MP2 Level Research Articles

Hydrolysis versus aminolysis of a potential nerve agent tabun: a computational reaction mechanism study

The mechanism for the hydrolysis and aminolysis reactions of potential nerve agent tabun have been investigated both at DFT/M062X level and at ab initio MP2 level of theory. Effect of solvent water has also been incorporated using Minnesota SMD model. Based on leaving groups, there are three probable dissociation pathways of tabun: (1) elimination of HCN, (2) elimination of dimethyl amine and (3) elimination of ethanol. Each of the pathways follows a stepwise neutral route through two transition states. From the mechanism, it has been established that the HCN removal pathway is most favorable than the other two due to greater leaving tendency of the cyanide group. The reaction possesses two four-membered transition state in each path, i.e., for the addition of ammonia/water and for the release of leaving groups. As the four-membered cyclic TSs are not so favorable, the investigated reactions were found quite a bit high energetic. The first addition step of the H2O or NH3 is found as the rate-determining step. The reactivity of ammonia toward tabun has been found highly favorable (by ~ 7.6 kcal mol−1) than the water. This can be easily explained using the fact that the nucleophilicity of NH3 is higher than the H2O. Further, we have seen that water can be a very effective catalyst in the aminolysis reaction as it reduces the barrier of activation of the RDS by ~ 10 kcal mol−1. Self-catalyzed hydrolysis of water has also been performed, and it decreases the activation of ~ 11 kcal mol−1 than the uncatalyzed pathways. The significant reduction of energy of activation takes place due to the formation of six-membered transition states that makes much easier hydrogen transfer compared to the four-membered transition state formed in case of uncatalyzed aminolysis reactions.

Computation of NMR Shielding Constants for Solids Using an Embedded Cluster Approach with DFT, Double-Hybrid DFT, and MP2.

In this work, we explore the accuracy of post-Hartree–Fock (HF) methods and double-hybrid density functional theory (DFT) for the computation of solid-state NMR chemical shifts. We apply an embedded cluster approach and investigate the convergence with cluster size and embedding for a series of inorganic solids with long-range electrostatic interactions. In a systematic study, we discuss the cluster design, the embedding procedure, and basis set convergence using gauge-including atomic orbital (GIAO) NMR calculations at the DFT and MP2 levels of theory. We demonstrate that the accuracy obtained for the prediction of NMR chemical shifts, which can be achieved for molecular systems, can be carried over to solid systems. An appropriate embedded cluster approach allows one to apply methods beyond standard DFT even for systems for which long-range electrostatic effects are important. We find that an embedded cluster should include at least one sphere of explicit neighbors around the nuclei of interest, given that a sufficiently large point charge and boundary effective potential embedding is applied. Using the pcSseg-3 basis set and GIAOs for the computation of nuclear shielding constants, accuracies of 1.6 ppm for 7Li, 1.5 ppm for 23Na, and 5.1 ppm for 39K as well as 9.3 ppm for 19F, 6.5 ppm for 35Cl, 7.4 ppm for 79Br, and 7.5 ppm for 25Mg as well as 3.8 ppm for 67Zn can be achieved with MP2. Comparing various DFT functionals with HF and MP2, we report the superior quality of results for methods that include post-HF correlation like MP2 and double-hybrid DFT.

Simulation of main chain liquid crystalline polymers using a Gay-Berne/Lennard-Jones hybrid model

Main chain liquid crystalline polymers (MCLCP) offer strong potential to exhibit auxetic properties. However, the first synthesized molecules did not show the expected results. To address this issue, simulation provides an interesting advantage as it can grasp the molecular reasons why the auxetism is not reached, and thus it can guide the synthesis of successful candidates. However, the crucial step of validation is mandatory. In this study, we report the simulation of MCLCP at the coarse-grained level. Interactions are represented by an hybrid Gay-Berne/Lennard Jones (GB/LJ) potential which is particulary adapted in the simulation of anisotropic systems. Energies stemming from different configurations of pairs of ellipsoids are computed at the MP2 level, and are fitted using the GB potential. The methylene groups are represented by spheres whose interactions are depicted by the LJ potential. Molecular dynamics in the NPT ensemble (number of particles, pressure and temperature are kept constant) are thus carried out beginning at 800 K to 375 K, by cooling the system by 25 K steps. It is shown that the smectic A phase emerges at about 500 K, and the smectic B phase at about 425 K. Such mesophases occur without the use of any external stimulus. These findings pave the way to simulate LCP which have been specifically designed to potentially exhibit auxetic properties.

Pentavalent P…π phosphorus bonding with associated Cl…π halogen bonding in influencing the geometry of POCl3-Phenylacetylene heterodimers: Evidence from matrix isolation infrared spectroscopy and ab initio computations

Of the two diverse oxidation states, phosphorus exists in its pentavalent state in a majority of real-life systems. In the present study, the role of Cl…π halogen bonding with co-operative pentavalent P…π phosphorus bonding in influencing the geometry of POCl3-PhAc heterodimers has been experimentally proved at low temperatures. The experiments were performed by co-deposition of POCl3 and PhAc under matrix isolated conditions followed by infrared spectral characterization. The structural elucidation of all possible 1:1 POCl3-PhAc heterodimers was accomplished using ab initio and DFT computational methodologies. Of the four minima revealed by computations performed at MP2 level of theory using aug-cc-pVDZ basis set, the energetically favoured minimum generated experimentally was stabilized dominantly by Cl…π halogen bonding interactions. However, the associated primary role of P…π phosphorus bonding in determining the geometry of this dimer has been firmly established, with reinforcements from Electrostatic Potential Mapping, Natural Bond Orbital, Energy Decomposition and Non-Covalent Interaction analyses.

Cis-trans isomerization is not rate determining for b2 ion structures: A guided ion beam and computational study of the decomposition of H+(GlyProAla)

Decomposition of the protonated tripeptide, GlyProAla (H+GPA), through collision-induced dissociation with Xe in a guided ion beam tandem mass spectrometer (GIBMS) is examined. Cross sections for the formation of [b2]+, [y2 + 2H]+, [a1]+, [b3]+, [a3]+, [a2]+, and H+(1-pyrroline) fragment ions were collected as a function of kinetic energy. Analysis of these cross sections include consideration of the effects of multiple collisions, dissociation lifetimes, reactant internal and kinetic energy distributions, competition among channels, and evolution into sequential channels. Structures and molecular parameters of reactants, transition states, intermediates, and products were identified using the B3LYP/6-311+G(d,p) level of theory, with single-point energy calculations performed at the B3LYP, B3P86, and MP2(full) levels of theory using a 6-311+G(2d,2p) basis set. Good agreement between experimental threshold energies and those calculated for rate-limiting transition states allow key reaction pathways for the formation of each product to be identified. The MP2(full) level of theory is found to agree best with the experimental results. Notably, even though H+GPA starts with a cis-peptide bond, it forms an oxazolone as its [b2]+ fragment and the absence of a diketopiperazine [b2]+ fragment is verified by other key observations.

End‐substituted thiahelicenes for electronic device applications

AbstractMinimum energy structures of neutral and radical cations of end‐substituted thia[n]helicenes (n = 1‐10) in DCM solvent are reported. For both neutral and radical cations of these helicenes, calculated structures are nonplanar for n = 3 to 10. Helical structures are obtained for higher helicenes, and the thia[8]helicene system has a helical structure with one complete turn. Equilibrium structures are predicted by using B3LYP‐D/6‐311++G(d,p) method in conjunction with the solvation model based on solute density. Single‐point energy calculations are also performed at the MP2 level to improve certain energy parameters. Excited‐state calculations are performed using time‐dependent density functional theory formalism to predict UV‐Visible spectra of neutral and radical cations of thia[n]helicenes in DCM solvent. Thia[n]helicenes radical cation have strong absorption in the near‐infrared region. Calculations also suggest that dimerization is not a favorable process in the DCM solvent for the end‐substituted neutral and radical cation of thia[7]helicene. The present theoretical study examines the molecular and electronic properties of thia[n]helicenes in search of near‐infrared electronic devices.

A New Basis Set for the Calculation of 13C NMR Chemical Shifts within a Non-empirical Correlated Framework.

A new basis set of triple-ζ quality for carbon, 3z-S, is developed and tested at the DFT, MP2, and CCSD(T) levels, taking into account solvent and vibrational corrections for a number of molecules ranging from the smallest fluoromethane, CH3F, to the largest 5,10,15,20-tetraphenylporphyrin, C44H30N4. The proposed highly economical 3z-S basis set has been proven to provide very good accuracy in all examinations, comparable to that of the NMR-oriented Jensen's pcS-2 basis set, which is about 50% larger than 3z-S.

Can an Elusive Platinum(III) Oxidation State be Exposed in an Isolated Complex?

AbstractPlatinum(IV) complexes are extensively studied for their activity against cancer cells as potential substitutes for the widely used platinum(II) drugs. PtIV complexes are kinetically inert and need to be reduced to PtII species to play their pharmacological action, thus acting as prodrugs. The mechanism of the reduction step inside the cell is however still largely unknown. Gas‐phase activation of deprotonated platinum(IV) prodrugs was found to generate products in which platinum has a formal +3 oxidation state. IR multiple photon dissociation spectroscopy is thus used to obtain structural information helping to define the nature of both the platinum atom and the ligands. In particular, comparison of calculations at DFT, MP2 and CCSD levels with experimental results demonstrates that the localization of the radical is about equally shared between the dxz orbital of platinum and the pz of nitrogen on the amino group, the latter acting as a non‐innocent ligand.

Can an Elusive Platinum(III) Oxidation State be Exposed in an Isolated Complex?

Platinum(IV) complexes are extensively studied for their activity against cancer cells as potential substitutes for the widely used platinum(II) drugs. PtIV complexes are kinetically inert and need to be reduced to PtII species to play their pharmacological action, thus acting as prodrugs. The mechanism of the reduction step inside the cell is however still largely unknown. Gas-phase activation of deprotonated platinum(IV) prodrugs was found to generate products in which platinum has a formal +3 oxidation state. IR multiple photon dissociation spectroscopy is thus used to obtain structural information helping to define the nature of both the platinum atom and the ligands. In particular, comparison of calculations at DFT, MP2 and CCSD levels with experimental results demonstrates that the localization of the radical is about equally shared between the dxz orbital of platinum and the pz of nitrogen on the amino group, the latter acting as a non-innocent ligand.

A general purpose acetonitrile interaction potential to describe its liquid, solid and gas phases

A flexible and polarizable force field to describe acetonitrile in its three states of matter has been developed on the basis of an ab initio potential energy surface at the MP2 level. The acetonitrile molecule is represented by a sophisticated twelve-site model: the six nuclei plus six mobile charges. Three thousands structures have been employed for the fitting including monomers, dimers and trimers. Gas phase behavior has been tested by analyzing aggregates from dimers to 27-mer which give accurate reproducibility of the experimental and quantum-mechanical results. Classical MD simulations have been performed for the liquid and its crystalline α- and β-forms. An analysis of liquid in a wide range of structural, dynamic, energetics and spectroscopic properties has been performed, as well as neutron diffraction data. Comparison with experimental information is satisfactory. Due to the first principles nature and the polarizable character of this force field properties of the three states of matter are properly reproduced.

Analyzing the local basis set superposition error for CO adsorbed on rutile(110)

AbstractOne of the main tasks of quantum chemistry is to predict total energies for a given system within an almost nonapproximate method for a complete basis set. Unfortunately, although computational power is growing, approximate methods such as MP2 or CCSD(T) still have to be used as higher‐level methods such as full CI are computationally too demanding. Nevertheless, when using these approximations, at least an almost‐complete basis set should be used in order to avoid errors from basis set superposition or incompleteness. The aim of this work is to introduce a new method to analyze the local basis set superposition error (LBSSE) using local counterpoise corrections in order to converge a basis set for a given compound. Using this approach, we are able to define a basis set composition for a CO molecule adsorbed on rutile(110), which can be regarded as complete. In the presented work, CO adsorbed on rutile(110) and CO2 adsorbed on a model Ti3O9 cluster will be used as case examples. Therefore, in addition to a new LBSSE analysis method, adsorption energies of CO on rutile(110) at the MP2 and CCSD levels of theory are presented.

Exploring ground and low-lying excited states for diquat, paraquat, and dipyridyl isomers

In this work, we present a computational investigation on diquat, paraquat, and six dipyridyl isomers (2,2′-dipyridyl, 2,3′-dipyridyl, 2,4′-dipyridyl, 3,3′-dipyridyl, 3,4′-dipyridyl, and 4,4′-dipyridyl). Ground state properties such as equilibrium structures, relative energetics, transition states for cis–trans interconversion, and vibrational frequencies were determined for all the isomers at the MP2 level of theory with the cc-pVTZ basis set in the gas-phase; the MP2/cc-pVTZ and MP2/6-311+G(d,p) levels of theory in water were employed for diquat and paraquat. The trans structures are the most stable ones among the compounds that present such isomeric forms, with relative energies of 6.24 kcal/mol, 0.61 kcal/mol, and 0.12 kcal/mol lower than the cis counterparts in 2,2′-dipyridyl, 2,3′-dipyridyl, and 3,3′-dipyridyl, respectively. The transition state lies at 7.65 kcal/mol above the trans form in the case of 2,2′-dipyridyl, 3.68 kcal/mol for 2,3′-dipyridyl, and 2.02 kcal/mol for 3,3′-dipyridyl, indicating that the interconversion is feasible in the cases of 2,3′-dipyridyl and 3,3′-dipyridyl and unlikely to occur in 2,2′-dipyridyl at room temperature. Vertical excitation energies and respective generalized oscillator strengths (GOS) were determined using time-dependent density functional theory (CAM-B3LYP/cc-pVTZ and PBE0/cc-pVTZ) and EOM-CCSD/cc-pVTZ. In terms of excitation (and independent of computational method), all the isomers except 4,4′-dipyridyl, presented excited electronic states that are both bright (with GOS > 0.1) and energetically accessible at UV–vis wavelengths. Two bright states were found for diquat and paraquat in the UV region. Therefore, we expect that photoinduced degradation of both compounds can benefit from the utilization of techniques combining more than one source of radiation.

A Theoretical Approach to New Triplet and Quintet (nitrenoethynyl)alkylmethylenes, (nitrenoethynyl)alkylsilylenes, (nitrenoethynyl)alkylgermylenes

Experimentally unreachable reactive intermediates of triplet and quintet (nitrenoethynyl)-X-methylenes, (nitrenoethynyl)-X-silylenes, and (nitrenoethynyl)-X-germylenes were compared and contrasted at B3LYP, M06-2X, WB97XD, HF, MP2, MP4, CCSD, and QCISD(T) levels with 6-311++G(d,p) basis set (X–M–C≡C–N; M=C, Si, and Ge; X = H (1), Me (2), Et (3), Pr (4), i-Pr (5), and t-Bu (6)). The effect of small and bulky groups on these acetylene linked reactive intermediates were studied. All triplet (nitrenoethynyl)-X-methylene species were identified as ground states with one local open-shell singlet carbene (δ1π1) and other local triplet nitrene moiety (π1π1) with 47.75-55.70 kcal/mol quintet-triplet energy gap (ΔEq-t). Silylene and germylene substitutions caused the reduction of ΔEq-t. One local closed-shell singlet silylene or germylene moiety (δ2π0) and one local triplet nitrene moiety (π1π1) were connected to make triplet (nitrenoethynyl)silylenes, and (nitrenoethynyl)germylenes. The species of (nitrenoethynyl)silylenes, and nitrenoethynyl)germylenes could be applied as dipolar intermediates in mechanism identification of chemical reactions. Quintet states were found as ground states with one local triplet divalency moiety (π 1π1) and also other local triplet nitrene moiety (π1π1).

1-t-Butyl-1-phenyl-1-silacyclohexane: Synthesis, conformational analysis in gas and solution by GED, FT-IR and theoretical calculations

1-t-Butyl-1-phenyl-1-silacyclohexane 1, the first disubstituted silacyclohexane with the most bulky substituent, t-Bu group, at silicon, was synthesized via the sequence of reactions PhSiCl3 → Ph(Cl)Si(CH2)5 → Ph(t-Bu)Si(CH2)5, and its molecular structure and conformational preferences were studied by gas-phase electron diffraction (GED), temperature variable IR spectroscopy and quantum chemical calculations of the isolated conformers and their solvate complexes in gas and in polar medium. The predominance of the t-Bueq conformer in gas phase (1-Phax:1-Pheq = 92:8, ΔG° = 1.63 kcal/mol) determined from GED is consistent with the results of quantum chemical calculations at the DFT and MP2 level of theory.

Structural, spectroscopic, and photochemical study of ethyl propiolate isolated in cryogenic argon and nitrogen matrices.

Ethyl propiolate (HC≡CCOOCH2CH3, EP) was studied experimentally by infrared spectroscopy in argon and nitrogen cryomatrices (15K) and by quantum chemical calculations (at the DFT(B3LYP) and MP2 levels of theory). Calculations predict the existence of four conformers: two low-energy conformers (I and II) possessing the carboxylic moiety in the cis configuration (O=C-O-C dihedral equal to ~0°) and two higher-energy trans forms (O=C-O-C dihedral equal to ~180°; III and IV). The conformation of the ethyl ester group within each pair of conformers is either anti (C-O-C-C equal to 180°; in conformers I and III) or gauche (C-O-C-C equal to ±86.6° in II, and±92.5° in IV). The two low-energy cis conformers (I and II) were predicted to differ in energy by less than 2.5kJmol-1 and were shown to be present in the studied cryogenic matrices. Characteristic bands for each one of these conformers were identified in the infrared spectra of the matrix-isolated compound and assigned taking into account the results of normal coordinate analysis, which used the geometries and harmonic force constants obtained in the DFT calculations. The two trans conformers (III and IV) were estimated to be 17.5kJmol-1 higher in energy than the conformational ground state (form I) and were not observed experimentally. The unimolecular photochemistry of matrix-isolated EP (in N2 matrix) was also investigated. In situ irradiation with UV light (λ>235nm) leads mainly to decarbonylation of the compound, with generation of ethoxyethyne, which in a subsequent photoreaction generates ketene (plus ethene).

Metastable Dianions and Dications.

A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX32- and LX42- (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M3 X2+ (M=Li and Na, X=F and Cl), YH32+ and ZH42+ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono-ions. The dissociation profile of the molecules in two mono-ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.

Molecular hydration of carbohydrates: quantum chemical study of xylofuranose–(H2O)n clusters

The structure, energetics and vibrational spectra of xylofuranose–(H2O)n where n = 2 to 10 cluster have been investigated by using Moller–Plesset second-order perturbation theory (MP) with aug-cc-pvdz as a basis set. Complete basis set limit for the xylofuranose–water clusters were calculate at MP2 level of theory. The incoming water molecule prefers the water–water interaction over the xylose–water interaction. The structural analysis shows that the average water–water distances are observed to be of similar. The calculated O–H stretching frequency is seen to blue shift in all except di-, penta- and hepta-hydrated clusters. In these clusters, the O–H frequency red shifts from isolated xylofuranose molecule. Because the OH group in these clusters is taking part either in intermolecular hydrogen bonding with water molecule or in intramolecular H-bonding with other OH groups present in xylose ring.

The structure of benzonitrile-water complex as unveiled by matrix isolation infrared spectroscopy: Is it linear or cyclic at low temperatures?

The hydrogen bonded interaction of benzonitrile (C6H5CN)-water (H2O) complexes have been studied experimentally using matrix isolation infrared spectroscopy to elucidate the structure(s) of the binary complexes produced at low temperatures. Computations performed at MP2 and B3LYP-D3 level of theory with aug-cc-pVDZ basis set predicted two complexes, of which global minimum complex A has a cyclic structure with the interactions occurring between ortho-hydrogen of C6H5CN and oxygen of H2O and the hydrogen of H2O with π-cloud of CN in C6H5CN. The linear acylic complex B, a local minimum is stabilized through a straight C-H⋯N interaction between nitrogen of C6H5CN and hydrogen of H2O and is present at a relative energy of ∼0.7 kcal/mol with respect to global minimum. While previous gas phase studies using a number of spectroscopic probes identify exclusively the cyclic global complex, our experiments performed under isolated conditions at low temperatures uniquely produced the acyclic linear C6H5CN-H2O complex, a local minimum in the potential energy surface. The CN stretching vibrational mode of C6H5CN was exploited as a unique marker to confirm the generation of local minimum. The effect of matrixes was simulated using Onsager self-consistent reaction field model and as a result, the linear complex (complex B) turned out to be energetically favored isomer under the influence of matrixes. The hydrogen bonding interaction in both the complexes was characterized using Atoms in Molecules, Natural Bond Orbital, Energy Decomposition and Non-Covalent Interaction analyses.

Theoretical study of isomers XBEY, BEXY, and XYBE (E = N, P, and As, and X, Y = F and Cl): Substituent effect

In order to obtain significant insights into effects of the substituents on characters of the novel boron-containing molecules, the optimized structures, energetics, and potential energy surfaces of the three series isomers, XBEY, BEXY, and XYBE (E = N, P, and As, and X, Y = F and Cl), have been examined in detail using high-accuracy quantum chemical calculations, in which the corresponding values are obtained at the M06-2X, MP2, and QCISD(T) levels of theory, respectively. Our findings demonstrate that the BEXY isomers possess less stable with respect to the XYBE derivatives, implying the boron-containing molecules prefer B-substitution much more than E-substitution. Moreover, stability of the XBEY is comparable to that of the XYBE, however, the corresponding difference can be identified by substituent effect as well, that is, a more X and Y electronegativity, a larger E atomic radius, and a more B-substitution result in greater structure stabilization.

Computational analysis of vibrational frequencies and rovibrational spectroscopic constants of hydrogen sulfide dimer using MP2 and CCSD(T).

Previous studies have shown that the weakly bonded H2S dimer demands high level quantum chemical calculations to reproduce experimental values. We investigated the hydrogen bonding of H2S dimer using MP2 and CCSD(T) levels of theory in combination with aug-cc-pV(D,T,Q)Z basis sets. More precisely, the binding energies, potential energy curves, rovibrational spectroscopic constants, decomposition lifetime, and normal vibrational frequencies were calculated. In addition, we introduced the local mode analysis of Konkoli-Cremer to quantify the hydrogen bonding in the H2S dimer as well as providing for the first time the comprehensive decomposition of normal vibrational modes into local modes contributions, and a decomposition lifetime based on rate constant. The local mode force constant of the H2S dimer hydrogen bond is smaller than that of the water dimer, in accordance with the weaker hydrogen bonding in the H2S dimer.