The Effects of Ligand Deprotonation on the Binding Selectivity of the Phenylalanine Hydroxylase Active Site
We report promising novel catechols that do not inhibit this enzyme. Results show deprotonation of the ligands by the active site can strongly affecting their binding strength, thus the pKas for all novel ligands were calculated and are reported.Graphical abstractNew family of molecules (PG-X) that do not inhibit Phenylalanine Hydroxylase, thus making them possible drug candidates for raising levels of dopamine in the brain. Shown above is PG-OH, which has the weakest interaction energy when optimized in the Phenylalanine Hydroxylase active site. Optimization is performed with M062X/6-31G, implicit solvation, and relaxed a...
Source: Computational and Theoretical Chemistry - February 25, 2019 Category: Chemistry Source Type: research

First-principles studies on the doping effect of Nin−1TM (n = 13, 19, 55)
Publication date: 15 March 2019Source: Computational and Theoretical Chemistry, Volume 1152Author(s): Wei Song, Tao Kuang, Zhe Fu, Jin-long Wang, Wei Zhang, Peng-fei MaAbstractThe structural and electronic properties of different transition-metal atoms (TM = Cr, Mn, Fe, Co, Cu, Zn, Pd, Ag, Pt, Au) doped into Nin neutral and ionic clusters (n = 13, 19, 55) were investigated using density functional theory calculations with the PBE exchange-correlation energy functional. The properties of the Nin−1TM clusters differed substantially from those of Nin, implying that the substitution of a transition-metal atom (TM...
Source: Computational and Theoretical Chemistry - February 25, 2019 Category: Chemistry Source Type: research

Cyclic dimers of formamidine with its N-halogenated formamidine analogues: structure, energetics, and proton-halonium transfer
Publication date: Available online 22 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Ruben D. Parra, Samuel Knewstub, Patrick Kusion, Gonzalo MorenoAbstractAb initio calculations were carried out to investigate cyclic dimers of formamidine with its N-halogenated analogues, HN=CHNHX (X = Cl, Br, or I). Geometry optimizations and frequency calculations were completed with the MP2 method and both the aug-cc-pVDZ and the aug-cc-pVTZ basis sets. BSSE-corrected interaction energies were calculated at the MP2, QCISD, and CCSD(T) methods. Electron density at relevant critical points, and charge transfers we...
Source: Computational and Theoretical Chemistry - February 23, 2019 Category: Chemistry Source Type: research

The Perlin effect in 2-halocyclohexanones and 2-halocyclohexanethiones
Publication date: 15 March 2019Source: Computational and Theoretical Chemistry, Volume 1152Author(s): Fátima M.P. de Rezende, Matheus P. Freitas, Teodorico C. RamalhoAbstractThe Perlin effect is an NMR phenomenon observed in six-membered rings and it is referred to as 1JC−Hax 
Source: Computational and Theoretical Chemistry - February 23, 2019 Category: Chemistry Source Type: research

Editorial Board
Publication date: 1 March 2019Source: Computational and Theoretical Chemistry, Volume 1151Author(s): (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - February 21, 2019 Category: Chemistry Source Type: research

The Perlin Effect in 2-halocyclohexanones and 2- halocyclohexanethiones
Publication date: Available online 19 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Fátima M.P. de Rezende, Matheus P. Freitas, Teodorico C. RamalhoAbstractThe Perlin effect is an NMR phenomenon observed in six-membered rings and it is referred to as1JC−Hax
Source: Computational and Theoretical Chemistry - February 20, 2019 Category: Chemistry Source Type: research

Structure, stability, and electronic structure properties of quasi-fullerenes Cn-q (n = 42, 48 and 60) doped with transition metal atoms (M = Sc, Ti, V and Cr): A Density Functional Theory study
Publication date: 15 March 2019Source: Computational and Theoretical Chemistry, Volume 1152Author(s): Christian A. Celaya, Jesús Muñiz, Luis Enrique SansoresAbstractQuasi-fullerenes (Cn-q, where q stands for quasi) are novel molecules that exhibit geometries such as carbon cages with interesting electronic structure properties due to the diversity on the shape of the rings in their structure. In this work, we studied the structural stability and electronic structure properties of possible endohedral metallo quasi-fullerenes M@Cn-q (M = Sc, Ti, V, Cr; n = 42, 48 and 60). These systems have been systema...
Source: Computational and Theoretical Chemistry - February 19, 2019 Category: Chemistry Source Type: research

Comparison of the Coulomb and non-orthogonal approaches to the construction of the exciton Hamiltonian
Publication date: Available online 14 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Ilya O. Glebov, Maxim I. Kozlov, Vladimir V. PoddubnyyAbstractA description for systems consisting of many different interacting fragments is one of the most prominent problems in computational chemistry. When excited states of such systems are considered, the exciton Hamiltonian method is generally used, where the total supramolecular Hamiltonian is constructed based on the wavefunctions of the fragments. In the current study, we compare two non-orthogonal methods to calculate intermolecular interactions (exciton c...
Source: Computational and Theoretical Chemistry - February 15, 2019 Category: Chemistry Source Type: research

Spectroscopic, vibrational and structural properties analysis of CaXen (n = 1–4) clusters
Publication date: 1 March 2019Source: Computational and Theoretical Chemistry, Volume 1151Author(s): Safa Mtiri, Brahim OujiaAbstractA systematic ab initio calculations based on a complete Configuration Interaction (CI) including the pseudo-potential model where the core valence correlation was presented by the Core Polarization Potential (CPP), were employed to determine the geometric structures of CaXen (n = 1–4) neutral clusters. For the diatomic (CaXe) and tri-atomic (CaXe2) systems, the potential energy curves for the ground and several excited states are determined and the different spectroscopic constants ...
Source: Computational and Theoretical Chemistry - February 14, 2019 Category: Chemistry Source Type: research

Structure, stability, and electronic structure properties of quasi-fullernes Cn-q (n=42, 48 and 60) doped with transition metal atoms (M= Sc, Ti, V and Cr): A Density Functional Theory study
Publication date: Available online 12 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Christian A. Celaya, Jesús Muñiz, Luis Enrique SansoresAbstractQuasi-fullerenes (Cn-q, where q stands for quasi) are novel molecules that exhibit geometries such as carbon cages with interesting electronic structure properties due to the diversity on the shape of the rings in their structure. In this work, we studied the structural stability and electronic structure properties of possible endohedral metallo quasi-fullerenes M@Cn-q (M= Sc, Ti, V, Cr; n= 42, 48 and 60). These systems have been systematic...
Source: Computational and Theoretical Chemistry - February 13, 2019 Category: Chemistry Source Type: research

Excited state dynamics of some nonsteroidal anti-inflammatory drugs: a surface-hopping investigation
Publication date: Available online 13 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Neus Aguilera-Porta, Inés Corral, Jordi Munoz-Muriedas, Giovanni GranucciAbstractHere we present a computational investigation of the excited state dynamics of 5 different active medical substances (aspirin, ibuprofen, carprofen, suprofen, indomethacin) which belong to the family of nonsteroidal anti-inflammatory drugs (NSAIDs). The nonadiabatic dynamics simulations were performed using the surface hopping method, with electronic energies and couplings evaluated on the fly in a semiempirical framework. For as...
Source: Computational and Theoretical Chemistry - February 13, 2019 Category: Chemistry Source Type: research

CO catalytic oxidation over C59X heterofullerenes (X = B, Si, P, S): A DFT study
Publication date: 1 March 2019Source: Computational and Theoretical Chemistry, Volume 1151Author(s): Mehdi D. Esrafili, Safa HeidariAbstractThe aim of this study is to explore the mechanisms of CO oxidation to CO2 over some C59X heterofullerenes (X = B, P, Si and S) through systematic dispersion-corrected density functional theory calculations. The adsorption energy of O2 over these fullerenes becomes more negative in the order of C59S 
Source: Computational and Theoretical Chemistry - February 13, 2019 Category: Chemistry Source Type: research

Spectroscopic, Vibrational and Structural properties analysis of CaXen (n=1-4) clusters
Publication date: Available online 11 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Safa Mtiri, Brahim OujiaAbstractA systematic ab initio calculations based on a complete Configuration Interaction (CI) including the pseudo-potential model where the core valence correlation was presented by the Core Polarization Potential (CPP), were employed to determine the geometric structures of CaXen (n =1-4) neutral clusters. For the diatomic (CaXe) and tri-atomic (CaXe2) systems, the potential energy curves for the ground and several excited states are determined and the different spectroscopic constants are...
Source: Computational and Theoretical Chemistry - February 11, 2019 Category: Chemistry Source Type: research

CO catalytic oxidation over C59X heterofullerenes (X=B, Si, P, S): A DFT study
Publication date: Available online 11 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Mehdi D. Esrafili, Safa HeidariAbstractThe aim of this study is to explore the mechanisms of CO oxidation to CO2 over some C59X heterofullerenes (X = B, P, Si and S) through systematic dispersion-corrected density functional theory calculations. The adsorption energy of O2 over these fullerenes becomes more negative in the order of C59S
Source: Computational and Theoretical Chemistry - February 11, 2019 Category: Chemistry Source Type: research

Theoretical Study on the Gas Phase Reaction of Methyl Chavicol with Hydroxyl Radical
Publication date: Available online 8 February 2019Source: Computational and Theoretical ChemistryAuthor(s): R. Bhuvaneswari, K. SenthilkumarAbstractMethyl chavicol (MC) is an oxygenated aromatic compound, suspected to be harmful to human health at high concentration. The present study focuses on the gas-phase oxidation mechanism of methyl chavicol initiated by OH radical by employing combined quantum chemical calculations and kinetic modelling. The initiation of the reaction is dominated by the abstraction of methyl chavicol hydrogen atom by OH radical and electrophilic addition of OH radical to the methyl chavicol. Energe...
Source: Computational and Theoretical Chemistry - February 9, 2019 Category: Chemistry Source Type: research

A reaction force perspective of a model amide bond formation reaction
Publication date: Available online 7 February 2019Source: Computational and Theoretical ChemistryAuthor(s): V. Suresh Kumar Neelamraju, Tanashree JaganadeAbstractA reaction force approach of amide bond formation between ammonia and formic acid is demonstrated along with each atom’s contribution to structural changes and electronic reordering of the chemical reaction. The B3LYP/6-31G(d,p) level of density functional theory based calculations were carried out to explore transition states (TSs) of stepwise and concerted amide bond formation reaction pathways. Various stages that characterize structural and electronic pr...
Source: Computational and Theoretical Chemistry - February 8, 2019 Category: Chemistry Source Type: research

The Damped Ehrenfest (D-Eh) Method: Application to Non-Adiabatic Reaction Paths
Publication date: Available online 8 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Andrew J. Jenkins, Michael A RobbAbstractAn implementation of the Ehrenfest method with damped velocity is discussed. The method is then applied to study the non-adiabatic reaction paths for two simple chemical systems: the isomerization of the allene radical cation in its excited state and the channel 3 photochemical transformation of benzene to benzvalene. For both systems the initial conditions for the Ehrenfest trajectory were either an adiabatic eigenstate with the geometry close to a conical intersection, or a ...
Source: Computational and Theoretical Chemistry - February 8, 2019 Category: Chemistry Source Type: research

Malleable parallelism with minimal effort for maximal throughput and maximal hardware load
Publication date: Available online 7 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Florian Spenke, Karsten Balzer, Sascha Frick, Bernd Hartke, Johannes M. DieterichAbstractIn practice, standard scheduling of parallel computing jobs almost always leaves significant portions of the available hardware unused, even with many jobs still waiting in the queue. The simple reason is that the resource requests of these waiting jobs are fixed and do not match the available, unused resources. However, with alternative but existing and well-established techniques it is possible to achieve a fully automated, ada...
Source: Computational and Theoretical Chemistry - February 7, 2019 Category: Chemistry Source Type: research

Editorial Board
Publication date: 15 February 2019Source: Computational and Theoretical Chemistry, Volume 1150Author(s): (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - February 6, 2019 Category: Chemistry Source Type: research

Intermolecular Association of Some Selected Melanin Monomers and Their Optical Absorption
Publication date: Available online 5 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Subhrangshu Supakar, Aulie Banerjee, Tarun JhaAbstractMelanin is a black-brown pigment with varied functions found widely distributed in living bodies across the globe. The exact molecular structure is still debatable/undefined and is considered to be formed by polymerization of 5,6-dihydroxyindole (DHI), 5,6- dihydroxyindole carboxylic acid (DHICA) and their quinonoid products. For eumelanin, an oligomeric view is proposed in this article where the protomolecules are in stacked conformation and comprises of the hydr...
Source: Computational and Theoretical Chemistry - February 5, 2019 Category: Chemistry Source Type: research

DFT characterization on the effect of redox-inactive cation Ca2+ on water oxidation by CoII-based cuboidal catalyst
Publication date: Available online 2 February 2019Source: Computational and Theoretical ChemistryAuthor(s): Xiao-Fang Su, Bo Zhu, Li Liu, Li-Kai Yan, Zhong-Min SuAbstractThe activity of the biomimetic CoII-based cuboidal water oxidation catalyst (WOC) [CoII4(hmp)4(μ-OAc)2(μ2-OAc)2(H2O)] ([CoII4O4]) and its Ca2+-substitute [CoII3CaO4] were theoretically investigated to evaluate the effect of redox-inactive Ca2+ on water oxidation by CoII-based cuboidal catalyst. Compared with [CoII4O4], the smaller redox potential of [CoII3CaO4] results in the more efficient oxidation-equivalents accumulation for water oxidation. By c...
Source: Computational and Theoretical Chemistry - February 3, 2019 Category: Chemistry Source Type: research

Unveiling the photophysics of thiourea from CASPT2/CASSCF potential energy surfaces and singlet/triplet excited state molecular dynamics simulations
Publication date: Available online 31 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Neus Aguilera Porta, Giovanni Granucci, Jordi Munoz-Muriedas, Inés CorralAbstractThis work describes the decay mechanism of photoexcited thiourea, both in gas phase and in solution, from the information inferred from the topography of the excited and ground state potential energy surfaces and mixed singlet/triplet quantum classical molecular dynamics simulations. Our gas phase results reveal T1/S0 intersystem crossing as the dominant (49%) intrinsic decay channel to the ground state, which reaches a population...
Source: Computational and Theoretical Chemistry - February 2, 2019 Category: Chemistry Source Type: research

Optical properties and Quasiparticle energies in the two-layered hydrogenated Gallium Nitrate nanosheet: A DFT study
Publication date: Available online 31 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Somayeh Faghihzadeh, Nasser Shahtamasebi, Davoud Vahedi FakhrabadAbstractIn this work, the electronic structure and optical properties of two-layered hydrogenated GaN were investigated. The results were obtained via first principle calculations based on density functional theory (DFT) using GW approximation and two particle Bethe–Salpeter equation along with electron-hole effect. The results show that direct band gap of the sample change from 1.67eV to, 4.1eV considering electron-electron effects. Based on our ...
Source: Computational and Theoretical Chemistry - February 2, 2019 Category: Chemistry Source Type: research

Electronic structure of boron and nitrogen doped isomeric graphene nanoflakes
Publication date: Available online 29 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Cesar Gabriel Vera de la Garza, Esaú Martínez Olmedo, Serguei FomineAbstractElectronic properties of nitrogen and boron doped isomeric graphene nanoflakes have been explored using dispersion corrected B3LYP functional and CASSCF methods. The most thermodynamically stable isomers of nitrogen and boron doped systems contain phenalene and azulene motifs substituted in positions 7 and 9, respectively. Nitrogen doping promotes nanoflake planarity, increases singlet-triplet gap and a band gap, while boron dop...
Source: Computational and Theoretical Chemistry - January 30, 2019 Category: Chemistry Source Type: research

First-principles Studies on the Doping Effect of Nin-1TM (n = 13, 19, 55)
Publication date: Available online 30 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Wei Song, Tao Kuang, Zhe Fu, Jin-long Wang, Wei Zhang, Peng-fei MaAbstractThe structural and electronic properties of different transition-metal atoms (TM = Cr, Mn, Fe, Co, Cu, Zn, Pd, Ag, Pt, Au) doped into Nin neutral and ionic clusters (n = 13, 19, 55) were investigated using density functional theory calculations with the PBE exchange-correlation energy functional. The properties of the Nin-1TM clusters differed substantially from those of Nin, implying that the substitution of a transition-metal atom (TMA) stron...
Source: Computational and Theoretical Chemistry - January 30, 2019 Category: Chemistry Source Type: research

Electron-Nuclear Entanglement in the Time-Dependent Molecular Wavefunction
Publication date: Available online 28 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Federica Agostini, E.K.U. Gross, Basile F.E. CurchodAbstractWe address the problem of electron-nuclear entanglement in time-dependent molecular wavefunctions, key quantities of quantum nonadiabatic molecular dynamics. The most natural way of tackling this question consists in comparing the nonadiabatic dynamics obtained from time-dependent self-consistent field and the exact factorization of the time-dependent electron-nuclear wavefunction. Both approaches are based on a single-product Ansatz for the molecular wavefu...
Source: Computational and Theoretical Chemistry - January 29, 2019 Category: Chemistry Source Type: research

How boron is adsorbed by d-glucamine: A density functional theory study
In this study, we carried out a molecular scale analysis of boron adsorption by density functional theory (DFT) computations.All 30 species of boron-bonding d-glucamine were considered in an adsorption site model. Moreover, a total of 24 bis-d-glucamine adsorption sites, including five-membered and six-membered chelate rings were calculated. The values of ΔH and ΔG in the boron adsorption reaction were obtained by the PW6B95-D3ATM/ma-def2-TZVP//PBE0/6-31 + G(d,p) level of theory with the SMD solvation energy. Moreover, the 11B NMR chemical shift was also computed to compare the experimental results.Our comp...
Source: Computational and Theoretical Chemistry - January 29, 2019 Category: Chemistry Source Type: research

Insight into the optical properties of meso-pentafluorophenyl(PFP)-BODIPY: an attractive platform for functionalization of BODIPY dyes
Publication date: Available online 25 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Martina De Vetta, Inés CorralAbstractThe pentafluorophenyl (PFP) moiety is an important and versatile substituent in the chemistry of BODIPYs, porphyrins and corroles. The widespread use of PFP meso-substituted compounds, as intermediates in the synthesis of more complex pyrrole derivatives, is the motivation behind this work, which investigates the optical properties of the meso-PFP-BODIPY from a theoretical point of view. From the panoply of computational tools available for this purpose, we have considered ...
Source: Computational and Theoretical Chemistry - January 25, 2019 Category: Chemistry Source Type: research

Diabatic and Adiabatic Representations: Electronic Structure Caveats
Publication date: Available online 25 January 2019Source: Computational and Theoretical ChemistryAuthor(s): David R. Yarkony, Changjian Xie, Xiaolei Zhu, Yuchen Wang, Christopher L. Malbon, Hua GuoAbstractIn this Viewpoint issues in the construction and use of adiabatic and diabatic representations in describing spin-conserving electronically nonadiabatic processes using the Born-Huang ansatz are reviewed and illustrated. We address issues which limit the accuracy of commonly used approximate equations of motion. The following caveats are discussed. (i) The use of adiabatic states for Nstate>2 is complicated by the fact...
Source: Computational and Theoretical Chemistry - January 25, 2019 Category: Chemistry Source Type: research

Molecular Design of Organoplatinum(II) Complexes Through a DFT/TDDFT Study: Photophysical Properties and Intermolecular Interactions
Publication date: Available online 22 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Hongyan Ning, Xiuxue Huang, Li Yang, Jiaxu ZhangAbstractA series of organoplatinum (II) complexes with different electron-donating substituents are designed and investigated using density functional theory (DFT) and time-dependent DFT approaches. By analyzing the ground and excited structures, absorption spectra, charge transport, and phosphorescence properties of five Pt(II) complexes, it is possible to forecast that [Pt(trpy)(C≡CAŕ)]PF6 (Aŕ=2,6-Me2C6H3) (complex 2c•PF6) could be an efficient phosphores...
Source: Computational and Theoretical Chemistry - January 24, 2019 Category: Chemistry Source Type: research

Theoretical study for conformational analysis and kinetics on the internal halogen exchange thermally induced of trichloro-(1,1-difluoroethyl)silane in the gas phase
Publication date: Available online 22 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Yeljair Monascal, Alexis Maldonado, Loriett Cartaya, Alvaro Alvarez-AularAbstractConsecutive first-order, homogeneous intramolecular fluorine-chlorine exchange reactions of trichloro-(1,1-difluoroethyl)silane have been theoretically studied using ab initio post-Hartree-Fock G4MP2 and DFT (B3LYP, M06, M06-2X) levels of theory. The reactions were studied at 127 oC and 0.1 Torr of temperature and pressure respectively, yielding (1-choro-1-fluoroethyl)-dichlorofluorosilane, and chloro-difluoro(1,1-dichloroethyl)silane. A...
Source: Computational and Theoretical Chemistry - January 24, 2019 Category: Chemistry Source Type: research

Computational Study on the Removal of Photolabile Protecting Groups by Photochemical Reactions
Publication date: Available online 23 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Chou-Hsun Yang, Johanna Denne, Scott Reed, Haobin WangAbstractThe application and versatility of photolabile protecting groups (PPGs) have continued to expand since their inception almost 50 years ago. In the present work we employ density functional theory (DFT) to characterize ground and excited state properties of several compounds with PPGs and to explore possible, controllable photodissociation reactions that remove these PPGs. The reaction mechanism is examined by analyzing the DFT results as well as dynamical ...
Source: Computational and Theoretical Chemistry - January 24, 2019 Category: Chemistry Source Type: research

Editorial Board
Publication date: 1 February 2019Source: Computational and Theoretical Chemistry, Volume 1149Author(s): (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - January 24, 2019 Category: Chemistry Source Type: research

Coupled Cluster Investigation of the interaction of Beryllium, Magnesium, and Calcium with Pyridine: Implications for the Adsorption on Nitrogen-Doped Graphene
Publication date: Available online 22 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Saif Ullah, Pablo A. Denis, Fernando SatoAbstractWe performed benchmark calculations to study the complexes of pyridine with beryllium, magnesium, and calcium. In all cases, the σ structures, in which the alkaline-earth element interacts with nitrogen, were found to be more stable than the ones featuring interactions with the π cloud. At the CCSD(T)/CBS level of theory, the dissociation energies (De) are 6.5, 3.7 and 7.2 kcal/mol, for beryllium, magnesium, and calcium, respectively. Our estimation of the D0 ...
Source: Computational and Theoretical Chemistry - January 22, 2019 Category: Chemistry Source Type: research

Fully quantal treatment of nonadiabatic molecular photodynamics: General considerations and application to the benzene cation
Publication date: Available online 22 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Simona Scheit, Sugata Goswami, Hans-Dieter Meyer, Horst KöppelAbstractThe merits and drawbacks of a mixed quantum-classical description of nuclear motion on coupled potential energy surfaces are discussed and compared with a fully quantal treatment. For the latter a particular approach is highlighted in which an efficient wavepacket propagation scheme, the Multiconfiguration Time-Dependent Hartree (MCTDH) method, is combined with a versatile modeling of the Hamiltonian for interacting potential energy surfaces, ...
Source: Computational and Theoretical Chemistry - January 22, 2019 Category: Chemistry Source Type: research

Structural Patterns in Carbon Chemisorption on Ultrasmall Iron Clusters: A First-principles Study
Publication date: Available online 22 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Zongying Wang, Huiting Bian, Jing Li, Wei Zhong, Tianshui Liang, Jun ZhaoAbstractTo get a better understanding of the catalyst chemistry of iron clusters, four representative Fen (n = 1-4) clusters were chosen to systematically investigate the carbonization processes through subsequently adding carbon atoms by using density functional theory calculations. With respect to the quantum results, the analysis of structures, stabilities, and magnetic moments were conducted. It is found that there are three typical peaks of...
Source: Computational and Theoretical Chemistry - January 22, 2019 Category: Chemistry Source Type: research

Probing cyanogen chloride gas molecules using blue phosphorene nanosheets based on adsorption properties: a first-principles study
Publication date: Available online 22 January 2019Source: Computational and Theoretical ChemistryAuthor(s): V. Nagarajan, R. ChandiramouliAbstractThe interaction behavior and sensing ability of cyanogen chloride (CNCl) molecules on blue phosphorene nanosheet (βP-NS) were explored using first-principles calculation. The geometric stability of both pristine and Al incorporated βP-NS are established by the formation energy. The core stimulus of the current research is to probe hazardous CNCl gas molecules using βP-nanostructures rapidly. The interaction of various orientation sites of CNCl on βP-base mater...
Source: Computational and Theoretical Chemistry - January 22, 2019 Category: Chemistry Source Type: research

Structures, Metallophilic Interactions and Electronic Excitation Energy of Linear Metal Chain Complexes PdmPtn[PH2(CH2PH)m+n-2CH2PH2]3, A Theoretical Investigation
Publication date: Available online 21 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Mingrui Shen, Congjie ZhangAbstractThe structures, metallophilic interactions and electronic excitation energy of linear metal chain complexes PdmPtn[PH2(CH2PH)m+n-2CH2PH2]3 (m+n=2-5) (1-18) have been investigated by using MP2 and density functional theory (DFT) methods. Calculated results indicated that geometries of PdmPtn(PH2CH2PH2)3 (m+n=2) (1-3) optimized by SVWN5 method are well consistent with those by MP2 method and experiment. Then, SVWN5 functional was used to the investigation of the large system of PdmPtn...
Source: Computational and Theoretical Chemistry - January 21, 2019 Category: Chemistry Source Type: research

Effect of solvent polarity on the potential energy surface in the SN2 reaction of F− + CH3Cl
Publication date: 15 February 2019Source: Computational and Theoretical Chemistry, Volume 1150Author(s): Lopamudra Satpathy, Sagarika Sahoo, Prabhat K. Sahu, Pradipta K. Behera, Bijay K. MishraAbstractThe SN2 reaction of F− + CH3Cl covers a conducive energy domain described by its potential energy surface with varied ∠FCCl and CF distance. Loci of the potential energy surface produce two reaction wells, one is due to nonconventional F∙∙∙HC hydrogen bonding and the other is due to linear backside attack. The effect of solvent polarity on the PESs leads to (i) a significant increase in the energy barrier of t...
Source: Computational and Theoretical Chemistry - January 20, 2019 Category: Chemistry Source Type: research

First-Principles Investigation of Native Point Defects in Two-Dimensional Ti3C2
Publication date: Available online 14 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Ruijiao He, Yun Wan, Puju Zhao, Ping Guo, Zhenyi Jiang, Jiming ZhengAbstractTwo-dimensional transition metal carbides or nitrides (MXenes) have attracted much research interest and have shown very promising applications. Recently, the Ti vacancies in Ti3C2 were observed in an experiment (ACS Nano, 2016, 10, 9193-9200) and demonstrated an important influence on the electronic properties of Ti3C2. Based on the first-principles method, this study systemically investigated these issues and found that the formation energy...
Source: Computational and Theoretical Chemistry - January 15, 2019 Category: Chemistry Source Type: research

Ab initio surface hopping molecular dynamics on the dissociative recombination of CH3+
Publication date: Available online 14 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Tetsuya Taketsugu, Yuta KobayashiAbstractAb initio molecular dynamics (AIMD) simulations were carried out to investigate dynamics in the dissociative recombination of CH3+ at the state-averaged complete active space self-consistent field (SA-CASSCF) level. Nonadiabatic transitions between adiabatic electronic states were taken into account by the Tully's fewest switches algorithm. The direct process was examined by trajectories starting from the crossing points of the potential energy surfaces of the CH3+ ground stat...
Source: Computational and Theoretical Chemistry - January 15, 2019 Category: Chemistry Source Type: research

Effect of solvent polarity on the potential energy surface in the SN2 reaction of F- + CH3Cl
Publication date: Available online 11 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Lopamudra Satpathy, Sagarika Sahoo, Prabhat K. Sahu, Pradipta K. Behera, Bijay K. MishraAbstractThe SN2 reaction of F- + CH3Cl covers a conducive energy domain described by its potential energy surface with varied ∠F-C-Cl and C-F distance. Loci of the potential energy surface produce two reaction wells, one is due to nonconventional F∙∙∙H-C hydrogen bonding and the other is due to linear backside attack. The effect of solvent polarity on the PESs leads to (i) a significant increase in the energy barrier of ...
Source: Computational and Theoretical Chemistry - January 12, 2019 Category: Chemistry Source Type: research

How Does Boron Is Adsorbed by D-glucamine: A Density Functional Theory Study
In this study, we carried out a molecular scale analysis of boron adsorption by density functional theory (DFT) computations.All 30 species of boron bonding D-glucamine which is an adsorption site model was considered. Moreover, A total of 24 bis-D-glucamine adsorption site including the five- and the six-membered chelate ring was calculated. The value of ΔH and ΔG regarded boron adsorption reaction was obtained by PW6B95-D3ATM/ma-def2-TZVP//PBE0/6-31+G(d,p) level of theory with the SMD solvation energy. Moreover, 11B NMR chemical shift was also computed to compare the experimental results.Our computational res...
Source: Computational and Theoretical Chemistry - January 11, 2019 Category: Chemistry Source Type: research

A theoretical study about reactivity and spectroscopic properties of copper ions toward sulfur-containing species
Publication date: Available online 11 January 2019Source: Computational and Theoretical ChemistryAuthor(s): N.P. De Oliveira, M.G. Cardoso, M.C. Guerreiro, K.J. de AlmeidaAbstractSulfur-containing compounds have a major impact on the negative sensory quality of cachaça and other alcoholic beverages. These sulfide “off-odors” can be often removed by the presence of copper ions – a process that remains poorly understood. The DFT and CCSD(T) calculations were used to evaluate the reactivity of the copper(I) and copper(II) ions toward the volatile H2S, MeHS and EtHS species. The main results indicate t...
Source: Computational and Theoretical Chemistry - January 11, 2019 Category: Chemistry Source Type: research

A quasiclassical trajectory calculation to compute the reaction cross section and thermal rate constant for the cesium exchange reaction 133CsI + 135Cs → 133Cs + I135Cs
Publication date: Available online 11 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Takanori Kobayashi, Leo Matsuoka, Keiichi YokoyamaAbstractTo compute the reaction cross section and the thermal rate constant of the cesium exchange reaction 133CsI + 135Cs → 133Cs + I135Cs in the temperature range 500–1,500 K, we performed a quasiclassical trajectory calculation using a potential energy surface developed from an ab initio calculation at the MP2/def2-QZVPPD level. The state-specific cross sections and their dependences on the initial vibrational and rotational quantum numbers of 133CsI (v ...
Source: Computational and Theoretical Chemistry - January 11, 2019 Category: Chemistry Source Type: research

Editorial Board
Publication date: 15 January 2019Source: Computational and Theoretical Chemistry, Volume 1148Author(s): (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - January 11, 2019 Category: Chemistry Source Type: research

Distributed polarizability of fullerene [2+1]-adducts C60Xn (n = 1 and 2) with symmetric addends X  = CH2 and O: A fresh view on the effect of positional isomerism
Publication date: 1 February 2019Source: Computational and Theoretical Chemistry, Volume 1149Author(s): Alina A. Tukhbatullina, Edward M. Khamitov, Denis Sh. SabirovAbstractWe have performed a site-specific analysis of the mean polarizability of fullerene [2+1]-adducts C60Xn (n = 1 and 2) with symmetric addends X  = CH2 and O using the distributed polarizability model. We have found that the contributions from the fullerene core and addends to the molecular polarizability are not the same for different regioisomeric C60X2: the core contribution linearly decreases and the addend contribution linearly increases w...
Source: Computational and Theoretical Chemistry - January 9, 2019 Category: Chemistry Source Type: research

Computational Study of Structural, Vibrational and Electronic Properties of the Highly Symmetric Molecules M4S6 (M= P, As, Sb, Bi)
Publication date: Available online 8 January 2019Source: Computational and Theoretical ChemistryAuthor(s): E. Semidalas, A. ChrissanthopoulosAbstractA systematic computational investigation of the structural, electronic and vibrational properties of the group 15 sulfides M4S6 at Td symmetry was carried out. The performance of DFT and MP2 theoretical methods was assessed compared to the high-level CCSD method. The M-S bond is based on the association between p valence orbitals of M and the 3p of sulfur according to the natural population analysis. Both polarizability and polarizability volume of the cage molecules increase ...
Source: Computational and Theoretical Chemistry - January 9, 2019 Category: Chemistry Source Type: research

Extrapolation Functions for Calculating Stretching Frequencies of Local OH Bonds of Water Molecules
Publication date: Available online 8 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Kiyoung Jeon, Mino YangAbstractComplete basis set (CBS) limit extrapolation of ab initio electronic energies of a water dimer has been performed over a range of OH bond distances. The inverse power, exponential, and stretched exponential functions used as an extrapolation function give different extrapolated electronic energies. Using the extrapolated energies, we calculated the fundamental and the first overtone transition frequencies of the OH bonds of the hydrogen-bond (HB) donor in the dimer. The three extrapolati...
Source: Computational and Theoretical Chemistry - January 9, 2019 Category: Chemistry Source Type: research

The Effect of Electric Fields in Methane Hydrate Growth and Dissociation: A Molecular Dynamics Simulation
Publication date: Available online 4 January 2019Source: Computational and Theoretical ChemistryAuthor(s): Tingting Xu, Xuemei Lang, Shuanshi Fan, Yanhong Wang, Jianbiao ChenAbstractMolecular dynamics simulation was employed to examine the growth and dissociation process of methane hydrate in the presence of static/oscillation electric fields at T=260 K and P =100 bars. The intensity of electric field was in range of 1.0-2.0 v/nm, and the frequency of applied e/m field was in range of 2.45 GHz – 1.0 THz. Electric field would be a factor controlling the hydrate growth and dissociation because the migration of water mo...
Source: Computational and Theoretical Chemistry - January 5, 2019 Category: Chemistry Source Type: research