Benchmark ab initio characterization of the multi-channel Cl + CH3X [X = F, Cl, Br, I] reactive potential energy surfaces.

We determine benchmark geometries and relative energies for the stationary points of the Cl + CH3X [X = F, Cl, Br, I] reactions. We consider four possible reaction pathways: hydrogen abstraction, hydrogen substitution, halogen abstraction, and halogen substitution, where the substitution processes can proceed via either Walden inversion or front-side attack. We perform geometry optimizations and obtain harmonic vibrational frequencies at the explicitly-correlated UCCSD(T)-F12b/aug-cc-pVTZ level of theory, followed by UCCSD(T)-F12b/aug-cc-pVQZ single-point computations to make finite-basis-set error negligible. To reach chemical (<1 kcal mol-1), or even subchemical (<0.5 kcal mol-1) accuracy, we include core-correlation, scalar relativistic, post-(T), spin-orbit-splitting and zero-point-energy contributions, as well, in the relative energies of all the stationary points. Our benchmark 0 K reaction enthalpies are compared to available experimental results and show good agreement. The stationary-point structures and energetics are interpreted in terms of Hammond's postulate and used to make predictions related to the dynamical behavior of these reactive systems.

First-principles mode-specific reaction dynamics.

Controlling the outcome of chemical reactions by exciting specific vibrational and/or rotational modes of the reactants is one of the major goals of modern reaction dynamics studies. In the present Perspective, we focus on first-principles vibrational and rotational mode-specific dynamics computations on reactions of neutral and anionic systems beyond six atoms such as X + C2H6 [X = F, Cl, OH], HX + C2H5 [X = Br, I], OH- + CH3I, and F- + CH3CH2Cl. The dynamics simulations utilize high-level ab initio analytical potential energy surfaces and the quasi-classical trajectory method. Besides initial state specificity and the validity of the Polanyi rules, mode-specific vibrational-state assignment for polyatomic product species using normal-mode analysis and Gaussian binning is also discussed and compared with experiment.

Dynamics of the HCl + C2H5 Multichannel Reaction on a Full-Dimensional Ab Initio Potential Energy Surface.

We report a full-dimensional ab initio analytical potential energy surface (PES), which accurately describes the HCl + C2H5 multichannel reaction. The new PES is developed by iteratively adding selected configurations along HCl + C2H5 quasi-classical trajectories (QCTs), thereby improving our previous Cl(2P3/2) + C2H6 PES using the Robosurfer program package. QCT simulations for the H'Cl + C2H5 reaction reveal hydrogen-abstraction, chlorine-abstraction, and hydrogen-exchange channels leading to Cl + C2H5H', H' + C2H5Cl, and HCl + C2H4H', respectively. Hydrogen abstraction dominates in the collision energy (Ecoll) range of 1-80 kcal/mol and proceeds with indirect isotropic scattering at low Ecoll and forward-scattered direct stripping at high Ecoll. Chlorine abstraction opens around 40 kcal/mol collision energy and becomes competitive with hydrogen abstraction at Ecoll = 80 kcal/mol. A restricted opening of the cone of acceptance in the Cl-abstraction reaction is found to result in the preference for a backward-scattering direct-rebound mechanism at all energies studied. Initial attack-angle distributions show mainly side-on collision preference of C2H5 for both abstraction reactions, and in the case of the HCl reactant, H/Cl-side preference for the H/Cl abstraction. For hydrogen abstraction, the collision energy transfer into the product translational and internal energy is almost equally significant, whereas in the case of chlorine abstraction, most of the available energy goes into the internal degrees of freedom. Hydrogen exchange is a minor channel with nearly constant reactivity in the Ecoll range of 10-80 kcal/mol.

Imaging the Ion-Molecule Reaction Dynamics of O- + CD4.

While neutral reactions involved in methane oxidation have been intensively studied, much less information is known about the reaction dynamics of the oxygen radical anion with methane. Here, we study the scattering dynamics of this anion-molecule reaction using crossed-beam velocity map imaging with deuterated methane. Differential scattering cross sections for the deuterium abstraction channel have been determined at relative collision energies between 0.2 and 1.5 eV and ab initio calculations of the important stationary points along the reaction pathway have been performed. At lower collision energies, direct backscattering and indirect complex-mediated reaction dynamics are observed, whereas at higher energies, sideways deuterium stripping dominates the reaction. Above 0.7 eV collision energy, a suppressed cross section is observed at low product ion velocities, which is likely caused by the endoergic pathway of combined deuteron/deuterium transfer, forming heavy water. The measured product internal energy is attributed mainly to the low-lying deformation and out-of-plane bending vibrations of the methyl radical product. The results are compared with a previous crossed-beam result for the reaction of oxygen anions with nondeuterated ̧methane and with the related neutral-neutral reactions, showing similar dynamics and qualitative agreement.

Alternating Stereospecificity upon Central-Atom Change: Dynamics of the F- +PH2 Cl SN 2 Reaction Compared to its C- and N-Centered Analogues.

Central-atom effects on bimolecular nucleophilic substitution (SN 2) reactions are well-known in chemistry, however, the atomic-level SN 2 dynamics at phosphorous (P) centers has never been studied. We investigate the dynamics of the F- +PH2 Cl reaction with the quasi-classical trajectory method on a novel full-dimensional analytical potential energy surface fitted on high-level ab initio data. Our computations reveal intermediate dynamics compared to the F- +CH3 Cl and the F- +NH2 Cl SN 2 reactions: phosphorus as central atom leads to a more indirect SN 2 reaction with extensive complex-formation with respect to the carbon-centered one, however, the title reaction is more direct than its N-centered pair. Stereospecificity, characteristic at C-center, does not appear here either, due to the submerged front-side-attack retention path and the repeated entrance-channel inversional motion, whereas the multi-inversion mechanism discovered at nitrogen center is also undermined by the deep Walden-well. At low collision energies, 6 % of the PH2 F products form with retained configuration, mostly through complex-mediated mechanisms, while this ratio reaches 24 % at the highest energy due to the increasing dominance of the direct front-side mechanism and the smaller chance for hitting the deep Walden-inversion minimum. Our results suggest pronounced central-atom effects in SN 2 reactions, which can fundamentally change their (stereo)dynamics.

Phosphorus-centered ion-molecule reactions: benchmark ab initio characterization of the potential energy surfaces of the X- + PH2Y [X, Y = F, Cl, Br, I] systems.

In the present work we determine the benchmark relative energies and geometries of all the relevant stationary points of the X- + PH2Y [X, Y = F, Cl, Br, I] identity and non-identity reactions using state-of-the-art electronic-structure methods. These phosphorus-centered ion-molecule reactions follow two main reaction routes: bimolecular nucleophilic substitution (SN2), leading to Y- + PH2X, and proton transfer, resulting in HX + PHY- products. The SN2 route can proceed through Walden-inversion, front-side-attack retention, and double-/multiple-inversion pathways. In addition, we also identify the following product channels: H--formation, PH2-- and PH2-formation, 1PH- and 3PH-formation, H2-formation and HY + PHX- formation. The benchmark classical relative energies are obtained by taking into account the core-correlation, scalar relativistic, and post-(T) corrections, which turn out to be necessary to reach subchemical (<1 kcal mol-1) accuracy of the results. Classical relative energies are augmented with zero-point-energy contributions to gain the benchmark adiabatic energies.

Rotational Mode-Specificity in the Cl + C2H6 → HCl + C2H5 Reaction.

We perform rotational mode-specific quasi-classical trajectory simulations using a high-quality ab initio analytical potential energy surface for the Cl(2P3/2) + C2H6 → HCl + C2H5 reaction. As ethane, being a prolate-type symmetric top, can be characterized by the J and K rotational quantum numbers, the excitation of two rotational modes, the tumbling (J, K = 0) and spinning (J, K = J) rotations of the reactant is carried out with J = 10, 20, 30, and 40 at a wide range of collision energies. The impacts of rotational excitation on the reactivity, the mechanism, and the post-reaction distribution of energy are investigated: (1) exciting both rotational modes enhances the reactivity with the spinning rotation being more effective due to its coupling to the C-H stretching vibrational normal modes (C-H bond elongating effect) and larger rotational energies, (2) rotational excitation increases the dominance of direct rebound over the stripping mechanism, while collision energy favors the latter, (3) investing energy in tumbling rotation excites the translational motion of the products, while the excess spinning rotational energy readily flows into the internal degrees of freedom of the ethyl radical or, less significantly, into the HCl vibration, probably due to the pronounced rovibrational coupling in this case. We also study the relative efficiency of vibrational and rotational excitation on the reactivity of the barrierless and thus translationally hindered title reaction.

First-Principles Reaction Dynamics beyond Six-Atom Systems.

Moving beyond the six-atomic benchmark systems, we discuss the new age and future of first-principles reaction dynamics, which investigates complex, multichannel chemical reactions. We describe the methodology starting from the benchmark ab initio characterization of the stationary points, followed by full-dimensional potential energy surface (PES) developments and reaction dynamics computations. We highlight our composite ab initio approach providing benchmark stationary-point properties with subchemical accuracy, the Robosurfer program system enabling automatic PES development, and applications for the Cl + C2H6, F + C2H6, and OH- + CH3I post-six-atom reactions focusing on ab initio issues and their solutions as well as showing the excellent agreement between theory and experiment.

Vibrational mode-specific dynamics of the F(2P3/2) + C2H6 → HF + C2H5 reaction.

We investigate the competing effect of vibrational and translational excitation and the validity of the Polanyi rules in the early- and negative-barrier F(2P3/2) + C2H6 → HF + C2H5 reaction by performing quasi-classical dynamics simulations on a recently developed full-dimensional multi-reference analytical potential energy surface. The effect of five normal-mode excitations of ethane on the reactivity, the mechanism, and the post-reaction energy flow is followed through a wide range of collision energies. Promoting effects of vibrational excitations and interaction time, related to the slightly submerged barrier, are found to be suppressed by the early-barrier-induced translational enhancement, in contrast to the slightly late-barrier Cl + C2H6 reaction. The excess vibrational energy mostly converts into ethyl internal excitation while collision energy is transformed into product separation. The substantial reaction energy excites the HF vibration, which tends to show mode-specificity and translational energy dependence as well. With increasing collision energy, direct stripping becomes dominant over the direct rebound and indirect mechanisms, being basically independent of reactant excitation.

Vibrational mode-specificity in the dynamics of the Cl + C2H6 → HCl + C2H5 reaction.

We report a detailed dynamics study on the mode-specificity of the Cl + C2H6 → HCl + C2H5 H-abstraction reaction. We perform quasi-classical trajectory simulations using a recently developed high-level ab initio full-dimensional potential energy surface by exciting five different vibrational modes of ethane at four collision energies. We find that all the studied vibrational excitations, except that of the CC-stretching mode, clearly promote the title reaction, and the vibrational enhancements are consistent with the predictions of the Sudden Vector Projection (SVP) model, with the largest effect caused by the CH-stretching excitations. Intramolecular vibrational redistribution is also monitored for the differently excited ethane molecule. Our results indicate that the mechanism of the reaction changes with increasing collision energy, with no mode-specificity at high energies. The initial translational energy mostly converts into product recoil, while a significant part of the excess vibrational energy remains in the ethyl radical. An interesting competition between translational and vibrational energies is observed for the HCl vibrational distribution: the effect of exciting the low-frequency ethane modes, having small SVP values, is suppressed by translational excitation, whereas a part of the excess vibrational energy pumped into the CH-stretching modes (larger SVP values) efficiently flows into the HCl vibration.

Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short ß-Sheets Coupled to Phase Transition.

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small ß-sheets, the key motifs of proteins, undergoing structural changes in liquid-liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3-0.5 kcal·mol-1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2-2.3 kcal·mol-1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol-1 per residue excess stabilization.

Exact quantum dynamics background of dispersion interactions: case study for CH4·Ar in full (12) dimensions.

A full-dimensional ab initio potential energy surface of spectroscopic quality is developed for the van-der-Waals complex of a methane molecule and an argon atom. Variational vibrational states are computed on this surface including all twelve (12) vibrational degrees of freedom of the methane-argon complex using the GENIUSH computer program and the Smolyak sparse grid method. The full-dimensional computations make it possible to study the fine details of the interaction and distortion effects and to make a direct assessment of the reduced-dimensionality models often used in the quantum dynamics study of weakly-bound complexes. A 12-dimensional (12D) vibrational computation including only a single harmonic oscillator basis function (9D) to describe the methane fragment (for which we use the ground-state effective structure as the reference structure) has a 0.40 cm-1 root-mean-square error (rms) with respect to the converged 12D bound-state excitation energies, which is less than half of the rms of the 3D model set up with the 〈r〉0 methane structure. Allowing 10 basis functions for the methane fragment in a 12D computation performs much better than the 3D models by reducing the rms of the bound state vibrational energies to 0.07 cm-1. The full-dimensional potential energy surface correctly describes the dissociation of the system, which together with further development of the variational (ro)vibrational methodology opens a route to the study of the role of dispersion forces in the excited methane vibrations and the energy transfer from the intra- to the intermolecular vibrational modes.

Benchmark ab initio and dynamical characterization of the stationary points of reactive atom + alkane and SN2 potential energy surfaces.

We describe a composite ab initio approach to determine the best technically feasible relative energies of stationary points considering additive contributions of the CCSD(T)/complete-basis-set limit, core and post-CCSD(T) correlation, scalar relativistic and spin-orbit effects, and zero-point energy corrections. The importance and magnitude of the different energy terms are discussed using examples of atom/ion + molecule reactions, such as X + CH4/C2H6 and X- + CH3Y/CH3CH2Cl [X, Y = F, Cl, Br, I, OH, etc.]. We test the performance of various ab initio levels and recommend the modern explicitly-correlated CCSD(T)-F12 methods for potential energy surface (PES) developments. We show that the choice of the level of electronic structure theory may significantly affect the reaction dynamics and the CCSD(T)-F12/double-zeta PESs provide nearly converged cross sections. Trajectory orthogonal projection and an Eckart-transformation-based stationary-point assignment technique are proposed to provide dynamical characterization of the stationary points, thereby revealing front-side complex formation in SN2 reactions and transition probabilities between different stationary-point regions.

Full-dimensional MRCI-F12 potential energy surface and dynamics of the F(2P3/2) + C2H6 → HF + C2H5 reaction.

We report a detailed quasi-classical dynamics study on a new full-dimensional multireference spin-orbit-corrected potential energy surface (PES) for the F(2P3/2) + C2H6 → HF + C2H5 reaction. For the PES development, the Robosurfer program package is applied and the MRCI-F12+Q(5,3)/aug-cc-pVDZ energy points are fitted using the monomial symmetrization approach of the permutationally invariant polynomial method. Our simulations provide substantial reaction probabilities and sharply increasing cross sections with an increase in collision energy for this early- and negative-barrier reaction. A direct rebound/stripping mechanism is preferred at low/high collision energies, and the initial translational energy turns out to convert mostly into product recoil, whereas the reaction energy excites the HF vibration. Vibrational and vibrationally resolved rotational state distributions of the HF product obtained from our computations agree well with the single-collision experimental data for the vHF = 1, 2, and 3 states.

Detailed benchmark ab initio mapping of the potential energy surfaces of the X + C2H6 [X = F, Cl, Br, I] reactions.

We investigate three reaction pathways of the X + C2H6 [X = F, Cl, Br, I] reactions: H-abstraction, methyl-substitution, and H-substitution, with the latter two proceeding via either Walden-inversion or front-side-attack mechanisms. We report classical and adiabatic relative energies of unprecedented accuracy for the corresponding stationary points of the reaction potential energy surfaces (PESs) by augmenting the CCSD(T)-F12b/aug-cc-pVQZ energies by core-correlation, post-CCSD(T) and spin-orbit corrections. Taking these correction terms into account turns out to be essential to reach subchemical, i.e. <0.5 kcal mol-1, accuracy. Our new benchmark 0 K reaction enthalpies show excellent agreement with experimental data. Spin-orbit coupling in these open-shell systems is also monitored throughout the reaction paths and found to be non-negligible even in some transition-state geometries. Barrier heights corresponding to the different channels of the title reactions appear in the same order with increasing energy: H-abstraction, Walden-inversion methyl-substitution, Walden-inversion H-substitution, front-side-attack H-substitution and front-side-attack methyl-substitution, except for X = I where the latter two come in reverse order. Similarly, product channels follow the energy order of the corresponding barrier heights in all four cases. We find strongly reactant-like transition-state structures for the exothermic F + C2H6 reaction paths, while more and more product-like transition states are observed along with increasing endothermicity as going from Cl to I. Several entrance and exit channel minima are also identified for the studied reactions with significant spin-orbit effects for the formers.

Four faces of the interaction between ions and aromatic rings.

Non-covalent interactions between ions and aromatic rings play an important role in the stabilization of macromolecular complexes; of particular interest are peptides and proteins containing aromatic side chains (Phe, Trp, and Tyr) interacting with negatively (Asp and Glu) and positively (Arg and Lys) charged amino acid residues. The structures of the ion-aromatic-ring complexes are the result of an interaction between the large quadrupole moment of the ring and the charge of the ion. Four attractive interaction types are proposed to be distinguished based on the position of the ion with respect to the plane of the ring: perpendicular cation-π (CP⊥ ), co-planar cation-π (CP∥ ), perpendicular anion-π (AP⊥ ), and co-planar anion-π (AP∥ ). To understand more than the basic features of these four interaction types, a systematic, high-level quantum chemical study is performed, using the X- + C6 H6 , M+ + C6 H6 , X- + C6 F6 , and M+ + C6 F6 model systems with X- = H- , F- , Cl- , HCOO- , CH3 COO- and M+ = H+ , Li+ , Na+ , NH4+, CH3 NH3+, whereby C6 H6 and C6 F6 represent an electron-rich and an electron-deficient π system, respectively. Benchmark-quality interaction energies with small uncertainties, obtained via the so-called focal-point analysis (FPA) technique, are reported for the four interaction types. The computations reveal that the interactions lead to significant stabilization, and that the interaction energy order, given in kcal mol-1 in parentheses, is CP⊥ (23-37) > AP⊥ (14-21) > CP∥ (9-22) > AP∥ (6-16). A natural bond orbital analysis performed leads to a deeper qualitative understanding of the four interaction types. To facilitate the future quantum chemical characterization of ion-aromatic-ring interactions in large biomolecules, the performance of three density functional theory methods, B3LYP, BHandHLYP, and M06-2X, is tested against the FPA benchmarks, with the result that the M06-2X functional performs best. © 2017 Wiley Periodicals, Inc.

Complex rovibrational dynamics of the Ar·NO+ complex.

Rotational-vibrational states of the Ar·NO+ cationic complex are computed, below, above, and well above the complex's first dissociation energy, using variational nuclear motion and close-coupling scattering computations. The HSLH potential energy surface used in this study (J. Chem. Phys., 2011, 135, 044312) is characterized by a first dissociation energy of D0 = 887.0 cm-1 and supports 200 bound vibrational states. The bound-state vibrational energies and the corresponding wave functions allow the interpretation of the scarcely available experimental results about the intermonomer vibrational motion of the complex. A very large number of long-lived quasibound combination states of the three vibrational modes, exhibiting a very similar energy-level structure as that of the bound states, are found embedded in the continuum. Additional short-lived resonance states are also identified and their properties are analyzed.

A general variational approach for computing rovibrational resonances of polyatomic molecules. Application to the weakly bound H2He+ and H2⋠CO systems.

The quasi-variational quantum chemical protocol and code GENIUSH [E. Mátyus et al., J. Chem. Phys. 130, 134112 (2009) and C. Fábri et al., J. Chem. Phys. 134, 074105 (2011)] has been augmented with the complex absorbing potential (CAP) technique, yielding a method for the determination of rovibrational resonance states. Due to the effective implementation of the CAP technique within GENIUSH, the GENIUSH-CAP code is a powerful tool for the study of important dynamical features of arbitrary-sized molecular systems with arbitrary composition above their first dissociation limit. The GENIUSH-CAP code has been tested and validated on the H2He+ cation: the computed resonance energies and lifetimes are compared to those obtained with a previously developed triatomic rovibrational resonance-computing code, D2FOPI-CCS [T. Szidarovszky and A. G. Császár Mol. Phys. 111, 2131 (2013)], utilizing the complex coordinate scaling method. A unique feature of the GENIUSH-CAP protocol is that it allows the simple implementation of reduced-dimensional dynamical models. To prove this, resonance energies and lifetimes of the H2⋅CO van der Waals complex have been computed utilizing a four-dimensional model (freezing the two monomer stretches), and a related potential energy surface, of the complex.

The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization.

The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins. In order to investigate the thermodynamics of oligomerization, full geometry optimizations and frequency calculations were performed both on parallel and antiparallel ß-pleated sheet model structures of [HCO-(Ala)(1-6)-NH(2)](2) and (For-Ala(1-2)-NH(2))(1-6) peptides, both at the B3LYP and M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) levels of theory, both in vacuum and in water. Our results show that relative entropy and enthalpy both show a hyperbolic decrease with increasing residue number and with increasing number of strands as well. Thus, di- and oligomerization are always thermodynamically favored. Antiparallel arrangements were found to have greater stability than parallel arrangements of the polypeptide backbones. During our study the relative changes in thermodynamic functions are found to be constant for long enough peptides, indicating that stability and entropy terms are predictable. All thermodynamic functions of antiparallel di- and oligomers show a staggered nature along the increasing residue number. By identifying and analyzing the 6 newly emerging dimer vibrational modes of the 10- and 14-membered building units, the staggered nature of the entropy function can be rationalized. Thus, the vanishing rotational and translational modes with respect to single strands are converted into entropy terms "holding tight" the dimers and oligomers formed, rationalizing the intrinsic adherence of natural polypeptide backbones to aggregate.

Hydrolysis of Edible Oils by Fungal Lipases: An Effective Tool to Produce Bioactive Extracts with Antioxidant and Antimicrobial Potential.

Hydrolysis of olive, rapeseed, linseed, almond, peanut, grape seed and menhaden oils was performed with commercial lipases of Aspergillus niger, Rhizopus oryzae, Rhizopus niveus, Rhizomucor miehei and Candida rugosa. In chromogenic plate tests, olive, rapeseed, peanut and linseed oils degraded well even after 2 h of incubation, and the R. miehei, A. niger and R. oryzae lipases exhibited the highest overall action against the oils. Gas chromatography analysis of vegetable oils hydrolyzed by R. miehei lipase revealed about 1.1 to 38.4-fold increases in the concentrations of palmitic, stearic, oleic, linoleic and α-linolenic acids after the treatment, depending on the fatty acids and the oil. The major polyunsaturated fatty acids produced by R. miehei lipase treatment from menhaden oil were linoleic, α-linolenic, hexadecanedioic, eicosapentaenoic, docosapentaenoic and docosahexaenoic acids, with yields from 12.02 to 52.85 µg/mL reaction mixture. Folin-Ciocalteu and ferric reducing power assays demonstrated improved antioxidant capacity for most tested oils after the lipase treatment in relation to the concentrations of some fatty acids. Some lipase-treated and untreated samples of oils, at 1.25 mg/mL lipid concentration, inhibited the growth of food-contaminating bacteria. The lipid mixtures obtained can be reliable sources of extractable fatty acids with health benefits.