Molecules

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1026 KiB

Open AccessArticle

Concerted Halogen Bonding and Orthogonal Metal-Halogen Interactions in Dimers of Lithium Formamidinate and Halogenated Formamidines: An ab Initio Study

by Ruben D. Parra

Molecules 2014, 19(1), 1069-1084; https://doi.org/10.3390/molecules19011069 - 17 Jan 2014

Cited by 13 | Viewed by 9573

Abstract

Dimers of lithium formamidinate, CH(NH)₂Li, and halogenated formamidines, HN=CHNHX, (X=Cl, Br, or I) are used as model systems to investigate simultaneous N-X···N and N-Li···N interactions, in tandem with orthogonal Li···X interactions. Geometry optimizations and energy calculations for the dimers are examined [...] Read more.

Dimers of lithium formamidinate, CH(NH)₂Li, and halogenated formamidines, HN=CHNHX, (X=Cl, Br, or I) are used as model systems to investigate simultaneous N-X···N and N-Li···N interactions, in tandem with orthogonal Li···X interactions. Geometry optimizations and energy calculations for the dimers are examined with the MP2 method and the M06-2X hybrid functional and the aug-cc-pVTZ basis set (the aug-cc-pVTZ-PP basis set is used for the iodine atom). Both methods predict the formation of a planar structure of C_2v symmetry, regardless of the identity of the halogen atom. In this structure, the identities of the constituent monomers are essentially lost. Accordingly, the N-X···N interactions emerge as a rather symmetric quasi-linear N···X···N, where the covalent N-X bond in the halogenated formamidine is replaced by a partly covalent N···X interaction. Formation of the C_2v structure is also driven by a fairly linear N···Li···N interaction parallel to the N···X···N interaction, and a Li···X interaction orthogonal to both the N···X···N and N···Li···N interactions. The strength of the interactions increases with the size of the halogen. The robustness of the interactions suggests that the dimers studied here or suitable analogues may find diverse applications including their use as novel polymeric synthons. Full article

(This article belongs to the Special Issue Computational Chemistry)

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1309 KiB

Open AccessArticle

Electronic Structure and Mesoscopic Simulations of Nonylphenol Ethoxylate Surfactants. A Combined DFT and DPD Study

by Diego Valencia, Jorge Aburto and Isidoro García-Cruz

Molecules 2013, 18(8), 9441-9450; https://doi.org/10.3390/molecules18089441 - 7 Aug 2013

Cited by 10 | Viewed by 6719

Abstract

The aim of this work was to gain insight into the effect of ethylene oxide (EO) chains on the properties of a series of nonylphenol ethoxylate (NPE) surfactants. We performed a theoretical study of NPE surfactants by means of density functional theory (DFT) [...] Read more.

The aim of this work was to gain insight into the effect of ethylene oxide (EO) chains on the properties of a series of nonylphenol ethoxylate (NPE) surfactants. We performed a theoretical study of NPE surfactants by means of density functional theory (DFT) and dissipative particle dynamics (DPD). Both approximations were used separately to obtain different properties. Four NPEs were selected for this purpose (EO = 4, 7, 11 and 15 length chains). DFT methods provided some electronic properties that are related to the EO units. One of them is the solvation Gibbs energy, which exhibited a linear trend with EO chain length. DPD calculations allow us to observe the dynamic behavior in water of the NPE surfactants. We propose a coarse-grained model which properly simulates the mesophases of each surfactant. This model can be used in other NPEs applications. Full article

(This article belongs to the Special Issue Computational Chemistry)

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1641 KiB

Open AccessArticle

Determining Chemical Reactivity Driving Biological Activity from SMILES Transformations: The Bonding Mechanism of Anti-HIV Pyrimidines

by Mihai V. Putz and Nicoleta A. Dudaş

Molecules 2013, 18(8), 9061-9116; https://doi.org/10.3390/molecules18089061 - 30 Jul 2013

Cited by 31 | Viewed by 6668

Abstract

Assessing the molecular mechanism of a chemical-biological interaction and bonding stands as the ultimate goal of any modern quantitative structure-activity relationship (QSAR) study. To this end the present work employs the main chemical reactivity structural descriptors (electronegativity, chemical hardness, chemical power, electrophilicity) to [...] Read more.

Assessing the molecular mechanism of a chemical-biological interaction and bonding stands as the ultimate goal of any modern quantitative structure-activity relationship (QSAR) study. To this end the present work employs the main chemical reactivity structural descriptors (electronegativity, chemical hardness, chemical power, electrophilicity) to unfold the variational QSAR though their min-max correspondence principles as applied to the Simplified Molecular Input Line Entry System (SMILES) transformation of selected uracil derivatives with anti-HIV potential with the aim of establishing the main stages whereby the given compounds may inhibit HIV infection. The bonding can be completely described by explicitly considering by means of basic indices and chemical reactivity principles two forms of SMILES structures of the pyrimidines, the Longest SMILES Molecular Chain (LoSMoC) and the Branching SMILES (BraS), respectively, as the effective forms involved in the anti-HIV activity mechanism and according to the present work, also necessary intermediates in molecular pathways targeting/docking biological sites of interest. Full article

(This article belongs to the Special Issue Computational Chemistry)

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908 KiB

Open AccessArticle

Ab Initio Calculations of Possible γ-Gauche Effects in the ¹³C-NMR for Methine and Carbonyl Carbons in Precise Polyethylene Acrylic Acid Copolymers

by Todd M. Alam

Molecules 2013, 18(8), 9010-9020; https://doi.org/10.3390/molecules18089010 - 29 Jul 2013

Cited by 1 | Viewed by 6682

Abstract

The impacts of local polymer chain conformations on the methine and carbonyl ¹³C-NMR chemical shifts for polyethylene acrylic acid p(E-AA) copolymers were predicted using ab initio methods. Using small molecular cluster models, the magnitude and sign of the γ-gauche torsional angle [...] Read more.

The impacts of local polymer chain conformations on the methine and carbonyl ¹³C-NMR chemical shifts for polyethylene acrylic acid p(E-AA) copolymers were predicted using ab initio methods. Using small molecular cluster models, the magnitude and sign of the γ-gauche torsional angle effect, along with the impact of local tetrahedral structure distortions near the carbonyl group, on the ¹³C-NMR chemical shifts were determined. These ¹³C-NMR chemical shift variations were compared to the experimental trends observed for precise p(E-AA) copolymers as a function acid group spacing and degree of zinc-neutralization in the corresponding p(E-AA) ionomers. These ab initio calculations address the future ability of ¹³C-NMR chemical shift variations to provide information about the local chain conformations in p(E-AA) copolymer materials. Full article

(This article belongs to the Special Issue Computational Chemistry)

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9040 KiB

Open AccessArticle

Decomposition Mechanisms and Kinetics of Novel Energetic Molecules BNFF-1 and ANFF-1: Quantum-Chemical Modeling

by Roman V. Tsyshevsky and Maija M. Kuklja

Molecules 2013, 18(7), 8500-8517; https://doi.org/10.3390/molecules18078500 - 18 Jul 2013

Cited by 39 | Viewed by 6713

Abstract

Decomposition mechanisms, activation barriers, Arrhenius parameters, and reaction kinetics of the novel explosive compounds, 3,4-bis(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (BNFF-1), and 3-(4-amino-1,2,5-oxadiazol-3-yl)-4-(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (ANFF-1) were explored by means of density functional theory with a range of functionals combined with variational transition state theory. BNFF-1 and ANFF-1 were recently [...] Read more.

Decomposition mechanisms, activation barriers, Arrhenius parameters, and reaction kinetics of the novel explosive compounds, 3,4-bis(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (BNFF-1), and 3-(4-amino-1,2,5-oxadiazol-3-yl)-4-(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (ANFF-1) were explored by means of density functional theory with a range of functionals combined with variational transition state theory. BNFF-1 and ANFF-1 were recently suggested to be good candidates for insensitive high energy density materials. Our modeling reveals that the decomposition initiation in both BNFF-1 and ANFF-1 molecules is triggered by ring cleavage reactions while the further process is defined by a competition between two major pathways, the fast C-NO₂ homolysis and slow nitro-nitrite isomerization releasing NO. We discuss insights on design of new energetic materials with targeted properties gained from our modeling. Full article

(This article belongs to the Special Issue Computational Chemistry)

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253 KiB

Open AccessArticle

In-Solution Conformational Analysis of the XCYCH₃ Moiety for Small Esters and Ethers with all Combinations of X, Y = O, S

by Peter I. Nagy

Molecules 2013, 18(7), 8063-8082; https://doi.org/10.3390/molecules18078063 - 8 Jul 2013

Cited by 6 | Viewed by 5882

Abstract

Favorable steric and electrostatic fit of a ligand to a receptor is of central interest in theoretical drug design. This paper considers the effects of non-protic solvents, in comparison with the gas phase, on the preferred conformation of the XCYCH₃ moiety of [...] Read more.

Favorable steric and electrostatic fit of a ligand to a receptor is of central interest in theoretical drug design. This paper considers the effects of non-protic solvents, in comparison with the gas phase, on the preferred conformation of the XCYCH₃ moiety of simple aliphatic esters and heterocyclic methyl ethers with all combinations of the X and Y atoms as oxygen and sulfur. An IEF-PCM/B97D/aug-cc-pv(t+d)z continuum dielectric solvent study in chloroform and acetonitrile explores the through-space polarization effect of the environment on the conformational preference, not affected by possible solute-solvent hydrogen bond formation. The inherently favored structure for the present molecules is important, since the hypothetical oxygen and sulfur lone-pairs point approximately in opposite directions in the cis conformation of esters, whereas the trans and gauche conformations for the methyl group in ethers define nearly parallel or perpendicular directionality for the lone pairs of the ring heteroatoms and the O or S atoms connecting to the ring. These different preferences for the studied two families of compounds allow for designing formation of hydrogen bonds with a protein in fairly different regions of the latter still within the ligand-binding cavity. For a fine-tuning of these hydrogen bonds, a replacement of an oxygen atom of the ligand by a sulfur atom could be a straightforward possibility. Full article

(This article belongs to the Special Issue Computational Chemistry)

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1768 KiB

Open AccessArticle

Comprehensive Theoretical Studies on the Reaction of 1-Bromo-3,3,3-trifluoropropene with OH Free Radicals

by Meiling Zhang, Ce Song and Yan Tian

Molecules 2013, 18(7), 7873-7885; https://doi.org/10.3390/molecules18077873 - 4 Jul 2013

Cited by 3 | Viewed by 5098

Abstract

The potential energy surfaces (PES) for the reaction of 1-bromo-3,3,3-trifluoropropene (CF₃CHCBrH) with hydroxyl (OH) free radicals is probed theoretically at the CCSD/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of theory. All the possible stationary and first-order saddle points along the reaction paths were verified by the [...] Read more.

The potential energy surfaces (PES) for the reaction of 1-bromo-3,3,3-trifluoropropene (CF₃CHCBrH) with hydroxyl (OH) free radicals is probed theoretically at the CCSD/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of theory. All the possible stationary and first-order saddle points along the reaction paths were verified by the vibrational analysis. The calculations account for all the product channels. Based on the calculated CCSD/aug-cc-pVDZ potential energy surface, the possible reaction mechanism is discussed. Six distinct reaction pathways of 1-bromo-3,3,3-trifluoropropene (BTP) with OH are investigated. The geometries, reaction enthalpies and energy barriers are determined. Canonical transition-state theory with Wigner tunneling correction was used to predict the rate constants for the temperature range of 290–3,000 K without any artificial adjustment, and the computed rate constants for elementary channels can be accurately fitted with three-parameter Arrhenius expressions. OH addition reaction channel and the H atom abstraction channels related to the carbon-carbon double bond are found to be the main reaction channels for the reaction of 1-bromo-3,3,3-trifluoropropene (CF₃CHCBrH) with hydroxyl (OH) free radicals while the products leading to CF₃CHCH + BrOH and COHF₂CHCBrH + F play a negligible role. Full article

(This article belongs to the Special Issue Computational Chemistry)

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316 KiB

Open AccessArticle

Water Complexes of Cytochrome P450: Insights from Energy Decomposition Analysis

by Nandun Thellamurege and Hajime Hirao

Molecules 2013, 18(6), 6782-6791; https://doi.org/10.3390/molecules18066782 - 10 Jun 2013

Cited by 43 | Viewed by 6820

Abstract

Water is a small molecule that nevertheless perturbs, sometimes significantly, the electronic properties of an enzyme’s active site. In this study, interactions of a water molecule with the ferric heme and the compound I (Cpd I) intermediate of cytochrome P450 are studied. Energy [...] Read more.

Water is a small molecule that nevertheless perturbs, sometimes significantly, the electronic properties of an enzyme’s active site. In this study, interactions of a water molecule with the ferric heme and the compound I (Cpd I) intermediate of cytochrome P450 are studied. Energy decomposition analysis (EDA) schemes are used to investigate the physical origins of these interactions. Localized molecular orbital EDA (LMOEDA) implemented in the quantum chemistry software GAMESS and the EDA method implemented in the ADF quantum chemistry program are used. EDA reveals that the electrostatic and polarization effects act as the major driving force in both of these interactions. The hydrogen bonding in the Cpd I•••H₂O complex is similar to that in the water dimer; however, the relative importance of the electrostatic effect is somewhat larger in the water dimer. Full article

(This article belongs to the Special Issue Computational Chemistry)

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1810 KiB

Open AccessArticle

The Mathematics of a Successful Deconvolution: A Quantitative Assessment of Mixture-Based Combinatorial Libraries Screened Against Two Formylpeptide Receptors

by Radleigh G. Santos, Jon R. Appel, Marc A. Giulianotti, Bruce S. Edwards, Larry A. Sklar, Richard A. Houghten and Clemencia Pinilla

Molecules 2013, 18(6), 6408-6424; https://doi.org/10.3390/molecules18066408 - 30 May 2013

Cited by 14 | Viewed by 5625

Abstract

In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds [...] Read more.

In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds and active ligands. Here we present a quantitative assessment of the screening of 32 positional scanning libraries in the identification of highly specific and selective ligands for two formylpeptide receptors. We also compare and contrast two mixture-based library approaches using a mathematical model to facilitate the selection of active scaffolds and libraries to be pursued for further evaluation. The flexibility demonstrated in the differently formatted mixture-based libraries allows for their screening in a wide range of assays. Full article

(This article belongs to the Special Issue Computational Chemistry)

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974 KiB

Open AccessArticle

Computational Modeling of the Size Effects on the Optical Vibrational Modes of H-Terminated Ge Nanostructures

by Alejandro Trejo and Miguel Cruz-Irisson

Molecules 2013, 18(4), 4776-4785; https://doi.org/10.3390/molecules18044776 - 22 Apr 2013

Cited by 8 | Viewed by 6136

Abstract

The vibrational dispersion relations of porous germanium (pGe) and germanium nanowires (GeNWs) were calculated using the ab initio density functional perturbation theory with a generalized gradient approximation with norm-conserving pseudopotentials. Both pores and nanowires were modeled using the supercell technique. All of the [...] Read more.

The vibrational dispersion relations of porous germanium (pGe) and germanium nanowires (GeNWs) were calculated using the ab initio density functional perturbation theory with a generalized gradient approximation with norm-conserving pseudopotentials. Both pores and nanowires were modeled using the supercell technique. All of the surface dangling bonds were saturated with hydrogen atoms. To address the difference in the confinement between the pores and the nanowires, we calculated the vibrational density of states of the two materials. The results indicate that there is a slight shift in the highest optical mode of the Ge-Ge vibration interval in all of the nanostructures due to the phonon confinement effects. The GeNWs exhibit a reduced phonon confinement compared with the porous Ge due to the mixed Ge-dihydride vibrational modes around the maximum bulk Ge optical mode of approximately 300 cm⁻¹; however, the general effects of such confinements could still be noticed, such as the shift to lower frequencies of the highest optical mode belonging to the Ge vibrations. Full article

(This article belongs to the Special Issue Computational Chemistry)

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1365 KiB

Open AccessArticle

First-Principles Elucidation of the Surface Chemistry of the C₂H_x (x = 0–6) Adsorbate Series on Fe(100)

by Ashriti Govender, Daniel Curulla-Ferré, Manuel Pérez-Jigato and Hans Niemantsverdriet

Molecules 2013, 18(4), 3806-3824; https://doi.org/10.3390/molecules18043806 - 26 Mar 2013

Cited by 23 | Viewed by 6138

Abstract

Ab initio total-energy calculations of the elementary reaction steps leading to acetylene, ethylene and ethane formation and their decomposition on Fe(100) are described. Alongside the endothermicity of all the formation reactions, the crucial role played by adsorbed ethyl as main precursor towards both [...] Read more.

Ab initio total-energy calculations of the elementary reaction steps leading to acetylene, ethylene and ethane formation and their decomposition on Fe(100) are described. Alongside the endothermicity of all the formation reactions, the crucial role played by adsorbed ethyl as main precursor towards both ethylene and ethane formation, characterises Fe(100) surface reactivity towards C₂H_x (x = 0–6) hydrocarbon formation in the low coverage limit. A comprehensive scheme based on three viable mechanisms towards ethyl formation on Fe(100), including methyl/methylene coupling, methyl/methylidyne coupling followed by one hydrogenation and methyl/carbon coupling followed by two hydrogenations, is the main result of this article. Full article

(This article belongs to the Special Issue Computational Chemistry)

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911 KiB

Open AccessArticle

The Interactions of Oxygen with Small Gold Clusters on Nitrogen-Doped Graphene

by Xin Chen, Shaorui Sun, Fan Li, Xiayan Wang and Dingguo Xia

Molecules 2013, 18(3), 3279-3291; https://doi.org/10.3390/molecules18033279 - 13 Mar 2013

Cited by 17 | Viewed by 8180

Abstract

By means of density functional theory, the adsorption properties of O₂ molecule on both isolated and N-graphene supported gold clusters have been studied. The N-graphene is modeled by a C₆₅NH₂₂ cluster of finite size. The results indicate that the [...] Read more.

By means of density functional theory, the adsorption properties of O₂ molecule on both isolated and N-graphene supported gold clusters have been studied. The N-graphene is modeled by a C₆₅NH₂₂ cluster of finite size. The results indicate that the catalytic activity and the O₂ adsorption energies of odd-numbered Au clusters are larger than those of adjacent even-numbered ones. The O₂ molecule is in favor of bonding to the bridge sites of odd-numbered Au clusters, whereas for odd-numbered ones, the end-on adsorption mode is favored. The perpendicular adsorption orientation on N-graphene is preferred than the parallel one for Au₂, Au₃ and Au₄ clusters, while for Au₅, Au₆ and Au₇, the parallel ones are favored. When O₂ is adsorbed on N-graphene supported Au clusters, the adsorption energies are largely increased compared with those on gas-phase ones. The increased adsorption energies would significantly facilitate the electron transfer from Au d-orbital to π* orbital of O₂, which would further weakening the O–O bond and therefore enhancing the catalytic activity. The carbon atoms on N-graphene could anchor the clusters, which could make them more difficult to structural distortion, therefore enhance their stability. Full article

(This article belongs to the Special Issue Computational Chemistry)

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