Rotational Energy Surface Research Articles

Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations.

N-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the E and Z conformers spectrally affect, on average, 3.4 and 2.5 of the closest H2O molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the Z conformer of HU is found here to be more stable by 17.4 kJ·mol-1 than the E conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in Z-HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its N-alkyl-substituted derivatives, N-hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.

Vibrational Spectroscopy and Structural Analysis of V+(C2H6)n Clusters (n = 1-4).

The vibrational structure and binding motifs of vanadium cation-ethane clusters, V+(C2H6)n, for n = 1-4 are probed using infrared photodissociation spectroscopy in the C-H stretching region (2550-3100 cm-1). Comparison of spectra to scaled harmonic frequency spectra obtained using density functional theory suggests that ethane exhibits two primary binding motifs when interacting with the vanadium cation: an end-on η2 configuration and a side-on configuration. Determining the denticity of the side on isomer is complicated by the rotational motion of ethane, implying that structural analysis based solely on Born-Oppenheimer potential energy surface minimizations is insufficient and that a more sophisticated vibrationally adiabatic approach is necessary to interpret spectra. The lower-energy side-on configuration predominates in smaller clusters, but the end-on configuration becomes important for larger clusters as it helps to maintain a roughly square-planar geometry about the central vanadium. Proximate C-H bonds exhibit elongation and large red-shifts when compared to bare ethane, particularly in the case of the side-on isomer, demonstrating initial effects of C-H bond activation, which are underestimated by scaled harmonic frequency calculations. Tagging several of the clusters with argon and nitrogen results in nontrivial effects. The high binding energy of N2 can lead to the displacement of ethane from a side-on configuration into an end-on configuration. The presence of either one or two Ar or N2 can impact the overall symmetry of the cluster, which can alter the potential energy surface for ethane rotation in the side-on isomer and may affect the accessibility of low-lying electronic excited states of V+.

The role of the local environment on the structural heterogeneity of carotenoid β-ionone rings.

Our analysis of the X-ray crystal structure of canthaxanthin (CAN) showed that its ketolated β-ionone rings can adopt two energetically equal, but structurally distinct puckers. Quantum chemistry calculations revealed that the potential energy surface of the β-ionone ring rotation over the plane of the conjugated π-system in carotenoids depends on the pucker state of the β-ring. Considering different pucker states and β-ionone ring rotation, we found six separate local minima on the potential energy surface defining the geometry of the keto-β-ionone ring-two cis and one trans orientation for each of two pucker states. We observed a small difference in energy and no difference in relative orientation for the cis-minima, but a pronounced difference for the position of trans-minimum in alternative pucker configurations. An energetic advantage of β-ionone ring rotation from a specific pucker type can reach up to 8kJ/mol ([Formula: see text]). In addition, we performed the simulation of linear absorption of CAN in hexane and in a unit cell of the CAN crystal. The electronic energies of [Formula: see text] transition were estimated both for the CAN monomer and in the CAN crystal. The difference between them reached [Formula: see text], which roughly corresponds to the energy gap between A and B pucker states predicted by theoretical estimations. Finally, we have discussed the importance of such effects for biological systems whose local environment determines conformational mobility, and optical/functional characteristics of carotenoid.

On light surfaces in black hole thermodynamics

We discuss the fundamentals of classical black hole (BH) thermodynamics in a new framework determined by light surfaces and their frequencies. This new approach allows us to study BH transitions inside the Kerr geometry. In the case of BHs, we introduce a new parametrization of the metric in terms of the maximum extractable rotational energy or, correspondingly, the irreducible mass, which is an alternative to the spin parametrization. It turns out that BH spacetimes with spins a/M= sqrt{8/9} and a/M=1/sqrt{2} show anomalies in the rotational energy extraction and surface gravity whereas the case a/M=sqrt{3}/2 is of particular relevance to study the variations of the horizon area. We find the general conditions under which BH transitions can occur and express them in terms of the masses of the initial and final states. This shows that BH transitions in the Kerr geometry are not arbitrary but depend on the relationship between the mass and spin of the initial and final states. From an observational point of view, we argue that near the BH poles it is possible to detect photon orbits with frequencies that characterize the light surfaces analyzed in this work.

Computational analysis of the proton-bound acetonitrile dimer, (ACN)2 H.

In atmospheric pressure ionization mass spectrometry the theoretical thermodynamic treatment of proton-bound cluster stabilities helps us to understand the prevailing chemical processes. However, such calculations are rather challenging because low-barrier internal rotations and strong anharmonicity of the hydrogen bonds cause the breakdown of the usually applied harmonic approximation. Even the implemented anharmonic treatment in standard ab initio software failed in the case of (ACN)2 H+ . For a case study of the proton-bound acetonitrile dimer, (ACN)2 H+ , we scan the potential energy surface (PES) for the internal rotation and the proton movement in all three spatial directions. We correct the partition functions by treating the internal rotation as a free rotor and by solving the nuclear Schrödinger equation explicitly for the proton movement. An additional PES scan for the dissociation surface further improves the understanding of the cluster behavior. The internal rotation is essentially barrier free (V0 = 2.6 × 10-6 eV) and the proton's movement between the two nitrogen atoms follows a quartic rather than quadratic potential. As a figure of merit we calculate the free dissociation enthalpy of the dimer. Our description significantly improves the standard results from about 118.3 kJ/mol to 99.6 kJ/mol, compared with the experimentally determined value of 92.2 kJ/mol. The dissociation surface reveals strong crosstalk between modes and is essentially responsible for the observed errors. The presented corrections to the partition functions significantly improve their accuracy and are rather easy to implement. In addition, this work stresses the importance of alternative theoretical methods for proton-bound cluster systems besides the standard harmonic approximations.

Complete OSV-MP2 Analytical Gradient Theory for Molecular Structure and Dynamics Simulations.

We propose an exact algorithm for computing the analytical gradient within the framework of the orbital-specific-virtual (OSV) second-order Møller-Plesset (MP2) theory in resolution-of-identity (RI) approximation. We implement the relaxation of perturbed OSVs through the explicit constraints of the perturbed orthonormality, the perturbed diagonality, and the perturbed eigenvalue condition. We show that the rotation of OSVs within the retained OSV subspace makes no contribution to gradients, as long as the unperturbed Hylleraas energy functional reaches minimum. The OSV relaxation is solved as the perturbed nondegenerate eigenvalue problem between the retained and discarded OSV subspaces. The detailed derivation and preliminary implementations for gradient working equations are discussed. The coupled-perturbed localization method is implemented for meta-Löwdin localization function. The numerical accuracy of computed OSV-MP2 gradients is demonstrated for the geometries of selected molecules that are often discussed in other theories. From OSV-MP2 with the normal OSV selection, the canonical RI-MP2/def2-TZVP gradients can be reproduced within 10-4 au. The OSV-MP2/def2-TZVPP covalent bond lengths, angles, and dihedral angles are in good agreement with canonical RI-MP2 structures by 0.017 pm, 0.03°, and 0.2°, respectively. No particular accuracy gains have been observed for molecular geometries compared to the recent local pair-natural-orbital MP2 by using the predefined orbital domains. Moreover, the OSV-MP2 analytical gradients can generate atomic forces that are utilized to drive the Born-Oppenheimer molecular dynamics (BOMD) simulation for studying structural and vibrational properties with respect to OSV selections. By performing the OSV-MP2 NVE BOMD calculation using the normal OSV selection, the structural and vibrational details of protonated water cations are well reproduced. The 200 ps NVT well-tempered metadynamics at 300 K has been simulated to compute the OSV-MP2 rotational free-energy surface of coupled hydroxyl and methyl rotors for ethanol molecule.

The infrared spectrum of PF3 and analysis of rotational energy clustering effect

The first variational calculations of the rotational-vibrational levels of PF are performed and intensities for dipole transitions between them computed. This is accomplished using new state of the art potential energy and dipole moment surfaces. This allows the infrared spectrum of PF to be simulated, providing a complete overview of the ro-vibrational spectrum up to J=100 in the wavenumber range 0–3100 cm−1. The behaviour of PF at high rotational excitations is also investigated. The formation of quasi-degenerate 6-fold rotational energy clusters at high rotational excitation are investigated up to J=270 and are found to occur around J=200. The clustering effect is analysed in terms of semi-classical rotational energy surfaces.

Noble gas dimers confined inside C70.

The potential energy surfaces for the interior rotation of a series of pairs of noble gas atoms encapsulated in the C70 cavity have been explored. He2@C70, Ne2@C70, Ar2@C70, HeNe@C70, HeAr@C70 and NeAr@C70 were chosen as case studies. Our calculations suggest stable minima with the two noble gas atoms lying along the symmetry axis of the fullerene. Transition states for the rotations are expected to occur when the two atoms are located in the symmetry plane perpendicular to the C5 axis. The energy barriers for the rotations are predicted to be in the 5-64 kcal mol-1 range, significantly increasing with the size of the noble gas atoms inside C70. These energy barriers lead to a wide range of rate constants, including those characteristic of very fast internal rotations, of the order of k = 2.40 × 109 s-1 for He2@C70, and those describing very slow rotations, of the order of k = 1.80 × 10-33 s-1 for Ar2@C70. It is mandatory to correct for the basis set superposition error to calculate accurate binding energies.

Dynamic structure of organic compounds in solution according to NMR data and quantum chemical calculations: II. Styrene

Dynamic structure of Soman diastereoisomers has been studied with the goal of obtaining accurate information to simulate molecular mechanisms of its action on living systems. The potential energy surface for internal rotation about the single P–O and O–C bonds has been constructed in terms of the Moller–Plesset second-order perturbation theory using 6-311G(d,p) basis set. The relative contributions of different conformers have been estimated by solving the vibrational problem according to the large-amplitude vibration model. The conformational dependences of the 4 J CF and 3 J CP coupling constants for the S,S and S,R diastereoisomers of Soman have been calculated at the FPT DFT B3LYP/6-311++G(2df,2p) level of theory. The calculated vibrationally averaged coupling constants have been compared with the available experimental data to determine the structure of the most toxic Soman stereoisomer.

Computational investigation of π-bond strengths in fluorinated ethylenes

The strengths of π-bonds in a series of fluorinated ethylenes have been computationally investigated, and the potential energy surfaces for thermal CC bond rotation in fluorinated ethylenes, as well as in ethylene, have been explored. The computed thermal rotational barrier values and the π-bond strengths obtained using Benson’s procedure show parallel trends. Our calculations indicate that the π-bond in CH2=CHF is slightly stronger, and the one in CF2=CF2 is noticeably weaker than that in CH2=CH2. In addition, the stabilization effects of fluorine substitution have been evaluated for fluorinated ethylene molecules and for singlet biradical thermal rotation transition states. Considering these fluorine substituent effects, the change in the π-bond strength of a series of fluorinated ethylenes can be qualitatively interpreted.

PP-Rotation, P-Inversion and Metathesis in Diphosphines Studied by DFT Calculations: Comments on Some Literature Conflicts

The potential energy surface for internal rotation about the phosphorus–phosphorus bond was calculated at the PCMDCM/B3LYP/6-311++G(d,p) computational level for a set of eight symmetrical, unsymmetrical and P-stereogenic diphosphines; H4P2, Me4P2, (CF3)4P2, Ph4P2, Me2P–P(CF3)2, Me2P–PPh2, and the meso- and dl-isomers of Me(CF3)P–PMe(CF3) and MePhP–PMePh. Certain trends in the data were elucidated and compared with conflicting data from the literature regarding the relative population of anti and gauche rotational isomers. The pyramidal inversion barriers (stereomutation barriers in P-stereogenic cases) for the same set of diphosphines was estimated through the inversion transition states and also compared to literature values. Finally, the Me4P2 + (CF3)4P2 → 2Me2(CF3)2P2 metathesis reaction was also explored to evaluate its feasibility versus inversion. The finding of larger barriers in the metathesis than in the inversion rules in favour of an inversion mechanism for the stereomutation of P-stereogenic diphosphines.

Features of the Interaction of Hydroxyl and Methyl Tops in the Ethanol Molecule: 2D-Calculation of the Torsion Energy Levels

Geometric parameters and vibrational spectra of the trans- and gauche-conformers of the ethanol molecule were calculated using the B3LYP/cc-pVQZ and B3LYP/acc-pVQZ approximations. 2D potential energy surfaces for internal rotation of the hydroxyl and methyl tops were built. Kinetic parameters associated with torsion coordinates were calculated using Wilson’s s vectors at the same 2D grid nodes at which the potential energy values were found. Features of the kinematic and force interaction of the two tops were analyzed. Energies of torsion levels and frequencies of torsional vibrations of CH 3 and OH groups were calculated. Good agreement between the calculated (199.8 cm −1 ) and experimental (202.6 cm −1 ) values for the fundamental frequency of OH torsional vibrations was achieved. Essential differences in the corresponding values for the fundamental torsional vibrations of CH 3 groups were analyzed.

Conformations of Organophosphine Oxides.

The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P-C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 force field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes-an essential part of understanding the chemistry of these compounds. The predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.

Spatial structure of 2-(2´-hydroxyphenyl)-4-methylchromanes and some specific features of intramolecular hydrogen bond

The B3LYP/6-311++G(2d,2p) method was used to study spatial structures in the gas phase of 2S*,4S*- and 2S*,4R*-2-(2´-hydroxyphenyl)-4-methylchromanes (1 and 2), which are the products of thermal dimerization of o-vinylphenol. A two-dimensional potential energy surface of the internal rotation of the cyclic fragments of the molecule around the C(2)—C(1´) bond and the OH group around the C(2´)—O(2´) bond was built for chromane 1. The appearance of the stretching vibration absorption band for free OH groups in the IR spectra of solutions of chromanes 1 and 2 in low polar solvents allowed us to draw a conclusion that, despite the presence of a "classic" strong enough intramolecular hydrogen bond (IMHB) O—H...O between the OH group and the O atom of heterocycle, some molecules 1 and 2 exist in solutions as rotamers with the free OH group. Theoretical evaluation shows that the amount of such rotamers in the gas phase is ~8%, while in solution, according to the IR spectroscopy data, it is ~12%. Theoretical evaluation of the IMHB enthalpy for o-phenylchromanes 1 and 2 gives the value of 1.9 kcal mol−1.

RETRACTED ARTICLE: Quantum effects on translation and rotation of molecular chlorine in solid para-hydrogen

Structure and quantum effects of a Cl2 molecule embedded in fcc and hcp para-hydrogen (pH2) crystals are investigated in the zero-temperature limit. The interaction is modelled in terms of Cl2–pH2 and pH2–pH2 pair potentials from ab initio CCSD(T) and MP2 calculations. Translational and rotational motions of the molecules are described within three-dimensional anharmonic Einstein and Devonshire models, respectively, where the crystals are either treated as rigid or allowed to relax. The pH2 molecules, as well as the heavier Cl2 molecule, show large translational zero-point energies (ZPEs) and undergo large-amplitude translational motions. This gives rise to substantial reductions in the cohesive energies and expansions of the lattices, in agreement with experimental results for pure hydrogen crystals. The rotational dynamics of the Cl2 impurity is restricted to small-amplitude librations, again with high librational ZPEs, which are described in terms of two-dimensional non-degenerate anharmonic oscillators. The lattice relaxation causes qualitative changes of the rotational energy surfaces, which finally favour librations around the crystallographic directions pointing towards the nearest neighbours, both for fcc and hcp lattices. Implications on the reactant orientation in the experimentally observed laser-induced chemical reaction, Cl + H2 → HCl + H, are discussed.

Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N′-methyl-l-alanylamide Dipeptide

We propose an articulated computational experiment in which both quantum mechanics (QM) and molecular mechanics (MM) methods are employed to investigate environment effects on the free energy surface for the backbone dihedral angles rotation of the small dipeptide N-acetyl-N′-methyl-l-alanylamide. This computation exercise is appropriate for an upper-level physical chemistry course. The purposes are (i) to show the importance of solvent effects on the free energy surface of molecules in solution and (ii) to compare different computational chemistry tools in terms of computation complexity versus detail of information obtained from calculus. The QM section is divided in three parts: in vacuo, implicit solvent, and explicit solvent calculations. Similarly, also the MM section is divided in three parts: molecular mechanics, molecular dynamics, and adaptive biasing force molecular dynamics. QM and MM sections can be proposed by the instructor as different and complementary parts of the experiment or as independent QM or MM class lessons. Together, the two sections can be used to set up a computational chemistry laboratory exercise targeted to the study of solvent effects on molecular properties.

Hydration and Proton Transfer in Highly Sulfonated Poly(phenylene sulfone) Ionomers: An Ab Initio Study

The need to operate proton exchange membrane fuel cells under hot and dry conditions has driven the synthesis and testing of sulfonated poly(phenylene) sulfone (sPSO(2)) ionomers. The primary hydration and energetics associated with the transfer of protons in oligomeric fragments of two sPSO(2)ionomers were evaluated through first-principles electronic structures calculations. Our results indicate that the interaction between neighboring sulfonic acid groups affect both theconformation and stability of the fragments. The number of water molecules required to affect the transfer of a proton in the first hydration shell was observed to be a function of the hydrogen bonding in proximity of the sulfonic acid groups: three H(2)O for the meta- and four H(2)O for the ortho-conformations. Calculations of the rotational energy surfaces indicate that the aromatic backbones of sPSO(2) are much stiffer than the polytetrafluoroethylene (PTFE) backbones in perfluorosulfonic acid (PFSA) ionomers: the largest energy penalty for rotating phenylene rings (i.e., 15.5 kcal/mol for ortho-ortho-sPSO(2)) is nearly twice that computed for the rotation of a CF(2) unit in a PTFE backbone. The energetics for the transfer of various protons in proximity to one or two sulfonate groups (-SO(3)(-)) was also determined. The computed energy barrier for proton transfer when only one sulfonic acid group is present is approximately 1.9 kcal/mol, which is 2.1 kcal/mol lower than similar calculations for PFSA systems. When two sulfonic acid groups are bridged by water molecules, a symmetric bidirectional transfer occurs, which gives a substantially small energy barrier of only 0.7 kcal/mol.

Conformational analysis of 2-acetylcyclopentanone by the density functional and MP2 methods

Two-dimensional potential energy surfaces for internal rotation of the acetyl substituent and inversion of the five-membered ring in the gas phase and in acetonitrile were constructed by the B3LYP/6-31G(d) method for the diketo form of the 2-acetylcyclopentanone (2-ACPN) molecule. The diketo form of 2-ACPN exists in the gas phase and in low-polarity cyclohexane as a mixture of four rotamers K1, K2, K3, and K4. The fifth isomeric form K3a exists in polar acetonitrile. The estimation of the tautomeric composition of 2-ACPN taking into account the influence of the cyclohexane medium in the framework of the polarizable continuum model (PCM) using the MP 2/cc-pVTZ method agrees better with experimental data than the estimate obtained by the B3LYP/cc-pVTZ method. The constants of the enol-enol and keto-enol tautomeric equilibria of the 2-ACPN tautomers in solutions of aprotic solvents were estimated.

Derivatives of benzo[b]furan. Part I. Conformational studies of khellinone and visnaginone

The structural analysis of khellinone and visnaginone indicated the planarity of the benzo[b]furan ring system. The oxygen or carbon atoms of the substituents, –OH, –OCH3, and –C(=O)CH3, are nearly coplanar with the aromatic ring. The molecular conformation is stabilized by the intramolecular O–H···O hydrogen bond formed between the ortho-substituted hydroxyl and acetyl groups. The intermolecular contacts present in the crystal structure are the C–H···O and C–H···π interactions and the π··· π stacking. The energy surface for the internal rotation about the Csp2–O/C bonds in the khellinone and visnaginone molecules has been explored by quantum-chemical calculations. The density functional theory (DFT) methods yielded three stable conformers of khellinone and two of visnaginone obtained by a rotation of the methoxy group about the C4sp2–OCH3 bond. The most stable conformation in the gas phase is consistent with the stereochemistry of the molecules adopted in the solid. The secondary minima conformers have energies higher by 0.3–1.8 kcal/mol. The energy of the intramolecular O–H···O interactions, present in the molecular structure of all stable conformers, is around 18 kcal/mol at the DFT level. A complete and reliable assignment of the bands in the IR and Raman spectra of both compounds has been performed.

High-resolution spectroscopy and analysis of the ν3/2ν4 dyad of CF4

CF4 is a strong greenhouse gas of both anthropogenic and natural origin [D.R. Worton et al., Environ. Sci. Technol. 41, 2184 (2007)]. However, high-resolution infrared spectroscopy of this molecule has received only a limited interest up to now. Until very recently, the public databases only contained cross-sections for this species, but no detailed line list. We reinvestigate here the strongly absorbing ν3 region around 7.8 μm. New Fourier transform infrared (FTIR) spectra up to a maximal resolution of 0.0025 cm−1 have been recorded: (i) room-temperature spectra in a static cell and (ii) a supersonic expansion jet spectrum at a 23 K estimated temperature. Following the work of Gabard et al. [Mol. Phys. 85, 735 (1995)], we perform a simultaneous analysis of both the ν3 and 2ν4 bands since a strong Coriolis interaction occurs between them, perturbing the ν3 R-branch rotational clusters around J = 20. Similarly to Gabard et al. , we also include ν4 FTIR data and microwave data in the fit. The analysis is performed thanks to the XTDS and SPVIEW programs [Ch. Wenger et al., J. Mol. Spectrosc., 251 102 (2008)]. Compared to Gabard et al. , the present work extends the analysis up to higher J values (56 instead of 32). Absorption intensities are estimated thanks to the dipole moment derivative from D. Papoušek et al. [J. Phys. Chem. 99, 15387 (1995)] and compare well with the experiment. We have produced a synthetic linelist that is included in the HITRAN 2008 and GEISA 2009 public databases. The rotational energy surfaces for the dyad are also examined in detail in order to understand the distribution and clustering patterns of rovibrational levels.