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 MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol(-1) RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol(-1). The nonlocal VV10 dispersion functional is especially beneficial for the double hybrids, particularly in DSD-PBEP86-NL (RMSD = 0.12 kcal mol(-1)). Other recommended dispersion-corrected functionals with favorable price/performance ratios are ωB97X-V, and, surprisingly, B3LYP-D3BJ and BLYP-D3BJ (RMSDs of 0.23, 0.20 and 0.23 kcal mol(-1), respectively). Without dispersion correction (but parametrized for midrange interactions) M06-2X has the lead (RMSD = 0.45 kcal mol(-1)). A collection of three energy-based diagnostics yields similar information to an SAPT analysis about the nature of the noncovalent interaction. Two of those are the percentages of Hartree-Fock and of post-MP2 correlation effects in the interaction energy; the third, CSPI = [IE - IE]/[IE + IE] or its derived quantity DEBC = CSPI/(1 + CSPI(2))(1/2), describes the character of the MP2 correlation contribution, ranging from 0 (purely dispersion) to 1 (purely other effects). In addition, we propose an improved, parameter-free scaling for the (T) contribution based on the Ecorr[CCSD-F12b]/Ecorr[CCSD] and Ecorr[CCSD(F12*)]/Ecorr[CCSD] ratios. For Hartree-Fock and conventional DFT calculations, full counterpoise generally yields the fastest basis set convergence, while for double hybrids, half-counterpoise yields faster convergence, as previously established for correlated ab initio methods.

Frequency and zero-point vibrational energy scale factors for double-hybrid density functionals (and other selected methods): can anharmonic force fields be avoided?

We have obtained uniform frequency scaling factors λ(harm) (for harmonic frequencies), λ(fund) (for fundamentals), and λ(ZPVE) (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.

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.

When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations.

Investigations of reaction pathways between a proton and cellobiose (CB), a glucose disaccharide of importance, were carried out in cis and trans CB using Ab Initio Molecular Dynamics (AIMD) simulations starting from optimized configurations where the proton is initially placed near groups with affinity for it. Near and above 300 K, protonated CB (H(+)CB) undergoes several transient reactions including charge transfer to the sugar backbone, water formation and dehydration, ring breaking and glycosidic bond breaking events as well as mutarotation and ring puckering events, all on a 10 ps timescale. cis H(+)CB is energetically favoured over trans H(+)CB in vacuo, with an energy gap larger than for the neutral CB.

Revealing the hot bands in the regions of the N-H and C-H stretch fundamentals of pyrrole.

Photoacoustic Raman spectra of gaseous pyrrole in the 3504-3535 and 3068-3152 cm(-1) energetic windows were measured, to obtain new information about the hot bands in the vicinity of the N-H(ν1) and C-H(ν2) stretch fundamentals, respectively. The observed vibrational patterns are characterized by sharp Q-branches, where the strong bands reflect the fundamentals and the weaker ones, as established from their temperature dependence, are hot bands. From the simulation of the observed spectra, the band origins and nondiagonal anharmonicities were determined. Comparison of the latter values to the anharmonicities, x(ij) (i = 1, 2 and j = 16, 15, 14, 12, 11) obtained from anharmonic calculations at the B3LYP/6-311++G(d,p), B3LYP/cc-pVQZ and MP2/cc-pVTZ levels, aided the tentative assignment of the hot bands. The retrieved parameters add new data to the extensive set of already known vibrational constants of pyrrole.

Isotopic hydration of cellobiose: vibrational spectroscopy and dynamical simulations.

The conformation and structural dynamics of cellobiose, one of the fundamental building blocks in nature, its C4' epimer, lactose, and their microhydrated complexes, isolated in the gas phase, have been explored through a combination of experiment and theory. Their structures at low temperature have been determined through double resonance, IR-UV vibrational spectroscopy conducted under molecular beam conditions, substituting D(2)O for H(2)O to separate isotopically, the carbohydrate (OH) bands from the hydration (OD) bands. Car-Parrinello (CP2K) simulations, employing dispersion corrected density functional potentials and conducted "on-the-fly" from ∼20 to ∼300 K, have been used to explore the consequences of raising the temperature. Comparisons between the experimental data, anharmonic vibrational self-consistent field calculations based upon ab initio potentials, and the CP2K simulations have established the role of anharmonicity; the reliability of classical molecular dynamics predictions of the vibrational spectra of carbohydrates and the accuracy of the dispersion corrected (BLYP-D) force fields employed; the structural consequences of increasing hydration; and the dynamical consequences of increasing temperature. The isolated and hydrated cellobiose and lactose units both present remarkably rigid structures: their glycosidic linkages adopt a "cis" (anti-ϕ and syn-ψ) conformation bound by inter-ring hydrogen bonds. This conformation is maintained when the temperature is increased to ∼300 K and it continues to be maintained when the cellobiose (or lactose) unit is hydrated by one or two explicitly bound water molecules. Despite individual fluctuations in the intra- and intermolecular hydrogen bonding pattern and some local structural motions, the water molecules remain locally bound and the isolated carbohydrates remain trapped within the cis potential well. The Car-Parrinello dynamical simulations do not suggest any accessible pathway to the trans conformations that are formed in aqueous solution and are widespread in nature.

Vibrational spectra of α-glucose, ß-glucose, and sucrose: anharmonic calculations and experiment.

The anharmonic vibrational spectra of α-D-glucose, ß-D-glucose, and sucrose are computed by the vibrational self-consistent field (VSCF) method, using potential energy surfaces from electronic structure theory, for the lowest energy conformers that correspond to the gas phase and to the crystalline phase, respectively. The results are compared with ultraviolet-infrared (UV-IR) spectra of phenyl ß-D-glucopyranoside in a molecular beam, with literature results for sugars in matrices and with new experimental data for the crystalline state. Car-Parrinello dynamics simulations are also used to study temperature effects on the spectra of α-D-glucose and ß-D-glucose and to predict their vibrational spectra at 50, 150, and 300 K. The effects of temperature on the spectral features are analyzed and compared with results of the VSCF calculations conducted at 0 K. The main results include: (i) new potential surfaces, constructed from Hartree-Fock, adjusted to fit harmonic frequencies from Møller-Plesset (MP2) calculations, that give very good agreement with gas phase, matrix, and solid state spectra; (ii) computed infrared spectra of the crystalline solid of α-glucose, which are substantially improved by including mimic groups that represent the effect of the solid environment on the sugar; and (iii) identification of a small number of combination-mode transitions, which are predicted to be strong enough for experimental observation. The results are used to assess the role of anharmonic effects in the spectra of the sugars in isolation and in the solid state and to discuss the spectroscopic accuracy of potentials from different electronic structure methods.

Sugar-salt and sugar-salt-water complexes: structure and dynamics of glucose-KNO3-(H2O)n.

Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and for complexes of the type glucose-KNO(3)-(H(2)O)(n), for n < or = 11. Structure and dynamic properties of the systems are explored. The MD simulations are carried out using primarily the DL_POLY/OPLS force field, and global and local minimum energy structures of some of the systems are compared with ab initio calculations. The main findings include: (1) complexation with KNO(3) leads to an "inverse anomeric effect", with the beta-glucose complex more stable than the alpha-glucose by approximately 1.74 kcal mol(-1); (2) as temperature is increased to 600 K, the KNO(3) remains undissociated in the 1 : 1 complex, with the K(+) hooked to the equilibrium site, and the NO(3)(-) bound to it, undergoing large-amplitude bending/torsional motions; (3) for n > or = 3 water molecules added to the system, charge separation into K(+) and NO(3)(-) ions takes place; (4) for the sugar-water system with n = 11 water molecules all hydroxyl groups are hydrated with the glucose adopting a surface position, indicative of a surfactant property of the sugar; and (5) comparison of DL_POLY with MP2/TZP structure predictions indicates that the empirical force field predicts global and local minimum structures reasonably well, but errs in giving the energy rankings of the different minima. The implications of the results on the effects of salts on saccharides are discussed.

Vibrational spectroscopy of triacetone triperoxide (TATP): anharmonic fundamentals, overtones and combination bands.

The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed.

Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings.

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.