MP2 Methods Research Articles

A theoretical investigation on the complexes of B3O3H3 with acetylene and its substituted derivatives.

The complexes of B3O3H3 with acetylene and its substituted derivatives C2HX (X=H, F, Cl, Br, CH3, NH2) are explored by theoretical calculations using MP2 and M06-2X methods with aug-cc-pVDZ as the basis set. The different molecular electrostatic potential features of B3O3H3 with benzene (C6H6) and borazine (B3N3H6) result in different stable structures of the complexes with C2HX. The geometric analysis indicates that the global minimum is the parallel stacked (PS) structure with the linear C-C triple bond lies on the top of B3O3H3, and this is much different from that of the B3N3H6...C2HX complex, in which the C-H bond directs towards the B3N3H6 ring (T-shaped). The H-bonded structure where the C-H interacts with the O atom of B3O3H3 is found to be a local minimum. Besides, there is an additional X…O halogen-bonded structures for the B3O3H3…C2HX (X=Cl, Br) complexes. As for the PS geometry, when one H atom in C2H2 is replaced by different X groups, the binding energies of the complexes increases in the order of F<H<Cl<Br<CH3<NH2, which is mainly determined by the strength of the π-hole bond. The nature of interaction in these complexes is further studied by the atoms-in-molecules (AIM) and noncovalent interaction (NCI) analysis. The natural bond orbital (NBO) analysis indicates that the main orbital interaction arises from LPX→BD*B‑O for B3O3H3…C2HX (X=Cl, Br, NH2), and BDC‑C→BD*B‑O for B3O3H3…C2HX (X=H, CH3) complexes. Complexes of B3O3H3 with acetylene and its substituted derivatives.

Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies.

Bacterial proteins dubbed virulence factors (VFs) are a highly diverse group of sequences, whose only obvious commonality is the very property of being, more or less directly, involved in virulence. It is therefore tempting to speculate whether their prediction, based on direct sequence similarity (seqsim) to known VFs, could be enhanced or even replaced by using machine-learning methods. Specifically, when trained on a large and diverse set of VFs, such may be able to detect putative, non-trivial characteristics shared by otherwise unrelated VF families and therefore better predict novel VFs with insignificant similarity to each individual family. We therefore first reassess the performance of dimer-based Support Vector Machines, as used in the widely used MP3 method, in light of seqsim-only and seqsim/dimer-hybrid classifiers. We then repeat the analysis with a novel, considerably more diverse data set, also addressing the important problem of negative data selection. Finally, we move on to the real-world use case of proteome-wide VF prediction, outlining different approaches to estimating specificity in this scenario. We find that direct seqsim is of unparalleled importance and therefore should always be exploited. Further, we observe strikingly low correlations between different feature and classifier types when ranking proteins by VF likeness. We therefore propose a 'best of each world' approach to prioritize proteins for experimental testing, focussing on the top predictions of each classifier. Further, classifiers for individual VF families should be developed.

Reactivity of Hydrated Hydroxide Anion Clusters with H and Rb: An ab Initio Study.

We present a theoretical investigation of the hydrated hydroxide anion clusters, OH(H2O)n-, and of the collisional complexes, H-OH(H2O)n- and Rb-OH(H2O)n- (with n = 1-4). The MP2 and CCSD(T) methods are used to calculate interaction energies, optimized geometries, and vertical detachment energies. Parts of the potential energy surfaces are explored with a focus on the autodetachment region. We point out the importance of diffuse functions to correctly describe the latter. We use our results to discuss the different water loss and electronic detachment channels, which are the main reaction routes at room temperature and below. In particular, we have considered a direct and an indirect process for the electronic detachment, depending on whether water loss follows or precedes the detachment of the excess electron. We use our results to discuss the implications for astrochemistry and hybrid trap experiments in the context of cold chemistry.

Spectroscopic constants and anharmonic force fields of F2SO: An ab inito study

The equilibrium geometry, spectroscopic constants and anharmonic force field of F2SO (X∼1A′) have been reported employing B3LYP, B3P86, B3PW91 and MP2 methods combining with Dunning’s correlation-consistent cc-pVQZ, cc-pV5Z, aug-cc-pVQZ and aug-cc-pV5Z basis sets. The calculated equilibrium geometry, equilibrium rotational constants and fundamental vibrational frequencies of F2SO well reproduce the previous theoretical or experimental values. The calculated equilibrium geometry verifies that F2SO has pyramidal structure and Cs symmetry instead of C1 symmetry. The ground-state rotational constants, harmonic vibrational frequencies, anharmonic constants, quartic and sextic centrifugal distortion constants, cubic and quartic force constants, vibration-rotation interaction constants, and Coriolis coupling constants of F2SO are also predicted. The calculated results show that B3P86 and MP2 methods are superior to B3LYP and B3PW91 methods for the spectroscopic constants of F2SO, we hope that our predictions can provide the useful data for the experiment study of the corresponding spectroscopic constants of F2SO.

Cyclonona‐3,5,7‐trienylidene and its Si, Ge, Sn, and Pb analogs versus their α‐halogenated derivatives at B3LYP and MP2 methods

AbstractFive sets of group 14 sextet cyclic unsaturated divalent species including carbenes (1X), silylenes (2X), germylenes (3X), stannylenes (4X), and plumbylenes (5X) are compared and contrasted at B3LYP/AUG‐cc‐pVTZ//B3LYP/6‐311 + G* and MP2/AUG‐cc‐pVTZ//MP2/6‐311 + G* levels of theory, where X = H, F, Cl, and Br. The scrutinized carbenes consisting of cyclonona‐3,5,7‐trienylidene (1H) and its 2,2,9,9‐tetrahalo derivatives (1Cl, 1Br) appear as boat shaped minima except for 1H which turns out as a boat shaped transition state for having a negative force constant. All of carbenes (1H, 1Cl, and 1Br) have triplet ground states except for 1F. In contrast, all of the corresponding 2X‐ 5X metallylenes appear as singlet boat shaped minima on their potential energy surfaces. Stability (estimated by ΔEs‐t, ie, energy gap between singlet [s] and triplet states) appear as a function of size and decreases by going down in group 14 column: 5X &gt; 4X &gt; 3X &gt; 2X &gt; 1X. Exclusive of carbene set, within other four sets stability decreases by going down in group 17 column: Br &gt; Cl &gt; F &gt; H. Hence, singlet 2,2,9,9‐tetrabromocyclonona‐3,5,7‐trienplumbylene, 5Br, appears as the most stable sextet divalent with no tendency for dimerization. Comparison is extended to the structural parameters, band gap, nucleophilicity, electrophilicity, isodesmic reactions, and dimerization.

Theoretical study of the internal rotational barriers of fluorine, chlorine, bromine, and iodine-substituted ethanes

Physical and chemical characteristics of flexible compounds are extremely dependent of internal rotation barriers. On the other hand, halides of organic compounds are extremely common, and the nature of their rotation barriers are still poorly understood. As a simple example, the experimental height of the internal rotational barrier decreases with the number of fluorine-substituted in ethane, C2H5F, C2H4F2, and C2H3F3. For chlorine-substituted ethane C2H5Cl, C2H4Cl2 and C2H3Cl3 the internal rotational barrier converges in an opposite manner. No experimental results are available for the bromine- and iodine-substituted compounds C2H5Br, C2H4Br2, C2H3Br3, C2H5I, C2H4I2, and C2H3I3. In light of lack of both an adequate explanation for this phenomenon and experimental results for Br and I, the present work studied these compounds using different levels of theory: MP2, MP3, MP4, QCISD(T) and CCSD(T) methods, and the G3 and G3CEP composite theories. The results showed that the G3 and G3CEP theories were the most accurate calculations for the F- and Cl-substituted compounds as a result of the additive contributions of the energy values. From Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Energy Decomposition Analysis (EDA) it was verified that the internal rotational barriers decrease with the addition of Fluorine atoms for fluorine-containing ethanes and can be explained by: π character in the CF bond and delocalization indexes (DI(A)) by QTAIM analysis; the interaction of the ligand and anti-ligand orbitals by NBO analysis and for the descriptors by EDA. On the other hand, the enlargement of the barriers with the addition of Cl, Br and I atoms for substituted ethanes, are dominated by the large electronic cloud of these halogens, which generates significant steric repulsion.

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

The conformational equilibrium of thymidine and deuterothymidine molecules in low-temperature Ar matrices has been studied using low-temperature matrix-isolation Fourier IR spectroscopy and quantum-chemical calculations by the DFT/B3LYP and MP2 methods. It has been found that two anti-conformers ta2_0 and ta3_0 with different structures of the sugar ring, C2′-endo and C3′-endo, predominate in low-temperature matrices. In isolated state, each of these conformers has a few low-barrier satellites that can fully pass into more stable structures when a molecule enters the matrix. The main syn conformer ts2_0 is stabilized by an intramolecular hydrogen bond between the O5′H group of the sugar and the C2O group of the base (O5′H⋅⋅⋅O2), while C2′-endo is the predominant conformation of the deoxyribose ring. The considerably lower population of ts2_0 compared to the anti-conformers ta2_0, ta3_0 can be explained by the smaller population of satellite conformations. It has been shown that the absorption band of νN3D stretching vibration is split by the Fermi resonance.

Theoretical study of the substituent effect on corrosion inhibition performance of benzimidazole and its derivatives

The substituent effects of electron-donating and -withdrawing on the efficiency of corrosion inhibition of benzimidazole and its derivatives have been studied by density functional theory DFT and Moller – Plesset perturbation theory MP2 calculations at aqueous medium. For this investigation, the corrosion inhibition efficiencies of the protonated and non-protonated spesies of benzimidazole and its derivatives were correlated with molecular electronic properties: high occupied molecular orbital (HOMO) and low unoccuppied molecular orbital (LUMO) energies, ionization potential, electron affinity, electronegativity and fraction number of electron transfer. The dipole moment and interaction energy represent the total surface coverage and the strength of the adsorption of inhibitors on the metal surface. Natural bond orbital NBO analysis in term of the second order interaction energies were used to study the contributions of the active sites of inhibitors toward corrosion inhibition performances. The ionization potential of the inhibitors has a strong influence on the efficiency of corrosion inhibitors. It was found that the MP2 method accurately predicted the ionization potential while the DFT failed to mimic the ionization potential of the experimental results. The linear correlation was shown between electronic properties and corrosion inhibition efficiency. Electron donating substituents increase the corrosion inhibition efficiency, whereas electron withdrawing substituents give the opposite effect. The NH2 substituent contributes highest, whereas NO2 provides the weakest contribution to the corrosion inhibition efficiency for both non-protonated and protonated species of inhibitors. The second order interaction energy indicated that heteroatom at imidazole position was the main center of electron donating and they received simultaneously significant amount of electron back donation from the metal

Theoretical insights on nonradiative deactivation mechanisms of protonated xanthine

The nonradiative deactivation mechanisms of the lowest 1ππ excited states in four protonated isomers of the 7H- and 9H-xanthine, based on the MP2, CC2, ADC(2) and CASSCF theoretical methods have been investigated. It has been predicted that out-of-plane driving coordinates are effectively responsible for photostability of these systems at the Franck-Condon region of the 1ππ* excited state, while the NH or OH stretching coordinates can be suggested to play the deactivation role in the higher energetic range based on the 1πσ* state. The different deactivation mechanisms provide significant supports for photostability of protonated xanthine in the wide range of UV radiation as well as its neutral homologue. Also, from spectroscopy points of view, no significant alteration in the 1ππ*-S0 electronic transition has been predicted to occur following protonation.

Physical nature of silane⋯carbene dimers revealed by state-of-the-art ab initio calculations.

Using the SAPT2 + 3(CCD)δMP2 method in complete basis set (CBS) limit, it is shown that the interactions in the recently studied silane⋯carbene dimers are mainly dispersive in nature. Consequently, slow convergence of dispersion energy also forces slow convergence of the interaction energy. Therefore, obtaining very accurate values requires extrapolation of the correlation part to the CBS limit. The most accurate values obtained at the CCSD(T)/CBS level of theory show that the studied silane⋯carbene dimers are rather weakly bound, with interaction energies ranging from about -1.9 to -1.3 kcal/mol. Comparing to CCSD(T)/CBS, it will be shown that SCS-MP2 and MP2C methods clearly underestimate and methods based on SAPT2+ and having some third-order corrections, as well as the MP2 method, overestimate values of interaction energies. Popular SAPT(DFT) method performs better than SCS-MP2 and MP2C; nevertheless, underestimation is still considerable. The underestimation is slightly quenched if third-order dispersion energy and its exchange counterpart is added to the SAPT(DFT). The closest value of CCSD(T)/CBS has been given by the SAPT2 + (3)(CCD)δMP2 method in quadruple-ζ basis set. © 2019 Wiley Periodicals, Inc.

Theoretical insight into a feasible strategy of capturing, storing and releasing toxic HCN at the surface of doped BN-sheets by charge modulation

The response of boron nitride nanosheets (BNNSs), with the chemical composition of B25N25H20, serving as an adsorbent of toxic hydrogen cyanide (HCN) is explored by using density functional theory (M06-2X variant of DFT). Atoms were treated with a triple-zeta quality basis set with p- and d-polarized functions, namely 6-311G(d,p). The primary focus of this study is to explore adsorption properties (adsorption energies and structures and interaction types) by introducing a single dopant (C/Si or Al) atom, by substituting either B or N at the center of the BNNS. Also considered is the effect of charge modulation on the neutral pristine and doped BNNS-HCN systems by inserting and extracting an electron. Adsorption energy varied in the range from 2.9 to 71.5 kcal/mol. The source of interactions between adsorbent and adsorbate varies from weak H-bonding to strong N→ B dative bond formation. Removal of an electron from C- or Si-doped BNNS-HCN binds both units more tightly (25.8 to 49.5 kcal/mol) than in their neutral form (2.8-6.2 kcal/mol). Thus, storage of HCN is possible by removing an electron from the neutral complexes and desorption or releasing process (to reuse captured HCN) may be easier by adding an electron to the cationic forms. The most striking feature evolved by doping and charge modulation is the cleavage of the H-CN bond in the reduced form of C-BNNS-HCN complex, where B is replaced by the C atom and a product-end transition state was identified. Electron-correlation MP2 method with 6-31G(d) basis set confirmed DFT prediction of such HC activation. In Al-doped BNNS-HCN, dative (HC)-N → Al(BNNS) bond formation in most of the complexes (neutral, as well as charged) is quite stable (20 to 33 kcal/mol) which would inhibit release of HCN from Al-doped BNNS. Overall charge modulation can make doped BNNSs an excellent adsorbent with different characteristics and several uncommon and unusual but useful features evolved from this study.

Calculation of Vibrational Parameters of an Electride-Like Molecule Li4C4H2N2 and the Pyridazine Molecule C4H4N2

The frequencies and intensities are calculated for fundamental transitions between vibrational states of an electride-like molecule Li4C4H2N2 that can be obtained from the pyridazine molecule C4H4N2 by replacing two hydrogen atoms by lithium atoms and adding two other lithium atoms to nitrogen atoms. Spectral parameters of Li4C4H2N2 are calculated in the harmonic and anharmonic approximations using the MP2, CCSD, and QCISD methods with the sets of atomic functions aug-cc-pVDZ and aug-cc-pVTZ. For comparison the absorption spectrum of a pyridazine molecule was calculated in the same approximations. The calculations showed that, upon introducing lithium atoms into the pyridazine molecule, new intense bands appear and the spectral parameters of the bands present in the pyridazine spectrum are significantly changed. The results obtained may be useful for spectroscopic observation and identification of the new c-ompound.

Ab initio study on the six lowest energy conformers of iso-octane: conformational stability, barriers to internal rotation, natural bond orbital and first-order hyperpolarizability analyses, UV and NMR predictions, spectral temperature sensitivity, and scaled vibrational assignment

In this paper, we present the quantum electronic study of iso-octane, based on MP2 and B3LYP methods using the 6-311++G(d,p) basis set. In addition to conformational stability and internal rotation barriers studies, the delocalization energies associated with the internal charge transfer (ICT) within each of the six lowest energy conformers were evaluated using NBO analysis. With the aim to differentiate even more between these conformers, the energy gap between HOMO and LUMO orbitals, chemical softness, and first-order hyperpolarizability (nonlinear optics property) were evaluated. Similarly, their spectral behavior was investigated at different levels; the ultraviolet (UV) absorption bands were assigned using molecular orbitals data obtained by TD-B3LYP calculations with 6-311++G(d,p) basis set, while carbon 13C NMR and proton 1H signal peaks were assigned using the GIAO-B3LYP/6-311++G(d,p) method. In addition, the normal mode calculations of the most and least stable conformers using a scaled force field in terms of nonredundant local symmetry coordinates were carried out to approach the vibrational spectra temperature dependency.

The mechanism of tert-butylthiol formation via hydrosulfurization of isobutene catalyzed by superacids (HBF4, HAsF6, and HSbF6)

The mechanism of the (CH3)2CCH2 + H2S → (CH3)3CSH reaction catalyzed by various superacids (HBF4, HAsF6, and HSbF6) was investigated theoretically using the ab initio CCSD(T) and MP2 methods and the aug-cc-pVDZ/LANL2DZ basis sets. The effects of surrounding solvent molecules were approximated by employing the PCM solvation model. The most important findings include the observation that each superacid considered is capable of effectively catalyzing isobutene hydrosulfurization as it reduces the activation barrier by ca. 95% in comparison to the uncatalyzed process.

PF5 and PCl5 interacting with water – Comparative study at the molecular level

The isomeric structures formed by the interaction of PF5 and PCl5 with up to four water molecules were theoretically examined by employing the MP2 method and the aug-cc-pVDZ basis set. The additional effects of surrounding water molecules were approximated by employing the polarized continuum solvation model (PCM) within a self-consistent reaction field treatment. The calculations indicate that the global minimum resulting from the interaction of PF5 and one H2O molecule corresponds to the PF5–H2O adduct and remains the most stable isomer after addition of second and third H2O, whereas the presence of fourth H2O molecule renders the PF5OH−/H3O+/2H2O structure the most stable. On the contrary, the interaction of PCl5 and a single H2O molecule leads to the global minimum structure corresponding to the PCl3O phosphoryl chloride with two HCl moieties attached. The lowest energy isomers resulting from the interaction of PCl5 with two, three, and four H2O molecules indicate the tendency of PCl3O to subsequent replacement of the Cl ligands with OH groups resulting in formation of H3PO4 (with five surrounding HCl fragments) when the number of available H2O molecules is sufficient. The presence of the competitive isomers containing H3O+ fragments in the case of the PCl5 interacting with water molecules is also predicted and discussed.

The role of hydrogen bonding in π···π stacking interactions in Ni(II) complex derived from triethanolamine: synthesis, crystal structure, antimicrobial, and DFT studies

A complex, Ni(C6H15NO3)2]·2C7H5O2 (1) has been synthesized from the reaction of nickel salt with triethanolamine (TEA) and benzoate in MeOH and characterized by FTIR, elemental analysis and single crystal X-ray diffraction. The complex exhibits moderate cytotoxicity against bovine erythrocytes (15%). Furthermore, high bacterial biofilm inhibition (90%) was recorded against Escherichia coli and moderate against Pasteurella multocida (75%) and Staphylococcus aureus (61%) bacterial species. Theoretical studies along with natural bond orbitals (NBOs) for 1 carried out with DFT and theory at B3LYP/6-31G(d,p) level. The theoretical results demonstrated good agreement with experimental along with answers about the electronic structure of the complex. B3LYP and MP2 methods were also employed to predict the strength of CH···π and π···π as the only attractive interaction in 1.

Quantum-mechanical study of energies, structures and vibrational spectra of the HF complexed with dimethyl ether

Interaction energies, geometry and vibrational frequencies of the gas-phase HF-dimethyl ether complex were obtained using quantum-chemical methods. Equilibrium and vibrationally averaged geometries, harmonic and anharmonic wavenumbers of the complex were calculated using second-order perturbation theory procedures with B3LYP, B2PLYP-D and MP2 methods with 6-311++G(2df, 2pd) basis set. Quantum-mechanical model describing anharmonic-type vibrational couplings within hydrogen bond was used to explain broadening, fine structure and temperature dependence of the FH stretching IR absorption bands as effect of hydrogen bond formation. Simulations of the rovibrational structure of the FH stretching bands were performed for different temperatures. The results were compared with experimental spectra.

The mechanisms of isobutene hydration yielding tert-butanol catalyzed by a strong mineral acid (H2SO4) and Lewis-Brønsted superacid (HF/SbF5)

The mechanism of the (CH3)2CCH2+H2O→(CH3)3COH reaction catalyzed by two strong acids (H2SO4 and HSbF6) was investigated theoretically using the ab initio MP2 and CCSD(T) methods and the aug-cc-pVDZ/LANL2DZ and aug-cc-pVTZ/LANL2DZ basis sets. The effects of surrounding solvent molecules were approximated by employing the polarized continuum solvation model. The most important findings include the observation that both acids are capable of catalyzing isobutene hydration but the reaction is predicted to proceed faster when the HSbF6 superacid plays the catalyst role.

Atmospheric reaction pathways of methanimine and nitroxyl: a theoretical study

The kinetics and mechanisms of atmospheric reaction of methanimine (H2CNH) with nitroxyl on the singlet surface were studied by employing DFT, MP2, and CCSD(T) methods along with the 6-311++G(3df, 3pd) and aug-cc-pVTZ basis sets. Also, thermodynamic parameters and rate constants have been computed in the temperature range of 300–3000 K using conventional transition state theory and RRKM theories at MP2/6-311++G(3df,3pd) level. The results show that seven adducts can be produced. Two of them are highly thermodynamically stable (CH4+N2O and HNCNH+H2O). In kinetic point of view, HCN + HNOH and H2CN + H2NO adducts (due to passing one corresponding low-level transition state) are favorable pathways of title reaction.

Thiadiazole-2-Thiol-5-Thione and 2,5-Dimercapto-1,3,4-Thiadiazol Tautomerism, Conformational Stability, Vibrational Assignments, Inhibitor Efficiency and Quantum Chemical Calculations

Abstract Raman (3700–100 cm−1) and infrared (4000–400 cm−1) spectra of 2,5-Dimercapto-1,3,4-thiadiazol (DMTD) were recorded in the solid phase. Six structures (1–6) were initially proposed for DMTD as a result of thiol-thione tautomerism and internal rotation(s) of thiol group(s) around the C–S bond. Quantum chemical calculations were carried out for an isolated molecule (1–6) using density functional theory (B3LYP) and ab initio MP2(full) methods utilizing 6-31G(d) and 6-311++G(d,p) basis sets which favor thiol-thione tautomerism (structure 4). Relaxed potential energy surface scans of structure 4 revealed an additional conformer (the thiol group is out-of-plane, structure 7) using the aforementioned methods at 6-311++G(d,p) basis set. For additional verification, plane-wave solid state calculations were carried out at PW91 and PBEsol came out in favor of conformer 7. This is in agreement with the computed/observed SH in-plane bending of S-7 (959/941 cm−1) rather than the one estimated at (880 cm−1) for S-4. Moreover, the observed split IR/Raman bands were found consistent with solid state calculated frequencies of S-7 assuming two molecules per unit cell bonded via H-bonding intermolecular interactions. Aided by vibrational frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed IR and Raman bands is proposed herein. Furthermore, we have estimated the frontier molecular orbitals and atomic charges to account for the corrosion inhibition efficiency of DMTD along with its binding sites to the metal surface. Our results are discussed herein and compared to similar molecules whenever appropriate.