Study of conformational and optical rotation for the alaninamide

Six stationary points of alaninamide have been located on the potential surface energy (PES) at the B3LYP/6‐311++G(2d,2p) level of theory both in the gas phase and in aqueous solution. In the aqueous solution, to take the water solvent effect into account, the polarizable continuum model (PCM) method has been used. Accurate geometric structures and their relative stabilities have been investigated. The results show that the intramolecular hydrogen bond plays a very important role in stabilizing the global minimum of the alaninamide. Moreover, the consistent result in relative energy using high‐level computations, including the MP2 and MP3 methods with the same basis set [6‐311++G(2d,2p)], indicates that the B3LYP/6‐311++G(d,p) level may be applied to the analogue system. More importantly, the optical rotation of the optimized conformers (both in the gas phase and in aqueous solution) of alaninamide have been calculated using the density functional theory (DFT) and Hartree–Fock (HF) method at various basis sets (6‐31+G*, 6‐311++G(d,p), 6‐311++G(2d,2p) and aug‐cc‐pvdz). The results show that the selection of the computation method and the basis set in calculation has great influence on the results of the optical rotations. The reliability of the HF method is less than that of DFT, and selecting the basis set of 6‐311++G(2d,2p) and aug‐cc‐pvDZ produces relative reliable results. Analysis of the computational results of the structure parameters and the optical rotations yields the conclusion that just the helixes in molecules caused the chiral molecules to be optical active. The Boltzmann equilibrium distributions for the six conformers (both in the gas phase and in the aqueous solution) are also carried out. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical study of chiral discrimination in the hydrogen bonding complexes of the hydrazine dimer

In this work, the discrimination of different chiral forms of the hydrazine dimer were investigated using Density Functional Theory (DFT) and second‐order Moller–Plesset Perturbation (MP2) theory at basis set levels from 6‐31g to 6‐31++g(d,p). Four chiral structures were studied. The optimized geometric parameters, interaction energies, and chirodiastatic energy for various isomers at different levels were estimated. Finally, the solvent effects on the geometries of the hydrazine dimers were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐31++g(d,p) level. The results indicate that the polarity of the solvent has played an important role in the structures and relative stabilities of different isomers. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n,n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n‐mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11‐mer and 12‐mer were also studied. The geometry optimization calculations were performed at the RHF/6‐311G* level for all the cases and at the MP2/6‐311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6‐311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero‐point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory, the 6‐311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6‐311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6‐311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas‐phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 90–104, 2001     

Potential-hypersurface local minima and temperature

Summary The presence of several local energy minima on a potential hypersurface is treated in terms of geometry, energy, and harmonic vibrations. Partition functions of the minima are employed in order to treat temperature excitations of rotational-vibrational motions. Proportions of relative stabilities of the individual structures change with temperature (including interchanges of the relative stabilities so that the global energy minimum can even be less populated than a higher local energy minimum). Illustrative examples are given on B₂H₄ and Ga₂H₄ systems. The treatment is suggested as a standard complement of the local-minimum hypersurface representation (before whole potential hypersurfaces are constructed and employed in molecular dynamics treatments).Dedicated to Prof. Klaus Ruedenberg on the occasion of his 70th birthday     

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

The hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ab initio conformational analysis of cyclooctane molecule

The potential energy surface (PES) for the cyclooctane molecule was comprehensively investigated at the Hartree–Fock (HF) level of theory employing the 3–21G, 6–31G, and 6–31G* basis sets. Six distinct true minimum energy structures (named B, BB, BC, CROWN, TBC, and TCC₁), characterized through harmonic frequency analysis, were located on the multidimensional PES. Two transition state structures were also located on the PES for the cyclooctane molecule. Electron correlation effects were accounted for using the Møller–Plesset second-order perturbation theory (MP2) approach. The predicted global minimum energy structure on the ab initio PES for the cyclooctane molecule is the BC conformer. A gas phase electron diffraction study at 300 K suggested a conformational mixture while an NMR study in solution at 161.5 K predicted the BC conformer as the predominant form. The equilibrium constants reported in the present study, which were evaluated from the ab initio calculated total Gibbs free energy change values, were in good agreement with both experimental investigations. The ab initio results showed that the low temperature condition significantly favored the BC conformer while above room temperature both BC and CROWN structures can coexist. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 524–534, 1998     

Theoretical studies of structural and electronic properties of AlnAsn clusters

We present theoretical results of size dependent structural, electronic, and optical properties of ligand‐free stoichiometric Al_nAs_n clusters of zinc‐blende modification. The investigation is done using a simplified parametrized linear combination of atomic orbital–density functional theory‐local density approximation–tight‐binding (LCAO–DFT–LDA–TB) method and consider clusters with n up to around 100. Initial structures have assumed as spherical parts of infinite zinc‐blende structure and then allowed to relax to the closest local‐energy‐minimum structure. We analyze the radial distributions of atoms, Mulliken populations, electronic energy levels (in particular, HOMO and LUMO), bandgap, and stability as a function of size and composition. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Structures and electronic properties of the small rubidium‐doped silicon RbSin (n = 1–12) clusters

The geometries, relative stabilities, and electronic properties of small rubidium‐doped silicon clusters RbSi_n (n = 1–12) have been systematically investigated using the density functional theory at the B3LYP/GENECP level. The optimized structures show that lowest‐energy isomers of RbSi_n are similar with the ground state isomers of pure Si_n clusters and prefer the three‐dimensional for n = 3–12. The relative stabilities of RbSi_n clusters have been analyzed on the averaged binding energy, fragmentation energy, second‐order energy difference, and highest occupied molecular orbital‐lowest unoccupied molecular orbital energy gap. The calculated results indicate that the doping of Rb atom enhances the chemical activity of Si_n frame and the magic number is RbSi₂. The Mulliken population analysis reveals that the charges in the corresponding RbSi_n clusters transfer from the Rb atom to Si atoms. The partial density of states and chemical hardness are also discussed. © 2014 Wiley Periodicals, Inc.     

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase,in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution

Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were determined by means of the RI-MP2 method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set. The relative energies of isolated tautomers included the correction to higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ level. The relative enthalpies at 0 K and relative free energies at 298 K were based on the above-mentioned relative energies and zero-point vibration energies, temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31G level. The keto form having hydrogen atom at N7 is the global minimum while the canonical form having hydrogen atom at N9 represents the first local minimum at all theoretical levels in vacuo and in the presence of 1 and 2 water molecules. All three unusual rare tautomers having hydrogens at N3 and N7, at N3 and N9, and also at N9 and N7 are systematically considerably less stable and can be hardly detected in the gas phase. The theoretical predictions fully agree with existing theoretical as well as experimental results. The effect of bulk solvent on the relative stability of guanine tautomers was studied by self-consistent reaction field and molecular dynamics free energy calculations using the thermodynamic integration method. Bulk solvent, surprisingly, strongly favored these three rare tautomers over all remaining low-energy tautomers and probably only these forms can exist in water phase. The global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol more stable than the canonical form (3rd local minimum). Addition of one or two water molecules does not change the relative stability order of isolated guanine tautomers but the respective trend clearly supports the surprising stabilization of three rare forms.     

Chiral discrimination in hydrogen‐bonded complexes of hydrogen peroxide with methyl hydroperoxide: Theoretical study

For the first time, the discrimination of different chiral forms of 1:1 complexes with hydrogen peroxide and methyl hydroperoxide have been investigated using density functional theory (DFT) and Møller–Plesset type 2 (MP2) methods at varied basis set levels from 6‐31+G(d,p) to 6‐31++G(2d,2p). Three pairs of chiral enantiomers were considered. The optimized geometric parameters, interaction energies, and chirodiastatic energies for various isomers at different levels are estimated. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the ΔG_solv. The gas phase results show that the heterochiral six‐membered ring complex (structure I) and homochiral five‐membered ring complexes (structures IV and V) are preferred configurations for the three pairs of chiral enantiomers. The solvation effect on six‐membered ring complexes (structures I and II) shows nonsignificant changes in the configurations preferred, but on five‐membered ring complexes, the homo‐/heterochiral preference is found to be inverse in the polar solvent. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Computational Studies on the Sc<Subscript>n</Subscript>N<Subscript>m</Subscript> (n + m=10) Clusters: Structure,Electronic and Vibrational Properties

Besides the size and structure, compositions also dramatically affect the properties of clusters. In fact, the increased degree of freedom poses much more challenges to determine the global minimum structure of multi-component clusters. In this thesis, based on the CALYPSO structure searching method, the global minimum structures are obtained for Sc_nN_m (n + m=10) clusters at PW91/6-311+G(d) level. The growth behavior indicates that the cage unit tends to arrange into the compact configurations, and the occupied positions of N atoms shift from the surface towards the center of coordination site with the increasing number of Sc atoms. The relative stabilities have been discussed by analyzing the average binding energies and HOMO–LUMO gaps. In addition, the molecular orbitals, dipole moments, polarizability, hyperpolarizabilities, natural population, natural electron configuration, and Infared and Raman spectra calculations allow complete characterization of the electronic and vibrational properties for the global minimum structural clusters.     

Density functional study of HO(H2O)n (n = 1–3) clusters

The hydrogen bonding complexes HO(H₂O)_n (n = 1–3) were completely investigated in the present study using DFT and MP2 methods at varied basis set levels from 6‐31++G(d,p) to 6‐311++G(2d,2p). For n = 1 two, for n = 2 two, and for n = 3 five reasonable geometries are considered. The optimized geometric parameters and interaction energies for various complexes at different levels are estimated. The infrared spectrum frequencies and IR intensities of the most stable structures are reported. Finally, thermochemistry studies are also carried out. The results indicate that the formation and the number of hydrogen bonding have played an important role in the structures and relative stabilities of different complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Structural,spectroscopic aspects,and electronic properties of (TiO2)n clusters: A study based on the use of natural algorithms in association with quantum chemical methods

In this article, we propose a stochastic search‐based method, namely genetic algorithm (GA) and simulated annealing (SA) in conjunction with density functional theory (DFT) to evaluate global and local minimum structures of (TiO₂)_n clusters with n = 1–12. Once the structures are established, we evaluate the infrared spectroscopic modes, cluster formation energy, vertical excitation energy, vertical ionization potential, vertical electron affinity, highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) gaps, and so forth. We show that an initial determination of structure using stochastic techniques (GA/SA), also popularly known as natural algorithms as their working principle mimics certain natural processes, and following it up with density functional calculations lead to high‐quality structures for these systems. We have shown that the clusters tend to form three‐dimensional networks. We compare our results with the available experimental and theoretical results. The results obtained from SA/GA‐DFT technique agree well with available theoretical and experimental data of literature. © 2013 Wiley Periodicals, Inc.     

Theoretical Study of Rotational Isomerism in Ethyl Pseudohalides

The structure and conformational stability of ethyl pseudohalides CH₃CH₂ — XCN (X = O, S, Se) were investigated using ab initiocalculations at the MP2 level of theory with a triple- basis set augmented with polarization and diffusion functions. Full optimization was performed on the minimum energy structures as well as on the transition state forms. The relative stabilities of rotational conformers were calculated at the MP4 level using MP2 optimized reference geometries. The nature of all considered stationary points was verified by calculation of the harmonic vibrational frequencies. The calculated bond lengths, bond angles, dipole moments, and rotational constants of optimized global minima structures agree very well with the corresponding experimental data obtained from microwave spectroscopic studies. Also, available experimental frequencies are in good accord with the theoretical values. For ethyl cyanate CH₃CH₂ — OCN, the antiperiplanar (trans) form is predicted to be more stable than the synclinal (gauche) form, and the synperiplanar (cis) form corresponds to the transition state. For both ethyl thiocyanate CH₃CH₂ — SCN and ethyl selenocyanate CH₃CH₂ — SeCN, the gaucheform is the global minimum while the trans-conformer is a local minimum and the cis-form is a transition state.     

Search for the global minimum structures of AlB3H2n (n = 0 − 6) clusters

The global minimum structures of AlB₃H_2n (n = 0–6) clusters are determined using the stochastic search method at the B3LYP/6–31G level of theory. These initially specified geometries are recalculated using B3LYP and CCSD(T) methods using the 6–311++G^** basis set. The structural and electronic properties of the two lowest‐lying isomers are presented. The structural parameters obtained for aluminum borohydride are compared with the experimental and theoretical results. The H₂ fragmentation energies of the most stable isomers are investigated. Chemical bonding analyses for the global minimum of AlB₃H_2n (n = 0–6) clusters are performed using the adaptive natural density partitioning method. © 2014 Wiley Periodicals, Inc.     

A series of novel side chain liquid crystalline polysiloxanes containing cyano‐ and cholesterol‐terminated substituents: Where will the structure‐dependence of terminal behavior of the side chain reappear?

A series of polysiloxane side chain liquid crystal polymers with strong polarity cyano substitution‐terminated achiral side chains and cholesterol‐terminated chiral side chains was successfully synthesized via thiol‐ene click chemistry. ¹H‐NMR, FT‐IR, and thermogravimetric analysis were used to confirm their chemical structures and thermal stabilities. Their phase transition behaviors and phase structures were systematically investigated by a combination of analysis methods such as differential scanning calorimetry, polarized optical microscopy, and X‐ray. Results revealed that attributing to the decisive role of the polarity interaction, all the polymers only developed a monolayer interdigitated SmA phase in which the period arrangement was determined by the cyano‐terminated side chains, the increased content of cholesterol‐terminated chiral side chains (X_chol) just expanded the distance between neighboring molecules within a layer. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 1765–1772     

Theoretical prediction for the structures of gas phase lithium oxide clusters: (Li2O)n (n = 1–8)

We apply genetic algorithm combining directly with density functional method to search the potential energy surface of lithium‐oxide clusters (Li₂O)_n up to n = 8. In (Li₂O)_n (n = 1–8) clusters, the planar structures are found to be global minimum up to n = 2, and the global minimum structures are all three‐dimensional at n ≥ 3. At n ≥ 4, the tetrahedral unit (TU) is found in most of the stable structures. In the TU, the central Li is bonded with four O atoms in sp³ interactions, which leads to unusual charge transformation, and the probability of the central Li participating in the bonding is higher by adaptive natural density partitioning analysis, so the central Li is in particularly low positive charge. At large cluster size, distortion of structures is viewed, which breaks the symmetry and may make energy higher. The global minimum structures of (Li₂O)₂, (Li₂O)₆, and (Li₂O)₇ clusters are the most stable magic numbers, where the first one is planar and the later both have stable structural units of tetrahedral and C_4v. © 2012 Wiley Periodicals, Inc.     

Quantum chemical exploration of formaldehyde clusters (H2CO)n (n = 2–4)

Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H₂CO)n (n = 2–4) by using the Scaled Hypersphere Search‐Anharmonic Downward Distortion Following (SHS‐ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT‐D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S₄ structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.     

Investigation of the Benzene–Naphthalene and Naphthalene–Naphthalene Potential Energy Surfaces: DFT/CCSD(T) Correction Scheme

The potential energy surfaces of the naphthalene dimer and benzene–naphthalene complexes are investigated using the recently developed DFT/CCSD(T) correction scheme [J. Chem. Phys. 2008 , 128, 114 102]. One and three minima are located on the PES of the benzene–naphthalene and the naphthalene dimer complexes, respectively, all of which are of the parallel‐displaced type. The stabilities of benzene–naphthalene and the naphthalene dimer are ?4.2 and ?6.2 kcal mol^?1, respectively. Unlike the benzene dimer, where the T‐shaped complex is the global minimum, the lowest‐energy T‐shaped structure is about 0.2 and 1.6 kcal mol^?1 above the global minimum on the benzene–naphthalene and the naphthalene dimer potential energy surfaces, respectively.