Respective Potential Energy Surfaces Research Articles

Paddlanes revisited: Which are the smallest possible?

AbstractPaddlanes are tricyclic molecules with four bridging chains that share the same two bridgehead carbon atoms. The smallest known paddlane containing only carbon atoms in the main framework has a total of 18 atoms. We utilized computational chemistry (MP2/cc‐pVTZ) to locate the smallest possible all‐carbon paddlanes that meet the criterion suggested by Hoffmann, Schleyer, and Schaefer as being “fleeting,” meaning frequency calculations suggest the structures are energy minima on their respective potential energy surfaces (PES). Our results suggest that paddlane compounds with a total of 10 or fewer atoms can be considered to be non‐viable either because they are not energy minima on the PES or due to strain in the system that manifests as especially long carbon–carbon bonds. Some paddlanes with a total of 11 carbon atoms proved to be energy minima but still exhibited longer carbon–carbon bonds than normal. Finally, several paddlanes with a total of 12 carbons appear to be the least strained since carbon–carbon bond lengths remain reasonable.

Vibrational Spectroscopic, 13C NMR, DFT Studies on Chlorofullerene (C60Cl6): A Potential Bioactive Agent

Abstract. The present work comprises the systematic computational chemical findings on Chlorofullerene (C60Cl6). The molecular structure of C60Cl6 was optimized by density function theory (DFT)/B3LYP model of 6-31G(d,p) basis set using Gaussian 09 program. The infrared and Raman spectra were simulated and assigned for C60Cl6 molecule. Carbon – chlorine stretching vibrations are found to be in the range 150-900 cm-1 and the chains are strongly affected with the radial vibrations of the carbon sphere. The optimized geometries at ground-state of the molecules are calculated without any geometrical restriction, except those enforced by symmetry and the molecules are found to be minima on their respective potential energy surfaces. The optimized structures have been subjected to Gauge including atomic orbital (GIAO), the chemical shielding tensors using B3LYP/6-31G(d,p) in solvent phase with the aim of calculating 13C chemical shift values with respect to trimethylsilane (TMS) as computational reference. Molecular acuteness and stability were investigated using the Frontier molecular orbitals (FMO) analysis. The molecular electrostatic potential (MEP) mapping provides a valuable information regarding the net electrostatic effect produced by net charge distribution of the molecule. Chlorofullerenes are considered to be promising compounds for the investigation of biological action which show pronounced anti-HIV action and low toxicity. Hence, these results set goal in scheming the biocompatible molecules which will be useful in the field of carbon nano medicine and drug delivery application.

Unimolecular Reactions of 2-Methyloxetanyl and 2-Methyloxetanylperoxy Radicals.

Alkyl-substituted cyclic ethers are intermediates formed in abundance during the low-temperature oxidation of hydrocarbons and biofuels via a chain-propagating step with ȮH. Subsequent reactions of cyclic ether radicals involve a competition between ring opening and reaction with O2, the latter of which enables pathways mediated by hydroperoxy-substituted carbon-centered radicals (Q̇OOH). Due to the resultant implications of competing unimolecular and bimolecular reactions on overall populations of ȮH, detailed insight into the chemical kinetics of cyclic ethers remains critical to high-fidelity numerical modeling of combustion. Cl-initiated oxidation experiments were conducted on 2-methyloxetane (an intermediate of n-butane oxidation) using multiplexed photoionization mass spectrometry (MPIMS), in tandem with calculations of stationary point energies on potential energy surfaces for unimolecular reactions of 2-methyloxetanyl and 2-methyloxetanylperoxy isomers. The potential energy surfaces were computed using the KinBot algorithm with stationary points calculated at the CCSD(T)-F12/cc-pVDZ-F12 level of theory. The experiments were conducted at 6 Torr and two temperatures (650 K and 800 K) under pseudo-first-order conditions to facilitate Ṙ + O2 reactions. Photoionization spectra were measured from 8.5 eV to 11.0 eV in 50-meV steps, and relative yields were quantified for species consistent with Ṙ → products and Q̇OOH → products. Species detected in the MPIMS experiments are linked to specific radicals of 2-methyloxetane. Species from Ṙ → products include methyl, ethene, formaldehyde, propene, ketene, 1,3-butadiene, and acrolein. Ion signals consistent with products from alkyl radical oxidation were detected, including for Q̇OOH-mediated species, which are also low-lying channels on their respective potential energy surfaces. In addition to species common to alkyl oxidation pathways, ring-opening reactions of Q̇OOH radicals derived from 2-methyloxetane produced ketohydroperoxide species (performic acid and 2-hydroperoxyacetaldehyde), which may impart additional chain-branching potential, and dicarbonyl species (3-oxobutanal and 2-methylpropanedial), which often serve as proxies for modeling reaction rates of ketohydroperoxides. The experimental and computational results underscore that reactions of cyclic ethers are inherently more complex than currently prescribed in chemical kinetic models utilized for combustion.

Accessing unusual heterocycles: ring expansion of benzoborirenes by formal cycloaddition reactions.

Benzoborirenes are a very rare class of strained boron heterobicyclic systems. In this study a kinetically stabilized benzoborirene 1 is shown to react with multiple bonds of trimethylphosphine oxide, acetaldehyde, and tert-butyl isonitrile. The (2 + 2) cycloaddition product with trimethylphosphine oxide, benzo[c][1,2,5]oxaphosphaborole, has a long apical PO bond (194.0 pm) that must be considered on the border line between ionic and covalent according to the natural bond orbital, quantum theory of atoms in molecules, and compliance matrix approaches to the description of chemical bonding. The coordination compound between the benzoborirene and phosphine oxide was observed by NMR spectroscopy at 213 K. The Lewis acidity of 1 is similar to that of B(OCH2CF3)3 and B(C6F5)3 based on the 31P{1H} NMR chemical shift of the Lewis acid base complexes with trimethylphosphine oxide at 213 K. Benzoboriene 1 does not react with acetone, but forms a (2 + 2) cycloaddition product, an oxaborole, with acetaldehyde. In contrast, it undergoes a double (2 + 1) reaction with tert-butyl isonitrile to yield a boro-indane derivative under mild conditions. The observed reactivity of 1 is in agreement with computational analyses of the respective potential energy surfaces.

The many-body expansion for metals. I. The alkaline earth metals Be, Mg, and Ca

We examine the many-body expansion (MBE) for alkaline earth metal clusters, Ben, Mgn, Can (n = 4, 5, 6), at the Møller–Plesset second order perturbation theory, coupled-cluster singles and doubles with perturbative triples, multi-reference perturbation theory, and multi-reference configuration interaction levels of theory. The magnitude of each term in the MBE is evaluated for several geometrical configurations. We find that the behavior of the MBE for these clusters depends strongly on the geometrical arrangement and, to a lesser extent, on the level of theory used. Another factor that affects the MBE is the in situ (ground or excited) electronic state of the individual atoms in the cluster. For most geometries, the three-body term is the largest, followed by a steady decrease in absolute energy for subsequent terms. Though these systems exhibit non-negligible multi-reference effects, there was little qualitative difference in the MBE when employing single vs multi-reference methods. Useful insights into the connectivity and stability of these clusters have been drawn from the respective potential energy surfaces and quasi-atomic orbitals for the various dimers, trimers, and tetramers. Through these analyses, we investigate the similarities and differences in the binding energies of different-sized clusters for these metals.

Better force fields start with better data: A data set of cation dipeptide interactions

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids – including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.

Computational discovery of two-dimensional copper chalcogenidesCuX(X= S, Se, Te)

We investigate the energy landscape of 2D CuS, CuSe, and CuTe compounds using a global evolutionary algorithm in combination with density functional theory. Four low-lying energy ${\mathrm{Cu}}_{2}{X}_{2}$ (X=S, Se, Te) slabs with $P\overline{3}m1$, $P4/mmm$, $P4/nmm$, and $Pmmn$ symmetries have been identified on their respective potential energy surfaces. Three structures present tetrahedral ${\mathrm{Cu}X}_{4}$ motifs which pave the 2D slabs, while the latter is based on shared ${\mathrm{Cu}}_{4}{X}_{2}$ octahedra. The viability of each phase was examined by looking at dynamical, thermodynamic, and thermal stability criteria. We find that 2D copper monosulfide crystallizes in the $P\overline{3}m1$ phase, reminiscent of the covalent slab found in the $\mathrm{Ca}{\mathrm{Al}}_{2}{\mathrm{Si}}_{2}$ prototype. Two polymorphs of 2D copper selenide with symmetries $P\overline{3}m1$ and $P4/mmm$ are close in energy. The latter ${\mathrm{Cu}}_{2}{\mathrm{Se}}_{2}$ slab is made of fused ${\mathrm{Cu}}_{4}{\mathrm{Se}}_{2}$ square bipyramids with electronegative Se atoms in apical positions. Finally, the ground-state 2D CuTe has a $Pmmn$ space group containing distorted ${\mathrm{CuTe}}_{4}$ tetrahedra with some Te--Te bonding. The electronic and bond analyses show that all of these predicted 2D CuX phases are metallic with ionocovalent bonds.

Molecular simulation of flows in thermochemical non-equilibrium around a cylinder using ab initio potential energy surfaces for N2 + N and N2 + N2 interactions

We present two-dimensional direct molecular simulation (DMS) results for high-enthalpy nitrogen flows in thermochemical non-equilibrium around a circular cylinder. The simulations are carried out using accurate ab initio potential energy surfaces (PES) to describe N2 + N and N2 + N2 interactions. Select comparisons with the direct simulation Monte Carlo method are presented to demonstrate how the high-fidelity DMS data, both at the level of bulk flow quantities and local molecular distributions, can be used to thoroughly inform or validate simplified reduced-order descriptions. Then, a partially dissociated nitrogen flow around a circular cylinder is obtained from two successive refinements of a well-established ab initio nitrogen PES. The only input in both calculations is the respective PESs, all other simulation parameters being precisely equal. This work, enabled by large scale computing, represents the first attempt at establishing a rigorous methodology for (i) the validation of lower-fidelity, computationally efficient models using ab initio, assumption-free calculations (DMS) as benchmarks and (ii) a systematic assessment of ab initio PES accuracy using entire flow field results.

Generation, Characterization, and Dissociation of Radical Cations Derived from Prolyl-glycyl-glycine.

Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG•+) and its sequence ions [a3 + H]•+ and [b2 - H]•+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)]•2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG•+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a3 + H]•+ and [b2 - H]•+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG•+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a3 + H]•+ and [b2 - H]•+ ions.

Nonadiabatic Excited-State Molecular Dynamics for Open-Shell Systems.

Nonadiabatic Molecular Dynamics (NAMD) of excited states has been widely used in the simulation of photoinduced phenomena. However, the inability to treat bond breaking and forming processes with single-reference electronic structure methods limits their application in photochemistry for extended molecular systems. In this work, the extension of excited-state NAMD for open-shell systems is developed and implemented in the NEXMD software. We present the spin-unrestricted CIS and TD-SCF formalism for the ground and excited states, analytical derivatives, and nonadiabatic derivative couplings for the respective potential energy surfaces. This methodology is employed to study the photochemical reaction of three model molecules. The results demonstrate the advantage of the open-shell approach in modeling photochemical reactions, especially involving bond breaking processes. We find that the open-shell method lowers the reaction barrier at the bond-breaking limits resulting in larger calculated photochemical quantum yields compared to the respective closed-shell results. We also address problems related to spin contamination in the open-shell method, especially when molecular geometries are far from equilibrium.

C → N coordination bonds in (CCC) → N + ← (L) complexes

Quantum chemical calculations were performed on a series of novel divalent NI compounds, CCC → N+ ← CO (1), CCC → N+ ← N2 (2), CCC → N+ ← PPh3 (3), CCC → N+ ← C(NH2)2 (4), CCC → N+ ← NHCMe (5) CCC → N+ ← N-methyl-4-pyridylidene (6) and CCC → N+ ← Cyclopropenylidene (7), where CCC is a carbocyclic carbene (cyclohexa-2,5-diene-4-(diaminomethynyl)-1-ylidene). Complete optimization of 3D structures indicates that the chosen structures are the global minima on their respective potential energy surfaces (tautomeric alternatives are much less stable). The CCC → N+ coordination bond length is in the range of 1.353–1.399 A, supporting the C → N coordination bond character. This is also supplemented by very low CCC → N bond rotational barriers (> 8 kcal/mol). The CCC → N ← L angles are in the range of 118°–131°, suggesting that there is no heteroallene-type character at the central nitrogen atom. Electron localization function, lone pair occupancy calculations and partial charge analysis indicate the presence of excess electron density at the N+ centre. The nucleophilicity of the designed compounds was further measured by calculating the proton affinity and complexation energies with various Lewis acids like BH3, AlCl3 and AuCl at the N+ centre. All these studies suggest the presence of divalent NI character in the designed compounds 1–7.

The role of Li+ ions in the gas phase dehydrohalogenation and dehydration reactions of i-C3H7Br and i-C3H7OH molecules studied by radiofrequency-guided ion beam techniques and ab initio methods.

Gas phase reactive collisions between lithium ions and i-C3H7X (X = Br, OH) molecules have been studied under single collision conditions in the center of mass (CM) 0.01-10.00 eV energy range using a radiofrequency-guided ion beam apparatus. Mass spectrometry analysis of the products did show the presence of [C3H6-Li]+, [HX-Li]+, C3H7+, and C2H3+ as well as of the [Li-i-C3H7Br]+ adduct while [Li-i-C3H7OH]+ was hardly detected. For all these reactive processes, the corresponding cross sections have been measured in absolute units as a function of the CM collision energy. Quantum chemistry ab initio calculations done at the second order Möller Plesset level have provided relevant information on the topology of the potential energy surfaces (PESs) where a reaction takes place allowing the characterization of the stationary points on the respective PESs along their reaction pathways. The connectivity of the different stationary points localized on the PESs was ensured by using the intrinsic reaction coordinate (IRC) method, confirming the adiabatic character of the reactions. The main topology features of the reactive PESs, in the absence of dynamical calculations, were used to interpret at the qualitative level the behavior of the experimental excitations functions, evidencing the role played by the potential energy barriers on the experimental dynamics of the reactions. Reaction rate constants at 303.2 K for different reactions have been calculated from measured excitation functions.

Formation of Potential Interstellar Noble Gas Molecules in Gas and Adsorbed Phases.

The discovery of naturally occurring ArH+ in various regions of the interstellar medium has shown the need for more understanding of the reactions that lead to covalently bonded noble gas molecules. The test comes with trying to predict the formation of other small noble gas molecules. Many molecules have been observed in various interstellar environments, which possess the possibility of bonding with noble gases. This work explores how both argon and neon can form bonds to ligands made of these species through quantum chemical computations. Argon and neon are chosen as they are among the most abundant atoms in the universe but are more polarizable than the more common but smaller helium atom. Reactions leading to noble gas molecules are modeled in the gas phase as well as through the adsorbed phase by catalysis with a polycyclic aromatic hydrocarbon (PAH) surface. The adsorption energy of the neutral noble gas atoms to the surface increases as the size of the PAH also increases but this is still less than 10 kcal/mol. It is proposed and supported herein that an incoming molecule can bond with the noble gas atom adsorbed onto the PAH, form a stable structure, and allow the PAH to function as the leaving group. This work shows that the noble gas molecules ArCCH+, ArOH+, ArNH+, and NeCCH+ are not only stable minima on their respective potential energy surfaces but also can be formed in either the gas phase or through PAH adsorption with known or hypothesized interstellar molecules. Most notably, NeCCH+ does not appear to form in the gas phase but could be catalyzed on PAH surfaces. Hence, the interstellar detection of such molecules could also serve as a probe for the observation of interstellar PAHs.

ChemInform Abstract: Experimental and Theoretical Determination of Dissociation Energies of Dispersion‐Dominated Aromatic Molecular Complexes

AbstractReview: 305 refs.

Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes

The dissociation energy (D0) of an isolated and cold molecular complex in the gas-phase is a fundamental measure of the strength of the intermolecular interactions between its constituent moieties. Accurate D0 values are important for the understanding of intermolecular bonding, for benchmarking high-level theoretical calculations, and for the parametrization of force-field models used in fields ranging from crystallography to biochemistry. We review experimental and theoretical methods for determining gas-phase D0 values of M·S complexes, where M is a (hetero)aromatic molecule and S is a closed-shell "solvent" atom or molecule. The experimental methods discussed involve M-centered (S0 → S1) electronic excitation, which is often followed by ionization to the M(+)·S ion. The D0 is measured by depositing a defined amount of vibrational energy in the neutral ground state, giving M(‡)·S, the neutral S1 excited state, giving M*·S, or the M(+)·S ion ground state. The experimental methods and their relative advantages and disadvantages are discussed. Based on the electronic structure of M and S, we classify the M·S complexes as Type I, II, or III, and discuss characteristic properties of their respective potential energy surfaces that affect or hinder the determination of D0. Current theoretical approaches are reviewed, which comprise methods based on a Kohn-Sham reference determinant as well as wave function-based methods based on coupled-cluster theory.

The Design of "Neutral" Carbanions with Intramolecular Charge Compensation.

Strategies to construct zwitterionic anions from the parent anions are proposed. Two principles are employed; the cationic counterpart is (a) attached as a substituent or (b) inserted as an integral part at a remote location in the assembly. The optimized geometries reveal that a striking similarity exists between the zwitterions and the respective precursor parent anion. The computed vibrational frequencies emphasize that these novel entities are minima on their respective potential energy surfaces. A substantial HOMO-LUMO gap indicates that the proposed structures do not show instability in their respective electronic states and that the higher energy configuration states do not contribute to the ground state viability. The separation of charge between the monopoles in these zwitterions is demonstrated by moderately large nonzero dipole moments. Significant large energy barriers for rearrangement to the closely related positional isomers, demonstrated in a few cases, advocate the thermal stability (associated with spectroscopic viability) of the novel molecules. The donor capacity (basicity) of the anionic subunit in these zwitterions is comparable to that of the respective parent anions. Since the qualitative and quantitative features in the designed charged compensated complexes are conserved as anions, these molecules may perhaps be employed in synthetic organic or organometallic chemistry.

Computational prediction of electronic excited-state structures and properties of 2,4-dinitroanisole (DNAN)

This manuscript reports results of density functional theory (DFT) investigation on ground-state and electronic excited-state structures of 2,4-dinitroanisole (DNAN) in the bulk water solution. The cam-B3LYP functional along with 6-311G(d,p) basis set was used, and time-dependent DFT (TD-DFT) method was used for excited-state calculations. The effect of bulk water was modeled using the CPCM approach. Nature of potential energy surfaces (PESs) was ascertained through the harmonic vibrational frequency analysis; all optimized geometries were found to be minima at the respective PESs. It was predicted that singlet excited-state geometries are significantly changed compared to the ground state. Further, it was also revealed that irrespective of nature of the electronic singlet excited states, the length of C7O1 bond is increased compared to the ground state. Further, electronic structures and properties consequent to electronic excitations are also discussed.

Accurate ab initio vibrational energies of methyl chloride

Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( HL), are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-1), respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.

Noble-Gas-Inserted Fluoro(sulphido)boron (FNgBS, Ng = Ar, Kr, and Xe): A Theoretical Prediction.

The possibility of the existence of a new series of neutral noble gas compound, FNgBS (where Ng = Ar, Kr, Xe), is explored theoretically through the insertion of a Ng atom into the fluoroborosulfide molecule (FBS). Second-order Møller-Plesset perturbation theory, density functional theory, and coupled cluster theory based methods have been employed to predict the structure, stability, harmonic vibrational frequencies, and charge distribution of FNgBS molecules. Through energetics study, it has been found that the molecules could dissociate into global minima products (Ng + FBS) on the respective singlet potential energy surface via a unimolecular dissociation channel; however, the sufficiently large activation energy barriers provide enough kinetic stability to the predicted molecules, which, in turn, prevent them from dissociating into the global minima products. Moreover, the FNgBS species are thermodynamically stable, owing to very high positive energies with respect to other two two-body dissociation channels, leading to FNg + BS and F(-) + NgBS(+), and two three-body dissociation channels, corresponding to the dissociation into F + Ng + BS and F(-) + Ng + BS(+). Furthermore, the Mulliken and NBO charge analysis together with the AIM results reveal that the Ng-B bond is more of covalent in nature, whereas the F-Ng bond is predominantly ionic in character. Thus, these compounds can be better represented as F(-)[NgBS](+). This fact is also supported by the detail analysis of bond length, bond dissociation energy, and stretching force constant values. All of the calculated results reported in this work clearly indicate that it might be possible to prepare and characterize the FNgBS molecules in cryogenic environment through matrix isolation technique by using a mixture of OCS/BF3 in the presence of large quantity of noble gas under suitable experimental conditions.

Kinetics and mechanism of gas-phase reaction of CF3OCH2CH3 (HFE-263) with the OH radical — a theoretical study

In the present study, the density functional method with recently developed M06 functionals has been used to study the reaction of CF3OCH2CH3 with the OH radical. All possible hydrogen abstraction and displacement reaction channels have been modeled. The minimum energy path on the respective potential energy surface and energetics were calculated at the M06-2X/6-311++G(d,p) level of theory. Two different reaction mechanisms were considered: (i) reactant and product complexes called the complex mechanism and (ii) the direct mechanism (reactant → transition state → product). Tunneling corrections were made using the Eckart unsymmetrical potential. The overall rate constant calculated by the complex mechanism (keff = 1.8 × 10−13 cm3 molecule−1 s−1) has been found to be in good agreement with the experimentally determined value (1.5 ± 0.25 × 10−13 cm3 molecule−1 s−1), while the rate constant calculated by the direct mechanism (kD = 7.6 × 10−14 cm3 molecule−1 s−1) is about two times lower than the experimental value. The theoretical studies show that hydrogen atom abstraction from the –CH2– site is the most favorable reaction pathway and the reaction involves prereactive and product complexes before leading to stable product formation.