Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

Our previous benchmark CCSD(T)/ complete basis set limit calculations were collected into a database named begdb - Benchmark Energy and Geometry DataBase. Web-based interface to this database was prepared and is available at www.begdb.com. Users can browse, search and plot the data online or download structures and energy tables.

Application of Berlin's Theorem to Bond-Length Changes in Isolated Molecules and Red- and Blue-Shifting H-Bonded Clusters

The origin of the bond-length change in molecule or molecular cluster has been investigated at the MP2/aug-cc-pVDZ level of theory using the electrostatic potential or the electron density difference analysis method. Our results have clearly shown that the bond-length change of a chemical bond is determined mainly by the balance of the electrostatic forces exerted by electrons on the two nuclei. The factors that affect the balance of the electrostatic forces include four parts: (i) The abstraction of the electron density from Berlin's binding region between the two nuclei. (ii) The accumulation of the electron density in Berlin's antibinding regions. (iii) The accumulation of the electron density in Berlin's binding region between the two nuclei. (iv) The abstraction of the electron density from Berlin's antibinding regions. Using the change of the electron density around the two nuclei of a chemical bond, we have succeeded in explaining two important chemical phenomena: (i) breakdown of bond length-bond strength correlation; (ii) the bond-length change in the hydrogen bond.

CH Stretching Vibrational Shift of Benzene Dimer: Consistency of Experiment and Calculation

Three low-energy structures of the benzene dimer are investigated by several theoretical procedures (RI-MP2, CCSD(T), RI-DFT-D, DFT/BH&H) covering London dispersion energy. The RI-DFT-D and CCSD(T) calculations are used to verify the DFT/BH&H dimer characteristics, as only at this level can anharmonic calculations be performed. It is ascertained that the T-shaped (C(2v)) structure, in which the C-H stretching frequency of the proton donor shows a significant blue shift, is not stable at any level of theory. It is either a transition structure or a minimum which is easily transformed into a parallel-displaced structure or a T-shaped (C(s)) structure, even at low temperature. Consequently, no blue shift can be detected. On the other hand, the calculated anharmonic IR spectra of the two most stable structures of benzene dimer, namely, the T-shaped (C(s)) and the parallel-displaced ones, give rise to a small red (and no blue) shift of the C-H stretching vibration. This finding is fully consistent with the experimental results.

Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest

In this work we investigate the performance of the DFT method, augmented with an empirical dispersion function (DFT-D), paired with the PCM implicit solvation model, for the computation of noncovalent interaction energies of biologically-relevant, solvated model complexes. It is found that this method describes intermolecular interactions within water and ether (protein-like) environments with roughly the same accuracy as in the gas phase. Another important finding is that, when environmental effects are taken into account, the empirical dispersion term associated with the DFT-D method need be modified very little (or not at all), in order to obtain the optimum, most well balanced, performance.

Model of Peptide Bond−Aromatic Ring Interaction: Correlated Ab Initio Quantum Chemical Study

Aromatic ring-peptide bond interactions (modeled as benzene and formamide, N-methylformamide and N-methylacetamide) are studied by means of advanced computational chemistry methods: second-order Möller-Plesset (MP2), coupled-cluster single and double excitation model [CCSD(T)], and density functional theory with dispersion (DFT-D). The geometrical preferences of these interactions as well as their interaction energy content, in both parallel and T-shaped arrangements, are investigated. The stabilization energy reaches a value of over 5 kcal/mol for the N-methylformamide-benzene complex at the CCSD(T)/complete basis set (CBS) level. Decomposition of interaction energy by the DFT-symmetry-adapted perturbation treatment (SAPT) technique shows that the parallel and T-shaped arrangements, although similar in their total interaction energies, differ significantly in the proportion of electrostatic and dispersion terms.

Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes

In the past several years the MP2 method has been used extensively in studies of noncovalent interactions within biological systems such as proteins, DNA/RNA, and protein-ligand complexes. In this work we assess the performance that can be expected of this method, when paired with several different medium and extended basis sets, for the accurate computation of binding energies of hydrogen bonded and dispersion bound biologically derived complexes. It is found that, overall, the MP2/cc-pVTZ method produces the best, most well balanced, description of noncovalent interactions. Another interesting observation made in this study is that generally the MP2 technique, when paired with any basis set, does not yield reliable results for cyclic hydrogen bonds such as those found in nucleic acid base pairs.

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.

The mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine

We present the mid-IR (400-1800 cm(-1)) spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine measured by IR-UV double-resonance spectroscopy. We compare the recorded mid-IR spectra with the spectra of the most stable structures obtained from RI-MP2 and RI-DFT-D calculations. The results confirm the enol form for all structures and demonstrate the efficacy of a new approach to DFT calculations that includes dispersion interactions.

Benchmark RI-MP2 database of nucleic acid base trimers: performance of different density functional models for prediction of structures and binding energies

A new database of nucleic acid base trimers has been developed that includes 141 geometries and stabilization energies obtained at the RI-MP2 level of theory with the TZVPP basis set. Compared to previously compiled biologically oriented databases, this new construct includes considerably more complicated structures; the various intermolecular interactions in the trimers are quite heterogeneous and in particular include simultaneous hydrogen bonding and stacking interactions, which is similar to the situation in actual biopolymers. Validation against these benchmark data is therefore a more demanding task for approximate models, since correct descriptions of all energy terms are unlikely to be accomplished by fortuitous cancellations of systematic errors. The density functionals TPSS (both with and without an empirical dispersion term), PWB6K, M05-2X, and BH&H, and the self-consistent charge density functional tight binding method augmented with an empirical dispersion term (SCC-DFTB-D) were assessed for their abilities accurately to compute structures and energies. The best reproduction of the BSSE corrected RI-MP2 stabilization energies was achieved by the TPSS functional (TZVPP basis set) combined with empirical dispersion; removal of the dispersion correction leads to significantly degraded performance. The M05-2X and PWB6K functionals performed very well in reproducing the RI-MP2 geometries, but showed a systematic moderate underestimation of the magnitude of base stacking interactions. The SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2; given its computational efficiency it represents a good option for initial scanning of analogous biopolymeric potential energy surfaces. BH&H gives geometries of comparable quality to the other functionals but significantly overestimates interaction energies other than stacking.

Accurate Theoretical Determination of the Structure of Aromatic Complexes Is Complicated: The Phenol Dimer and Phenol···Methanol Cases

The structure of the phenol dimer and phenol...methanol complexes was determined by gradient optimization using the Hartree-Fock (HF), MP2, DFT, and RI-DFT-D methods with various basis sets. Theoretical rotational constants were compared with experimental values and the following conclusions were made: (1) HF and DFT methods fail to predict cluster geometries; (2) MP2 with a medium basis set yields reliable cluster geometries but only because of a compensation for errors; (3) when the AO basis set is enlarged, the geometry becomes incorrect, and the theoretical geometry becomes reliable only when the higher correlation energy contributions (CCSD(T)) are included; and (4) the RI-DFT-D procedure covering the dispersion energy provides excellent geometries.

Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue

A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.

On the Nature of the Surprisingly Small (Red) Shift in the Halothane⋅⋅⋅Acetone Complex

The halothaneacetone and fluoroformacetone complexes are studied using the second-order Møller-Plesset (MP2) method with a cc-pVTZ basis set and the density functional theory (DFT) method with a TZVP basis set. Whereas halothane exhibits a small red shift upon complexation, fluoroform shows a pronounced blue shift. To explain this difference in behavior, we perform symmetry-adapted perturbation theory (SAPT) and natural bond orbital (NBO) analyses. Although the composition of the total stabilization energy of each complex is different, that alone does not provide a satisfactory explanation for the difference in the spectral shifts. This difference is interpreted as a result of the interplay of the hyperconjugation and rehybridization mechanisms. The small and surprising red shift of the C-H stretching frequency of halothane, which resulted from the complexation of this species with acetone,is explained by the compensation of the two above-mentioned mechanisms. On the other hand, the fluoroformacetone complex exhibits a blue shift of the C--H stretching frequency upon complexation, the most likely reason for this shift being a concerted occurrence of the hyperconjugation and rehybridization mechanisms. The calculated shift of the C-H stretching vibration frequencies of halothane (+27 cm(-1)) agree with the experimental value of +5 cm(-1).

Non-covalent interactions in biomacromolecules

Non-covalent interactions play an important role in chemistry, physics and especially in biodisciplines. They determine the structure of biomacromolecules such as DNA and proteins and are responsible for the molecular recognition process. Theoretical evaluation of interaction energies is difficult; however, perturbation as well as variation (supermolecular) methods are briefly described. Accurate interaction energies can be obtained by complete basis set limit calculations providing a large portion of correlation energy is covered (e.g. by performing CCSD(T) calculations). The role of H-bonding and stacking interactions in the stabilisation of DNA, oligopeptides and proteins is described, and the importance of London dispersion energy is shown.

Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge-transfer terms are also important. The DeltaG of ethidium intercalation to DNA was estimated at -4.5 kcal mol(-1) and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non-covalent stacking (including charge-transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.

Glycine in an Electronically Excited State: Ab Initio Electronic Structure and Dynamical Calculations

The goal of this study is to explore the photochemical processes following optical excitation of the glycine molecule into its two low-lying excited states. We employed electronic structure methods at various levels to map the PES of the ground state and the two low-lying excited states of glycine. It follows from our calculations that the photochemistry of glycine can be regarded as a combination of photochemical behavior of amines and carboxylic acid. The first channel (connected to the presence of amino group) results in ultrafast decay, while the channels characteristic for the carboxylic group occur on a longer time scale. Dynamical calculations provided the branching ratio for these channels. We also addressed the question whether conformationally dependent photochemistry can be observed for glycine. While electronic structure calculations favor this possibility, the ab initio multiple spawning (AIMS) calculations showed only minor relevance of the reaction path resulting in conformationally dependent dynamics.

Gas-Phase Spectroscopy of Biomolecular Building Blocks

Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.

Understanding of Assembly Phenomena by Aromatic−Aromatic Interactions: Benzene Dimer and the Substituted Systems

Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.