Minimum Energy Geometry Research Articles

Binding of singlet oxygen with a stacked guanine dimer

AbstractGeometry optimization calculations were performed using the B3LYP/6‐31+G* method on the complexes of 1O2 and 3O2 molecules with a stacked dimer of planar guanine, varying the distance (D) between the planes of the guanine molecules. In this process, geometries of the guanine molecules were held fixed, D was fixed at different values, while the bond lengths of 1O2 and 3O2 as well as their orientations with respect to the guanine molecules were optimized for each value of D. The complexes in their most stable geometries were solvated in water using the integral equation formalism of the polarized continuum model of the self‐consistent reaction field theory. In gas phase, the most stable complex between 1O2 and the guanine dimer (2G.1O2) is formed when D is about 6 Å, while the most stable complex between 3O2 and the guanine dimer (2G.3O2) is formed when D is about 3.75 Å. In the minimum total energy geometry of 2G.1O2, 1O2 is located between the guanine molecules, above the imidazole ring of one of them. However, in the minimum total energy geometry of 2G.3O2, 3O2 is located outside the stack of guanine molecules, near the amino group of one of them. The solvation calculations showed that in aqueous media, 1O2 would bind with the stacked guanine dimer more strongly than in gas phase, while 3O2 would not bind with the same. The mode of binding of 1O2 with the stacked guanine dimer is such that it seems that 1O2 would replace one basepair in DNA, as happens in the intercalative mode of binding of drugs and other molecules, and it can lead to the formation of 8‐oxoguanine that has a mutagenic nature. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

FT-Raman spectroscopic study, aided by quantum chemical DFT calculations, of a series of oligothiophenes end-capped by nitriles

We report on the FT-Raman spectroscopic characterization, aided by DFT model chemistry calculations, of a bunch of α,ω-dicyano end-capped oligothiophenes, ranging in length from the dimer to the hexamer, which have been previously shown to display quite promissing amphoteric redox properties for their potential use in new technological applications. The attention is mainly focused to the role played by the CN⋯H hydrogen bonding interactions between adjacent molecules on various molecular properties, such as the minimum-energy geometry, atomic charges equilibrium distribution,topologies/energies of the frontier molecular orbitals and the Raman scattering spectral profile. To this end we have performed to two sets of quantum chemical calculations, at the DFT//B3LYP/3-21G* level, on: (a) a single terthiophene in the vacuum and (b) a suited dimeric model with a fully coplanar array of the two terthienyl segments interacting through the cyano end-caps.

Electronic excitation and ionisation of 1-azabicyclo[2.2.2]octane (ABCO): evidence for a twisted structure from experiment and theory

The first excited neutral and ground cationic states of 1-azabicyclo[2.2.2]octane (ABCO) have been studied using a combination of (1 + 1′) REMPI and ZEKE spectroscopy, supported by ab initio molecular orbital calculations. In common with the related tertiary alkyl amines, analysis of both REMPI and ZEKE spectra indicate that the overriding impulse upon electronic excitation and ionisation is for a flattening of the nitrogen end of the molecule, albeit hindered by the cage. In addition, the activity of the torsion mode (19) in both REMPI and ZEKE spectra suggests geometry changes along the torsion coordinate between the three electronic states sampled in these experiments. Ab initio molecular orbital calculations conducted at the MP2/cc-pVDZ level of theory yield minimum energy geometries with CNCC dihedral angles of 6.011° and 7.86° for the S 0 and D 0 states, respectively, which indicates that the torsion coordinate is described by a double minimum potential. However, the degree of perturbation to the vibrational eigenvalues suggests that the zero point level lies a few wavenumbers above a small barrier and that ABCO is pseudo-twisted with a vibrationally averaged C 3v symmetry.

Femtosecond study of Cu(H2O) dynamics

The short-time nuclear dynamics of Cu(H(2)O) is investigated using femtosecond photodetachment-photoionization spectroscopy and time-dependent quantum wave packet calculations. The Cu(H(2)O) dynamics is initiated in the electronic ground state of the complex by electron photodetachment from the Cu(-)(H(2)O) complex, where hydrogen atoms are oriented toward Cu. Several time-resolved resonant multiphoton ionization schemes are used to probe the ensuing reorientation and dissociation. Immediately following photodetachment, the neutral complex is far from its minimum energy geometry and possesses an internal energy comparable to the Cu-H(2)O dissociation energy and undergoes both large-amplitude H(2)O motion and dissociation. Dissociation is observed to occur on three distinct time scales: 0.6, 8, and 100 ps. These results are compared to the results of time-dependent J=0 wave packet calculations, propagating the initial anion vibrational wave functions on the ground-state potential of the neutral complex. An excellent agreement is obtained between the experimental results and the ionization signals derived from the calculated probability amplitudes. Related experiments and calculations are carried out on the Cu(D(2)O) complex, with results very similar to those of Cu(H(2)O).

C, D, and E Electronic States of the SO2+ Ion Studied Using Multiconfiguration Second-Order Perturbation Theory

For exploring the C, D, and E states of the SO2+ ion, eight excited states of SO2+, 22A1, 32A1, 22B2, 32B2, 12B1, 22B1, 32B1, and 22A2, have been studied using the complete active-space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) methods in conjunction with two contracted atomic natural orbital basis sets, S[6s4p3d1f]/O[5s3p2d1f] (ANO-L) and S[4s3p2d]/O[3s2p1d] (ANO-S) (the 12A1, 12B2, and 12A2 states were previously studied and assigned to the X, A, and B states, respectively). Equilibrium geometries and the v1 and v2 vibrational frequencies for the eight excited states were predicted at the CASSCF/ANO-L level. For the eight states, the CASPT2/ANO-L adiabatic excitation energy (T0) and vertical excitation energy (Tv) values were calculated using the CASSCF/ANO-L geometries, and the CASPT2/ANO-L relative energy (Tv‘) values to X2A1 were calculated at the SO2 molecular geometry. The CASPT2/ANO-L T0 ordering is: 12B1, 22B1, 22A2, 22A1, 32A1, 22B2, 32B2, and 32B1 (in increasing order of energy), and five of these states have shake-up ionization character. We assign the observed C, D, and E states of SO2+ to 12B1, 22A1, and 22B2, respectively, and the three calculated states have primary ionization character at the molecular geometry. The CASPT2/ANO-L T0 values and the CASSCF/ANO-L v1 and v2 values for 12B1 and 22A1 are in good agreement with the experimental T0, v1, and v2 values for the C and D states, respectively. The CASPT2/ANO-L T0 value and the CASSCF/ANO-L v1 and v2 values for 22B2 are in reasonable agreement with the experimental T0, v1, and v2 values for the E state, respectively. For preliminarily exploring the potential energy surfaces (PESs), potential energy curves (PECs) of the eight excited states, as functions of the OSO bond angle, were calculated at the CASPT2/ANO-S level, and then in the CASSCF/ANO-L PESs of 12B1 and 22A1 we found other minimum energy geometries which have lower CASPT2/ANO-L energies than the “equilibrium geometries” of the respective states. However, these geometries are far away from the Franck−Condon regions for the ground-state molecule and ion. For preliminarily exploring dissociation processes of SO2+, a Jacobi coordinate system (Cs symmetry) was adopted and dissociation potential energy curves (DPECs) for the 1-62A‘ and 1-52A‘ ‘ states were calculated at the CASPT2/ANO-S level. The calculations indicate that the 12A‘, 22A‘, 32A‘, 12A‘ ‘, 22A‘ ‘, and 32A‘ ‘ DPECs converge to the first dissociation limit [SO+ (X2Π) + O (3Pg)]. By considering the correlation relations of the Cs states with the C2v states and our assignments for the C, D, and E states, we conclude that, among the C, D, and E states, only two directly correlate to the first dissociation limit.

Structure and Thermodynamics of the Tin Dichloride DimerA Computational Study

The molecular structures of SnCl2 and Sn2Cl4 have been calculated by high-level quantum chemical methods. The global minimum structure found for the tin dichloride dimer is of Cs symmetry and has two halogen bridges. This structure is very different from the one suggested earlier by Fields et al. based on their gas-phase Raman spectroscopic measurements. Thermodynamic functions for gaseous SnCl2 and Sn2Cl4 have also been calculated. The minimum-energy geometry of the trimeric molecule, Sn3Cl6, has a six-membered ring with alternating Sn and Cl atoms in the highly puckered ring. The possible structural changes during evaporation are discussed in some detail.

Ultrafast Excited-State Proton Transfer of 2-(2‘-Hydroxyphenyl)benzothiazole: Theoretical Analysis of the Skeletal Deformations and the Active Vibrational Modes

The involvement of skeletal deformations in the ultrafast excited-state proton transfer of 2-(2‘-hydroxyphenyl)benzothiazole (HBT) and the identification of the vibrational modes active in the process are reported. A multidimensional ab initio calculation of ground and excited states at the HF/DFT and CIS/TDDFT level renders the relevant portions of the potential energy surfaces around the minimum-energy path connecting the enol and keto configuration. The frequencies and potential energy distributions of the normal modes and the corresponding deformations of the molecule are calculated for all minimum-energy geometries. Along the minimum-energy path, the nuclear deformation is projected onto the relevant normal modes. This normal-mode analysis shows that mainly five low-frequency in-plane vibrations are associated with the electronic rearrangement and the transfer of the proton. The theoretical findings are in quantitative agreement with the experimental study presented in the accompanying paper.

New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy.

Benchmark full quantum mechanical Hartree-Fock calculation has been carried out to compute interaction energies for the streptavidin-biotin binding complex. In this report, the entire streptavidin-biotin interaction system with a total of 1775 atoms is treated by quantum mechanics. The full quantum energy calculation for this protein system is made possible by applying a recently developed MFCC approach in which the protein molecule is decomposed into amino-acid-based fragments that are properly capped. Ab initio calculations are performed at the Hartree-Fock level with a 3-21G basis set. The energies are computed for geometries of the binding complex near two configurations, corresponding to the crystal structure of the binding complex and a minimum energy geometry found from molecular force field, respectively. Comparisons are made of the computed ab initio energies with those from a force field. The present calculation shows that ab initio binding energies (at HF/3-21G level) are almost 30 kcal/mol larger than those given by a force field.

Structural and electronic properties of novel nanoscale C 4 nS 4 n molecules

We have designed novel ring molecules, C 4 n S 4 n , which contain only carbon and sulfur atoms and performed Density Functional Theory (DFT) calculations on C 4 n S 4 n for n=4,6,8. We have also done Hartree–Fock (HF) calculations on C 24S 24 and compared HF and DFT results for C 24S 24. DFT calculations showed that the minimum energy (optimized) geometries of neutral C 4 n S 4 n molecules have D nh symmetry for n=4,6,8. However, for (C 24S 24) Q molecules with Q=+1,+2, DFT geometry optimizations lead to the structures with the point group symmetry to C 2, C 2 v and D 2 h for (C 24S 24) +, (C 24S 24) 2+ (singlet state) and (C 24S 24) 2+ (triplet state), respectively. Large structural differences between HF and DFT results for (C 24S 24) + indicate the importance of electron correlation effects for these molecules. It is also found that the triplet state of (C 24S 24) 2+ has lower energy.

Quantifying multiple-body interaction terms in H-bonded HCN chains with many-body perturbation/coupled-cluster theories

Many-body perturbation/coupled-cluster calculations have been carried out to investigate the multiple-body energy terms and their contribution to the interaction energy of linear (HCN)N chains. All minimum energy geometries of the clusters (N=2–7) are obtained at the second-order many-body perturbation (MP2) levels of theory. Electron correlation and cooperative effects in the C–H⋯N hydrogen bonds are also quantitatively characterized during the aggregation process. It is found that the two- and three-body terms account for nearly all of the total interaction energy, but all high-body terms increase with the size of the cluster. Detailed numerical values are given for all the many-body contributions of the (HCN)N chains. Electron correlation effects are found to be important for the two- and three-body terms but have decreased importance for the higher-body terms. Cooperative effects are also investigated for the binding energy and dipole moment. The dipole moments of the HCN oligomers are larger than the sum of the individual monomers with differences ranging between 12% (N=2) and 28% (N=7). The limiting values for the binding energy and dipole moment of (HCN)N, per monomer, corresponding to very large N values, are estimated to be 22.9 kJ/mol and 3.87 D, per monomer, respectively. These results correspond to cooperative contributions of 5.8 kJ/mol to the energy, and 1.0 D to the dipole moment.

Competition between π- and σ-based interactions in metal ion complexes of the phenyl radical

Hybrid density functional theory (B3-LYP and B3-PW91) and counterpoise-corrected ab initio (MP2) calculations have been performed for the adducts of the main-group metal ions Na +, Mg +, Al +, K +, and Ca + with the phenyl radical C 6H 5. While the calculated bond dissociation energies (BDEs) and complexation geometries of the alkali metal ion adducts do not differ substantially from those determined for the analogous M +/benzene π-complexes, the alkaline earth ions exhibit a strong preference for σ-bond formation at the bare C atom of the phenyl ring, with calculated BDEs exceeding those determined for benzene complexation by approximately 80 and 150 kJ mol −1 for Mg + and Ca +, respectively. This σ-coordination is only feasible when the unpaired spins on the reactant Mg + (or Ca +) and C 6H 5 radicals are opposed, thereby leading to a closed-shell (singlet state) adduct ion. When the unpaired spins are aligned, the triplet-state adduct thus produced adopts π-complex minimum energy geometry with a BDE significantly below that of the corresponding M +/benzene complex. Both π- and σ-coordination are also found to be local minima on the AlC 6H 5 + potential energy surface, with the BDE of the Al +/C 6H 5 σ-complex being approximately 50 kJ mol −1 larger than that of the corresponding π-complex, and about 20 kJ mol −1 above the BDE for Al +/benzene. The overall results of our study show that the phenyl radical exhibits a much greater degree of selectivity between the main-group metal ions represented here than is evident for benzene. The phenyl radical BDEs range from 59.7 (K +) to 264.7 kJ mol −1 (Ca +) according to calculations at the B3-PW91/6-311+G(2df,p) level of theory, which contrasts with the 65.5 (K +) to 147.9 kJ mol −1 (Al +) BDE values determined for benzene at the same level of theory.

Stereoelectronic substituent effects on intramolecular H-bonding in crowded o-anisic acids

The minimum energy geometries, OH stretching frequencies, and fractional distributions of the free and intramolecularly hydrogen-bonded conformers of eleven substituted o-anisic acids were determined by density functional theory. The structural changes that are associated with formation of the intramolecular H-bond are discussed. Intensities and areas of pertinent peaks in the measured infrared spectra were used to obtain the mol fractions of the intramolecularly H-bonded conformer, in equilibrium with the intermolecularly H-bonded dimers in chloroform solution. These mol fractions follow the same order as the theoretically determined “gas phase” values. They also correlate linearly with the change in the time-averaged 13C NMR shift of the carboxyl group that is produced by a change of solvent from DMSO to CDCl3. The same solvent change leads to an increase in the size of the one-bond C–H coupling constant of the methoxy group because of the greater polarization of the its H–C bonds in the intramolecular H-bonded conformer. The solvent-induced changes in the CH3O coupling constant correlate with those of the ipsoC2-OMe shift. The latter shift changes involve opposing effects of intra- and intermolecular H-bonding of the o-anisic acids.

Predicting the Phase Diagram of a Liquid Crystal Using the Convex Peg Model and the Semiempirical PM3 Method

A molecular theory to determine thermodynamic properties of isotropic and nematic phases of liquid crystals is proposed, based on a “convex peg” model and semiempirical PM3 (Parametrized Method 3) calculations. The Helmholtz-free energy of the molecular system, a convex hard core within an encircling spherical square-well (SW) potential, is obtained from a second-order perturbation theory for SW nonspherical particles, combined with the Parsons decoupling approximation of the translational and rotational degrees of freedom, and a long-range approximation for the evaluation of the perturbation terms. The theory is applied to predict the phase diagram and isotropic−nematic transition of p-azoxyanisole. To do this, an estimation of the volume of a p-azoxyanisole molecule is derived from a minimum-energy geometry, using PM3 calculations; the volume obtained is mapped into a hard ellipsoid revolution volume of a Convex Peg molecule. A very good agreement in the prediction of the thermodynamic properties is obtained when compared with experimental data.

Microsolvation of Hg and Hg2+: Energetics of Hg·H2O, Hg2+·H2O and HgOH+

High-level ab initio and DFT calculations are employed to calculate the geometries of monosolvated Hg and Hg2+. In agreement with previous studies on M2+·H2O species, we calculate the equilibrium geometry of the Hg2+·H2O dicationic complex as having the Hg2+ interacting with the oxygen atom of water, but we find that the minimum energy geometry is nonplanar and attribute this to covalency. For Hg·H2O, in contrast to many previous studies on neutral M·H2O species, but in agreement with our previous studies, we find that the Hg atom prefers to be situated on the hydrogen end of the water molecule, in a Cs orientation. We rationalize this in terms of electron−electron repulsion. We calculate the energies of the lowest states of HgOH+ and conclude that the ground state is a bent, closed-shell 1A‘ state, with a fair amount of covalency. CCSD(T) calculations employing very large basis sets, and employing the above geometries, allow us to calculate values for the interaction energies of Hg·H2O (213 cm-1) and Hg2+·H2O (90 kcal mol-1). In addition, the enthalpy of reaction for the process Hg2+ + H2O → HgOH+ + H+ is calculated to be −40 kcal mol-1 at the highest level of theory used herein. Finally, we conclude that the Hg2+·H2O complex should be observable, but that care in its preparation is required.

Ab initio quantum mechanical models of peptide helices and their vibrational spectra.

Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.

Stacking faults in close-packed clusters

Ground state geometries of small hard sphere clusters were studied using two different type of contact interaction, a pair-potential and a many-atom interaction. Monte Carlo method in an FCC lattice with all possible (111) stacking faults was used to obtain the minimum energy geometries for clusters up to 59 atoms. Due to the surface energy, FCC packing is generally favoured as opposite to the HCP structure. However, in most cluster sizes the ground state obtained with the many-atom interaction has one or more stacking faults. The most symmetric geometry is usually not the ground state. Clusters with 59 and 100 atoms were studied due the possibility of a high symmetry cluster with stacking faults in all four directions. The size dependence of the total energy has similarities with that of the average moment of inertia.

Bystander Effects on Carbene Rearrangements: A Computational Study

Methylcarbene, dimethylcarbene, chloromethylcarbene, and tert-butylmethylcarbene were studied at the HF/6-31G*, MP2/6-31G*, B3LYP/6-31G*, MP2/6-31+G(2d,p), QCISD(T)/6-31G*//MP2/6-31G*, and QCISD(T)/6-31+G(2d,p) levels. Minimum energy geometries of the singlet and triplet states of the carbenes were calculated. The barriers to 1,2-hydrogen migration for CH3CX → CH2CHX were calculated and found to increase for X = Cl > CH3 > C(CH3)3 > H. Isodesmic calculations indicate that the effect of the bystander group is to stabilize differentially the carbene reactant, thereby increasing the barrier to rearrangement for X = Cl > CH3 > C(CH3)3 > H.

Calculation of thermodynamic, electronic, and optical properties of monoclinic Mg2NiH4

Ab initio total-energy density functional theory is used to investigate the low temperature (LT) monoclinic form of Mg2NiH4. The calculated minimum energy geometry of LT Mg2NiH4 is close to that determined from neutron diffraction data, and the NiH4 complex is close to a regular tetrahedron. The enthalpies of the phase change to high temperature (HT) pseudo-cubic Mg2NiH4 and of hydrogen absorption by Mg2Ni are calculated and compared with experimental values. LT Mg2NiH4 is found to be a semiconductor with an indirect band gap of 1.4 eV. The optical dielectric function of LT Mg2NiH4 differs somewhat from that of the HT phase. A calculated thin film transmittance spectrum is consistent with an experimental spectrum.

Ab initio and DFT study of aliphatic diamines

The optimized minimum-energy geometries of different aliphatic diamines and of their protonated forms were determined using ab initio methods and density functionnal calculations. The molecular structures, vibrational frequencies and charge distributions of selected diamines and their protonated forms were also studied. The computed gas phase acidities as measured by the proton affinities of the diamines were obtained. Most methods used were able to predict it well, typically to within 10kcalmol−1.

Fenarimol solar degradation pathways and photoproducts in aqueous solution

The degradation photoproducts of the fungicide fenarimol obtained from irradiation of aqueous solutions with sunlight were characterised. The photoproducts resulting from samples with different exposure times were extracted and separated using chromatographic techniques. Seven main photoproducts were detected using high performance liquid chromatography with a photodiode array detector, gas chromatography with mass spectrometry detector and Fourier transform infrared spectroscopy. Structures are suggested for possible photoproducts based on the characterisation results, minimum energy geometry of the parent compound, and the mass spectral behaviour of fenarimol. These correspond to the compounds with m/ z 328 (three structural isomers (a), (b) and (c)), m/ z 294 (two structural isomers (a) and (b)), m/ z 292, 278 and 190. Of the various major products detected, the isomer 328(a) is seen to be particularly unstable under the action of sunlight. The most stable photoproducts are found to be those with m/ z 294(a), 278 and 190. However, upon prolonged solar irradiation all of these break down to produce polar, low molecular weight compounds. Comparison with our own and other results on fenarimol photolysis indicate significant solvent effects on the process. The combination of these structural characterisation results and previous data from spectroscopic and photodegradation kinetics studies allows us to suggest some possible mechanisms for the photodegradation of fenarimol under sunlight.