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Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane-cis-1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies. [ABSTRACT FROM AUTHOR]

Heterogeneity is a characteristic feature of all populations of living organisms. Here we make an attempt to validate a single-cell mass spectrometric method for detection of changes in metabolite levels occurring in populations of unicellular organisms. Selected metabolites involved in central metabolism (ADP, ATP, GTP, and UDP-Glucose) could readily be detected in single cells of Closterium acerosum by means of negative-mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The analytical capabilities of this approach were characterized using standard compounds. The method was then used to study populations of individual cells with different levels of the chosen metabolites. With principal component analysis and support vector machine algorithms, it was possible to achieve a clear separation of individual C. acerosum cells in different metabolic states. This study demonstrates the suitability of mass spectrometric analysis of metabolites in single cells to measure cell-population heterogeneity. 10.1021/ac1015326

The accuracy of quantum chemical treatment of biopolymers by means of density functional theory is brought into question in terms of intramolecular basis set superposition error (BSSE). Secondary structure forms—β-strands (C5; fully extended conformation), repeated γ-turns (C7), 310-helices (C10), and α-helices (C13)—of homopolypeptides (polyglycine and polyalanine) are used as representative examples. The studied molecules include Ace(Gly)5NH2, Ace(Gly)10NH2, Ace(Ala)5NH2, and Ace(Ala)10NH2. The counterpoise correction procedure was found to produce reliable estimations for the BSSE values (other methods of BSSE correction are discussed). The calculations reported here used the B3LYP, PBE0 (PBE1PBE), and BMK density functionals with different basis sets [from 6-31G(d) to 6-311+G(3df,3pd)] to estimate the influence of basis set size on intramolecular BSSE. Calculation of BSSE was used to determine the deviation of the current results from the complete basis set limit. Intramolecular BSSE was found to be nonadditive with respect to biopolymer size, in contrast to claims in recent literature. The error, which is produced by a basis set superposition, was found to exceed 4 kcal mol-1 when a medium-sized basis set was used. This indicates that this error has the same order of magnitude as the relative energy differences of secondary structure elements of biopolymers. This result makes all recent reports on the gas-phase stability of homopolypeptides and their analogs questionable. [ABSTRACT FROM AUTHOR]

One of only two error sources in the solution of the electronic Schrödinger equation is addressed: The basis set convergence (incompleteness) error (BSIE). The results of ab initio (first principles) correlated methods, for which the Mo\ller–Plesset second order perturbation theory (MP2) was chosen as an example, were extrapolated to the complete basis set (CBS) limit using a Dunning-type basis set series. Basis sets as large as cc-pV5Z and cc-pV6Z were used. A representative molecular set that included nitrogen (N2), acetylene (C2H2), ethylene (C2H4), carbon dioxide (CO2), water (H2O), ammonia (NH3), hydrogen cyanide (HCN), and ethanol (C2H5OH) molecules was used for the calculations. The intramolecular basis set superposition error (BSSE) was found to be correlated with BSIE, meaning that intramolecular BSSE can be used as a measure of basis set incompleteness. The BSIE dependence on BSSE could be qualitatively approximated (±25%) by a power-law dependence: BSIE=A×BSSEp, where log10(A)=1.45±0.21 and p=1.27±0.09. This leads to the fact that CBS values at the MP2 theory level can be obtained using only one energy value and the corresponding intermolecular BSSE. The same power-law dependence was confirmed for all of the molecular systems studied. The universality of the BSIE versus BSSE dependence presented was checked using Pople-type basis sets. Even the results obtained with 6-311G, 6-311G**, and 6-311G(2df,2pd) basis sets were found to be nicely described by the same (universal) power law. Benchmark studies of nitrogen and acetylene contraction (compaction) showed that BSIE can be decreased by up to 83% (at the cc-pVTZ level) using the CBS-BSSE strategy described. The presented BSIE versus BSSE dependence can greatly aid in obtaining CBS results for large molecular systems of chemical or biological interest. [ABSTRACT FROM AUTHOR]

High-level ab initio electronic structure calculations, including extrapolations to the complete basis set (CBS) limit, were performed, and highly precise relative energies of five-member N-heterocycles were determined. Nitrogen-containing heterocycles studied included tautomers of tetrazole (CH2N4) and triazoles (C2H3N3). Valence focal-point analysis of 1H-tetrazole, 2H-tetrazole, 5H-tetrazole, 1H-1,2,3-triazole, 2H-1,2,3-triazole, 1H-1,2,4-triazole, and 4H-1,2,4-triazole and a number of transition state (TS) calculations were performed, using energy values determined by CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z. An accuracy of 0.10–0.25 kcal mol-1 (35–87 cm-1) was obtained for comparison of tautomer energy differences. Relative CCSD(T)/CBS energies of 2.07, 3.98, and 6.25 kcal mol-1 for 1H-tetrazole, 1H-1,2,3-triazole, and 4H-1,2,4-triazole, respectively, were calculated. Use of electron correlation methods resulted in markedly different convergence behaviors for triazole and tetrazole tautomers. Similarly, differences in convergence were observed for TSs with respect to corresponding minima structures. It was confirmed that the MP2 method predicts an acyclic structure for 5H-tetrazole. The same was not observed for the corresponding TS geometry. Comparison with density functional theory (B3LYP) and model chemistry methods (CBS-4M and CBS-QB3) is reported. [ABSTRACT FROM AUTHOR]

Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree–Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided. [ABSTRACT FROM AUTHOR]

In this paper, an extra error source for high-quality ab initio calculation of conformation equilibrium in normal alkanes—intramolecular basis set superposition error (BSSE)—is discussed. Normal butane (n-butane) and normal hexane (n-hexane) are used as representative examples. Single-point energy difference and BSSE values of trans and gauche conformations for n-butane (and trans-trans-trans and gauche-gauche-gauche conformations for n-hexane) were calculated using popular electron correlation methods: The second-order Moller–Plesset (MP2), the fourth-order Moller–Plesset (MP4), and coupled cluster with single and double substitutions with noniterative triple excitation [CCSD(T)] levels of theory. Extrapolation to the complete basis set is applied. The difference between BSSE-corrected and uncorrected relative energy values ranges from ∼100 cal/mol (in case of n-butane) to more than 1000 cal/mol (in case of n-hexane). The influence of basis set type (Pople or Dunning) and size [up to 6-311G(3df,3pd) and aug-cc-pVQZ] is discussed. [ABSTRACT FROM AUTHOR]