Do CCSD and approximate CCSD-F12 variants converge to the same basis set limits? The case of atomization energies

While the title question is a clear "yes" from purely theoretical arguments, the case is less clear for practical calculations with finite (one-particle) basis sets. To shed further light on this issue, the convergence to the basis set limit of CCSD (coupled cluster theory with all single and double excitations) and of different approximate implementations of CCSD-F12 (explicitly correlated CCSD) has been investigated in detail for the W4-17 thermochemical benchmark. Near the CBS ([1-particle] complete basis set) limit, CCSD and CCSD(F12^*) agree to within their respective uncertainties (about ±0.04 kcal/mol) due to residual basis set incompleteness error, but a nontrivial difference remains between CCSD-F12b and CCSD(F12^*), which is roughly proportional to the degree of static correlation. The observed basis set convergence behavior results from the superposition of a rapidly converging, attractive, CCSD[F12]-CCSD-F12b difference (consisting mostly of third-order terms) and a more slowly converging, repulsive, fourth-order difference between CCSD(F12^*) and CCSD[F12]. For accurate thermochemistry, we recommend CCSD(F12^*) over CCSD-F12b if at all possible. There are some indications that the nZaPa family of basis sets exhibits somewhat smoother convergence than the correlation consistent family.

The S66 Non-Covalent Interactions Benchmark Reconsidered Using Explicitly Correlated Methods Near the Basis Set Limit

The S66 benchmark for non-covalent interactions has been re-evaluated using explicitly correlated methods with basis sets near the one-particle basis set limit. It is found that post-MP2 ‘high-level corrections’ are treated adequately well using a combination of CCSD(F12*) with (aug-)cc-pVTZ-F12 basis sets on the one hand, and (T) extrapolated from conventional CCSD(T)/heavy-aug-cc-pV{D,T}Z on the other hand. Implications for earlier benchmarks on the larger S66×8 problem set in particular, and for accurate calculations on non-covalent interactions in general, are discussed. At a slight cost in accuracy, (T) can be considerably accelerated by using sano-V{D,T}Z+ basis sets, whereas half-counterpoise CCSD(F12*)(T)/cc-pVDZ-F12 offers the best compromise between accuracy and computational cost.

Exploring the Accuracy Limits of Local Pair Natural Orbital Coupled-Cluster Theory

The domain based local pair natural orbital coupled cluster method with single-, double-, and perturbative triple excitations (DLPNO–CCSD(T)) is an efficient quantum chemical method that allows for coupled cluster calculations on molecules with hundreds of atoms. Because coupled-cluster theory is the method of choice if high-accuracy is needed, DLPNO–CCSD(T) is very promising for large-scale chemical application. However, the various approximations that have to be introduced in order to reach near linear scaling also introduce limited deviations from the canonical results. In the present work, we investigate how far the accuracy of the DLPNO–CCSD(T) method can be pushed for chemical applications. We also address the question at which additional computational cost improvements, relative to the previously established default scheme, come. To answer these questions, a series of benchmark sets covering a broad range of quantum chemical applications including reaction energies, hydrogen bonds, and other noncovalent interactions, conformer energies, and a prototype organometallic problem were selected. An accuracy of 1 kcal/mol or better can readily be obtained for all data sets using the default truncation scheme, which corresponds to the stated goal of the original implementation. Tightening of the three thresholds that control DLPNO leads to mean absolute errors and standard deviations from the canonical results of less than 0.25 kcal/mol (<1 kJ/mol). The price one has then to pay is an increased computational time by a factor close to 3. The applicability of the method is shown to be independent of the nature of the reaction. On the basis of the careful analysis of the results, three different sets of truncation thresholds (termed “LoosePNO”, “NormalPNO”, and “TightPNO”) have been chosen for “black box” use of DLPNO–CCSD(T). This will allow users of the method to optimally balance performance and accuracy.

The S66x8 benchmark for noncovalent interactions revisited: explicitly correlated ab initio methods and density functional theory

The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of CCSD(F12*)(T), DFT, and SAPT methods.

In silico study on aging and reactivation processes of tabun conjugated AChE

This study revealed that the reactivation of tabun inhibited AChE is feasible with neutral antidotes prior to the aging process.

Origin of reversal of stereoselectivity for [4+2] cycloaddition reaction between cyclopentadiene and methyl methacrylate in the presence of the chloroloaluminate ionic liquid (1-ethyl-3-methyl-imidazolium chloride): in silico studies

The origin of stereoselectivity for [4+2] cycloaddition reaction of methyl methacrylate with cyclopentadiene was investigated with the B3LYP-D3(BJ)/6-31+G(d)//B3LYP/6-31+G(d) level of theory in the presence of the ionic liquid 1-ethyl-3-methyl-imidazolium chloride (EMI+Cl–) and its acidic chloroaluminate melt, 1-ethyl-3-methyl-imidazolium heptachlorodialuminate (EMI+Al2Cl7–). The reaction of methyl methacrylate with cyclopentadiene was examined in the gas phase to rationalize the effect of the ionic liquid ion pairs EMI+Cl– and EMI+Al2Cl7–. The DFT calculated results were found to be in good agreement with the experimentally observed results. The much-discussed hydrogen bonding effect of the imidazolium cation with the dienophile is less important to govern the stereoselectivity for the cycloaddition reaction. The atoms in molecules theory was used to examine the role of hydrogen bonding between the EMI+ cation and methyl methacrylate in the transition state geometries. The calculated activation barriers with the M062X/6-31+G(d)//B3LYP/6-31+G(d) and MP2/6-311+G(d,p)//B3LYP/6-31+G(d) levels of theory also predict the similar exo/endo-stereoselectivity trend for the cycloaddition reactions.

Some Observations on Counterpoise Corrections for Explicitly Correlated Calculations on Noncovalent Interactions

The basis set convergence of explicitly correlated ab initio methods, when applied to noncovalent interactions, has been considered in the presence (and absence) of Boys-Bernardi counterpoise corrections, as well as using "half-counterpoise" (the average of raw and counterpoise-corrected values) as recently advocated in this journal [Burns, L. A.; Marshall, M. S.; Sherrill, C. D. J. Chem. Theory Comput. 2014, 10, 49-57]. Reference results were obtained using basis sets so large that BSSE (basis set superposition error) can be shown to be negligible. For the HF+CABS component, full counterpoise unequivocally exhibits the fastest basis set convergence. However, at the MP2-F12 and CCSD(T*)-F12b levels, surprisingly good uncorrected results can be obtained with small basis sets like cc-pVDZ-F12, owing to error compensation between basis set superposition error (which overbinds) and intrinsic basis set insufficiency (which underbinds). For intermediate sets like cc-pVTZ-F12, "half-half" averages work best, while for large basis sets like cc-pVQZ-F12, full counterpoise may be preferred but BSSE in uncorrected values is tolerably small for most purposes. A composite scheme in which CCSD(T)-MP2 "high level corrections" obtained at the CCSD(T*)-F12b/cc-pVDZ-F12 level are combined with "half-counterpoise" MP2-F12/cc-pVTZ-F12 interaction energies yields surprisingly good performance for standard benchmark sets like S22 and S66.

Hydrogen bonding interaction between active methylene hydrogen atoms and an anion as a binding motif for anion recognition: experimental studies and theoretical rationalization

Two new reagents, having similar spatial arrangements for hydrogen atoms of the active methylene functionalities, were synthesized and interactions of such reagents with different anionic analytes were studied using electronic spectroscopy as well as by using (1)H and (31)P NMR spectroscopic methods. Experimental studies revealed that these two reagents showed preference for binding to F(-) and OAc(-). Detailed theoretical studies along with the above-mentioned spectroscopic studies were carried out to understand the contribution of the positively charged phosphonium ion, along with methylene functionality, in achieving the observed preference of these two receptors for binding to F(-) and OAc(-). Observed differences in the binding affinities of these two reagents toward fluoride and acetate ions also reflected the role of acidity of such methylene hydrogen atoms in controlling the efficiencies of the hydrogen bonding in anion-Hmethylene interactions. Hydrogen bonding interactions at lower concentrations of these two anionic analytes and deprotonation equilibrium at higher concentration were observed with associated electronic spectral changes as well as visually detectable change in solution color, an observation that is generally common for other strong hydrogen bond donor functionalities like urea and thiourea. DFT calculations performed with the M06/6-31+G**//M05-2X/6-31G* level of theory showed that F(-) binds more strongly than OAc(-) with the reagent molecules. The deprotonation of methylene hydrogen atom of receptors with F(-) ion was observed computationally. The metal complex as reagent showed even stronger binding energies with these analytes, which corroborated the experimental results.

Dipicrylamine as a colorimetric sensor for anions: experimental and computational study

Dipicrylamine exhibited colorimetric sensing of F⁻, OAc⁻ and H₂PO₄⁻, detectable by bared-eye, out of a large number of anions. Interestingly, F⁻ binds with one of the phenyl carbon of dipicrylamine.

In silico studies in probing the role of kinetic and structural effects of different drugs for the reactivation of tabun-inhibited AChE

We have examined the reactivation mechanism of the tabun-conjugated AChE with various drugs using density functional theory (DFT) and post-Hartree-Fock methods. The electronic environments and structural features of neutral oximes (deazapralidoxime and 3-hydroxy-2-pyridinealdoxime) and charged monopyridinium oxime (2-PAM) and bispyridinium oxime (Ortho-7) are different, hence their efficacy varies towards the reactivation process of tabun-conjugated AChE. The calculated potential energy surfaces suggest that a monopyridinium reactivator is less favorable for the reactivation of tabun-inhibited AChE compared to a bis-quaternary reactivator, which substantiates the experimental study. The rate determining barrier with neutral oximes was found to be ∼2.5 kcal/mol, which was ∼5.0 kcal/mol lower than charged oxime drugs such as Ortho-7. The structural analysis of the calculated geometries suggest that the charged oximes form strong O^…H and N^…H hydrogen bonding and C-H^…π non-bonding interaction with the tabun-inhibited enzyme to stabilize the reactant complex compared to separated reactants, which influences the activation barrier. The ability of neutral drugs to cross the blood-brain barrier was also found to be superior to charged antidotes, which corroborates the available experimental observations. The calculated activation barriers support the superiority of neutral oximes for the activation of tabun-inhibited AChE compared to charged oximes. However, they lack effective interactions with their peripheral sites. Docking studies revealed that the poor binding affinity of simple neutral oxime drugs such as 3-hydroxy-2-pyridinealdoxime inside the active-site gorge of AChE was significantly augmented with the addition of neutral peripheral units compared to conventional charged peripheral sites. The newly designed oxime drug 2 appears to be an attractive candidate as efficient antidote to kinetically and structurally reactivate the tabun-inhibited enzyme.

Conformational preference of glycinamide in solution: an answer derived from combined experimental and computational studies

Conformational problems are often subtle but very important in controlling many intricate features in chemistry and biochemistry. We have performed the conformational analysis of glycinamide using NMR experiments and computational studies. (1)H NMR experiments suggest the prevalence of intramolecular hydrogen bonded conformation of glycinamide (2B) in acetonitrile, whereas, non-intramolecular hydrogen bonded conformation 2A is favoured in dimethylsulfoxide. The NOESY experiments carried out for glycinamide in DMSO-d6, showed stronger NOE interaction of the NHa-atom of amide group with CH2 than that of NHb-atom confirming the presence of conformer 2A. DFT calculations performed with explicit DMSO molecules also suggested a clear preference for the conformer 2A. The molecular dynamics simulations performed with the explicit DMSO molecules also showed that the intermolecular hydrogen bonding exists between the solvent and solute molecules to stabilize the conformer 2A. The present study sheds light on the debate of conformational preference of neutral glycinamide in the present literature.

In silico studies toward the recognition of fluoride ion by substituted borazines

The substituted borazines have been computationally investigated as new type of receptors for the recognition of fluoride ion. Fluorine, methyl and phenyl groups have been selected as electron-withdrawing, electron-releasing and aromatic substituents for the study employing DFT (B3LYP/6-311+G**) and ab initio (MP2/6-311+G**) levels of calculations. N-substituted borazines have shown higher fluoride ion affinity than their corresponding B-substituted borazines. In the case of fluorinated borazines, the binding affinity of fluoride is enhanced with the increasing number of substitutions. The F⁻ and Cl⁻ ions, generally, prefer to bind with the boron atom of substituted borazine rings, whereas, Br⁻ ion prefers to bind with NH hydrogens of the borazine receptor units. Phenyl derivatives of borazine also showed analogous behavior with halide anions. The binding affinities of halides with fluorinated and phenyl derivatives of borazine have been found to be much higher than the simple borazine receptor molecule. The NBO analyses performed for the complexation of F⁻ ion with fluorinated borazines suggest that the Lewis energy contribution in the total SCF energy enhanced with increasing the substitutions. However, in the case of methylated borazines, the delocalization energy is responsible for the stabilization of F⁻ ion complexes. The N-trifluoroborazine showed much higher fluoride ion affinity (30.9 kcal/mol) in aqueous phase than the simple borazine.

Ratiometric detection of Cr3+ and Hg2+ by a naphthalimide-rhodamine based fluorescent probe

Newly synthesized rhodamine derivatives, L(1) and L(2), are found to bind specifically to Hg(2+) or Cr(3+) in presence of large excess of other competing ions with associated changes in their optical and fluorescence spectral behavior. These spectral changes are significant enough in the visible region of the spectrum and thus, allow the visual detection. For L(1), the detection limit is even lower than the permissible [Cr(3+)] or [Hg(2+)] in drinking water as per standard U.S. EPA norms; while the receptor, L2 could be used as a ratiometric sensor for detection of Cr(3+) and Hg(2+) based on the resonance energy transfer (RET) process involving the donor naphthalimide and the acceptor Cr(3+)/Hg(2+)-bound xanthene fragment. Studies reveal that these two reagents could be used for recognition and sensing of Hg(2+)/Cr(3+). Further, confocal laser microscopic studies confirmed that the reagent L(2) could also be used as an imaging probe for detection of uptake of these ions in A431 cells.