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Journal of Computational Chemistry

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https://www.readbyqxmd.com/read/29143968/correlating-the-vibrational-spectra-of-structurally-related-molecules-a-spectroscopic-measure-of-similarity
#1
Yunwen Tao, Wenli Zou, Dieter Cremer, Elfi Kraka
Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates...
November 16, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29143346/a-comparative-view-on-the-potential-acting-on-an-electron-in-a-molecule-and-the-electrostatic-potential-through-the-typical-halogen-bonds
#2
Ekaterina Bartashevich, Vladimir Tsirelson
This work considers the features of the electrostatic potential (ESP), and the potential acting on an electron in a molecule (PAEM) for the series of isolated dihalide molecules and for their molecular complexes. The joint analysis of these functions enriches the vision of atomic predispositions to the halogen bond formation and reveals details for their characterization. The account for the exchange-correlation interaction in PAEM retains the specific anisotropy of the ESP, which is commonly used for the halogen bonding explanation within σ-hole concept...
November 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29143342/bonnmag-computer-program-for-ligand-field-analysis-of-f%C3%A2-n-systems-within-the-angular-overlap-model
#3
Anna Bronova, Thomas Bredow, Robert Glaum, Mark J Riley, Werner Urland
The program BonnMag has been developed to calculate the absorption spectra and temperature dependent magnetic susceptibilities of f (n) systems. The computations of the transition energies are performed within the angular overlap model. Using Judd-Ofelt theory BonnMag allows estimation of the relative absorption coefficients of the electronic transitions with reasonable accuracy. A description of the theoretical background of the implemented methods is given. Using Slater-Condon-Shortley parameters and spin-orbit coupling coefficients for free Ln(3+) ions from ab initio calculations, the transition energies of all Ln(3+) ions are calculated and compared to the results from CASSCF/NEV-PT2 calculations...
November 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29135037/analytical-hessian-fitting-schemes-for-efficient-determination-of-force-constant-parameters-in-molecular-mechanics
#4
Ruixing Wang, Mikhail Ozhgibesov, Hajime Hirao
Building upon our recently developed partial Hessian fitting (PHF) method (Wang et al., J. Comput. Chem. 2016, 37, 2349), we formulated and implemented two other rapid force-field parameterization schemes called full Hessian fitting (FHF) and internal Hessian fitting (IHF), and comparisons were made among these three parameterization schemes to assess their performance. FHF minimizes deviation between the Hessian matrices in Cartesian coordinates computed by quantum mechanics (QM) and molecular mechanics (MM), to determine the best possible MM force-constant parameters...
November 14, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29135034/implementation-and-performance-of-the-artificial-force-induced-reaction-method-in-the-grrm17-program
#5
Satoshi Maeda, Yu Harabuchi, Makito Takagi, Kenichiro Saita, Kimichi Suzuki, Tomoya Ichino, Yosuke Sumiya, Kanami Sugiyama, Yuriko Ono
This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version...
November 14, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29135029/quantum-crystallography-a-perspective
#6
Lou Massa, Chérif F Matta
Extraction of the complete quantum mechanics from X-ray scattering data is the ultimate goal of quantum crystallography. This article delivers a perspective for that possibility. It is desirable to have a method for the conversion of X-ray diffraction data into an electron density that reflects the antisymmetry of an N-electron wave function. A formalism for this was developed early on for the determination of a constrained idempotent one-body density matrix. The formalism ensures pure-state N-representability in the single determinant sense...
November 14, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29127720/breaking-the-polar-nonpolar-division-in-solvation-free-energy-prediction
#7
Bao Wang, Chengzhang Wang, Kedi Wu, Guo-Wei Wei
Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies...
November 11, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29125203/characterization-of-chalcogen-bonding-interactions-via-an-in-depth-conceptual-quantum-chemical-analysis
#8
Freija De Vleeschouwer, Mats Denayer, Balazs Pinter, Paul Geerlings, Frank De Proft
The chalcogen bond has been acknowledged as an influential noncovalent interaction (NCI) between an electron-deficient chalcogen (donor) and a Lewis base (acceptor). This work explores the main features of chalcogen bonding through a large-scale computational study on a series of donors and acceptors spanning a wide range in strength and character of this type of bond: (benzo)chalcogenadiazoles (with Ch = Te/Se/S) versus halides and neutral Lewis bases with O, N, and C as donor atoms. We start from Pearson's hard and soft acids and bases (HSAB) principle, where the hard nature of the chalcogen bond is quantified through the molecular electrostatic potential and the soft nature through the Fukui function...
November 10, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29125196/an-interacting-quantum-atom-study-of-model-sn-2-reactions-x-%C3%A2-%C3%A2-%C3%A2-ch3-x-x%C3%A2-%C3%A2-f-cl-br-and-i
#9
Ibon Alkorta, Joseph C R Thacker, Paul L A Popelier
The quantum chemical topology method has been used to analyze the energetic profiles in the X(-)  + CH3 X → XCH3  + X(-) SN 2 reactions, with X = F, Cl, Br, and I. The evolution of the electron density properties at the BCPs along the reaction coordinate has been analysed. The interacting quantum atoms (IQA) method has been used to evaluate the intra-atomic and interatomic energy variations along the reaction path. The different energetic terms have been examined by the relative energy gradient method and the ANANKE program, which enables automatic and unbiased IQA analysis...
November 10, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29125195/molecular-dynamics-simulation-of-liquid-water-and-ice-nanoclusters-using-a-new-effective-hfd-like-model
#10
Mohsen Abbaspour, Hamed Akbarzadeh, Sirous Salemi, Khodanazar Pirfalak
We have determined a new two-body interaction potential of water by the inversion of viscosity collision integrals of water vapor and fitted to achieve the Hartree-fock dispersion-like (HFD-like) potential function. The calculated two-body potential generates the thermal conductivity, viscosity, and self-diffusion coefficient of water vapor in an excellent accordance with experimental data at wide temperature ranges. We have also used a new many-body potential as a function of temperature and density with the HFD-like pair-potential of water to improve the two-body properties better than the SPC, SPC/E, TIP3P, and TIP4P models...
November 10, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29116648/nuclear-quantum-effects-induce-metallization-of-dense-solid-molecular-hydrogen
#11
Sam Azadi, Ranber Singh, Thomas D Kühne
We present an accurate computational study of the electronic structure and lattice dynamics of solid molecular hydrogen at high pressure. The band-gap energies of the C2/c, Pc, and P63/m structures at pressures of 250, 300, and 350 GPa are calculated using the diffusion quantum Monte Carlo (DMC) method. The atomic configurations are obtained from ab initio path-integral molecular dynamics (PIMD) simulations at 300 K and 300 GPa to investigate the impact of zero-point energy and temperature-induced motion of the protons including anharmonic effects...
November 8, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29116647/application-of-reference-modified-density-functional-theory-temperature-and-pressure-dependences-of-solvation-free-energy
#12
Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenji Mochizuki, Kenichiro Koga
Recently, we proposed a reference-modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard-sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard-sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water...
November 8, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29114892/hyperconjugative-effects-in-%C3%AF-hydrogen-bonding-theory-and-experiment
#13
Boris Galabov, Valia Nikolova, Diana Cheshmedzhieva, Boriana Hadjieva, Henry F Schaefer
Density functional theory computations with the B3LYP/6-311++G(2df,2p) method and IR spectroscopy are employed in investigating the properties of twenty π-hydrogen bonded complexes between substituted phenols and hexamethylbenzene. All complexes possess T-shaped structures. The methyl hyperconjugative effects on interactions energies and OH stretching frequencies are estimated via comparisons with previously reported theoretical and experimental results for analogous phenol complexes with benzene. The theoretical computations provide excellent quantitative predictions of the OH stretching frequency shifts (ΔνOH ) resulting from the hydrogen bonding...
November 8, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29105789/host-guest-interactions-between-octa-acid-and-cations-nucleobases
#14
Debdutta Chakraborty, Pratim Kumar Chattaraj
The nature of host-guest interaction in between octa acid cavitand (OA) and some representative cationic guests (Li(+) , Na(+) , K(+) , Be(+2) , Mg(+2) , Ca(+2) , Li3 O(+) , Na3 O(+) , K3 O(+) ) as well as heterocyclic moieties like [adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U), and tetrathiafulvalene (TTF)] has been examined with the aid of density functional theory (DFT)-based computations. Thermochemical results indicate that all the guests bind with OA in a thermodynamically favorable fashion at 298...
November 4, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29098697/interpreting-the-behavior-of-the-nicszz-by-resolving-in-orbitals-sign-and-positions
#15
Guillaume Acke, Sofie Van Damme, Remco W A Havenith, Patrick Bultinck
The zz component of the nucleus independent chemical shift or the NICSzz is commonly used as a quantifier of the (anti)aromatic character of a (sub)system. One of the underlying assumptions is that a position can be found where the "aromatic" ring currents are adequately reflected in the corresponding NICSzz value. However, as the NICSzz is the result of an integration over the entire space, it no longer explicitly contains the information needed to quantify the separate contributions arising from underlying current density patterns...
November 2, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29094421/confinement-induced-thermodynamic-and-kinetic-facilitation-of-some-diels-alder-reactions-inside-a-cb-7-cavitand
#16
Debdutta Chakraborty, Pratim Kumar Chattaraj
The effect of geometrical confinement on the Diels-Alder reactions between some model dienes viz. furan, thiophene, cyclopentadiene, benzene, and a classic dienophile, ethylene has been explored by performing density functional theory-based calculations. The effect of confinement has been imposed by a rigid macrocyclic molecule cucurbit[7]uril (CB[7]). Results indicate that all the reactions become thermodynamically more favorable at 298.15 K temperature and one atmospheric pressure inside CB[7] as compared to the corresponding free gaseous state reactions...
November 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29094387/reactions-involving-some-gas-molecules-through-sequestration-on-al12-be-cluster-an-electron-density-based-study
#17
Debdutta Chakraborty, Pratim Kumar Chattaraj
The viability of sequestering gas molecules (CO, NO, CO2 , NO2 , N2 O, O2 , O3 , H2 O, NH3 , H2 , CH3 OH, CH3 F, C2 H5 F, C2 H2 , C2 H4 , HCN, and SO2 ) on the Al12 Be cluster is investigated by carrying out density functional theory based computations. Thermochemical as well as energetic considerations suggest that Al12 Be cluster adsorbs the chosen gas molecules in a favorable fashion. The gas molecules attain an activated state on getting adsorbed on the metal cluster as vindicated by Atoms-in-Molecule analysis...
November 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29094379/electrostatics-for-probing-lone-pairs-and-their-interactions
#18
Padinjare Veetil Bijina, Cherumuttathu H Suresh, Shridhar R Gadre
The value of the molecular electrostatic potential minimum (Vmin ) and its topographical features (position, as well as the eigenvalues and eigenvectors of the corresponding Hessian matrix) are recently proposed as the criteria for characterizing a lone pair (Kumar A. et al., J. Phys. Chem. 2014, A118, 526). This electrostatic characterization of lone pairs is examined for a large number of small molecules employing MP4/6-311++G(d,p)//MP2/6-311++G(d,p) theory. The eigenvector of the Hessian matrix corresponding to its largest eigenvalue (λmax ), is found to be directed toward the lone pair-bearing-atom, with λmax showing a strong linear correlation with Vmin ...
November 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29094373/combined-molecular-and-periodic-dft-analysis-of-the-adsorption-of-co-macrocycles-on-graphene
#19
Adrian Calborean, Cristian Morari, Pascale Maldivi
The molecular doping of graphene with π-stacked conjugated molecules has been widely studied during the last 10 years, both experimentally or using first-principle calculations, mainly with strongly acceptor or donor molecules. Macrocyclic metal complexes have been far less studied and their behavior on graphene is less clear-cut. The present density functional theory study of cobalt porphyrin and phthalocyanine adsorbed on monolayer or bilayer graphene allows to compare the outcomes of two models, either a finite-sized flake of graphene or an infinite 2D material using periodic calculations...
November 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29083034/comparison-of-various-means-of-evaluating-molecular-electrostatic-potentials-for-noncovalent-interactions
#20
Steve Scheiner
The various heterodimers formed by a series of Lewis acids with NH3 as Lewis base are identified. Lewis acids include those that can form chalcogen (HSF and HSBr), pnicogen (H2 PF and H2 PBr), and tetrel (H3 SiF and H3 SiBr) bonds, as well as H-bonds and halogen bonds. The molecular electrostatic potential (MEP) of each Lewis acid is considered in a number of ways. Pictorial versions show broad regions of positive and negative MEP, on surfaces that vary with respect to either the value of the chosen isopotential, or their distance from the nuclei...
October 30, 2017: Journal of Computational Chemistry
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