Chemical Physics Letters (v.545, #C)
Editorial Board (IFC).
Intrinsic lifetimes and kinetic stability in media of noble-gas hydrides by R. Benny Gerber; Ehud Tsivion; Leonid Khriachtchev; Markku Räsänen (1-8).
Display Omitted► Matrix media can greatly affect the kinetic stability of HNgY species. ► HXeCCH can be stable in organic media (by simulations; matrix experiments). ► Simulations show that HXeCCH can be stable up to near room temperature.Noble-gas hydrides, generally prepared in noble-gas matrices, have fascinating chemical bonding and properties. However, very little is known on the kinetic stability of these compounds, and how it can be affected by different molecular environments and conditions. In this Letter, recent computational and experimental results bearing on this topic are discussed and analyzed. For the important case of HXeOH, there appears to be a gap between the predicted long lifetime for the isolated molecule and much shorter lifetime observed experimentally in a Xe matrix. Understanding of this gap is an important challenge in this field.
Ketone physics – structure, conformations, and dynamics of methyl isobutyl ketone explored by microwave spectroscopy and quantum chemical calculations by Yueyue Zhao; Wolfgang Stahl; Ha Vinh Lam Nguyen (9-13).
Display Omitted► Methyl isobutyl ketone has C1 symmetry and a similar geometry to isopropyl acetate. ► The acetyl methyl group shows internal rotation. ► Rotorsional spectrum was fitted with the programs XIAM and Erham. ► The calculated structure was validated by microwave spectroscopy.The microwave spectrum of methyl isobutyl ketone was recorded using a molecular beam Fourier transform microwave spectrometer and analyzed to determine the rotational constants A = 4.7517(17) GHz, B = 1.496 115(79) GHz, C = 1.324 364(39) GHz, and centrifugal distortion constants. A–E splittings from 250 MHz up to 1 GHz were observed due to internal rotation of the acetyl methyl group with a potential barrier of 250.3(19) cm−1. 59 A and 57 E species lines were fitted to experimental accuracy. The experimental rotational constants were compared with results from quantum chemical calculations to validate the molecular structure.
A molecular beam scattering investigation of methanol–noble gas complexes: Characterization of the isotropic potential and insights into the nature of the interaction by D. Cappelletti; P. Candori; S. Falcinelli; M. Albertí; F. Pirani (14-20).
Display Omitted► We measured cross sections for the scattering of CH3OH onto noble gases (Ng) targets. ► We obtained the phenomenological radial interaction for all the studied complexes. ► We formulated potential energy surfaces as pairwise additive multicenter model. ► The nature of interaction is mainly due to van der Waals and induction components. ► This is at variance with the behavior of analogous water or ammonia complexes.Integral cross section experiments involving rotationally hot CH3OH projectiles and noble gas (Ng = Ne, Ar, Kr and Xe) targets are reported for the first time. Measured data have been exploited to characterize the phenomenological radial interaction in the CH3OH–Ng weakly bound complexes. Potential energy surfaces for all the systems have been formulated on the basis of a pairwise additive multicenter model. The comparison of model predictions with the most relevant experimental findings suggests that in CH3OH–Ng complexes, at variance with the behavior of the analogous complexes involving water or ammonia, the interaction is mainly due to van der Waals and induction components.
Photoelectron spectroscopy and density functional calculations of Cu n BO2(OH)− (n = 1,2) clusters by Yuan Feng; Gao-Lei Hou; Hong-Guang Xu; Zeng-Guang Zhang; Wei-Jun Zheng (21-25).
CuBO2(OH) can be viewed as a superhalogen because its electron affinity exceeds that of halogen atoms, demonstrating that OH can behave like a halogen atom to participate in the formation of superhalogens.Display Omitted► OH can behave like a halogen atom to participate in the formation of superhalogens. ► Provide information about the interaction between OH and CuBO2. ► CuBO2(OH) can be regarded as a superhalogen.Cu n BO2(OH)− (n = 1, 2) clusters were studied by anion photoelectron spectroscopy and density functional calculations. From the experimental photoelectron spectra, the adiabatic detachment energy (ADE) and vertical detachment energy (VDE) of CuBO2(OH)− are determined to be 4.00 ± 0.08 and 4.26 ± 0.08 eV, and those of Cu2BO2(OH)− to be 2.30 ± 0.08 and 2.58 ± 0.08 eV. The structures of Cu n BO2(OH)− and their corresponding neutrals are assigned by comparison between theoretical calculations and experimental measurements. Both experiment and theory show that CuBO2(OH) can be viewed as a superhalogen, thus, confirmed that OH can behave like a halogen atom to participate in superhalogen formation.
Magnesium amidoborane monoammoniate: Plane-wave DFT calculations by H.J. Gotsis; N. Russo; E. Sicilia (26-28).
A DFT periodic approach, has been used to calculate the structural and electronic properties of the newly synthesized magnesium amidoborane monoammoniate (Mg (NH2BH3)2 ·NH3). The results of our first-principles calculations establish the insulating nature of this material and used to analyze the chemical bonding between different atoms.Display Omitted► Theoretical calculations were carried out on the newly developed magnesium amidoborane monoammoniate (Mg(NH2BH3)2· NH3). ► The lattice parameters of the crystal and the N–H δ+⋯ δ-H–B bond lengths were found to be in good agreement with experiment. ► The calculations predict a wide band-gap insulator with a gap size of between 4.6 and 6.4 eV. ► Electronic density of states analyses indicate the covalent bond nature of N–H and B–H bonds but ionic bonding between Mg and N.Recently it has been reported that magnesium amidoborane monoammoniate ( Mg ( NH 2 BH 3 ) 2 · NH 3 ) has a high hydrogen content and consequently is an attractive candidate for hydrogen storage applications. The electronic and structural properties of the amidoborane Mg ( NH 2 BH 3 ) 2 · NH 3 have been calculated within the generalized gradient approximation (GGA) in the Perdew–Burke–Ernzerhof (PBE) parameterization. The role of the ammonia ligand is to stabilize magnesium amidoborane ( Mg ( NH 2 BH 3 ) 2 ) by increasing the number of H ⋯ H contacts. The band gap of the GGA-PBE relaxed structure is computed using the conventional density functionals and the semiempirical hybrid functional approach HSE06. It is shown that this compound is an insulator with a gap size of between 4.6 and 6.4 eV. These calculations reveal the covalent nature of N–H and B–H bonds. The interaction character between Mg and N atoms is essentially ionic.
Antiferroelectric domains in liquid crystalline methacrylic polymers by C.M. González-Henríquez; E.A. Soto-Bustamante; W. Haase (29-34).
The formation of a polymer with polar domains allows obtaining antiferroelectric structures. Crystalline polymers are able to show electric response, when an electric field is applied due to the polarization of the material. The same characteristic is not present for the semi-crystalline polymers.Display Omitted► For all polymers, a smectic C2 phase occurs over broad temperature range. ► Crystalline polymers show anticlinic antiferroelectric phases. ► Semi-crystalline polymers were paraelectric. ► The arrangement of side chain within the network is related with the kinetic of precipitation.The preparation of several liquid crystalline polymers obtained using different AIBN concentration and polymerization times are reported. The compounds were characterized by 1H NMR, differential thermal analysis (DTA), X-ray diffraction and pyroelectric measurements. For all polymers, a smectic C2 phase occurs over broad temperature range, where the molecules adopt an opposite tilt direction for alternate smectic layer. Crystalline polymers show an antiferroelectric behavior, developing an anticlinic phase responsible for the electric behavior. The arrangement of the side chain molecules within the partial crystalline network in these electrically active polymers is related with the kinetic of precipitation.
Dynamics of ultrafast photoinduced heterogeneous electron transfer, implications for recent solar energy conversion scenarios by Lars Gundlach; Bernd Burfeindt; Jürgen Mahrt; Frank Willig (35-39).
Display Omitted► Temperature dependent electron transfer spectra have been measured. ► The role of high-energy (quantum) vibrational modes for heterogeneous electron transfer has been identified. ► Different theoretical models are compared with the measurements. ► Implications for recent solar energy conversion scenarios are discussed.The general case of a heterogeneous electron transfer reaction is realized by ultrafast electron transfer from a photo-excited molecule to a wide continuum of electronic acceptor states. Two different theoretical model calculations addressing the injection dynamics have recently been presented. The first scenario predicts a wide energy distribution for the injected electron via excitations of high-energy vibrational modes in the ionized molecule, whereas the second scenario ascribes the width to thermal fluctuations. We present experimental data at different temperatures and identify the valid injection scenario for perylene/TiO2 systems. The results are discussed in view of recent solar energy conversion scenarios.
Vibrational vs. electronic coherences in 2D spectrum of molecular systems by Vytautas Butkus; Donatas Zigmantas; Leonas Valkunas; Darius Abramavicius (40-43).
Display Omitted► Vibrational and excitonic wavepackets are distinguished in 2D spectra. ► The displacement from the peak maxima determines the phase of spectral oscillations. ► The phase of vibronic oscillations depends on the electron–phonon coupling strength. ► Oscillatory diagonal peaks in accord with cross-peaks signify vibronic origins.Two-dimensional spectroscopy has recently revealed the oscillatory behavior of the excitation dynamics of molecular systems. However, in the majority of cases there is considerable debate over what is actually being observed: excitonic or vibrational wavepacket motion or evidence of quantum transport. In this letter we present a method for distinguishing between vibrational and excitonic wavepacket motion, based on the phase and amplitude relationships of oscillations of distinct peaks as revealed through a fundamental analysis of the two-dimensional spectra of two representative systems.
Hydrogen trapped in Be n cluster cages: The atomic encapsulation option by Fedor Y. Naumkin; David J. Wales (44-49).
Display Omitted► Small beryllium cluster cages can trap hydrogen atoms endohedrally starting from Be6. ► H@Be6 units can be merged together, preserving integrity. ► Such assemblies are metastable to release of H2 and stabilized by an energy barrier. ► Extended to a nanofoam material, such systems may enable a high storage capacity. ► Shapes and electronic properties of the Be n shells are modified by the H cores.Core–shell (kH)@Be n (k = 1–3, n = 6–11) systems are studied computationally. The smallest system with endohedral hydrogen is H@Be6 with a central H anion, thermodynamically stable to dissociation into H + Be6. Larger structures are constructed by merging a few such units and have reduced stability. Potential energy barriers to hydrogen exit from the cage assemblies are estimated. Face- and edge-sharing combinations of the structural units are considered. The extrapolated upper bound for the potential ‘nanofoam’ material storage capacity is 10 weight-% of hydrogen. The changes in shape and electronic properties of the Be n cages upon insertion of hydrogen are also analyzed.
The aromaticity of the [Re3(μ-X)3X9]3− clusters, X = Cl, Br, I by Leonor Alvarado-Soto; Eduardo Schott V; Ximena Zarate; Ramiro Arratia-Pérez; Rodrigo Ramirez-Tagle (50-53).
NICSzz scan profile (NICS in ppm, R in Ǻ) for the all the clusters.Display Omitted► We studied the [Re3(μ-Cl)3Cl9]3−, [Re3(μ-Br)3Br9]3−, [Re3(μ-I)3I9]3− clusters. ► The clusters exhibit aromaticity which is decreased by the SO effect. ► The [Re3(μ-I)3I9]3− is the most aromatic cluster. ► The TDDFT calculations corroborate the aromaticity.The results of this Letter reveals that the [Re3(μ-Cl)3Cl9]3−, [Re3(μ-Br)3Br9]3−, [Re3(μ-I)3I9]3− clusters exhibit aromaticity and that spin–orbit effect decreases the aromaticity due to the fact that the 5d3/2 spinors are more contracted than the scalar 5d orbitals. The [Re3(μ-I)3I9]3− and [Re3(μ-Br)3Br9]3− clusters are the most aromatic clusters. This can be explained by the np1/2 and np3/2 spinors radial expectation (〈r〉) values which follows the Cl < Br < I sequence. Thus, the most extended spinors correspond to I and Br ligands, as indicated in the ELF plots. Furthermore we carried out TDDFT calculations which agrees with the fact that [Re3(μ-I)3I9]3− should show the highest value of aromaticity.
Stokes shift dynamics of [Na][TOTO] – A new class of ionic liquids: A comparative study with more common imidazolium analogs by Snehasis Daschakraborty; Ranjit Biswas (54-59).
Display Omitted► Dynamic Stokes shift values for [Na][TOTO] less than those for imidazolium ILs. ► Predicts a very weak temperature dependence for shift. ► Calculated dynamics is extremely slow because of large viscosity. ► Predicts bi-phasic dynamics in accordance with experimental dielectric relaxation. ► Calculations suggest Arrhenius-type temperature dependence.A semi-molecular theory has been employed to predict temperature dependent Stokes shift dynamics of a dipolar probe in sodium 2,5,8,11-tetraoxatridecan-13-oate ([Na][TOTO]), and compared with imidazolium ionic liquids (ILs). Predicted dynamic Stokes shift for [Na][TOTO]is ∼60–70% of that calculated for imidazolium ILs. The calculated biphasic dynamics is, however, extremely slow because of large viscosity, average solvation time (〈τ ss〉) being in ∼1 s–10 ns range at 254 ⩽ T/(K) ⩽ 344. This is much slower than those in imidazolium ILs (0.1 ⩽ 〈τ ss〉/ns ⩽ 6 at 278 ⩽ T/(K) ⩽ 338). Predicted temperature dependence of shift is very weak and suggests near-Arrhenius behavior for the dynamics.
Assessing the importance of Van der Waals interactions on the adsorption of azobenzene on the rutile TiO2(1 1 0) surface by J.P. Prates Ramalho; Francesc Illas (60-65).
The interaction of azobenzene on TiO2(110) is largely dominated by dispersion terms with litle participation of standard covalent chemical bond.Display Omitted► The effect of dispersion in the stability of the cis- and trans- azobenzene on TiO2(1 1 0) is analyzed. ► Dispersion terms are crucial to explain relative stability. ► Dispersion terms are crucial to describe the cleavage of the N＝N azo bond reaction energy. ► Dispersion terms do not affect the main qualitative features of the interaction.The role of dispersion in the adsorption of cis- and trans-azobenzene on rutile TiO2(1 1 0) has been investigated by means of density functional theory methods. Dispersion is crucial to properly describe the relative values of the adsorption energy since it differently affects each isomer. Dispersion terms are also crucial to describe the energy reaction corresponding to the cleavage of the N＝N azo bond. However, the main features of the interaction remain unchanged since the density of states, electron density difference plots and Bader charges are only slightly affected by the inclusion of dispersion terms.
Nonclassical hydrides of Ni+ in ZSM-5 zeolite structures: A hybrid DFT study by P.A. Georgiev; A. Albinati (66-70).
Display Omitted► DFT calculations suggest the formation of (η2-H2)2Ni+ complex in ZSM-5 zeolite. ► Its spectral features are in a very good agreement with experimental data. ► Associated thermodynamics favour ambient temperature formation/decomposition. ► The complex may serve as a model in the design of novel hydride materials.We have studied the reactivity towards dihydrogen of Ni2+–Ni+ reduced ions, residing above two framework oxygen atoms, using a 18 SiO4 tetrahedrals (18T) model cluster representing the intersection of the straight and the sinusoidal channels in ZSM-5 zeolite. Reported are a detailed analysis of the Ni+–H2 orbital interactions, the thermodynamic stability, and characteristic spectral signatures of the predicted Ni+(H2) n nonclassical hydrides for n = 1 and 2, at the B3LYP level of theory. Comparison is made to existing spectroscopy data for a Ni+(H2) complex formed in Ni-exchanged ZSM-5 zeolite .
Structural phase transition and band gap of uniaxially deformed (6, 0) carbon nanotube by Nikolai A. Poklonski; Sergey V. Ratkevich; Sergey A. Vyrko; Eugene F. Kislyakov; Oleg N. Bubel’; Andrei M. Popov; Yurii E. Lozovik; Nguyen Ngoc Hieu; Nguyen Ai Viet (71-77).
Display Omitted► The ground state of (6, 0) nanotube is found to have the Kekule structure. ► Structural phase transition is revealed at approximately 9% elongation. ► The abrupt increase (about five times) of the band gap is revealed at the phase transition.The atomic and band structures of the (6, 0) zigzag carbon nanotube at its axial elongation are calculated by semiempirical molecular orbital and by tight-binding methods. The ground state of the nanotube is found to have a Kekule structure with four types of bonds and difference between lengths of long and short bonds of about 0.005 nm. The structural phase transition is revealed at ≈ 9 % elongation, resulting in a quinoid structure with two types of bonds. This structural phase transition is followed by the transition from a narrow gap to moderate gap semiconductor. Validity of the semiempirical PM3 method is discussed.
Fluorinated derivatives of sp 2 graphene allotropes: Structure, stability, and electronic properties by A.N. Enyashin; A.L. Ivanovskii (78-82).
Display Omitted► Thirty two various isomers of fluorinated forms of sp 2 graphene allotropes are examined. ► Using DFT method, their stability, structural and electronic properties are predicted. ► These fluorinated derivatives will be of interest as new semiconducting materials.By means of the DFT band structure calculations, we have explored the relative stability and electronic properties of 32 isomers of fluorinated derivatives of sp 2 graphene allotropes, which comprise various carbon cycles C n (n = 4, 5, 6, 7, 8, and 12). We have identified the most stable isomers of the examined systems. Besides, our data reveal that independently of the type of the electronic spectrum of parent sp 2 graphene allotropes, their fluorinated forms are wide-band-gap semiconductors with direct Г–Г inter-band transitions.
Binding properties of a nitrogen atom onto an anionic golden fullerene Au 16 - by Gunn Kim; Seoung-Hun Kang; Chan-young Lim; Young-Kyun Kwon (83-87).
Display Omitted► We examine the structural and electronic characteristics of an anionic golden cage with a nitrogen adatom. ► The triangular and bridge sites are preferred for exohedral nitrogen adsorption. ► To obtain the activation energy barriers, the minimum-energy transition paths are searched. ► For the infrared spectra, the exohedral doping causes larger intensities than the endohedral doping at higher frequencies.Using density functional theory, we examine the effects of a nitrogen atom adsorbed onto an anionic golden cage ( Au 16 - ) on the properties of the nanocage. For the exohedral adsorption that is more stable than the endohedral doping, the bridge and hollow sites have larger binding energies than the atop sites by ∼1 eV. When the N atom is adsorbed on the cage, electrons are transferred to nitrogen from Au 16 - . The nitrogen atom may move thermally from the exterior to the interior through a bridge site. In infrared spectra, exohedral doping causes greater intensities at higher frequencies than endohedral doping.
Methylation and the system-size effect over the structural, electronic, magnetic (NICS) and reactive properties of pentalene derivatives by Cristina A. Barboza; Ezequiel Barboza; Ramiro Arratia-Perez; Desmond Mac-Leod Carey (88-94).
Display Omitted► We study the electronic and molecular properties of polycyclic π systems. ► Optical properties are related to methylation and system size in these systems. ► Electronic excitations are assigned mainly to π → π∗ transitions. ► Antiaromaticity character decreasing with the increment of the system-size.The effects of increasing size and tetra-methylation over dimerization, electronic and magnetic properties of the pentalene, s-indacene, dicyclopenta-[b,g]-naphthalene and dicyclopenta-[b,i]-anthracene series, were studied. Potential energy surfaces were evaluated using the hybrid-density functionals BHandH and LC-wPBE. Our results suggest a linear scaling of the dimers stabilization and interaction energies. NICS values indicate that, there are no effects over the five member rings antiaromaticity, however the central rings are slightly aromatic for the largest molecules. The presence of methyl groups has a small effect over the reactivity of the molecules, while the increasing of system-size increases the reactivity of the five membered-rings.
Two-photon absorption of Si n (n = 3–10) clusters compared with Si bulk by You-Zhao Lan (95-99).
Two-photon absorption coefficients of the Si n (n = 3–10) clusters compared with Si bulk for 800–2200 nm.Display Omitted► TPA properties of the Si n (n = 3–10) clusters were investigated by using the sophisticated response approach. ► TPA coefficients of the Si clusters are systematically smaller than those of Si bulk for 800–2200 nm. ► TPA coefficients of the Si clusters as well as Si bulk increase with a decrease of the input light wavelength. ► Channel of double resonance results in large TPA coefficients of the Si clusters in the visible range.The two-photon absorption (TPA) properties of the Si n (n = 3–10) clusters were investigated by using the density functional response approach. The TPA coefficients of the Si clusters are systematically smaller than those of Si bulk for 800–2200 nm. The TPA coefficients of the Si clusters as well as Si bulk increase with a decrease of the input light wavelength. The analysis of the TPA enhancement shows that the channel of double resonance makes a significant contribution to the large TPA coefficients of the Si clusters in the visible range.
Computational study of bond dissociation enthalpies for lignin model compounds: β-5 Arylcoumaran by Jarod M. Younker; Ariana Beste; A.C. Buchanan (100-106).
Display Omitted► We report MCSCF and M06-2X carbon–oxygen and carbon–carbon BDEs for aryl- coumaran models related to common β-5 substructures in lignin. ► We find agreement between MCSCF and DFT BDEs for bi-radical products. ► Triplet BDEs are suffcient to understand trends. ► Substituent effects on BDEs are small, with the exception of a trans-vinyl lowering the C–O BDE.The biopolymer lignin is a potential source of valuable chemicals. The β-5 linkage comprises ∼10% of the linkages in lignin. Density Functional Theory (DFT) was used to calculate the Cα–O and C α – C β bond dissociation enthalpies (BDEs) for β-5 models with varied substituents, which are important for understanding initial lignin decomposition. The Cα–O ( C α – C β ) BDEs were in the range of 40–44 (57–62) kcal/mol. The products resulting from either homolysis are bi-radicals with multi-determinant character in the singlet electronic state. Multiconfiguration self-consistent field (MCSCF) theory results were used to verify that unrestricted DFT and broken-symmetry DFT were sufficient to study these reactions.
Which oxidation state is preferable at S 0 state in oxygen-evolving complex, Mn4(II, III, IV, IV) or Mn4(III, III, III, IV)? A B3LYP study by Tomoya Ichino; Yasunori Yoshioka (107-111).
CaMn4O5 core and H-bonds of water molecules in OEC.Display Omitted► The electronic structures of the CaMn4O5 core are theoretically examined. ► Two different states of Mn4[III, III, IV, III] and Mn4[III, IV, IV, II] are obtained. ► Mn4[II, III, IV, IV] at the S 0 state is ruled out. ► The geometries of the CaMn4O5 core are important. ► The patterns of the hydrogen-bonding networks of water molecules are also important.Based on the structure of 1.9 Å resolved OEC, which was published as PDBid = 3ARC, geometries and electronic structures of the CaMn4O5 core and surrounding water molecules at the S0 state are examined by the hybrid B3LYP and broken-symmetry methods. Two doublet states 1 and 2 with energy difference of 15.2 kcal/mol were obtained. 1 is lower than 2. The oxidation states of four manganese atoms of 1 are Mn4[III, III, IV, III], while those of 2 are Mn4[III, IV, IV, II]. It is concluded that the oxidation states of Mn4(II, III, IV, IV) is ruled out at the S 0 state.
Effects of the basis set superposition error on optimized geometries of trimer complexes (Part I) by Chang Kon Kim; Jongok Won; Chan Kyung Kim (112-117).
Display Omitted► We studied the BSSE of six hydrogen-bonded trimers using the CP approach. ► Two types of CP corrections were employed to examine the geometrical changes. ► Unusual structural changes were explained based on two opposing effects. ► Effects of angle strain and ghost orbitals depend on the methods and basis set.The basis set superposition error (BSSE) of hydrogen-bonded trimers, (NH3)3, (H2O)3, (HF)3, (PH3)3, (H2S)3 and (HCl)3, was examined using the Counterpoise (CP) approach at the MP2 level with various basis sets. Trimers from periods 1 and 2 elements showed a similar trend in the geometrical variations, even though the CP-corrections on the interaction energies of the latter were much larger. The degree of the changes in the bond length was not significant when a sufficiently large basis set was used. The CP-correction function, δE(fCP), made a considerable contribution to the complexation energy, ΔEc, even with the largest basis set.
MDMS: Molecular dynamics meta-simulator for evaluating exchange type sampling methods by Daniel B. Smith; Asim Okur; Bernard R. Brooks (118-124).
Display Omitted► We develop a model for testing exchange-based/replica-exchange sampling methods. ► The model can replicate many important features of biologically-relevant proteins. ► The model will greatly increase the speed of development for new replica-exchange-type methods.Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a molecular dynamics meta-simulator (MDMS) based on transition state theory to simulate a replica exchange simulation, eliminating the need to run explicit dynamics between exchange attempts. MDMS simulations allow for rapid testing of new replica exchange based methods, greatly reducing the amount of time needed for new method development.
Analysis of surface structures of hydrogen bonding in protein–ligand interactions using the alpha shape model by Weiqiang Zhou; Hong Yan; Quan Hao (125-131).
Display Omitted► Hydrogen bonds show consistent geometric patterns. ► Hydrogen atom–acceptor atom and donor atom–acceptor atom are spatially matched. ► Hydrogen bonding requires geometric complementarity.Hydrogen bonding provides useful information for the study of protein–ligand interactions. However, the physical role that a hydrogen bond plays and its 3D surface characteristics in protein–ligand interaction are still not well understood. We apply the 3D alpha shape model to reconstruct the interface of a protein–ligand structure and use solid angles at interface atoms to represent the surface geometric properties of a hydrogen bond. The result shows that 77.2% of the hydrogen bonds show complementary geometric patterns and 95.0% of the protein–ligand complexes contain at least one such hydrogen bond.
Electronic structure study of the triplet azulene-like molecules by Slavko Radenković; Svetlana Marković; Vladimir Milenković (132-137).
Display Omitted► We performed an electronic structure study of singlet and triplet states of a series of azulene-like molecules. ► We employed the unrestricted symmetry-broken and complete active space methods. ► We found that higher members of the investigated series of molecules are triplet diradicals. ► Singlet states of the azulene-like molecules exhibit pronounced diradical character.In this Letter a detailed electronic structure study of singlet and triplet states of a series of azulene-like molecules was performed using several DFT and complete active space (CAS) methods. According to the results obtained at the B3LYP level of theory using the unrestricted symmetry-broken method, the singlet–triplet splitting for the members of the series with three and more hexagons is quite small, and in addition, four members of the series were found to be triplet diradicals. The CASSCF calculations revealed that higher members of the series of the azulene-like molecules with six and more hexagons are triplet diradicals.
The conformational sensitivity of iterative stockholder partitioning schemes by T. Verstraelen; P.W. Ayers; V. Van Speybroeck; M. Waroquier (138-143).
Display Omitted► A new atoms-in-molecules scheme is proposed: Gaussian ISA. ► The robustness of GISA is compared with two existing schemes Hirshfeld-I and ISA. ► Hirshfeld-I is found to be superior in terms of (conformational) robustness. ► The robustness of an AIM scheme correlates with the locality of the AIM variations.Chemical interpretation and empirical modeling of partial charges requires a robust partitioning scheme to derive these charges from the molecular electronic density. The degree of undesirable conformational sensitivity is assessed for three iterative stockholder partitioning schemes: Hirshfeld-I (HI), Iterative Stockholder Analysis (ISA) and a new Gaussian ISA variant (GISA). GISA has fewer degrees of freedom than ISA and enforces monotonically decaying pro-atoms. These improvements accelerate the converge of GISA as compared to ISA. However, the conformational sensitivity of the charges does not decrease and is still large compared to HI.
An atoms-in-molecules study on selected tautomeric triads by Krzysztof K. Zborowski (144-147).
Display Omitted► A theoretical QTAIM study of tautomeric equilibria. ► Estimation of atomic energies in various environments. ► Huge energy changes of carbon atom for C＝X–C–X–H transformation (X = O, S). ► Different behavior of oxygen and sulfur in the C＝X group.A new method of investigating tautomeric equilibria is described. The method is based on the partition of the total molecular electronic energies among atoms, according to the quantum theory of the atoms in molecules. We employ our methodology to study several model tautomeric systems, so called tautomeric triads. The differences in the atomic energies between tautomers are exhaustively discussed and general trends in relative stabilities of C, S, N and O atoms calculated in different molecular environments are presented.