Showing papers in "Journal of Molecular Structure-theochem in 1998"

Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes

Abstract: An approach to the general extension of the OPLS all-atom (OPLS-AA) force field to heterocycles has been explored with testing for pyridine and the diazenes, pyridazine, pyrimidine, and pyrazine. For the non-bonded interactions, the partial atomic charges are obtained from fitting to the electrostatic potential surfaces from ab initio RHF/6–31G∗ calculations and standard OPLS values are used for the Lennard-Jones parameters. The harmonic bond-stretching and angle-bending parameters are largely adopted from the AMBER force field. The resultant OPLS-AA force field is shown to perform well for computing the structures of the heterocycles, heterocycle-water interaction energies, and thermodynamic properties of the four pure liquids. The latter quantities were computed from Monte Carlo statistical mechanics simulations; the average errors in computed densities and heats of vaporization are 0.8% and 2.7%. Free energies of hydration were also calculated for pyridine and pyrazine, and provided errors of under 1 kcal mol−1 in comparison to experimental data.

Statistical analysis of the molecular surface electrostatic potential: an approach to describing noncovalent interactions in condensed phases

Abstract: We discuss various means of characterizing the pattern of the electrostatic potential on a molecular surface These include determination of the most positive and most negative values of the potential, its average deviation, and its variance The latter, in conjunction with a measure of the degree of balance between the contributions from the positive and negative regions, has proven to be particularly useful in developing analytical representations of condensed phase properties that depend upon noncovalent interactions Some applications are briefly reviewed

A general survey of molecular quantum similarity

Abstract: A comprehensive survey of the theoretical foundations and definitions associated with quantum similarity is given. In this task care has been taken to determine the primary mathematical structure which can be associated with quantum similarity measures. Due to this, the concept of a tagged set is defined to demonstrate how molecular sets can be described systematically. The definition of quantum object, a notion introduced by our laboratory and employed for a long time in quantum similarity studies, is clarified by means of a blend involving quantum theory and the tagged set structure formalism, and used afterwards as the cornerstone of the subsequent development of the theory. In the definition of quantum objects, density functions play a fundamental role. To formally construct the quantum similarity measure, it is very interesting to study the main algorithmic ideas, which may serve to compute approximate density forms, accurate enough to be employed in the practical calculation of nuclear, atomic and molecular quantum similarity measures. Thus, the atomic shell approximation is defined accompanied by all the implied computational constraints and the consequences they have in the whole theory development as well as to the physical interpretation of the results. A wide and complex field appears from all these ideas, where convex sets play a fundamental role, and a new definition emerges: one associated with vector semispaces, where the main numerical formalism of quantum similarity seems perfectly adapted. Applications of this development embrace quantum taxonomy, visual representation of molecular sets, QSAR and QSPR, topological indices, molecular alignment, etc., and among this range of procedures and fields, there appears with distinct importance the discrete representation of molecular structures.

Computational Investigation of the Structures and Relative Stabilities of Amino/Nitro Derivatives of Ethylene

Abstract: Eight amino and/or nitro derivatives of ethylene have been investigated computationally at the density functional B3P86/631 + G** level. The molecular geometries and relative stabilities reflect the varying roles of ‘push‐pull’ electronic delocalization and intramolecular hydrogen bonding. The same two factors affect, to varying extents, the computed C‐NO2 and C‐NH2 bond dissociation energies, which are also presented, as are the heats of formation, vaporization and sublimation of the three diaminodinitroethylenes. The potential of the latter as energetic compounds is briefly discussed. q 1998 Elsevier Science B.V. All rights reserved

Calculation of the structure and absorption spectra of phthalocyanines in the gas-phase and in solution

Abstract: Ab initio calculations have been carried out on both gas-phase and solvated phthalocyanines in order to determine equilibrium structures, vibrational spectra, and electronic spectra. Density functional theory (DFT) optimized geometries have the expected symmetries of D 2h for free-base phthalocyanine, D 4h for copper phthalocyanine, and C 4v for tin phthalocyanine, whereas Hartree–Fock optimized geometries, which also include lead phthalocyanine, are slightly displaced from the expected symmetries. Both sets of optimized geometries agree reasonably well with the available experimental structures. Vibrational spectra, calculated by the Hartree–Fock method, are in partial agreement with measured spectra, whereas visible absorption spectra calculated using molecular geometries obtained at three different levels of theory (DFT, HF, and PM3) showed good agreement with the measured vapor-phase spectra in the Q-band, and using the DFT optimized geometry resulted in very good agreement with measurements in the B-band. The self-consistent reaction field method for including bulk solvent effects in HF calculations had a small, nearly negligible, effect on the molecular structure of SnPc, whereas the DFT/ cosmo solvation model yielded the predictable result of increasing the Sn–N bond length by pulling the Sn atom further out of the molecular plane.

A comparative study on the vibrational spectroscopy of pyridazine, pyrimidine and pyrazine

Abstract: In this work, the authors deal with the vibrational spectroscopy of the three diazine parent compounds, i.e. that of pyridazine, pyrimidine and pyrazine. Infrared spectra were recorded in vapour and condensed phases, and Raman spectra were measured in condensed phase using both parallel and perpendicular polarization of light. The vibrational fundamental frequencies were calculated applying ab initio quantum-chemical methods: Moller–Plesset perturbation and local density functional methods. The results of the calculations were applied to the assignment of the vibrational fundamentals and the measured fundamental frequencies were used to refine the vibrational force constants. The main deviations between the recalculated and the measured frequencies are about 2.5% or smaller.

On the bonding and the electric field gradient of the uranyl ion

Abstract: Molecular properties of the uranyl ion ([UO2](2+)) are studied using both a non-relativistic and a relativistic method. Inclusion of relativity leads to a bond length expansion and makes the electric field gradient (EFG) at the uranium nucleus strongly dependent on the U-O bond distance, The non-relativistic EFG value is found to be much larger than the relativistic value. An analysis of the non-relativistic and relativistic wave functions is given and shows the presence of a so-called 'U(6p) core-hole'. A different ordering of the valence spinors is found compared to previous work. It is confirmed that the HOMO has sigma(u) character and has a large U(5f) contribution. (C) 1999 Elsevier Science B.V. All rights reserved.

Qualitative thinking in the age of modern computational chemistry : or what lionel salem knows

Abstract: A personal assessment is given of the present state of computational chemistry, and in particular of the persistent need for qualitative orbital thinking at a time when exceedingly accurate calculations are possible. The need for the qualitative view arises, it is claimed, from the inherent difference between predictability and understanding, from certain potential impediments to chemical understanding intrinsic to human-computer interactions, from the peculiar yet productive way that experiment and theory interact in chemistry, and lastly from some special features of theory in science in general.

CH and Chalogen bond dissociation energies for fluorinated and chlorinated methane evaluated with hybrid B3LYP density functional theory methods and their comparison with experimental data and the CBS-Q ab initio computational approach

Abstract: The CH and Chalogen bond dissociation energies (BDEs) were computed with the hybrid B3LYP/6-311 + G(2d,2p) theory model for chlorinated and fluorinated methane. All computed values were substantially lower (5–10 kcal mol −1 ) than the experimental values. To obtain better agreement, a correlation factor was introduced. When this factor was applied, excellent agreement between the B3LYP/6-311 + G(2d,2p) computed energies and the experimental BDEs was observed. On the other hand, the CBS-Q ab initio computational approach generated BDEs which are in good agreement with experimental values without a correction factor.

A study of the structures and vibrations of c6h5nh2, c6h5nhd, c6h5nd2, c6d5nh2, c6d5nhd, and c6d5nd2 in the s1 state by ab initio calculations

Abstract: The structures and vibrations of C6H5NH2, C6H5NHD, C6H5ND2, C6D5NH2, C6D5NHD, and C6D5ND2 have been studied using ab initio molecular orbital (MO) calculations. Calculations at the CIS/6-31+G∗ level successfully predict that aniline is planar in the S1 state, and contracts along the long in-plane axis with a quinoid-like resonance structure. A comparison of the S0 and S1 state vibrational modes is presented and discussed in terms of the changes in reduced masses, force constants, and mode mixing for aniline and its isotopic species. The computed frequencies are found to be in very good agreement with the available experimental values.

An assessment of density functional methods for studying molecular adsorption in cluster models of zeolites

Abstract: The performance of six density functional theory (DFT) methods has been tested for a zeolite cluster containing three tetrahedral atoms (3T) and the complexes it forms with water and methanol molecules. The DFT methods (BLYP, BP86, BPW91, B3LYP, B3P86, B3PW91) give results in good agreement with second-order perturbation theory (MP2). The results in this paper provide evidence of the suitability of DFT methods for studying hydrogen-bonded adsorption complexes in zeolites. Generally, the hybrid DFT methods are in closer agreement with experiment and MP2 than the pure DFT methods for geometrical parameters. The only exception is the Z − geometry, perhaps due to its anionic character. All DFT methods give results in good overall agreement with MP2 for intramolecular geometrical parameters of the adsorption complexes, intramolecular vibrational frequencies, and adsorption energies. The B3LYP method gives intermolecular geometries and intermolecular vibrational frequencies which are closest to those obtained from the MP2 method. Thus, the B3LYP method seems to be the best choice for a density functional treatment of molecular adsorption in zeolite systems.

Infrared spectra of some isotopomers of ethylamine and the ethylammonium ion: a theoretical study

Abstract: The normal mode frequencies of some isotopomers of trans and gauche ethylamine and the ethylammonium ion are examined theoretically using the GAUSSIAN 94 set of quantum chemistry codes at the MP2 level of theory using a 6-311G** basis set In particular deuteration of the NH2 and NH+3 hydrogen atoms, as well as the deuteration of the CH2 hydrogen atoms, the CH3 hydrogen atoms, and total deuteration of the ethylamine and ethylammonium ion are examined The trans conformer of the ethylamine is found to be energetically more stable by 116 kJ mol−1 At 25°C the Gibbs free energy change ΔGo for the trans→gauche equilibrium is 107 kJ mol−1, but because there are two equivalent gauche conformers the relative population of gauche:trans is 130 Correction factors for predominant vibrational motions at each level of theory are reported and compared for the eight molecular species for trans and gauche ethylamine and the ethylammonium ion that are considered

Physical and chemical properties of airborne nanoscale particles and how to measure the impact on human health

Abstract: Suspended particles with a diameter below 1 μm act as vehicles transporting toxic chemicals into the human respiratory system. It is therefore of interest to record the intensity of these particles and to determine the source from which they were emitted. It is shown that this can be done by simultaneously measuring the light scattering (LS), the photoelectric charging (PC), and the diffusion charging (DC). Particles carrying polycyclic aromatic hydrocarbons (PPAH) are detected by their large PC and are generated in combustion of organic materials, whereas particles from other sources only exhibit LS and DC. With combustion-generated particles, the ratio of PC/DC allows to determine the type of combustion from which the particles were emitted. In particular, particles from diesel emission can be distinguished from cigarette smoke. It is further demonstrated how changes of chemical composition or of particle size that might occur in the atmosphere are detectable. As an example of an application, we studied the nanoscale particles found on motorways in the industrialized world. The sources of the majority of these particles are diesel motors. The fraction of particle mass due to PPAH is independent of location and weather conditions. However, the particle concentration is much larger in Tokyo and in Paris than in Zurich due to the higher density of diesel vehicles.

A proton NMR shielding model for the face of a benzene ring

Abstract: In a strong magnetic field, nuclei located over an aromatic ring experience a diminished magnetic field as a result of the induced magnetic field caused by circulating π electrons. The shielding effect of an aromatic ring can be substantial, causing an upfield shift of up to 3 ppm in proton NMR spectra, yet this effect is not considered in any of the empirical methods for predicting chemical shifts. We have used GIAO, an ab initio subroutine in Gaussian 94 to calculate isotropic shielding tensors and to predict the proton NMR chemical shift for a simple model system: methane held at various positions over a benzene ring. The NMR chemical shift shielding increments experienced by the protons of methane have been mapped as a function of their position x, y and z in Cartesian coordinates relative to the center of the aromatic ring. A mathematical function was fit to this three-dimensional shielding increment surface at each of six distances from the face of the benzene ring. In addition, a single mathematical equation was developed for predicting the shielding caused by a benzene ring. Chemical shifts predicted by this equation are compared with observed values. Incorporation of this function into a molecular mechanics–chemical shift prediction program should aid structure elucidation of structures having such features.

HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential

Abstract: The cleavage mechanism of HIV-1 protease (HIV-PR) is investigated with classical molecular dynamics (MD) simulation and with methods incorporating a hybrid quantum mechanical and molecular mechanical (QM/MM) potential function. An X-ray structure of an HIV-PR/inhibitor complex was used to generate model HIV-PR/substrate and HIV-PR/intermediate complexes. Analysis of the feasibility of reaction is based on three hypothetical reaction mechanisms and a variety of possible starting conditions. The classical MD simulations were analyzed for conformations consistent with reaction initiation, as reported previously. It was concluded that Asp125 is the general acid in the first reaction step and transfers a proton to the carbonyl oxygen. Simulations suggest that water 301 stabilizes productive reactant and intermediate conformations but does not participate directly in the reaction. A lytic water, when present, is held very tightly in a position propitious for nucleophilic attack at the scissile carbon. For mechanisms consistent with the classical simulations, reaction barriers were calculated using a QM/MM potential. The QM/MM potential and a restrained energy minimization method for calculating reaction paths and barriers are described. Preliminary results identify reasonable barrier heights and transition state conformations and predict that the first reaction step follows a predominantly stepwise rather than concerted pathway.

Model core potentials for the lanthanides

Abstract: Model core potential (MCP) parameters and valence basis sets are determined for the lanthanides La through Lu. The 46 (1s–4d) electrons are replaced by the MCP and the 5s, 5p, 4f, 5d, and 6s are treated explicitly as valence electrons. The major relativistic effects at the level of Gowan and Griffin's quasi-relativistic Hartree–Fock method (QRHF) are incorporated into the MCPs. The valence orbitals thus obtained have inner nodal structure. The MCP is tested for various states of Pr, Pr + , Pr 2 + and Pr 3 + at the SCF level, and it is confirmed that the MCP determined for neutral atom works very well even for Pr 3 + . The CASSCF and SDCI calculations are performed for the ground state ( 3 Φ) of CeO. The spectroscopic constants given by the SDCI including Davidson's correction ( r e =1.816 A, ω e =866 cm − 1 , and D e =7.89 eV) are in good agreement with the experimental values ( r e =1.820 A, ω e =862 cm − 1 , and D 0 =8.18 eV).

On spin density and hole distribution relations: valence and free valence

Abstract: The formalism of the average or mean number of particles in a many-body system is applied to the “hole” distribution of many-electron molecular systems. In this way we rigorously derive expressions for the atomic valence and free valence magnitudes. It is shown that spin densities and free valence are directly related to each other in the case of maximum information state functions like ROHF (restricted open-shell Hartree-Fock) and UHF (unrestricted Hartree-Fock). For the case of correlated CI-like expansions free valence is interpreted as a measure of the non-uniform character of the spin distribution even in the case of systems with zero total spin number. Ab initio calculations of some selected molecules are presented and discussed.

Relativistic dsp-model core potentials for main group elements in the fourth, fifth and sixth row and their applications

Abstract: We have developed advanced relativistic model core potentials (dsp-MCPs) for the fourth (Ga–Kr), fifth (In–Xe) and sixth-row (Tl–Rn) main-group elements, where the outermost core (n−1)d electrons were treated explicitly as well as the ns and np valence electrons. The remaining core electrons were replaced by dsp-MCPs. The major relativistic effects were incorporated into the dsp-MCPs at the level of Cowan and Griffin's quasi-relativistic Hartree–Fock method. We applied dsp-MCPs to calculate spectroscopic constants for the ground states of the rare-gas diatomic molecules Kr2 and Xe2. The results obtained by coupled pair approximation using atomic natural orbital (ANO) basis sets, in which the correlation of inner (n−1)d electrons was included as well as those of the valence ns and np electrons, give excellent agreement with experimental values.

Hybrid density functional theory and quadratic complete basis set ab initio computational study of structural properties, vibrational spectra, and bond dissociation energy for methyl aluminum and methyl gallium

Abstract: Geometries, harmonic frequencies, and homolytic and heterolytic bond dissociation energies were computed with ab initio and density functional theory (DFT) methods, the target being to determine the stability of GaCH 3 and AlCH 3 , generate their infra-red spectra, and evaluate the accuracy of hybrid DFT methods for these and similar molecular systems against highly accurate ab initio methods. For this study, the ab initio methods HF, MP2, CCSD(T), and quadratic complete basis set (CBSQ) were selected. Their computational data were used for comparison with DFT (B3LYP, B3P86, and B3PW91) computed values. The stability and physical properties of the GaCH 3 and AlCH 3 organometallic complexes are discussed on the basis of these computational results.

Density functional study on the structures and vibrational spectra of the radical anion and cation of biphenyl

Abstract: Density functional theory using the 6–31G ∗ basis set and two non-local exchange-correlation functionals (B-YLP and B3-LYP) has been applied to the calculations of the structures and vibrational spectra of the radical anion and cation, of biphenyl. The B3-LYP dihedral angles between the two phenyl rings are 5.8 ° and 19.5 ° for the radical anion and cation respectively. Upon ionization, structural changes occur in the direction from benzenoid to quinoid. The unsealed vibrational frequencies calculated at the B-YLP/6–31G ∗ level are mostly in agreement with the frequencies in the Raman spectra of the radical anion and cation of the normal and perdeuterated species reported in the literature. The calculations predict that both the radical anion and cation give rise to a very strong infrared band, and that this band arises from a mode in which the benzenoid-to-quinoid deformation occurs out of phase in the two phenyl rings.

On a topological interpretation of electronic and vibrational molecular energies

Abstract: A relationship between Randic's connectivity index and various quantum mechanical parameters derived from the Huckel Molecular Orbital (HMO) approach is demonstrated. When applied to conjugated hydrocarbons, this index represents the measure of the global π electron molecular energy and, therefore, of the resonance energy. Moreover, the development of the procedure, allows the introduction of a new definition of the bond order which, in turn, makes possible a better prediction not only for bond lengths of naphtalene but also for the resonance integral and conjugation energy for butadiene. Also, a corrected value for the Randic index is deduced, which allows for the reduction of the discrepancies between the spectroscopic and thermodynamic values for the resonance integral, the significant improvement in the prediction of the resonance energies as well as the accurate prediction of the vibrational CC energies for different substituents of the carbon atoms. Moreover, the use of the topological charge indices [Galvez, J., Garcia, R., Salabert, M.T., Soler, R., J. Chem. Inf. Comput. Sci. 34 (1994) 520–525] [1] (TCI), leads to a remarkable improvement in the prediction of the resonance energies of a set of non-alternant hydrocarbons in a cross-validation test. All these results reinforces the hypothesis, previously mentioned by us, that molecular topology may be considered as an alternative and independent way to describe chemical structure.

MNDO treatment of the Hückel and Möbius types of cyclacenes

Abstract: The Mobius-type cyclacenes with benzenoid rings of 8–14 are compared with the corresponding Huckel types in terms of various properties which are estimated within the framework of MNDO calculations. It has been found that, although in the homologous series of the Huckel types certain properties are dictated by the cryptoannulenic effect, they are only partly dependent on this effect in the case of Mobius cyclacenes.

A computational study of imidazole, 4-nitroimidazole, 5-nitroimidazole and 4,5-dinitroimidazole

Abstract: We have examined the molecular structure of imidazole (I), 4-nitroimidazole (II), 5-nitroimidazole (III) and 4,5-dinitroimidazole (IV) with semi-empirical, ab initio and density functional theory (DFT) calculations. Compared with experimental data, both B3LYP and MP2 calculations with the 6-31G∗ basis set furnish excellent geometric features with average errors of less than 0.01 A in bond lengths and of less than 1 ° in bond angles. Although the SCF results are slightly worse than those with electron correlation effects, HF/3-21G and HF/6-31G∗ calculations also provide reasonable geometries and are probably useful in a practical sense. Geometries obtained from semi-empirical methods have large errors in some of bond lengths and angles. Rotational barriers of the nitro group in II and III have been estimated to be 6.4 and 10.8 kcal/mol, respectively, at the QCISD(T)/6-31G∗//HF/6-31G∗ level. These barriers are largely overestimated at the SCF and B3LYP levels, although utilizing an extremely large basis set such as 6-311++G(3pd,3df) at the B3LYP level reduces the barriers to a comparable range with those of QCISD(T)/6-31G∗//HF/6-31G∗. On the other hand, both AM1 and PM3 underestimate these barriers considerably. According to the analysis of natural bond orbitals, a substantial difference in rotational barriers of between II and III is attributed to the relative stabilization energy due to π orbital conjugations between the C4C5 bond and NO bonds. In the global minimum of IV predicted by both ab initio and DFT calculations, both nitro groups are skewed, with more deformation of the nitro group attached to the C5 atom, although the degree of twisted angles in nitro groups is quite variant depending on the calculational levels. Both semi-empirical methods predict that the nitro group attached to the C4 atom is eclipsed and the one attached to the C5 atom is planar. The orientation of nitro groups in IV can be understood by a compromise between 1. (1) an increase of electrostatic repulsions as two electronegative nitro groups approach and 2. (2) a destabilization due to less π orbital overlaps as nitro groups are skewed.

Theoretical study of valence and Rydberg excited states of benzene revisited

Abstract: The multireference Moller–Plesset perturbation (MRMP) theory with complete active space self-consistent field (CASSCF) reference functions is applied to the study of the singlet and triplet valence π – π * excited states and Rydberg excited states of benzene in the ultraviolet region. The overall accuracy of MRMP is surprisingly high. The average deviations of the excitation energies from the available experimental values are 0.1 eV for the valence excited states and 0.15 eV for the Rydberg states. A comparison is made with recent results of single reference-based methods. It is concluded that MRMP is able to describe satisfactorily excited states with a double excitation character, while single reference-based methods are not.

Characterization of low-barrier hydrogen bonds 2. HF2−: a density functional and ab initio study

Abstract: Hartree-Fock, Moller-Plesset, QCISD, CCSD, and DFT calculations have been carried out using the 6–31+G(d,p), 6–31+G(2d,p), 6–31+G(3d,2p), and 6–31+G(3df,2p) basis sets to study the interaction of a fluoride ion with hydrogen fluoride. In each case the resulting hydrogen bond is extremely strong, resulting in a single well potential, with no barrier for proton transfer. Density functional methods employing non-local gradient-corrected exchange and correlation functionals were found to perform very similarly to other correlated methods, including calculations at the MP2, QCISD, and CCSD levels of theory. DFT calculations using the local functional SVWN gave results in very poor agreement with the other methods. SVWN gave interaction energies about 10 kcal mol −1 too high when compared to recent gas phase experiments.

Molecular dynamics study of hyaluronic acid in water

Abstract: Molecular dynamics (MD) simulations on hyaluronic acid (HA)-water systems were carried out to study the HA-water interactions. Employing the GROMOS force field and the SPC water model, HA dimer and trimer subunits surrounded by 490 water molecules were investigated. For each system pair distribution functions, diffusion coefficients and reorientation correlation times of the water molecules were calculated from 450 ps trajectories. The average values of the interglycosidic angles found in the simulations are φ 13 = 52 °, ψ 13 = 25 ° for the β(1,3) linkage, and φ 14 = 40 °, ψ 14 = 3 ° for the β(1,4) linkage well corresponding to the minimum regions in Ramachandran plots. The self-diffusion coefficients of the water molecules vary from 1.5 × 10 −9 m 2 s −1 to 2.3 × 10 −9 m 2 s −1 dependent on the distance between the water molecules and the atoms of the HA molecule. The reorientation correlation times of the water molecules were estimated to be about 2 ps at a polymer concentration of 7 wt.% HA. On the basis of energy and geometry criteria, the number of hydrogen bonds between the water molecules and the acceptor atoms of HA was determined to be between 10 and 15 per dimer unit indicating the high hydration ability of hyaluronic acid in comparison to other di- and oligosaccharides.

Hydrogen bonding effects in quantum mechanical fore fields of pyrimidine bases : uracil

Abstract: Using dihydrate uracil as a model of H-bonded compound formed by a uracil and two water molecules in the vicinity of HN1C2O and HN3C4O groups, DFT molecular orbital calculations have been performed in order to evaluate the changes in its simulated IR spectrum. To estimate the effect of intermolecular interactions on the vibrational properties of pyrimidine bases we have used the B3LYP functional and polarised 6–31G basis sets. The normal mode analysis enables us to assign the 30 modes of uracil, the 6 modes of the two water molecules along with the 12 additional modes resulting from their mutual interactions.

Combining genetic algorithm and simulated annealing: A molecular geometry optimization study

Abstract: We introduce a new hybrid approach to determine the ground state geometry of molecular systems. Firstly, we compared the ability of genetic algorithm (GA) and simulated annealing (SA) to find the lowest energy geometry of silicon clusters with six and 10 atoms. This comparison showed that GA exhibits fast initial convergence, but its performance deteriorates as it approaches the desired global extreme. Interestingly, SA showed a complementary convergence pattern, in addition to high accuracy. Our new procedure combines selected features from GA and SA to achieve weak dependence on initial parameters, parallel search strategy, fast convergence and high accuracy. This hybrid algorithm outperforms GA and SA by one order of magnitude for small silicon clusters (Si6 and Si10). Next, we applied the hybrid method to study the geometry of a 20-atom silicon cluster. It was able to find an original geometry, apparently lower in energy than those previously described in literature. In principle, our procedure can be applied successfully to any molecular system.

Peptide models xxii. a conformational model for aromatic amino acid residues in proteins. a comprehensive analysis of all the rhf/6-31+g conformers of for-l-phe-nh2

Abstract: Phenylalanine is expected to have conformational features similar to the other three naturally occurring aromatic amino acid residues: Tyr, Trp and His. Previous ab initio structure determinations resulted in 19 different conformers of HCO–L–Phe–NH2 at the RHF/3–21G level of theory. The present work summarises the results of a comprehensive analysis incorporating RHF/3–21G, RHF/6–31+G*, RHF/6–31+G*//RHF/3–21G and B3LYP/6–311++G**//RHF/3–21G data as some of the previously established minima have vanished with the larger basis set, three out of the 19 stationary points having migrated during the optimisation. On top of that, the conformational building unit of the right-handed helix-like (αL) conformation and that of the polyproline II (eL) conformation are still missing from the E=E(φ,ψ) surface. The optimised ab initio structures are also analysed in the context of –Phe– conformers taken from a large X-ray database on non-homologous proteins incorporating a total of 158 664 amino acid residues.

A theoretical study of ten n8 isomers

Abstract: The HF/3s2pld and MP2/3s2pld structures, energies and vibrational frequencies were calculated for ten N8 isomers, corresponding to ten analogous CH structures. Comparative calculations using density functional theory (DFT), with a cc-pVTZ basis set, were also performed. All ten structures were found to be local minima on the energy hypersurface at the Hartree-Fock (HF) level, whereas at the second-order Moller-Plesset (MP2) level nine structures were stable. At the DFT level, eight local minima were found. The total energies were recomputed using 4s3p2dlf basis sets at the HF and MP2 levels of theory.