Structures of 1,2,3-trihydroxybenzene in the S0 and S1 states

In this paper we report on the structure and vibrations of gaseous pyrogallol (1,2,3-trihydroxybenzene) in the electronic ground state (S₀) and its first electronically excited state (S₁). Both ab initio CASSCF/CASMP2 calculations as well as R2PI spectroscopy have been performed. From the ab initio calculations three minimum energy structures are obtained and the vibrations of two structures are observed in the R2PI spectra. The minimum energy structures differ by their OH torsional angles. The full three-dimensional potential energy surface of the coupled torsional motions is investigated and the three-dimensional eigenvalues are calculated. The most stable structure of pyrogallol contains two intramolecular hydrogen bonds and turns out to be planar in the S₀ state. In the S₁ state the free OH group is rotated out of the plane of the aromatic ring by about 40°. The strong change in geometry of this structure is predicted by the CASSCF calculations and confirmed by the R2PI spectra of pyrogallol and its deuterated species. The low frequency region of the R2PI spectra can be explained by a torsional motion and the out of plane vibration 17b.     

Density functional theory study on molecular structure and vibrational IR spectra of isocytosine

Density functional theory with the combined Becke3-LYP exchange-correlation energy functional [DFT(B3-LYP) method] using the 6-31G(d, p) basis set is applied to predict molecular parameters (geometries, rotational constants, dipole moments) and vibrational IR spectra (harmonic wavenumbers, absolute intensities) of six tautomers of the isocytosine molecule. The results are compared with the corresponding data calculated at the conventional ab initio Hartree-Fock (HF) level using the same basis set and with available experimental data. Calculations show that (a) three amino tautomers are slightly nonplanar species with, evidently, a distorted amino group, (b) the DFT (B3-LYP)/6-31G(d, p) method predicts better molecular parameters, than do the HF calculations, and (c) the DFT(B3-LYP)-calculated vibrational IR spectra of isocytosine agree well with the available recorded IR spectra, and they show marked improvement over the IR spectra predicted at the HF/6-31G(d, p) level. Tautomeric stabilities of isocytosine are discussed on the basis of computed electronic energies by the DFT(B3-LYP) and ab initio approaches [including the MP2 and MP4(SDQ) calculations of electronic energies] and predicted zero-point vibrational energies by DFT(B3-LYP) and HF methods. This relative energies at 0 K of the tautomeric forms of isocytosine predicted by both conventional ab initio and DFT(B3-LYP) methods correlate well with the experimental data, showing the predominance of the aminohydroxy tautomer of isocytosine for an isolated molecule. © 1997 John Wiley & Sons, Inc.     

Ab initio molecular dynamics of hydrogen dissociation on metal surfaces using neural networks and novelty sampling

We outline a hybrid multiscale approach for the construction of ab initio potential energy surfaces (PESs) useful for performing six-dimensional (6D) classical or quantum mechanical molecular dynamics (MD) simulations of diatomic molecules reacting at single crystal surfaces. The algorithm implements concepts from the corrugation reduction procedure, which reduces energetic variation in the PES, and uses neural networks for interpolation of smoothed ab initio data. A novelty sampling scheme is implemented and used to identify configurations that are most likely to be predicted inaccurately by the neural network. This hybrid multiscale approach, which couples PES construction at the electronic structure level to MD simulations at the atomistic scale, reduces the number of density functional theory (DFT) calculations needed to specify an accurate PES. Due to the iterative nature of the novelty sampling algorithm, it is possible to obtain a quantitative measure of the convergence of the PES with respect to the number of ab initio calculations used to train the neural network. We demonstrate the algorithm by first applying it to two analytic potentials, which model the H2/Pt(111) and H2/Cu(111) systems. These potentials are of the corrugated London-Eyring-Polanyi-Sato form, which are based on DFT calculations, but are not globally accurate. After demonstrating the convergence of the PES using these simple potentials, we use DFT calculations directly and obtain converged semiclassical trajectories for the H2/Pt(111) system at the PW91/generalized gradient approximation level. We obtain a converged PES for a 6D hydrogen-surface dissociation reaction using novelty sampling coupled directly to DFT. These results, in excellent agreement with experiments and previous theoretical work, are compared to previous simulations in order to explore the sensitivity of the PES (and therefore MD) to the choice of exchange and correlation functional. Despite having a lower energetic corrugation in our PES, we obtain a broader reaction probability curve than previous simulations, which is attributed to increased geometric corrugation in the PES and the effect of nonparallel dissociation pathways.     

Structures, energetics, and spectra of aqua-cesium (I) complexes: an ab initio and experimental study

The design of cesium-selective ionophores must include the nature of cesium-water interactions. The authors have carried out extensive ab initio and density functional theory calculations of hydrated cesium cations to obtain reasonably accurate energetics, thermodynamic quantities, and IR spectra. An extensive search was made to find the most stable structures. Since water...water interactions are important in the aqua-Cs+ clusters, the authors investigated the vibrational frequency shifts as a function of the number of water molecules and the frequency characteristics with and without the presence of outer-shell water molecules. The predicted vibrational frequencies were then compared with the infrared photodissociation spectra of argon-tagged hydrated cesium cluster ions. This comparison allowed the identification of specific hydrogen-bonding structures present in the experimental spectra.     

Formamide dimers: a computational and matrix isolation study

The dimerization of formamide (FMA) has been investigated by matrix isolation spectroscopy, static ab initio calculations, and ab initio molecular dynamics (AIMD) simulations. Comparison of the experimental matrix IR spectra with the ab initio calculations reveals that two types of dimers A and C are predominantly formed, with two and one strong NH...O hydrogen bonds, respectively. This is in accordance with previously published experiments. In addition, there is also experimental evidence for the formation of the thermally labile dimer B after deposition of high concentrations of FMA in solid xenon. The AIMD simulations of the aggregation process show that in all cases dimer C is initially formed, but rearrangement to the more stable doubly hydrogen-bonded structures A or B occurs for a fraction of collisions on the sub-picosecond time scale.     

l-Cysteine: Neutron spectroscopy, Raman, IR and ab initio study

Inelastic incoherent neutron scattering (IINS) spectra were obtained at 10K for normal and deuterated l-cysteine. Raman and infrared spectra were also recorded. Geometry of l-cysteine molecule was optimized for the zwitterion form using ab initio HF/6-31G* level. The theoretical frequencies of normal and d(4)-l-cysteine were compared with INS, Raman and IR spectra. Normal coordinate analysis and band assignments based on ab initio calculations and experimental data are presented.     

Ab initio calculations on low-energy conformers of alpha-cyclodextrin

In this article we carried out a comprehensive investigation of true minima on the potential energy surface (PES) for the alpha-cyclodextrin molecule using ab initio Hartree-Fock (HF) and density functional theory (DFT) quantum chemical methods, employing basis sets ranging from 6-31 G(d,p) to 6-311++G(2d,2p) triple-zeta quality. Thermodynamic quantities and the solvent effect were evaluated at the DFT level of theory. We believe that the most relevant conformers present on the multidimensional PES were sampled in our work, using an adequate treatment of electron correlation effects to describe the intramolecular hydrogen bonds that are present in cyclodextrin species. We present new structures not reported so far and discuss, in detail, the relevance of the DFT gas-phase equilibrium structures for the experimental and theoretical studies involving cyclodextrins and corresponding inclusion complexes, in the condensed phase. In addition, among the various true minimum energy structures located on the DFT PES, the preferred structures in the gas phase and aqueous media, needed to be used as representative minima on the PES in further studies involving the interaction of alpha-cyclodextrin with other species, were unambiguously identified.     

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.     

Insights into the structures, energetics, and vibrations of aqua-rubidium(I) complexes: ab initio study

We have carried out ab initio and density functional theory calculations of hydrated rubidium cations. The calculations involve a detailed evaluation of the structures, thermodynamic properties, and IR spectra of several plausible conformers of Rb+ (H2O)(n=1-8) clusters. An extensive search was made to find out the most stable conformers. Since the water-water interactions are important in hydrated Rb+ complexes, we investigated the vibrational frequency shifts of the OH stretching modes depending on the number of water molecules and the presence/absence of outer-shell water molecules. The predicted harmonic and anharmonic vibrational frequencies of the aqua-Rb+ clusters reflect the H-bonding signature, and would be used in experimental identification of the hydrated structures of Rb+ cation.     

Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations

The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic simulations combined with high-level correlated ab initio quantum chemical and statistical thermodynamic calculations. The lowest energy conformers were localized in the free energy surface. The structures of the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas phase have been for the first time reported and their scaled theoretical IR spectra unambiguously assigned and compared with previous gas-phase experimental results. Common geometrical features have been systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly. In addition, the peptide backbone of Trp-Gly-Gly has been compared with that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur. J. 2005, 11, 6803). From the observed systematic structural behavior between these peptide analogues, it is expected that the gas-phase conformers of other similar aromatic small peptides would present equivalent geometries. The DFT methodology failed to describe the potential energy surface of the studied peptides since the London dispersion energy (not covered in DFT) plays a significant role in the stabilization of most stable conformers.     

Vibrational spectra, ab initio calculations, and ring-puckering potential energy function for gamma-crotonolactone

The infrared and Raman spectra of liquid and vapor gamma-crotonolactone have been collected. Both the experimental data and ab initio calculations show that the molecule is rigidly planar in its electronic ground state. This conclusion agrees with the previously reported microwave studies and is attributed to the conjugation between the C=C and C=O double bonds of the ring. The ring-puckering potential energy function was generated from ab initio calculations and was confirmed by the vapor-phase Raman spectra to be nearly harmonic. Density functional theory (DFT) calculations predict a harmonic ring-puckering frequency of 203 cm(-1) as compared to the observed vapor-phase Raman value of 208 cm(-1). The DFT calculations were also used to compute the infrared and Raman spectra of gamma-crotonolactone, and these agree very well with the experimental spectra.     

Ab initio and DFT studies of the vibrational spectra of benzofuran and some of its derivatives

The vibrational spectra of benzofuran and some of its derivatives have been systematically investigated by ab initio and density functional B3LYP methods. The harmonic vibrational wavenumbers and intensity of vibrational bands were calculated at ab initio and DFT levels invoking different basis sets up to 6-311++g**. Vibrational assignments have been made and it has been found that the calculated DFT frequencies agree well in most cases with the observed frequencies for each molecule. Conformational studies have also been carried out and it is evident from ab initio calculations that 2(3H) benzofuranone is more stable than 3(2H) benzofuranone in support to our earlier semiempirical results.     

Low-lying isomers of the B9(-) boron cluster: the planar molecular wheel versus three-dimensional structures

The B(9)(-) cluster was found previously to be an unprecedented molecular wheel containing an octacoordinate planar boron with D(8h) symmetry in a combined photoelectron spectroscopy (PES) and theoretical study [H. J. Zhai et al., Angew. Chem., Int. Ed. 42, 6004 (2003)]. However, the PES spectra of B(9)(-) exhibit minor features that cannot be explained by the global minimum D(8h) structure, suggesting possible contributions from low-lying isomers at finite temperatures. Here we present Car-Parrinello molecular dynamics with simulated annealing simulations to fully explore the potential energy surface of B(9)(-) and search for low-lying isomers that may account for the minor PES features. We performed density functional theory (DFT) calculations with different exchange-correlation functionals and ab initio calculations at various levels of theory with different basis sets. Two three-dimensional low-lying isomers were found, both of C(s) symmetry, 6.29 (C(s)-2) and 10.23 (C(s)-1) kcal/mol higher in energy than the D(8h) structure at the highest CCSD(T) level of theory. Calculated detachment transitions from the C(s)-2 isomer are in excellent agreement with the minor features observed in the PES spectra of B(9)(-). The B(9)(-) cluster proves to be a challenge for most DFT methods and the calculated relative energies strongly depend on the exchange-correlation functionals, providing an excellent example for evaluating the accuracies of various DFT methods.     

The valence electronic structure and conformational flexibility of epichlorohydrin

The electronic structure of epichlorohydrin is investigated in the whole valence region by a combined experimental and theoretical study. The issue of controversial assignments of the molecular electronic structure is here addressed. Photoelectron spectra (PES) and Threshold Photoelectron spectra (TPES) of room temperature molecules in the gas phase are recorded. Geometries and energies of the stable conformers due to internal rotation of the C-C-C-Cl dihedral angle, gauche-II (g-II), gauche-I (g-I), and cis, are calculated, and the effect of the conformational flexibility on the photoionization energetics is studied by DFT and 2h-1p Configuration Interaction (CI) methods. Strong breakdown of the Koopmans Theorem (KT) is obtained for the four outermost ionizations, which are further investigated by higher level ab initio calculations. The full assignment of the spectrum is put on a firm basis by the combination of experimental and theoretical results. The orbital composition from correlated calculations is found closer to the DFT orbitals, which are then used to analyze the electronic structure of the molecule. The Highest Occupied Molecular Orbital (HOMO) and HOMO--2 are n(O)/n(Cl) mixed orbitals. The nature of each valence MO is generally preserved in all the conformers, although the magnitude of the n(O)/n(Cl) mixing in HOMO and HOMO--2 varies to some extent with the C-C-C-Cl dihedral angle. The low energy part of the HOMO PE band is predicted to be substantially affected by the conformational flexibility, as experimentally observed in the spectra. The rest of the spectrum is described in terms of the dominant conformer g-II, and a good agreement between experiment and theory is found. The inner-valence PE spectrum is characterized by satellite structures, due to electron correlation effects, which are interpreted by means of 2h-1p CI calculations.     

IR-UV double resonance spectroscopy of guanine-H2O clusters

We present the IR-UV double resonance spectrum of guanine monohydrate in the region 3100 cm(-1) to 3800 cm(-1) along with the energies and frequencies of these structures calculated at the non-empirical correlated ab initio RI-MP2/cc-pVDZ level. We assign the structures of guanine-water clusters by comparing the experimental spectra with the ab initio calculations and with the IR spectra of the bare guanine monomer. We find two clusters with guanine in the enol-amino tautomeric form and one structure with guanine in the keto-amino form.     

Structure of Au8: planar or nonplanar?

We have studied the structures and stabilities of Au6 and Au8 at the density-functional theory (DFT) and ab initio correlated levels of theory. For Au8, our ab initio calculations predict the lowest Au8 isomer to be planar, in line with the DFT calculations.     

Conformational Analysis of 2,2′-bifuran: Correlated High-level Ab initio and DFT Results

The torsional potential for inter-ring rotation in 2,2′-bifuran has been systematically tackled using highly accurate ab initio calculations as well as cost-effective DFT methods. The successful convergence of the ab initio results allowed to confirm the presence of a shallow gauche minimum in the torsional potential curve. The standard DFT methods failed to capture such a tiny energy barrier but, interestingly, the results could be remarkably improved by a mixture of wavefunction and DFT energies in a multi-coefficient fashion; thus, accurate DFT-based and ab initio reference data also become available. Since the experimental evaluation of torsional potentials faces quantitative problems, the outcome of high-level theoretical calculations is expected to be reliably used in further investigation on structure and conformational distribution of this system.     

Molecular structure of guanine-quartet supramolecular assemblies in a gel-state based on a DFT calculation of infrared and vibrational circular dichroism spectra

The infrared (IR) and vibrational circular dichroism (VCD) spectra of guanosine-5'-hydrazide ( G-1), a powerful hydrogelator, have been measured and analyzed on the basis of ab initio modeling. B3LYP/6-31G** DFT calculations predict that G-1, forming a clear solution in deuterated DMSO, is present in monomeric form in this solvent, whereas strong gelation in a phosphate buffer is due to the formation of a guanine-quartet structure, ( G-1)4, in which the four G-1 are linked by hydrogen-bonded guanine moieties and stabilized by an alkali metal cation. The B3LYP/6-31G** IR and VCD spectra of the nearly planar G-quartet, whose structure is slightly distorted from the C4h symmetry, in which the G-bases interact via four Hoogsteen-type hydrogen bonds and a sodium cation is positioned in the middle of the G-quartet, are in very good agreement with the experimental spectra, indicating that this structure is the predominant structure in the gel state. The geometric parameters are discussed. This study is the first to use IR and VCD spectroscopies coupled with DFT calculations to elucidate the structure of a supramolecular species in a gel state and shows the VCD spectroscopy as a powerful method for investigating the structure of complex supramolecular self-assemblies where the use of other structural methods is limited.     

Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): a promising tool for studying isolated small peptides

Resolution of identity standard density functional theory augmented with a damped empirical dispersion term (RI-DFT-D) calculations have been carried out on a set of lowest energy minima of tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides. RI-DFT-D (TPSS/TZVP) results are in excellent agreement with benchmark data based on the CCSD(T) method. Experimental spectra could be assigned according to the calculated IR frequencies. Central processing unit (CPU) time requirements are only slightly higher than those needed for the DFT calculations. Consequently, RI-DFT-D theory seems to be a promising methodology for studying oligopeptides with accuracy comparable to ab initio quantum chemical calculations.