Counterpoise Research Articles

Quantitative evaluation of noncovalent interactions with negative fragmentation approach including basis set superposition error correction

Abstract We propose a negative fragmentation approach (NFA), including counterpoise (CP) correction to basis set superposition error (BSSE) for quantitatively evaluating intra- and intermolecular noncovalent interactions. Noncovalent interactions are widely found in chemistry and biology and are regarded as essential interactions. However, there are few general methods for evaluating these individual intra- and intermolecular interaction energies because of two issues: (i) difficulty in the evaluation of intramolecular interactions due to the interacting sites connected with covalent bonds and (ii) BSSE affecting the quantitative accuracy of interaction analysis. In our scheme, we overcome the issue (i) using the NFA scheme, which can evaluate intra- and intermolecular interactions as a fragment–fragment interaction of interacting sites, and address the issue (ii) using the CP method. Here, NFA including the CP correction was applied to various molecular systems, providing comparable results for intermolecular interactions to supermolecule calculations with the CP correction and also succeeding in the evaluation of intramolecular interactions and its BSSEs. It is notable that our NFA scheme does not require any particular program or a modification of the program codes. These indicate that many researchers can apply our NFA scheme to various molecular systems.

Base pairs with 5-chloroorotic acid and comparison with the natural nucleobase. Structural and spectroscopic study, and three suggested antiviral modified nucleosides

A structural and spectroscopic study of 5-chloroorotic acid (5-ClOA) biomolecule was carried out by IR and FT-Raman and the results obtained were compared to those achieved in 5-fluoroorotic acid and 5-aminoorotic acid compounds. The structures of all possible tautomeric forms were determined using DFT and MP2 methods. To know the tautomer form present in the solid state, the crystal unit cell was optimized through dimer and tetramer forms in several tautomeric forms. The keto form was confirmed through an accurate assignment of all the bands. For this purpose, an additional improvement in the theoretical spectra was carried out using linear scaling equations (LSE) and polynomic equations (PSE) deduced from uracil molecule. Base pairs with uracil, thymine and cytosine nucleobases were optimized and compared to the natural Watson-Crick (WC) pairs. The counterpoise (CP) corrected interaction energies of the base pairs were also calculated. Three nucleosides were optimized based on 5-ClOA as nucleobase, and their corresponding WC pairs with adenosine. These modified nucleosides were inserted in DNA:DNA and RNA:RNA microhelices, which were optimized. The position of the -COOH group in the uracil ring of these microhelices interrupts the DNA/RNA helix formation. Because of the special characteristic of these molecules they can be used as antiviral drugs. Communicated by Ramaswamy H. Sarma

Counterpoise correction from a practical perspective: is the result worth the cost?

In the present study, we have examined the utility of counterpoise (CP) corrections, the zero-cost geometric counterpoise (gCP) correction, and the double-ζ vDZP basis set, in representative examples of computational chemistry investigations. The tests include reaction energies and barriers in mechanisms of catalysis, and binding of substrates with enzyme active sites. Drawbacks of the CP approach include: it is more costly than calculations with the same basis set without applying CP corrections, multiple computations may be required where a single species is used in multiple instances, and it is only applicable to intermolecular interactions. In comparison, using gCP or vDZP is less costly. Their overall accuracy is comparable to CP, although the three approaches show variable performances for different systems. Thus, the use of a large basis set remains more consistent in obtaining results that are closer to the basis-set limit. Where the computational cost poses a challenge, the use of gCP or vDZP would be more advantageous than CP in terms of cost and simplicity.

Systematic Evaluation of Counterpoise Correction in Density Functional Theory.

A widespread belief persists that the Boys-Bernardi function counterpoise (CP) procedure "overcorrects" supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ∼150 atoms and ligand-protein models with ∼300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. This is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP "overcorrects" for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.

Base pairs with 4-amino-3-nitrobenzonitrile: comparison with the natural WC pairs. Dimer and tetramer forms, Infrared and Raman spectra, and several proposed antiviral modified nucleosides

Base pairs of 4-amino-3-nitrobenzonitrile (4A-3NBN) molecule with uracil, thymine and cytosine nucleobases were optimized and compared to natural Watson-Crick (WC) pairs. The slightly greater flexibility of the -NO2 group of 4A-3NBN than the N3-H group of the natural nucleobases together with a noticeable higher dipole moment of its pairs can facilitate disruption of the DNA/RNA helix formation. Several new mutagenic modified nucleosides with 4A-3NBN and 3-amino-2-nitrobenzonitrile (3A-2NBN) were proposed as antiviral prodrugs and their base pairs optimized. The special characteristics of these prodrugs appear appropriated for their clinical use. The counterpoise (CP) corrected interaction energies of the base pairs were calculated and compared to the natural ones. The M06-2X DFT method was used for this purpose. The molecular structure of 4A-3NBN was analyzed in detail and the crystal unit cell was simulated by a tetramer form and eight dimer forms. The performance of the B3LYP, X3LYP and M06-2X methods was tested on the vibrational wavenumbers in the monomer, dimer and tetramer forms of 4A-3NBN. The observed IR and Raman bands were assigned according to the optimum dimer II form determined by B3LYP and by the tetramer form calculated by M06-2X, which is the expected unit cell that forms the crystal net. The two best scaling procedures were used. Communicated by Ramaswamy H. Sarma

Behavior of counterpoise correction in many-body molecular clusters of organic compounds: Hartree-Fock interaction energy perspective.

The counterpoise (CP) correction by Boys and Bernardi has been well accepted as a reliable strategy to account for basis set superposition error (BSSE) in intermolecular complexes. The behavior of the CP correction was thoroughly studied in individual molecules of molecular complexes. This work studies the performance of the CP correction in many‐body clusters including three‐body clusters of organic compounds in the 3B‐69 dataset. Additionally, we used crystal structures of polymorphs of benzene, aspirin, and oxalyl dihydrazide (ODH) to construct a many‐body cluster dataset, abbreviated as the MBC‐36 dataset, consisting of two, four and eight molecules, and 16 molecules in the case of benzene. A series of Dunning's basis sets—cc‐pXZ and aug‐cc‐pXZ (X = D and T)—were used to predict CP‐corrected Hartree–Fock (HF) interaction energies of the 3B‐69 and MBC‐36 datasets. The CP‐corrected interaction energies were found to be basis‐set independent, whereas the non‐CP corrected interaction energies were found not to a follow a smooth exponential fitting as previously found for electronic energies of individual molecules. This observation was attributed to the presence of non‐additive induction forces in some clusters. Two 2 × 2 × 2 supercells of benzene polymorphs were constructed to explore the local nature of BSSE effects. A cut‐off radius of 10 Å was demonstrated to be sufficient to fully recover these effects. Although the behavior of CP correction was found to be non‐conventional in many‐body clusters of organic compounds, the use of a small basis set such as cc‐pVDZ showed excellent performance in the prediction of HF interaction energies.

The ozone-water complex: CCSD(T)/CBS structures and anharmonic vibrational spectroscopy of O3(H2O)n, (n = 1 - 2).

Ozone-water complexes O3(H2O)n (n = 1-2) have been studied using coupled cluster theory with triple excitations CCSD(T) with correlation consistent basis sets aug-cc-pVnZ (n = D, T, Q) and complete basis set (CBS) extrapolation techniques. We identified seven dimer (n = 1) and nine trimer species (n = 2) with open C2v and cyclic D3h ozone. Calculations at the CCSD(T)/CBS level of theory for C2v O3(H2O) on the counterpoise (CP)-corrected potential energy surface yield a dissociation energy of De = 2.31 kcal/mol and an O3 central-oxygen (Oc) H2O oxygen (Ow) distance r[Oc⋯Ow] of 3.097 Å, which is in good agreement with an experimental value of 2.957 Å [J. Z. Gillies et al., J. Mol. Spectrosc. 146, 493 (1991)]. Combining our CCSD(T)/CBS value of De for C2v O3(H2O) with our best estimate anharmonic CCSD(T)/aVTZ ΔZPE yields a Do value of 1.82 kcal/mol; the CCSD(T)/CBS value of De for D3h O3(H2O) is 1.51 kcal/mol and yields an anharmonic CCSD(T)/aVTZ Do = 0.99 kcal/mol. CCSD(T)/aVTZ dissociation energies and structures for C2v O3(H2O)2 are De = 4.15 kcal/mol, (Do = 3.08 kcal/mol) and r[Oc⋯Ow] = 2.973 Å, and De = 2.64 kcal/mol (Do = 1.68 kcal/mol) with r[Oc⋯Ow] = 2.828 Å for D3h O3(H2O)2. The results from ab initio molecular dynamics simulations, which consider dynamic and thermal effects in O3(H2O), show that the O3(H2O) complex remains stable at 50 K and dynamically interconverts between two hydrogen-bonded conformers with short Oc⋯Ow contacts (3.85 Å). Carr-Parrinello molecular dynamic (CPMD) simulations for O3(H2O) and O3(H2O)2 at 100 K demonstrate that O3(H2O)2 remains structurally intact, whereas O3(H2O) dissociates to free ozone and water, a feature consistent with the larger average binding energy in O3(H2O)2 (2.2 kcal/mol) vs that in O3(H2O) (1.8 kcal/mol). Finally, the results from CCSD(T)/CBS and CPMD simulations demonstrate that the large inter-trimer binding energies in O3(H2O)2 would give rise to an elevated trimer/dimer population ratio, making O3(H2O)2 a particularly stable and spectroscopically detectable complex.

Effect of bromine atom on the different tautomeric forms of microhydrated 5-bromouracil, in the DNA:RNA microhelix and in the interaction with human proteins

This study focuses on the effects of the bromine atom on the molecular structure parameters in the main tautomeric forms of 5-bromouracil (5BrU), and as well, its effect on hydration and on the Watson-Crick (WC) pairs as compared to uracil molecule. The influence of the bromine atom was studied in several environments. The hydration effect on the molecular structure and energies of the main tautomeric forms of 5BrU was analyzed by considering a variable number of water molecules in explicit form up to 30 to simulate the first and second hydration shells. The ‘mutagenic’ 2-hydroxy-4-oxo (U2) enol tautomer of 5BrU, but not of uracil, was absolutely favored over the keto form in clusters with more than 20 water molecules. For all calculations, B3LYP and M06-2X Methods were used. The effect of the bromine atom when it was inserted into the natural and reverse WC pairs uridine-adenosine was also determined, and counterpoise (CP) corrected interaction energies were calculated. The effect of the bromine atom was analyzed in several DNA:RNA hybrid microhelices. Different backbone and helical parameters were calculated and compared. The bromine atom destabilizes its base pair, with a remarkable increase in the rise parameter (Dz) corresponding to the microhelix, and to a slight increase in the diameter (d). Molecular docking calculations were also carried out with 5BrU for targeted proteins associated with diabetes, hepatocellular carcinoma and breast and lung cancers. The molecular docking analysis confirms that the 5BrU molecule may play an important role as a promising inhibitor against breast cancer.Communicated by Ramaswamy H. Sarma

Synthesis, X-ray Diffraction Studies, and Hydrogen Bonding Analysis of a New Phosphoramide Counterion in Solid State

In the present study, we report the structure of one new phosphoramidate counter ion. The single crystal X-ray diffraction analysis revealed that C18H18N3O4P1, consists of a discrete [C18H18N2OP]+ cation and NO 3 − anion. The compound crystallizes in triclinic system, space group P-1, unit cell a = 9.4935 A, b = 10.4556(4) A, c = 11.1560(3) A, α = 63.951(3)°, β = 67.039(3)°, γ = 66.017(3)°. The interaction between cation and anion has occurred through hydrogen bonding. The strength of different hydrogen bonds between two counter ions was studied by DFT calculations in the gas phase. We optimized the hydrogen atoms and kept all other atoms invariant in the optimization process. The H-optimized systems included one nitrate anion and one phosphoramide cation which were connected by special intermolecular interactions. The binding energies of these interactions were calculated (M062X/6-311G*) and corrected for the basis set superposition error (BSSE) using by counterpoise (CP) procedure. Moreover, the main noncovalent inter-molecular interactions were studied by Hirshfeld surface analysis and finger print plots.

Computational Characterization of Nylon 4, a Biobased and Biodegradable Polyamide Superior to Nylon 6.

This study is an attempt to develop a theoretical methodology to elucidate or predict the structural characteristics and the physical properties of an isolated polymeric chain and its crystalline state precisely and quantitatively. To be more specific, conformational characteristics of a biobased and biodegradable polyamide, nylon 4, in the free state have been revealed by not only ab initio molecular orbital calculations on its model compound but also nuclear magnetic resonance experiments for the model and nylon 4. Furthermore, the crystal structure and solid-state properties of nylon 4 have been elucidated by density functional theory calculations with a dispersion force correction under periodic boundary conditions. In the free state, the nylon 4 chain forms intramolecular N–H···O=C hydrogen bonds, which force the polymeric chain into distorted conformations including a number of gauche bonds, whereas nylon 4 crystallizes in the fully extended all-trans structure (α form) that is stabilized by intermolecular N–H···O=C hydrogen bonds. The intermolecular interaction energy (ΔECP) in the crystal was accurately calculated via a counterpoise (CP) method contrived here to correct the basis set superposition error, and the ultimate crystalline modulus (Eb) in the chain axis (b axis) direction at 0 K was also evaluated theoretically. The results were compared with those obtained from the α and γ crystalline forms of nylon 6, and, consequently, the superiority of nylon 4 to nylon 6 in thermal stability and mechanical properties was indicated: the ΔECP and Eb values are, respectively, −214 cal g–1 and 334 GPa (nylon 4), −191 cal g–1 and 316 GPa (α form of nylon 6), and −184 cal g–1 and 120 GPa (γ form of nylon 6). In conclusion, nylon 4 is expected to be put to practical use as a tough environmentally friendly polyamide.

Drug Design Outlook by Calculation of Second Virial Coefficient as a Nano Study

Intermolecular potential energy surface for an interaction of drug with Na has been examined using HF level of theory with 6-31G* basis set. The name of drug is meso-tetrakis (p-sulphonatophenyl) porphyrin (here after abbreviated to TSPP) . The numbers of Na+ have a significant effect on the calculated potential energy curve (including position, depth, and width of the potential well). Counterpoise (CP) correction has been used to show the extent of the basis set superposition error (BSSE) on the potential energy curves obtained for TSPPNa. The second virial coefficients are calculated by these data.

Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs.

Papers I and II in this series [R. M. Richard et al., J. Chem. Phys. 141, 014108 (2014); K. U. Lao et al., ibid. 144, 164105 (2016)] have attempted to shed light on precision and accuracy issues affecting the many-body expansion (MBE), which only manifest in larger systems and thus have received scant attention in the literature. Many-body counterpoise (CP) corrections are shown to accelerate convergence of the MBE, which otherwise suffers from a mismatch between how basis-set superposition error affects subsystem versus supersystem calculations. In water clusters ranging in size up to (H2O)37, four-body terms prove necessary to achieve accurate results for both total interaction energies and relative isomer energies, but the sheer number of tetramers makes the use of cutoff schemes essential. To predict relative energies of (H2O)20 isomers, two approximations based on a lower level of theory are introduced and an ONIOM-type procedure is found to be very well converged with respect to the appropriate MBE benchmark, namely, a CP-corrected supersystem calculation at the same level of theory. Results using an energy-based cutoff scheme suggest that if reasonable approximations to the subsystem energies are available (based on classical multipoles, say), then the number of requisite subsystem calculations can be reduced even more dramatically than when distance-based thresholds are employed. The end result is several accurate four-body methods that do not require charge embedding, and which are stable in large basis sets such as aug-cc-pVTZ that have sometimes proven problematic for fragment-based quantum chemistry methods. Even with aggressive thresholding, however, the four-body approach at the self-consistent field level still requires roughly ten times more processors to outmatch the performance of the corresponding supersystem calculation, in test cases involving 1500-1800 basis functions.

Exploring potent ligand for proteins: insights from knowledge-based scoring functions and molecular interaction energies

Two different scoring functions, Hirshfeld fingerprint-based scoring (HFBS) and molecular operating environment (MOE), and the kernel energy method (KEM) along with counterpoise (CP)-corrected approach were used to estimate the binding energies of protein–ligand complexes and tested against a series of inhibitors of human aldose reductase enzyme. The new scoring function, HFBS, is based on Hirshfeld fingerprints, which are 2D histogram plots of the distances from the molecular Hirshfeld surface to the nearest atomic nuclei inside versus outside the surface and are highly sensitive to the immediate environment of the molecule. The Hirshfeld surface plotted over the ligand molecule helped to visualize the contacts with the active site residues and solvents, which were then taken into account for interaction energy calculations. Application of KEM-assisted CP-corrected approach facilitated an efficient way of calculating interaction energies in protein complex systems. Interaction energies calculated using MP2/6-31G(d) level of theory allowed us to rank the ligands by potency. We find that both the KEM-assisted CP-corrected interaction energies and the scoring functions used here predict comparable rankings for the strength of binding of the series of ligands as docked to the active site of the protein, which are also in good agreement with the experimental binding affinities in this case.

DSD-PBEP86-NL and DOD-PBEP86-NL functionals for noncovalent interactions: Basis set effects and tentative applications to large noncovalent systems

Basis set effects on the DSD-PBEP86-NL and DOD-PBEP86-NL functionals for noncovalent interactions have been extensively studied in this work. The cc-pVXZ (X = D, T, Q, 5, 6) and augmented aug-cc-pVXZ (X = D, T, Q) basis sets are systematically tested without counterpoise (CP) corrections against the well-known S66 database. Additionally, the basis sets of def2-TZVPP and def2-TZVPPD are also examined. Based on our computations, the performances of the aug-cc-pVQZ, cc-pV5Z, and cc-pV6Z basis sets are very approximate to those obtained with the def2-QZVP basis set for both the DSD-PBEP86-NL and DOD-PBEP86-NL functionals. Note that the short-range attenuation parameters for these two functionals were directly optimized using the def2-QZVP basis set without CP corrections against the S66 database. Generally speaking, the cc-pVXZ (X = D, T, Q), aug-cc-pVXZ (X = D, T, Q), def2-TZVPP, and def2-TZVPPD basis sets favor half CP correction for these two functionals. Nevertheless, the aug-cc-pVQZ basis set already performs well without any CP correction, especially for the DOD-PBEP86-NL functional. With respect to accuracy and computational cost, the cc-pVTZ and def2-TZVPP basis sets with half CP corrections are recommended for these two functionals to evaluate interaction energies of large noncovalent complexes.

Computational Design of a Selective Molecular Imprinted Polymer for Extraction of Pseudoephedrine from Plasma and Determination by HPLC

In this work we computationally designed and synthesized a molecular imprinted polymer as a selective sorbent for extracting of Pseudoephedrine (PSE) from plasma. The computational design has been performed by using of two different theoretical methods i.e., Density Functional Theory (DFT) and Restricted Hartree Fock (RHF). Also to computationally choice of best polymerization solvent we used the Polarizable Continuum Model (PCM). Additionally the basis set superposition error (BSSE) of all calculations was measured by using counterpoise (CP) correction, too. The results delivered that the methacrylic acid (MAA) and MeOH provide the best MIP for PSE. To evaluation of synthesized polymer the Langmuir-Freundlich (LF) isotherm and kinetic of adsorption of polymer were studied. The polymer was used in solid-phase extraction as a selective sorbent for extraction and enrichment of PSE from plasma samples. The calibration curve was linear ranging from 0.01 to 5 μg mL-1 (R2=0.999). The limit of detection (LOD) and quantification (LOQ) in plasma were 0.003 and 0.01 μg mL-1, respectively. Also, mean recovery of 0.1 and 0.5 μg mL-1 of PSE from plasma were 84.4±6.2% and 85.4±5.4%, respectively. The %RSD of intraday and interday was 5.6% and 6.3%, respectively.

Corrigendum: Competition between Hydrogen and Halogen Bonding in Halogenated 1-Methyluracil:Water Systems.

The counterpoise (CP)-corrected interaction energies of the I- and At-containing complexes consisting of halogenated 1-methyl-uracil and one water molecule (XmU-H2O; X = I, At) should be 2.20 kJ mol−1 more negative than reported, see updated Table 3 below, and the scans for ImU-H2O and AtU-H2O reported in Figure 5 should be shifted down by 2.20 kJ mol−1. Likewise, the interaction energies of the XmU-(H2O)2 complexes (X = I, At) should be 4.40 kJ mol−1 more negative than reported. Thus, the interaction energies of the halogen-bonded (X-bonded) ImU(H2O)2 and AtmU-(H2O)2 complexes (with the water dimer located between C5-X and C4=O4), reported in Table 4, should be −73.4 and −79.3 kJ mol−1, respectively, and those of the “Above ring” complexes should be −88.2 and −87.3 kJ mol−1, respectively. The CP-corrected interaction energies of the XmU-(H2O)n complexes (X = F, Cl, Br, I, At; n = 1, 2) were calculated by subtracting the energies of the optimized isolated fragments (XmU and water) from the CP-corrected dimer energy. We had used the 6-31+G(d) basis set for all atoms except I and At, for which the aug-cc-pVDZ-PP basis set was used. Gaussian1 uses by default 6 Cartesian d-functions in the 6-31+G(d) basis set. However, we had not realized that, when specifying basis sets via the “Gen” keyword (which is required when using different basis sets for different atoms), Gaussian uses by default five spherical harmonic d-functions for all atoms. Thus, five d-functions were used for the calculation of the CP-corrected dimer energy and isolated ImU and AtmU, whereas six d-functions were used for isolated H2O. For consistency, spherical harmonic (5 d) basis functions should have been used for isolated H2O (or, alternatively, six d-functions should have been used for all other calculations). Using five d-functions instead of six d-functions for the isolated water calculation makes the energy of the water molecule less negative by 2.20 kJ mol−1, leading to the corrections listed above. These corrections make the increase in halogen-bond interaction energy from Cl or Br to At more linear, particularly for the system containing two water molecules. Note that, with this correction, the hydrogen-bond (H-bond) strength of the H-bonded XmU-H2O systems increases going down the halogen-bond group, and does not peak at the BrmU-H2O complex, as initially reported. We report two additional corrections: (i) The C5-X•••Ow angle for the H-bonded minimum (X = F) should be 117° instead of 81° and (ii) In Table 4 (first line) and Table 6 (footnote), “C6 = O6” should read “C4 = O4.” This article corrects: Competition between hydrogen and halogen bonding in halogenated 1-methyluracil:water systems, Volume 37, Issue 8, 763-770. Article first published online: 15 January 2016.

Basis set convergence of the binding energies of strongly hydrogen-bonded atmospheric clusters.

We investigate the basis set convergence of second order Møller Plesset perturbation theory for the binding energies of 11 strongly hydrogen-bonded clusters relevant to the atmosphere. The binding energies are calculated both as the uncorrected (UC) value, as well as by employing the counterpoise (CP) and the Same Number Of Optimized Parameters (SNOOP) correction schemes, with and without explicit correlation (F12). We find that the use of the F12 corrections is of utter importance for obtaining converged binding energies. Without F12 corrections at least a quadruple-ζ basis set is generally required to yield errors below 1 kcal mol-1 compared to the complete basis set (CBS) limit. Using coupled cluster methods we obtain a best estimate of the CCSD(T) CBS limit of the binding energies of the considered clusters and compare it with approximate DLPNO-CCSD(T) and DFT methods. We identify a pragmatic approach, relying solely on a series of double-ζ basis set calculations, for obtaining results in remarkably good agreement with our CBS estimate.

Designing L-serine targeted molecularly imprinted polymer via theoretical investigation

Molecular imprinting is one of few general, nonbiological methods for creating molecular receptors, but the progress in molecular imprinting calls for the predictive tools capable of understanding molecular level complexities of these processes. Thus, computational chemistry which predicts the suitability of functional monomer in designing the sensor for a particular analyte was attempted to design an amino acid (L-serine) sensor based on the molecular imprinting approach using density functional theory (DFT). Here, the computations were carried out to check the feasibility of best suited monomers for imprinting an amino acid (L-serine) in water and allied solvents. DFT method was utilized at B3LYP/6-31[Formula: see text]G(d,p) level to optimize template, monomers and template-monomer complexes and basis set superposition error (BSSE) was corrected by means of the counterpoise (CP) method for complexes in gas phase. All monomers can be utilized for imprinting. 2-vinyl pyridine and acrylamide were found to be good for imprinting serine in water but toluene was found to be good porogen for imprinting serine with functional monomer acrylamide. This study will aid in designing a water-compatible MIP sensor for serine molecules, which could be a biomarker for certain neurological disorders.

The explicitly correlated same number of optimized parameters (SNOOP-F12) scheme for calculating intermolecular interaction energies.

We augment the recently introduced same number of optimized parameters (SNOOP) scheme [K. Kristensen et al., J. Chem. Phys. 142, 114116 (2015)] for calculating interaction energies of molecular dimers with an F12 correction and generalize the method to enable the determination of interaction energies of general molecular clusters. The SNOOP, uncorrected (UC), and counterpoise (CP) schemes with/without an F12 correction are compared for the S22 test set of Jurečka et al. [Phys. Chem. Chem. Phys. 8, 1985 (2006)]-which consists of 22 molecular dimers of biological importance-and for water and methane molecular clusters. The calculations have been performed using the Resolution of the Identity second-order Møller-Plesset perturbation theory method. We conclude from the results that the SNOOP scheme generally yields interaction energies closer to the complete basis set limit value than the UC and CP approaches, regardless of whether the F12 correction is applied or not. Specifically, using the SNOOP scheme with an F12 correction yields the computationally most efficient way of achieving accurate results at low basis set levels. These conclusions hold both for molecular dimers and more general molecular clusters.

Simulation of the solid state and the first and second hydration shell of the xanthine oxidase inhibitor allopurinol: Structures obtained using DFT and MP2 methods

Allopurinol (AL) was investigated in the isolated state, solid state, and in the hydrated form through an exhaustive quantum-chemical analysis. Full geometry optimization and energy calculations of the 11 most stable tautomers in the isolated state were performed. The most stable one corresponds to AL-15 at all the levels of computation. Several weak bands of the experimental spectrum in Ar-matrix were tentatively assigned to tautomer AL-25. The crystal unit cell of the solid state was simulated by a heptamer form. Comparisons with the experimental values confirm that only tautomer AL-15 appears in the solid state. The hydration of the two most stable tautomers: AL-15 and AL-25 was carried out. Solvent effects were considered using the Tomasi's polarized continuum model (PCM) and by the explicit model (EM) including a variable number of water molecules surrounding the base to simulate the first and second hydration shells. In this second hydration shell the calculated difference in the free energy between both tautomers is so small, that both tautomers can coexist in bull water. Some of the most important conclusions on the effects of the hydration on the molecular structure were presented. The deformation and interaction energies were corrected for basis set superposition error (BSSE) using the counterpoise (CP) procedure.