the interaction between penetrated EFs and enclosed molecules can still govern the orientational preferences of dipolar molecules and lower the rotational barrier for some dipolar molecules. But for other molecules, both the intrinsic electrostatic interaction and the Pauli repulsion respond to external EFs more sensitively and rule the changes of barrier heights and orientational preferences.

Adsorption and rotational barrier for a single azobenzene molecule on Au(111) surface* *Project supported by the National Natural Science Foundation of China (Grant Nos. 21961142021, 11774395, 91753136, and 11727902), the Beijing Natural Science Foundation, China (Grant No. 4181003), the Strategic Priority Research Program (B) of the Chinese Academy of Sciences (Grant Nos. XDB30201000 and XDB28000000).

The orientation switching of a single azobenzene molecule on Au(111) surface excited by tunneling electrons and/or photons has been demonstrated in recent experiments. Here we investigate the rotation behavior of this molecular rotor by first-principles density functional theory (DFT) calculation. The anchor phenyl ring prefers adsorption on top of the fcc hollow site, simulated by a benzene molecule on close packed atomic surface. The adsorption energy for an azobenzene molecule on Au(111) surface is calculated to be about 1.76 eV. The rotational energy profile has been mapped with one of the phenyl rings pivots around the fcc hollow site, illustrating a potential barrier about 50 meV. The results are consistent with experimental observations and valuable for exploring a broad spectrum of molecules on this noble metal surface.

Introduction of polar or nonpolar groups at the hydroquinone units can lead to the destruction of the columnar structure of Pillar[5]arenes

Pillar[5]arenes, a type of novel macrocycles containing di-substituted hydroquinone units linked by methylene bridges in para-positions, have attracted extensive attention in supramolecular chemistry as interesting candidates to be used in the preparation of host-guest complexes. Functionalization by means of rim substitution and sustaining an ordered substituent arrangement on both sides of the rim is important for the development of new pillararene-based materials. In order to achieve this, the rim inversion process of rotating the hydroquinone units through the pillar[5]arenes has to be controlled. In this context we have studied the effect of different types of hydroquinone substituents on the rotational energy profile using density functional theory combined with the hybrid M06-2X functional. The influence of polar (CH2F, CH2Cl, CH2OH, CH2SH, CH2NH2) and nonpolar alkyl (CH3, CH2CH3, CH2CH2CH3, CH(CH3)2 and CH2CH2CH2CH3) substituents on the on the energy barriers of the rotation mechanism, and different local minima was investigated. The stabilization of the intermediate structures by non-covalent van der Waals and interactions and also by hydrogen bonds constitute a major factor affecting barrier heights. In case of polar substituents, the largest barriers were found for CH2OH and CH3 substitutions and the lowest ones for CH2SH and CH2NH2. For the alkyl series, the barrier decreased significantly up to propyl due to increasing stabilizing dispersion interactions while it increased again for n-butyl since the chain did not fit in well the cavity to rotate through.

Symmetry Influence on the Rotation of Molecules in Crystals

It was shown that rotational mobility of molecules in crystals is affected by the symmetry of their surroundings. A hypothesis was proposed for the discovered correlation. Three cases are possible for the location of the molecules with respect to the crystallographic symmetry elements: I – the location in a general position; II – the location in special positions without symmetry disordering; III – the location in special positions with symmetry disordering. According to the experimental data, the rotation barrier heights at the location of the molecules in cases I and III are lower than in case II. This fact is explained by the amplitude and phase shifts of the rotational energy profiles of two parts of the molecule in case I and by increasing the number of minima on the rotation barrier profile at disordering the molecules by symmetry in case III. The way is proposed for lowering the rotational barrier of molecules in crystals.

Synthesis and conformational analysis of new arylated-diphenylurea derivatives related to sorafenib drug via Suzuki-Miyaura cross-coupling reaction

Sorafenib, is a relatively new cytostatic drug approved for the treatment of renal cell and hepatocellular carcinoma. The development of new sorafenib analogues offers the possibility of generating structures of increased potency. To this end, a series of arylated-diphenylurea analogues 17–31 were synthesized via Suzuki-Miyaura coupling reaction, related to sorafenib by treatment of three diarylureas 2–4 having 3-bromo, 4-chloro and 2-iodo groups with various arylboronic acids. Conformational analysis of the new arylated urea analogues has been investigated using MOPAC 2016 of semi empirical PM7 Hamiltonian computational method. Our results showed that all compounds preferred the trans-trans conformations. Compound 17 has been selected to calculate the torsional energy profiles for rotation around the urea bonds and found to be existed predominantly in the trans-trans conformation with only very minimal fluctuation in conformation.

Computational Exploration of Reactivity of 6-Methyluracil/Imidazole-2-Carbaldehyde Oxime Conjugate

Molecular docking and ab intio quantum mechanical calculations were used to assess the nucleophilic reactivity of conjugates of 6-methyluracil and imidazole-2-carbaldehyde oxime. Minimum energy profiles for oxime group rotation and proton transfer were calculated for isolated conjugate. Results indicated that proton transfer and activation are possible. Results suggests that the compound can be active itself, reacting with esters in a way, similar to enzymatic histidine-containing catalytic triad. Thus, this compound is of potential interest for direct scavenging organophosphorus inhibitors of cholinesterases and/or as co-reagent in cholinesterase-based pseudocatalytic bioscavengers.

Nascent rotational distribution for LiH(v = 0-3,J) states from collisions with H2(E = 4300 and 4800cm-1)

Rotationally state selective excitation of H2(v=1, J=1 or 3) was achieved by stimulated Raman pumping. The full state-resolved distribution of scattered LiH(v=0–3, J=0~13)molecules from collisions with excited H2(E=4300 and 4800cm−1) is reported. Nascent rotational and translational energy profiles for scattered LiH(v=0~3) molecules with J=0~13 were measured using high-resolution transient laser induced fluorescence(LIF). The product translational energy for individual J-states increases by 120% for a 13% increase in donor energy. The scattered LiH(v=0, J=0~13) molecules have a biexponential rotational distribution. Fitting the data with a two-component exponential model yields a low-energy distribution and a high-energy distribution. The rotational distribution is sensitive to donor energy. Rotational distributions of scatted LiH(v=1–3) molecules were also measured. The distribution yielded rotational temperatures at 690K for LiH/H2(E=4300cm−1) and 730K for LiH/H2(E=4800cm−1), respectively. The rate constants for appearance LiH(v=0–3,J) were determined.

Development of a two-dimensional binning model for N2–N relaxation in hypersonic shock conditions

A high fidelity internal energy relaxation model for N2–N suitable for use in direct simulation Monte Carlo (DSMC) modeling of chemically reacting flows is proposed. A novel two-dimensional binning approach with variable bin energy resolutions in the rotational and vibrational modes is developed for treating the internal mode of N2. Both bin-to-bin and state-specific relaxation cross sections are obtained using the molecular dynamics/quasi-classical trajectory (MD/QCT) method with two potential energy surfaces as well as the state-specific database of Jaffe et al. The MD/QCT simulations of inelastic energy exchange between N2 and N show that there is a strong forward-preferential scattering behavior at high collision velocities. The 99 bin model is used in homogeneous DSMC relaxation simulations and is found to be able to recover the state-specific master equation results of Panesi et al. when the Jaffe state-specific cross sections are used. Rotational relaxation energy profiles and relaxation times obtained using the ReaxFF and Jaffe potential energy surfaces (PESs) are in general agreement but there are larger differences between the vibrational relaxation times. These differences become smaller as the translational temperature increases because the difference in the PES energy barrier becomes less important.

α-Agostic Interactions and Growing Chain Orientation for Olefin Polymerization Catalysts

Growing chain orientational preference is one of the key factors determining the stereoselectivity of olefin polymerization and related reactions such as carboalumination; α-agostic interactions are an important component of this preference. Using insertion of ethene in the M–CH3 bond as a model, the intrinsic orientational preference was evaluated for a number of important catalyst types through determination of the energy profile for methyl group rotation at the insertion TS. Ti and Zr metallocenes show a pronounced preference (Ti, 10 kcal/mol; Zr, ∼6 kcal/mol) for a classical α-agostic arrangement with a single short M···CH contact and an elongated C–H bond; on CH3 rotation the agostic elongation mostly disappears. In contrast, for all non-metallocene systems studied the orientational preference is much smaller or even opposite that of metallocenes. Moreover, on CH3 rotation the agostic C–H bond elongation gets spread out over two C–H bonds rather than disappearing. These results point to greater chain...

Computational study of the rotational pathways of the amino group in 2-chloroaniline, azines and formamide: One or two rotational barriers?

Rotation of the amino group in five different molecular systems, 2-aminopyridine, 2-aminopyrimidine, 2-chloroaniline, N-methylamino-1,3,5-triazine, and formamide, has been studied at B3LYP/6-311++G(2d,2p), MP2/6-311++G(2d,2p), and CCSD(T)/6-311++G(2d,2p)//B3LYP/6-311++G(2d,2p) levels of density functional, MP2, and coupled cluster theories. To this end, detailed rotation energy profiles for the above amino systems were obtained in two different ways: (1) by computing the energy-values as a function of only one torsion angle; and (2) by taking into account that the pyramidal nature of the NH2 group changes as rotation progresses so that energy profiles should be defined by two torsion angles. In the first case, saw-toothed energy profiles exhibiting two rotational barriers were always obtained. Conversely, by using two torsion angles as reaction coordinates smooth pathways were found where a rotation cycle can be completed passing only through the lowest energy barrier. Implications of these conflicting pathways are discussed.

Theoretical analysis of the rotational barrier in ethane: cause and consequences

On the basis of energy decomposition analysis, the rotational energy profile of ethane is explained by using two models: rigid rotation with instantaneous geometry relaxations of the eclipsed and staggered conformations and relaxed rotation with continuous geometry relaxations. Both models can be applied to the real system. A distinction between the cause of an initial energy rise and energetic consequences of structural changes accompanying the rotation is made. It is concluded that the increased Pauli repulsion is the main cause for the initial energy rise and geometry changes. However, after the structural changes take place, the Pauli repulsion is not responsible for the higher energy of the eclipsed state. It then originates from energetic consequences of geometry changes, which include decrease in electrostatic and orbital stabilization energies, mainly due to the C–C bond lengthening, and an energy rise due to methyl groups bending.

Full State-Resolved Energy Gain Profiles of CO2 from Collisions with Highly Vibrationally Excited Molecules. II. Energy-Dependent Pyrazine (E = 32 700 and 37 900 cm–1) Relaxation

The full state-resolved distribution of scattered CO2 (00(0)0) molecules from collisions with highly vibrationally excited pyrazine (E = 32,700 cm(-1)) is reported and compared to previous studies on pyrazine (E = 37,900 cm(-1)) to investigate how internal energy content impacts the dynamics for collisional quenching of high energy molecules [J. Phys. Chem. A 2010, 113, 1569]. Nascent rotational and translational energy profiles for scattered CO2 (00(0)0) molecules with J = 2-72 were measured using high-resolution transient infrared absorption and combined with earlier results for the J = 56-78 states [J. Chem. Phys. 1999, 111, 7373]. The product translational energy for individual J-states increases by 50% for a 16% increase in donor vibrational energy. The nascent rotational distribution for scattered CO2 is biexponential, comprising 77% nearly elastic collisions and 23% inelastic collisions. The spread of the rotational distribution is sensitive to donor energy, but the branching ratio for elastic and inelastic collisions is the same for both donor energies. The measured collision rates are close to the Lennard-Jones values and are only weakly dependent on changes in donor energy. The nascent energy gain distribution function P(ΔE) depends strongly on the energy, and this energy dependence is stronger than the linear dependence seen in multicollision energy transfer studies for pyrazine(E) + CO2 collisions.

Side Chain Flexibility in Perfluorosulfonic Acid Ionomers: An ab Initio Study

Side chain flexibility in perfluorosulfonic acid (PFSA) ionomers has been explored through ab initio electronic structure calculations. Three different PFSA side chain fragments were considered with a CF3CFCF3 backbone representation: Nafion (-OCF2CF(CF3)O(CF2)2SO3H), Aquivion or the short side chain (SSC) (-O(CF2)2SO3H), and the 3M PFSA (-O(CF2)4SO3H). Rotational potential energy surfaces for each bond along the length of the side chains were obtained using density functional theory with the B3LYP and the dispersion-corrected B97D functionals with and without the inclusion of a solvation model. Solvent effects were found to have minimal effect on bond rotations close to the tetrafluoroethylene backbone but had greater impact near the terminal sulfonic acid group. The carbon-sulfur bond was found to be the most flexible portion of the side chain in each of the fragments which was further enhanced with the inclusion of the solvent. Complete rotation about either the O-CF2 or CF-O bond in the Nafion side chain resulted in fairly high energetic barriers, but significant portions of these rotational surfaces had energetic penalties less than 1.5 kcal/mol indicating substantial conformational freedom. Fully extended and folded conformations of the Nafion side chain exhibit considerable contraction in side chain end-to-end distance and were observed to be nearly isoenergetic using B3LYP, but the folded structures with the ether oxygen atoms in gauche conformations were ~1.5 kcal/mol lower in energy using B97D. Below the second ether linkage of the Nafion side chain, the rotational potential energy profiles were identical to that determined for the SSC side chain. The 3M side chain was generally found to be the most rigid with barriers for complete rotation about the central carbon-carbon bonds of approximately 7 kcal/mol. These results indicate that minor differences in side chain length and chemistry may have a pronounced effect on the rotational potential energy surfaces, particularly those involving rotation about different carbon-carbon bonds with distinctly different character.

A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol.

An extension 53A6OXY+D to the GROMOS 53A6OXY force field is reported that includes an accurate description of the vicinal diether function. The calibration is based on the model compound 1,2-dimethoxyethane (DXE) and involves a fitting of the relevant torsional-energy parameters against quantum-mechanical (QM) rotational energy profiles for the OCCO and CCOC dihedral angles in vacuum, followed by a validation against experimental conformer populations in the pure liquid and in aqueous mixtures. A systematic comparison between the 53A6, 56A6CARBO, 53A6OXY, and 53A6OXY+D parameter sets is also performed in terms of these properties, as well as in terms of the thermodynamic properties of dimethylether (DME), diethylether (DEE), 1-methoxypropane (MPH), and DXE. Finally, the new parameter set is further validated in the context of polyethers, namely polyethyleneoxide (PEO) and polyethylenegycol (PEG). The 53A6OXY+D set reproduces well the QM rotational profiles of DXE in vacuum (by calibration), the conformational populations of DXE in the pure liquid and in aqueous mixtures, and the experimental thermodynamic pure-liquid and (polar and nonpolar) solvation properties of DME, DEE, MPH, and DXE. In particular, it accounts appropriately for the gauche-effect, both in its solvent-independent stereoelectronic component and in its solvent-dependent dielectric-screening component. In contrast to 53A6OXY, it also suggests a higher affinity of DXE for water compared to octanol, in agreement with the experimental partition coefficient. In the context of aqueous polyethers, the calculated size (Flory) exponent (νg = 0.61) for the molecular-weight dependence of the radius of gyration and persistence length (Lp = 0.39 ± 0.04 nm) agree well with estimates based on experiment or previous simulations with other force fields. The simulations also suggest a picture of aqueous polyethers as "water sponges", in which the diether function "adsorbs" an essentially constant number of water molecules corresponding to first-shell hydrogen-bonded saturation of its oxygen atoms, with a tendency to include other ether oxygen atoms along the chain in the second shell, resulting in "water bridging".

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.

Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases.

The methane and toluene monooxygenase hydroxylases (MMOH and TMOH, respectively) have almost identical active sites, yet the physical and chemical properties of their oxygenated intermediates, designated P*, H(peroxo), Q, and Q* in MMOH and ToMOH(peroxo) in a subclass of TMOH, ToMOH, are substantially different. We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss which changes could give rise to the different behavior of H(peroxo) and Q. In particular, analysis of multiple crystal structures reveals that T213 in MMOH and the analogous T201 in TMOH, located in the immediate vicinity of the active site, have different rotatory configurations. We study the rotational energy profiles of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and put forward a hypothesis according to which T213 and T201 play an important role in the formation of different types of peroxodiiron(III) species in MMOH and ToMOH. The hypothesis is indirectly supported by the QM/MM calculations of the peroxodiiron(III) models of ToMOH and the theoretically computed Mössbauer spectra. It also helps explain the formation of two distinct peroxodiiron(III) species in the T201S mutant of ToMOH. Additionally, a role for the ToMOD regulatory protein, which is essential for intermediate formation and protein functioning in the ToMO system, is advanced. We find that the low quadrupole splitting parameter in the Mössbauer spectrum observed for a ToMOH(peroxo) intermediate can be explained by protonation of the peroxo moiety, possibly stabilized by the T201 residue. Finally, similarities between the oxygen activation mechanisms of the monooxygenases and cytochrome P450 are discussed.

Elucidating steric effects on enantioselective epoxidation catalyzed by (salen)Mn in metal-organic frameworks

The steric effects of a metal-organic framework (MOF) on the enantioselectivity of a (salen)Mn were studied using classical atomistic modeling. Rotational energy profiles for the approach of 2,2-dimethyl-2H-chromene to the active site of (salen)Mn were mapped for the homogeneous catalyst and the catalyst immobilized as a linker in a MOF. The model corroborated that the Re enantioface is favored by the homogeneous catalyst. It was shown that the predicted enantioselectivity when chromene approaches the more accessible (salen)Mn in the MOF is highly sensitive to the distance between the (salen)Mn linkers of the interpenetrated frameworks. Calculated rotational energy profiles for a hypothetical non-interpenetrated MOF revealed that this MOF catalyst should exhibit enantioselectivity intermediate to the interpenetrated MOF and the homogeneous catalyst. Finally, the continuous chirality measure of the catalyst was found to correlate well with the energy of the homogeneous catalyst–reactant complex, suggesting that high chirality content is related to high enantioselectivity. This correlation, however, did not apply for some of the MOF catalysts. For heterogeneous catalysts, the mechanism of asymmetric induction depends on the steric environment in addition to the chirality of the catalyst.

ChemInform Abstract: A Molecular Mechanics Study of Conformational Isomerism in 1- and 3- Aryl Hydantoins and 3-Aryl-2-thiohydantoins.

Energy profiles for internal rotation about the C—N pivot bond in a series of 1- and 3-aryl hydantoins and 3-aryl-2-thiohydantoins have been computed using the MMX molecular mechanics force field. ...

Synthesis, Crystal Structure, and Rotational Energy Profile of 3-Cyclopropyl-1,2,4-benzotriazine 1,4-Di-N-oxide

1,2,4-Benzotriazine 1,4-di-N-oxides are potent antitumor drug candidates that undergo in vivo bioreduction leading to selective DNA damage in the low oxygen (hypoxic) cells found in tumors. Tirapazamine (TPZ) is the lead compound in this family. Here we report on the synthesis, crystal structure, and conformational analysis of a new analog, 3-cyclopropyl-1,2,4-benzotriazine 1,4-di-N-oxide (3). Compound 3 (C(10)H(10)N(3)O(2)) crystallized in the monoclinic space group C2/c. Unit cell parameters for 3: a = 16.6306 (12), b = 7.799 (5), c = 16.0113 (11) Å, α = 90, β = 119.0440 (10), γ = 90, and z = 8.