DFT-derived atomic multipoles in AMOEBA force field for calculating intermolecular interactions of azabenzenes dimers
Publication date: Available online 6 April 2018 Source:Computational and Theoretical Chemistry Author(s): Qin Shi, Shiwei Yin, Yun Wang The understanding of intermolecular interactions holds the key for many applications of organic semiconductor materials, such as azabenzenes, since they govern molecular configurations and the electron transfer rate. While the high-level quantum mechanics (QM) method can supply accurate interaction energies, it is most often time-consuming, which limits its large-scale applications. To address this issue, the approach using the polarizable force field (e.g. AMOEBA) has been recently devel...
Source: Computational and Theoretical Chemistry - April 7, 2018 Category: Chemistry Source Type: research

Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening
Publication date: Available online 7 April 2018 Source:Computational and Theoretical Chemistry Author(s): Keiya Maruyama, Yinglei Sheng, Hirofumi Watanabe, Kaori Fukuzawa, Shigenori Tanaka We evaluated the binding affinity between p38 MAP kinase and various inhibitors through use of the fragment molecular orbital (FMO) method at MP2/6-31G∗ level in comparison to experimental values of half maximal inhibitory concentration (IC50). Initially, the calculated results of the FMO-IFIE (inter-fragment interaction energy) sums for 60 complex structures registered in the Protein Data Bank were not well correlated with the I...
Source: Computational and Theoretical Chemistry - April 7, 2018 Category: Chemistry Source Type: research

Transition-metal-free diboration of non-activated olefins: A reaction mechanism revisited
Publication date: 1 May 2018 Source:Computational and Theoretical Chemistry, Volume 1131 Author(s): Fredrik Haeffner Density functional theory (M06-2X/6-31+G∗) calculations were used to examine a mechanism (B2(1,1)) proposed by Fernández et al. (2011) that tries to rationalize the high SYN-stereoselectivity observed in their discovered transition-metal-free diboration of non-activated olefins. The results show that B2(1,1) incorrectly predicts ANTI-addition of bulky diboron esters, however correctly predicts less bulky and catecholic diboron esters. Alternative mechanisms (B2 ′(1,1), B2(1,2), and B3), ...
Source: Computational and Theoretical Chemistry - April 7, 2018 Category: Chemistry Source Type: research

Doping of the first row transition metals onto B12N12 nanocage: A DFT study
Publication date: Available online 6 April 2018 Source:Computational and Theoretical Chemistry Author(s): Mahdi Abbasi, Ebrahim Nemati-Kande, Mohsen Doust Mohammadi A comparative study of doping of the first row transition metals (from Sc to Zn) onto all available adsorption sites of the exterior surface of B12N12 nanocage has been performed by DFT method at B3LYP/def2-TZVP(-f) level of theory. The geometrical structures, electronic properties, population and quantum theory of atoms in molecules (QTAIM) analyses are also performed to better understand the cage/metal interactions. It can be inferred from results that nine ...
Source: Computational and Theoretical Chemistry - April 6, 2018 Category: Chemistry Source Type: research

Retraction notice to “Ab initio study of AlBui3 self-association” [Comput. Theoret. Chem. 1111 (2017) 27–32]
Publication date: 15 April 2018 Source:Computational and Theoretical Chemistry, Volume 1130 Author(s): Evgeniy Yu. Pankratyev (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - April 6, 2018 Category: Chemistry Source Type: research

Quasi-classical dynamics investigations of the F  + D2O → DF + OD reaction on a full dimensional accurate potential energy surface
Publication date: 15 April 2018 Source:Computational and Theoretical Chemistry, Volume 1130 Author(s): Aike Liu, Chunni Xie, Jun Li The influence of vibrational excitations in the fully deuterated water (D2O) reactant on the reaction with the fluorine atom (F) is investigated using the full-dimensional quasi-classical trajectory method on an accurate ground electronic state potential energy surface. The results show that the reactant vibrational excitation in each mode of D2O has very complicated effect on the reactivity. At low collision energy, excitations in all three modes are more effective than collision energy in p...
Source: Computational and Theoretical Chemistry - April 6, 2018 Category: Chemistry Source Type: research

Stability, structural and electronic properties of ternary PdxAuyAgz clusters (x  + y + z = 7): A theoretical study
Publication date: 1 May 2018 Source:Computational and Theoretical Chemistry, Volume 1131 Author(s): Shuang Zhao, YunLai Ren, KaiSheng Yao, XinZhe Tian, JianJi Wang, JunNa Liu Full range of Au and Ag doped Pd clusters, Pd x Au y Ag z with x + y + z = 7 in their ground states, are studied using the density functional theory (DFT) at TPSSTPSS method with SDD pseudopotential. The average interatomic distance, chemical order, charge distribution, binding energy, mixing energy, finite difference energy, vertical ionization potential, electron affinity and HOMO-LUMO gap of the ternary clusters are evaluated as a func...
Source: Computational and Theoretical Chemistry - April 5, 2018 Category: Chemistry Source Type: research

Transition-Metal-Free Diboration of Non-Activated Olefins: A Reaction Mechanism Revisited.
Publication date: Available online 3 April 2018 Source:Computational and Theoretical Chemistry Author(s): Fredrik Haeffner Density functional theory (M06-2X/6-31+G∗) calculations were used to examine a mechanism (B2(1,1)) proposed by Fernández et al. (Angew. Chem., Int. Ed. 2011, 50, 7158) that tries to rationalize the high SYN-stereoselectivity observed in their discovered transition-metal-free diboration of non-activated olefins. The results show that B2(1,1) incorrectly predicts ANTI-addition of bulky diboron esters, however correctly predicts less bulky and catecholic diboron esters. Alternative mechanis...
Source: Computational and Theoretical Chemistry - April 4, 2018 Category: Chemistry Source Type: research

Conformational Structures and Vibrational Spectroscopic Investigation of Isolated Dityrosine and Tryptophan-Tyrosine Dipeptides: A Theoretical Study
Publication date: Available online 3 April 2018 Source:Computational and Theoretical Chemistry Author(s): Maricris L. Mayes, Lisa Perreault Aromatic peptides can form dipeptides which could then self-assemble into nanostructures. However, there is still a lack of fundamental understanding between structures and properties of these materials. We use dispersion-corrected density functional theory and second-order Møller Plesset perturbation theory to study a few lowest energy structures and the corresponding vibrational spectra of linear and cyclic dityrosine (YY) and tryptophan-tyrosine (WY), the building blocks of ...
Source: Computational and Theoretical Chemistry - April 4, 2018 Category: Chemistry Source Type: research

Mechanism and kinetics of the reaction of methyl acetate with Cl atom – A theoretical study
Publication date: 1 May 2018 Source:Computational and Theoretical Chemistry, Volume 1131 Author(s): M. Gnanaprakasam, L. Sandhiya, K. Senthilkumar A mechanistic study on the H-atom abstraction and CO bond breaking reaction of methyl acetate with Cl atom is investigated by using electronic structure calculations. Three reaction pathways for the initial reactions were identified. Two pathways corresponding to H-atom abstraction from acetyl site (CH3CO) and methoxy site (OCH3), leading to the formation of alkyl radical intermediate along with HCl. In the third pathway, acetyl chloride and CH3O radical is formed through the b...
Source: Computational and Theoretical Chemistry - April 4, 2018 Category: Chemistry Source Type: research

Theoretically predicted divalent silicon(0) compounds: Structures and chemical bonding of silylone in molybdenum pentacarbonyl complexes [Mo(CO)5-Si(XCp ∗)2] (X = B–Tl)
Publication date: 1 May 2018 Source:Computational and Theoretical Chemistry, Volume 1131 Author(s): Huynh Thi Phuong Loan, Hoang Van Duc, Duong Tuan Quang, Pham Van Tat, Dang Tan Hiep, Nguyen Thi Ai Nhung Quantum chemical calculations of structures and bonding in the transition metal complexes with silylone ligands [Mo(CO)5-Si(XCp∗)2] (Mo5-SiX) (X = B–Tl) are reported at the BP86 level of theory with various basis sets SVP, TZVPP, TZ2P + . The calculated equilibrium structures of complexes show that the silylone ligands Si(XCp∗)2 are bonded in a tilted orientation to the metal fragment Mo(CO)5 ...
Source: Computational and Theoretical Chemistry - April 3, 2018 Category: Chemistry Source Type: research

Stability, structural and electronic properties of ternary PdxAuyAgz clusters (x+y+z=7): A theoretical study
Publication date: Available online 31 March 2018 Source:Computational and Theoretical Chemistry Author(s): Shuang Zhao, YunLai Ren, KaiSheng Yao, XinZhe Tian, JianJi Wang, JunNa Liu Full range of Au and Ag doped Pd clusters, Pd x Au y Ag z with x+y+z=7 in their ground states, are studied using the density functional theory (DFT) at TPSSTPSS method with SDD pseudopotential. The average interatomic distance, chemical order, charge distribution, binding energy, mixing energy, finite difference energy, vertical ionization potential, electron affinity and HOMO-LUMO gap of the ternary clusters are evaluated as a function of the...
Source: Computational and Theoretical Chemistry - April 1, 2018 Category: Chemistry Source Type: research

DFT study of nanotubes as the drug delivery vehicles of Efavirenz
Publication date: Available online 31 March 2018 Source:Computational and Theoretical Chemistry Author(s): Hong Xu, Long Li, Guohong Fan, Xiangfeng Chu Efavirenz (EFV) is an antiretroviral medication which is commonly used to treat and prevent HIV disease. However, some disadvantages such as the poor water solubility, low inherent dissolution rate, low oral bioavailability of EFV limited its therapeutic effect. Nanoparticles or nanostructures can overcome the resistance of the diseases to drugs and are extensively explored as drug delivery carriers in the diagnosis and treatments of many diseases. In the present work, the...
Source: Computational and Theoretical Chemistry - April 1, 2018 Category: Chemistry Source Type: research

Atomistic Level Understanding of the Stabilization of Protein Trp Cage in Denaturing and Mixed Osmolyte Solutions
Publication date: Available online 29 March 2018 Source:Computational and Theoretical Chemistry Author(s): Gargi Borgohain, Sandip Paul Using replica exchange molecular dynamics simulation technique we report urea-induced denaturation and its counteraction by TMAO (Trimethylamine-N-oxide) of protein Trp cage. We find that in binary solution urea molecules are very much prone to stay nearby the salt bridge. In presence of TMAO, salt bridge is protected from urea molecules. TMAO also prevents hydration of the hydrophobic core of the protein and thus provides counteraction. Emphasizing on the orientational preferences of dif...
Source: Computational and Theoretical Chemistry - March 30, 2018 Category: Chemistry Source Type: research

Mechanism and Kinetics of the Reaction of Methyl Acetate with Cl atom - A Theoretical Study
Publication date: Available online 29 March 2018 Source:Computational and Theoretical Chemistry Author(s): M. Gnanaprakasam, L. Sandhiya, K. Senthilkumar A mechanistic study on the H-atom abstraction and C-O bond breaking reaction of methyl acetate with Cl atom is investigated by using electronic structure calculations. Three reaction pathways for the initial reactions were identified. Two pathways corresponding to H-atom abstraction from acetyl site (CH3C=O) and methoxy site (-OCH3), leading to the formation of alkyl radical intermediate along with HCl. In the third pathway, acetyl chloride and CH3O● radical is formed ...
Source: Computational and Theoretical Chemistry - March 30, 2018 Category: Chemistry Source Type: research

Theoretical Study of N-thiazolyl-2-cyanoacetamide Derivatives as Corrosion Inhibitor for Aluminum in Alkaline Environments
This study can help understand the mechanism of similar inhibitors and develop more inhibitors for Al in alkaline environment. Graphical abstract (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - March 29, 2018 Category: Chemistry Source Type: research

Spectroscopic and DFT approach for structure property relationship of red emitting Rhodamine analogues: A study of Linear and Nonlinear Optical Properties
Publication date: Available online 29 March 2018 Source:Computational and Theoretical Chemistry Author(s): Amol G. Jadhav, Lydia Rhyman, Ibrahim A. Alswaidan, Ponnadurai Ramasami, Nagaiyan Sekar Linear and nonlinear optical (NLO) properties of triphenyl fused rhodamine analogues were estimated by spectroscopic based methametical calcultions and compared with computated values using density functional theory (DFT) calculations. Various Global hybrids (GHs) and range separated hybrids (RSHs) were utilized for reliable estimations of NLO properties. Spectroscopic based methametical calcultions of polarizability (αCT), ...
Source: Computational and Theoretical Chemistry - March 29, 2018 Category: Chemistry Source Type: research

Density functional reactivity theory characterizing the reactivity of frustrated Lewis pairs
Publication date: Available online 27 March 2018 Source:Computational and Theoretical Chemistry Author(s): Dongling Wu, Anjie Liu, Dianzeng Jia Previously, theoretical studies for 2,6-lutidine/BR3 (R = F, Me, C6F5) (J. Phys. Chem. A2010) and PR3/B(C6F5)3 (R = Me, Ph, tBu, C6F5) (Chem. Phys. Lett.2012) pairs have been carried out by us to fully understand the reactivity differences between classical Lewis adducts and frustrated Lewis pairs (FLPs). Fukui function, as a conceptual DFT-based reactivity descriptor, was calculated and shown to explain well the observed reactivity of these Lewis pairs. The initially promising re...
Source: Computational and Theoretical Chemistry - March 28, 2018 Category: Chemistry Source Type: research

Theoretical Insights on the C-C Bond Reductive Elimination from Co(III) Center
Publication date: Available online 26 March 2018 Source:Computational and Theoretical Chemistry Author(s): Khalil Ahmad, Bilal Ahmad Khan, Soumendra K. Roy, Zain-ul-Abdin, Rashid Mahmood, Jahanzeb Khan, Hamad Ashraf The density-functional theory (DFT) calculations using B3LYP functional were performed to inspect the mechanism of the reductive elimination of ethane from a cobalt(III) dimethyl complex, (PMe3)3Co(CH3)2I. Three different pathways, i.e., radical mechanism (path A), concerted C-C bond formation (path B) and α-hydride elimination (path C) were studied for the reductive elimination reaction. A PMe3 ligand o...
Source: Computational and Theoretical Chemistry - March 27, 2018 Category: Chemistry Source Type: research

Comparing the substituent effects about ESIPT process for HBO derivatives
Publication date: Available online 26 March 2018 Source:Computational and Theoretical Chemistry Author(s): Dapeng Yang, Guang Yang, Min Jia, Xiaoyan Song, Qiaoli Zhang In this present work, we theoretically investigate the four HBO derivatives (i.e., HBO-NH2, HBO-OH, HBO-NO2, HBO-COOH) about their different excited state behaviors involved in excited state intramolecular proton transfer (ESIPT) process. Based on density functional theory (DFT) and time-dependent density functional theory (TDDFT) theoretical level, we analyze the bond lengths, bond angles and relative chemical changes about these four structures. In additi...
Source: Computational and Theoretical Chemistry - March 26, 2018 Category: Chemistry Source Type: research

Multireference Equation of Motion Coupled Cluster Benchmark Study of Magnetic Model Systems
Publication date: Available online 23 March 2018 Source:Computational and Theoretical Chemistry Author(s): Siyuan Wu, Johnathan Steffen, Piaoyu Hu, Marcel Nooijen The multireference equation of motion coupled cluster (MREOM-CC) approach including spin-orbit coupling is applied to magnetic model systems FArO, FArOF and FArFOH, and compared to benchmark multireference Configuration Interaction (MRCI) approaches in the case of FArO. In the MREOM calculations, convenient high-spin states provide reference reduced density matrices, that are used to obtain a sequence of similarity transformations of the Hamiltonian. All low-lyi...
Source: Computational and Theoretical Chemistry - March 24, 2018 Category: Chemistry Source Type: research

Non-covalent Interaction in Benzene and Substituted Benzene: A Theoretical Study
Publication date: Available online 23 March 2018 Source:Computational and Theoretical Chemistry Author(s): Chayanika Kashyap, Sabnam S. Ullah, Lakhya J. Mazumder, Ankur Kanti Guha Non-covalent interaction is believed to play a vital role in stabilizing various complex chemical species. Herein, we have undertaken a theoretical study to understand the nature and extent of non-covalent interaction between the aromatic surfaces of benzene and its substituted derivatives with hydrogen bond donors as well as lone pair containing molecules. Molecular electrostatic potential (MESP) calculation has been used to identify the attrac...
Source: Computational and Theoretical Chemistry - March 24, 2018 Category: Chemistry Source Type: research

Theoretically predicted Divalent Silicon(0) compounds: Structures and Chemical Bonding ofSilylone inMolybdenum Pentacarbonyl Complexes[Mo(CO)5-Si(XCp ∗)2] (X = B – Tl)
Publication date: Available online 23 March 2018 Source:Computational and Theoretical Chemistry Author(s): Huynh Thi Phuong Loan, Hoang Van Duc, Duong Tuan Quang, Pham Van Tat, Dang Tan Hiep, Nguyen Thi Ai Nhung Quantum chemical calculations of structure and bonding of the transition metal complexes Mo(CO)5 with silylone ligands [Mo(CO)5-Si(XCp∗)2] (Mo5-SiX) (X = B – Tl) are reported at the level BP86 with basis sets SVP, TZVPP, TZ2P+. The calculated equilibrium structures of complexes show that ligands Si(XCp∗)2 are bonded in a tilted orientation to the metal fragment Mo(CO)5 in Mo5-SiX. The bond diss...
Source: Computational and Theoretical Chemistry - March 24, 2018 Category: Chemistry Source Type: research

Heat of Formation Prediction by G4MP2-SFM Schemes: An application to Various Nitroazole Derivatives
Publication date: Available online 24 March 2018 Source:Computational and Theoretical Chemistry Author(s): Md Al Mamunur Rashid, Soo Gyeong Cho, Cheol Ho Choi Our G4MP2-SFM parameterization schemes have been applied to the various azole derivatives including imidazole, triazole, tetrazole, imidazolidine, [1,2,4]triazolo[4,3-a][1,3,5]triazine, tetrazine and pyrimidine, in order to establish a set of parameters for the reliable and fast heat of formation ( Δ H f o ) predictions. It is shown that a parameterization on such complex systems is possible, yielding an overall mean absolute deviation (MAD) and root mean squa...
Source: Computational and Theoretical Chemistry - March 24, 2018 Category: Chemistry Source Type: research

The effect of radial and angular profiles of twisted laser beam on Coronene molecule located off the optical axis
Publication date: Available online 22 March 2018 Source:Computational and Theoretical Chemistry Author(s): Mehmet Öncan, Fatih Koç, Dilara Başat Dereli, Koray Köksal We theoretically investigate the electronic orbital currents and magnetic field induced by twisted light in C 24 H 12 named as Coronene molecule. Main reason of induced magnetic field is the transfer of orbital angular momentum of the light into the molecule. We consider that the molecule is much smaller than the size of light spot. The probability of angular momentum transfer and the strength of induced magnetic field depend on the loca...
Source: Computational and Theoretical Chemistry - March 23, 2018 Category: Chemistry Source Type: research

Theoretical investigations on the atmospheric C2H5O2  + ClO reaction
Publication date: Available online 20 March 2018 Source:Computational and Theoretical Chemistry Author(s): Chenggang Lu, Yizhen Tang, Dawei Li, Jing Feng, Jingyu Sun, Yunju Zhang, Mou Lv Mechanisms and channels of the C2H5O2 + ClO reaction in atmosphere were investigated using quantum chemistry methods, i.e., CCSD(T)/6-311++G(2d,2p)//B3LYP/6-311++G(d,p) levels of theory. Our result indicates that the title reaction occurs on both the singlet and triplet potential energy surfaces (PES). Kinetically, C2H5O3Cl and C2H5O + ClOO on the singlet PES were dominant in atmosphere; while other products including CH3CHO2 +...
Source: Computational and Theoretical Chemistry - March 21, 2018 Category: Chemistry Source Type: research

Understanding the kinetics and molecular mechanism of the Curtius rearrangement of 3-oxocyclobutane-1-carbonyl azide
Publication date: Available online 20 March 2018 Source:Computational and Theoretical Chemistry Author(s): Arezu Nouri, Ehsan Zahedi, Morteza Ehsani, Azita Nouri, Ebrahim Balali The approach presented here is an unprecedented insight into the understanding of kinetics and molecular mechanism of thermal Curtius rearrangement of 3-oxocyclobutane-1-carbonyl azide. Curtius rearrangement can proceed via concerted and stepwise mechanisms. The CBS-QB3 and CBS-APNO composite methods indicated that concerted pathway is dominant and 104-105 times faster than stepwise path. The bonding evolution theory analysis at the B3LYP/6-311G(d...
Source: Computational and Theoretical Chemistry - March 21, 2018 Category: Chemistry Source Type: research

Computational Design of Boron Doped Lithium (BLin) Cluster-Based Catalyst for N2 Fixation
Publication date: Available online 20 March 2018 Source:Computational and Theoretical Chemistry Author(s): Mohd Riyaz, Neetu Goel The activation of dinitrogen bond and its conversion to ammonia under ambient condition is one of the most attracted issues in chemistry. Based on first principle investigations, we propose a boron doped lithium (BLin, n=5-7) cluster based catalysts for N2 fixation. Our calculations predict BLi6 to be a suitable catalyst for conversion of N2 to ammonia with a limiting potential of 19.13kcal/mol. Two mechanistic routes i.e. distal and enzymatic pathways have been investigated in detail to unders...
Source: Computational and Theoretical Chemistry - March 21, 2018 Category: Chemistry Source Type: research

Theoretical study of the azo dyes dissociation by advanced oxidation using Fukui indices. DFT calculations.
This study is dedicated for advanced oxidation applications. Graphical abstract (Source: Computational and Theoretical Chemistry)
Source: Computational and Theoretical Chemistry - March 21, 2018 Category: Chemistry Source Type: research

H proton intramolecular transformation in OH-OO-isoprene radicals
In this study, ab initio calculations have been performed to investigate the H proton intramolecular transformation in OH-OO -isoprene radicals. Geometry optimizations and transition states were performed using density functional theory at the UB3LYP/6–31+G∗∗ and M06-2X/6-311++G∗∗ level. It was found that the migration H atoms was all from the hydroxy-H in the predominant energetic route of 1-OH-2-OO -isoprene and 4-OH-3-OO -isoprene radicals with the energy barrier of 17.7 and 17.0 kcal/mol at the UB3LYP/6-31+G∗∗ level, respectively. The migration H atoms were all from the...
Source: Computational and Theoretical Chemistry - March 21, 2018 Category: Chemistry Source Type: research

Novel nitrogen-doped Au-embedded graphene single-atom catalysts for acetylene hydrochlorination: a density functional theory study
Publication date: Available online 19 March 2018 Source:Computational and Theoretical Chemistry Author(s): Wanqi Gong, Fei Zhao, Lihua Kang The mechanisms of an Au-embedded graphene (AuG) single-atom catalyst (SAC) and AuG-SACs doped with nitrogen at different locations for acetylene hydrochlorination were investigated through density functional theory (DFT). The density functional dispersion correction was calculated with the DFT-D3 method. We studied the adsorption characteristics of HCl and C2H2 on these SACs and simulated the corresponding reaction mechanism. We also found that adding the heteroatom N to AuG-SACs can ...
Source: Computational and Theoretical Chemistry - March 20, 2018 Category: Chemistry Source Type: research

Effect of Dopants and Defect in Graphene Nanoribbons on Dehydrogenation of MXH4, where M=Na,Li and X=Al,B
Publication date: Available online 19 March 2018 Source:Computational and Theoretical Chemistry Author(s): Meenakshi, Sandeep Kumar, Kiran Jeet, Hitesh Sharma The present paper reports the effect of Graphene Nanoribbons (GNRs) for improving the dehydrogenation of MXH 4 , where M = Na , Li and X = Al , B through density functional calculations. The rectangular Armchair GNRs and ZigZag GNRs with width up to 7.57 Å & 10 Å and length of 15 Å &10 Å respectively were considered for the investigation. The effect of dopant and defect was introduced by doping with different dopants ( B , N ...
Source: Computational and Theoretical Chemistry - March 20, 2018 Category: Chemistry Source Type: research

Ligand field splitting in homoleptic tetrahedral d10 transition metal complexes. Spectrochemical series
Publication date: Available online 17 March 2018 Source:Computational and Theoretical Chemistry Author(s): Shati G. Patra, Dipankar Datta The ligand field splitting Δt in a number of homoleptic tetrahedral complexes of Cu(I) and Ni(0) are determined from electronic structure calculations by DFT at the BP86/6-31+G(d,p) and BP86/LanL2DZ levels. Some ligands are monodentate (e.g. CO, NH3, Cl- etc.) and some are bidentate (e.g. ethylenediamine, 2,2′-bipyridine etc.). The Δt values obtained with the two basis sets for a given metal ion are comparable except for the phosphines. They correlate linearly with Shi...
Source: Computational and Theoretical Chemistry - March 19, 2018 Category: Chemistry Source Type: research

Detection of nucleobases using 2D germanane nanosheet: a first-principles study
Publication date: Available online 15 March 2018 Source:Computational and Theoretical Chemistry Author(s): U. Srimathi, V. Nagarajan, R. Chandiramouli The electronic properties and geometric stability of germanane nanosheet is explored using first-principle studies. The germanane nanosheet exhibits semiconducting properties and stability of germanane sheet is ensured with formation energy. The adsorption behavior of deoxyribo nucleic acid (DNA)/ribo nucleic acid (RNA) nucleobases on monolayer germanane nanosheet have been investigated using density functional theory with van der Waals dispersion correction. The adsorption...
Source: Computational and Theoretical Chemistry - March 16, 2018 Category: Chemistry Source Type: research

The role of hyperconjugation in the unusual conformation of thymine: a natural bond orbital analysis
Publication date: Available online 13 March 2018 Source:Computational and Theoretical Chemistry Author(s): Emerson Rengifo, Sara Gómez, Julio C. Arce, Frank Weinhold, Albeiro Restrepo The diketo conformation of thymine inferred from a high-level ab initio calculation, where one of the C–H bonds of the methyl group lies in the ring plane eclipsing another C–H bond instead of the polar C=O bond, seems unexpected on the grounds of an analysis in terms of steric hindrance and long–distance inductive interactions. To assess the causes of such conformation, we carried out a natural bond orbital analysis...
Source: Computational and Theoretical Chemistry - March 14, 2018 Category: Chemistry Source Type: research

Computational Study of Effect of Solvents on Vibrational Spectra of Coumarin 500
Publication date: Available online 13 March 2018 Source:Computational and Theoretical Chemistry Author(s): Randhir Singh, Prabhjot Kaur, Ritika Sachdeva, Jaipratap Singh Grewal, Vasant Sathe, G.S.S. Saini Optimized structure of coumarin 500 has been obtained in gas phase and in solvents like methanol, ethanol, dimethyl sulfoxide and CCl4 using density functional theory calculations with B3LYP/6-311+G(d,p) functionals. The calculated frequencies of certain vibrational bands of coumarin 500 are observed to shift in solvents. To understand the origin of these shifts, HOMO-LUMO analysis of ultra-violet visible spectra of coum...
Source: Computational and Theoretical Chemistry - March 14, 2018 Category: Chemistry Source Type: research

Electronic structure of phosphorene nanoflakes. A theoretical insight
Publication date: Available online 10 March 2018 Source:Computational and Theoretical Chemistry Author(s): Esaú Martínez Olmeda, Cesar Gabriel Vera, Serguei Fomine Phosphorene nanoflakes of different shapes and sizes were studied at the hybrid BHandHLYP level of theory. This functional accurately reproduces the experimental bond lengths and valence angles of black phosphorus. All nanoflakes were found to have a singlet ground state and their band gaps (Es) decrease linearly with 1/N, where N is the number of P atoms in the nanoflakes. It seems that the topology of the nanoflake edges does not affect E. The i...
Source: Computational and Theoretical Chemistry - March 11, 2018 Category: Chemistry Source Type: research

A theoretical mechanistic study for CH and CC bond activations of cyclohexane catalyzed by NiAl+ in the gas phase
Publication date: 1 April 2018 Source:Computational and Theoretical Chemistry, Volume 1129 Author(s): Yong-Ning Yuan, Guang-Ying Wang, Xiao-Xia Zhang, Yu-Xiu Nie, Zhi-Yuan Geng The first thorough theoretical mechanism analysis of heteronuclear bimetallic cation NiAl+ with cyclohexane has been investigated on singlet and triplet potential energy surfaces (PESs) by using density functional theory. Our calculated results show that NiAl+ can assist in the decomposition of cyclohexane to form benzene through two types of reaction channel: CH bond activation and H2 formation; CC bond activation and HD formation. The most import...
Source: Computational and Theoretical Chemistry - March 10, 2018 Category: Chemistry Source Type: research

H proton intramolecular transformation in OH-OO •-isoprene radicals
In this study, ab initio calculations have been performed to investigate the H proton intramolecular transformation in OH-OO•-isoprene radicals. Geometry optimizations and transition states were performed using density functional theory at the UB3LYP/6-31+G∗∗ and M06-2X/6-311++G∗∗ level. It was found that the migration H atoms was all from the hydroxy-H in the predominant energetic route of 1-OH-2-OO•-isoprene and 4-OH-3-OO•-isoprene radicals with the energy barrier of 17.7 and 17.0 kcal/mol at the UB3LYP/6-31+G∗∗ level, respectively. The migration H atoms were all f...
Source: Computational and Theoretical Chemistry - March 9, 2018 Category: Chemistry Source Type: research

Cu, Ag and Au clusters as air pollutants hunters
Publication date: Available online 6 March 2018 Source:Computational and Theoretical Chemistry Author(s): Miguel Reina, Ana Martínez The reaction of small metal clusters (Cu, Ag and Au up to ten atoms and Au20) with two air pollutant (NO2 and SO2) molecules is investigated. All systems under study are capable of trapping NO2• and SO2, as the formation reactions are exergonic and thus thermodynamically viable. The products in the addition reactions are molecularly bonded and in most cases planar five member rings (M-O-N-O-M) are formed. Cu clusters present the most exergonic reactions followed by Ag and Au, res...
Source: Computational and Theoretical Chemistry - March 7, 2018 Category: Chemistry Source Type: research

RE-EVALUATION OF THE STANDARD THERMOCHEMICAL PROPERTIES OF THE Al2 CLUSTER ON THE BASIS OF CBS THERMOCHEMISTRY OF ISOGYRIC REACTIONS AND CORRELATION DEPENDENCIES
Publication date: Available online 5 March 2018 Source:Computational and Theoretical Chemistry Author(s): Gregory A. Poskrebyshev In the present study, the value of Δf H o 298.15(3Al2(3Πu))atom = 518.4, 521, 521.4, 521.3 and 517.7 kJ/mol have been calculated using, respectively, CBS-QB3, ROCBS-QB3, W1U, W1RO and CBS-Q approaches. The slightly lower values of Δf H o 298.15(3Al2)isog = 495±15, 513±7, 503±17, 513±9 and 507±8 kJ/mol have been determined, respectively, by the same quantum mechanical approaches, but on the basis of thermochemistry of the isogyric reactions. The ...
Source: Computational and Theoretical Chemistry - March 6, 2018 Category: Chemistry Source Type: research

The physicochemical properties and tyrosinase inhibitory activity of ectoine and its analogues: A theoretical study
Publication date: Available online 6 March 2018 Source:Computational and Theoretical Chemistry Author(s): Roya Behazin, Ali Ebrahimi Protonation, deprotonation, and proton transfer were considered in ectoine (ECT) and some of its derivatives in the gas phase and solution media by the quantum mechanical calculations. The results of present study help to understand the activity of mentioned compounds as osmolytes, which are also important in water activity and osmotic pressure within a cell. Proton diffuses through the water solvent, covers the distance between the acidic and basic groups, and leads to the protonation of ba...
Source: Computational and Theoretical Chemistry - March 6, 2018 Category: Chemistry Source Type: research

Adsorption and dissociation of carbon monoxide on iron and iron-carbon clusters: Fen  + 2CO and FenC + 2CO, n = 4 and 7. A theoretical study
Publication date: 1 April 2018 Source:Computational and Theoretical Chemistry, Volume 1129 Author(s): Patricio Limon, Alan Miralrio, Miguel Castro In this work is studied the adsorption and reduction of carbon monoxide, CO, catalyzed by neutral and charged iron clusters, through the Fen 0, ±1 + 2CO → FenC0, ±1 + CO2 (n = 4, 7) reactions in the gas phase. It was found, by means of all-electron density functional theory calculations, that the activation energy, Ea = 140 kcal/mol, for the Boudouard reaction, CO + CO → C + CO2, is considerably reduced, up to 33.6 and 5...
Source: Computational and Theoretical Chemistry - March 6, 2018 Category: Chemistry Source Type: research

Quasi-classical dynamics investigations of the F + D2O → DF + OD reaction on a full dimensional accurate potential energy surface
Publication date: Available online 5 March 2018 Source:Computational and Theoretical Chemistry Author(s): Aike Liu, Chunni Xie, Jun Li The influence of vibrational excitations in the fully deuterated water (D2O) reactant on the reaction with the fluorine atom (F) is investigated using the full-dimensional quasi-classical trajectory method on an accurate ground electronic state potential energy surface. The results show that the reactant vibrational excitation in each mode of D2O has very complicated effect on the reactivity. At low collision energy, excitations in all three modes are more effective than collision energy i...
Source: Computational and Theoretical Chemistry - March 5, 2018 Category: Chemistry Source Type: research

A theoretical mechanistic study for C-H and C-C bond activations of cyclohexane catalyzed by NiAl+ in the Gas Phase
Publication date: Available online 2 March 2018 Source:Computational and Theoretical Chemistry Author(s): Yong-Ning Yuan, Guang-Ying Wang, Xiao-Xia Zhang, Yu-Xiu Nie, Zhi-Yuan Geng The first thorough theoretical mechanism analysis of heteronuclear bimetallic cation NiAl+ with cyclohexane has been investigated on singlet and triplet potential energy surfaces (PESs) by using density functional theory. Our calculated results show that NiAl+ can assist in the decomposition of cyclohexane to form benzene through two types of reaction channel: C-H bond activation and H2 formation; C-C bond activation and HD formation. The most ...
Source: Computational and Theoretical Chemistry - March 3, 2018 Category: Chemistry Source Type: research

Intermolecular dispersion energies from coupled exact-exchange Kohn-Sham excitation energies and vectors
We present two different schemes to reduce the high computational cost for calculating the excitation energies and vectors of the monomers to be used to compute the dispersion energies via the TDDFT method. This is achieved by a decoupling of the occupied-virtual orbital product basis functions which are associated with single-particle excitations belonging to large and small oscillator strengths. It will be shown that this approach can lead to large speedups of 90% and more compared to a full diagonalisation of the hessian, while the fully coupled dispersion energies can be reproduced with a reasonable accuracy. We also i...
Source: Computational and Theoretical Chemistry - March 2, 2018 Category: Chemistry Source Type: research

DFT Studies on Interaction between Bimetallic [Au2M] Clusters and Cellobiose
Publication date: Available online 28 February 2018 Source:Computational and Theoretical Chemistry Author(s): Manohar Pillegowda, Ganga Periyasamy The interactions of cellobiose with [Au2M] clusters have been studied using density functional theoretical methods. The computed Donor-Acceptor Map (DAM) analyses provide evidence for the electron donating and accepting nature of the cellobiose, [Au2M] clusters respectively. The electronic structural studies indicate that metal clusters bind with conformers of cellobiose through oxygen atom of the glycosidic bond or other hydroxyl groups. The presence of negative binding energy...
Source: Computational and Theoretical Chemistry - February 28, 2018 Category: Chemistry Source Type: research

Quantum chemical study of the impact of protective association on the chemoselective synthesis of carboxybetaine from 2-(dimethylamino)ethanol and acrylic acid
Publication date: Available online 26 February 2018 Source:Computational and Theoretical Chemistry Author(s): Misha Rumyantsev, Oleg A. Kazantsev, Sergey Rumyantsev, Ivan Yu. Kalagaev Targeted carboxybetaine synthesis is an important process that one can apply to prepare polymeric materials with various unique properties or low molecular weight products, such as deep eutectic solvents based on acrylic acid formulated for the specific tasks. Analyzing the mechanism of carboxybetaine formation, it was found that with an excess of amine, the H-bond formed between amine nitrogen and the acidic proton of the acrylic acid was s...
Source: Computational and Theoretical Chemistry - February 26, 2018 Category: Chemistry Source Type: research

Mechanism and kinetic of nitrate radical-initiated atmospheric reactions of guaiacol (2-methoxyphenol)
Publication date: Available online 26 February 2018 Source:Computational and Theoretical Chemistry Author(s): Bo Wei, Jianfei Sun, Qiong Mei, Maoxia He Guaiacol is the main representative of methoxyphenols generated from the pyrolysis of ligin. The gas-phase reaction mechanism of guaiacol with NO3 radical was researched by using density functional theory at M06-2X/6-31+g(d,p)//M06-2X/6-311+g(3df,2p) level in this work, and the reaction rate constants were calculated by using RRKM theory. The relative complete gas phase reaction mechanism of guaiacol with nitrate radicals was obtained. The calculated results showed that, N...
Source: Computational and Theoretical Chemistry - February 26, 2018 Category: Chemistry Source Type: research

A computational study for the B30 bowl-like nanostructure as a possible candidate for drug delivery system for amantadine
Publication date: Available online 26 February 2018 Source:Computational and Theoretical Chemistry Author(s): Zeinab Noroozi, Rezvan Rahimi, Mohammad Solimannejad In this work, adsorption of amantadine drug on the bowl-like B30 nanocluster has been reported at WB97XD/6-31G(d,p) computational level in gas phase and water media. The results show that B30 nanostructure is a possible carrier for delivery of amantadine drug. Five stable configurations are obtained for the interaction of amantadine with the B30 nanocluster. The most favorite adsorption site of B30 is shown as B1 that leads to the adsorption energy of -194.2 and...
Source: Computational and Theoretical Chemistry - February 26, 2018 Category: Chemistry Source Type: research