Proton affinity of amino acids: Their interpretation with density functional theory-based descriptors

The calculation of group electronegativity and hardness for amino acid “functional groups,” considered as a biradical taken out of their protein environment, is performed for both the α-helix and β-sheet geometry of these amino acids. Group electronegativity and hardness are then used to interpret the experimental gas-phase proton affinity sequence of the amino acids. Group hardness was found to play the dominant role, whereas group electronegativity only had a minor influence on the sequence, thereby stressing the importance of the charged form in the acid-base equilibrium. An explanation for the deviations, seen for some of the amino acids, from the correlation between these group properties and the proton affinity was sought. © 1996 John Wiley & Sons, Inc.     

Understanding organic gas-phase anion molecule reactions

Although ionic reactions in the gas phase seem on the surface to be totally different from those in solution (e.g., they typically occur about 10(12) times more rapidly than their solution analogues and go about as fast at 10 K as they do at room temperature), they can, in fact, exhibit subtle steric, electronic, and isotopic effects. In this Perspective, we show how these differences arise, explain why gas-phase ion reactions can be both fast and selective, and discuss when they can and cannot be classified as "hot" reactions. We also give examples of the use of these reactions to devise new synthetic pathways, investigate reaction mechanisms, and generate important thermochemical data such as bond dissociation energies.     

A density functional theory-based chemical potential equalisation approach to molecular polarizability

The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the dipole polarizability within the framework of density functional theory based linear response theory. The resulting polarizability is expressed in terms of the contributions from individual atoms in the molecule. A few illustrative numerical calculations are shown to predict the molecular polarizabilities in good agreement with available results. The usefulness of the approach to the calculation of intermolecular interaction needed for computer simulation is highlighted.     

Modified corrections for London forces in solid-state density functional theory calculations of structure and lattice dynamics of molecular crystals

Dispersion forces are critical for defining the crystal structures and vibrational potentials of molecular crystals. It is, therefore, important to include corrections for these forces in periodic density functional theory (DFT) calculations of lattice vibrational frequencies. In this study, DFT was augmented with a correction term for London-type dispersion forces in the simulations of the structures and terahertz (THz) vibrational spectra of the dispersion-bound solids naphthalene and durene. The parameters of the correction term were modified to best reproduce the experimental crystal structures and THz spectra. It was found that the accurate reproduction of the lattice dimensions by adjusting the magnitude of the applied dispersion forces resulted in the highest-quality fit of the calculated vibrational modes with the observed THz absorptions. The method presented for the modification of the dispersion corrections provides a practical approach to accurately simulating the THz spectra of molecular crystals, accounting for inherent systematic errors imposed by computational and experimental factors.     

Progress on the optoelectronic functional organic crystals

Organic crystals constructed by pi-conjugated molecules have been paid great attention to in the field of organic optoelectronic materials. The superiorities of these organic crystal materials, such as high thermal stability, highly ordered structure, and high carrier mobility over the amorphous thin film ma-terials, make them attractive candidates for optoelectronic devices. Single crystal with definite struc-ture provides a model to investigate the basic interactions between the molecules (supramolecular interaction), and the relationship between molecular stacking modes and optoelectronic performance (luminescence and carrier mobility). Through modulating molecular arrangement in organic crystal, the luminescence efficiency of organic crystal has exceeded 80% and carrier mobility has been up to the level of 10 cm2·V?1·s?1. Amplified stimulated emission phenomena have been observed in many crys-tals. In this paper, we will emphatically introduce the progress in optoelectronic functional organic crystals and some correlative principle.     

A density functional study of chemical reactions

Density functional theory (DFT ) was used to study reactions involving small molecules. Relative energies of isomers and transition structures of diazene, formaldehyde, and methylenimine were determined using various DFT functionals and results were compared with MP 2 and MP 4 calculations. DFT reaction barriers were found to be consistently lower. For some reactions, such as OH + H₂→ H₂O + H, gradient-corrected functionals predict very low or nonexistent barriers. The hybrid Hartree–Fock–DFT adiabatic connection method (ACM ) often provides much better results in such cases. The performance of several density functionals, including ACM , was tested in calculations on over 100 atomization, hydrogenation, bond dissociation, and isodesmic reactions. The ACM functional provides consistently better geometries and reaction energetics than does any other functional studied. In cases where both HF and gradient-corrected DFT methods underestimate bond distances, the ACM geometries may be inferior to those predicted by gradient-corrected DFT methods. © 1995 John Wiley & Sons, Inc.     

Mechanisms of Staudinger reactions within density functional theory

The Staudinger reactions of substituted phosphanes and azides have been investigated by using density functional theory. Four different initial reaction mechanisms have been found. All systems studied go through a cis-transition state rather than a trans-transition state or a one-step transition state. The one-step pathway of the phosphorus atom attacking the substituted nitrogen atom is always unfavorable energetically. Depending on the substituents on the azide and the phosphane, the reaction mechanism with the lowest initial reaction barrier can be classified into three categories: (1). like the parent reaction, PH(3) + N(3)H, the reaction goes through a cis-transition state, approaches a cis-intermediate, overcomes a PN-bond-shifting transition state, reaches a four-membered ring intermediate, dissociates N(2) by overcoming a small barrier, and results in the final products: N(2) and a phosphazene; (2). once reaching the cis-intermediate, the reaction goes through the N(2)-eliminating transition state and produces the final products; (3). the reaction has a concerted initial cis-transition state, in which the phosphorus atom attacks the first and the third nitrogen atoms of the azide simultaneously and reaches an intermediate, and then the reaction goes through similar steps of the first reaction mechanism. In contrast to the previous predictions on the relative stability of the unsubstituted cis-configured phosphazide intermediate and the unsubstituted trans-configured phosphazide intermediate, the total energy of the substituted trans-configured phosphazide intermediate is close to that of the substituted cis-configured phosphazide intermediate. The preference of the initial cis-transition state reaction pathway is thoroughly discussed. The relative stability of the cis- and the trans-intermediates is explored and analyzed with the aid of molecular orbitals. The effects of substituents and solvent effects on the reaction mechanisms of the Staudinger reactions are discussed in detail.     

Applying the concepts of density functional theory to simple systems

Equations are derived for the chemical potential and local hardness of the ground states of helium and the related two electron ions. With these properties it is possible to correct the energies of the simple single‐zeta wave functions to the nearly exact values. The calculations are simple for these simple systems. In principle, it is possible to extend this method to all atoms and molecules. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Self-assembly of gold nanoparticles on functional organic molecular crystals

The utilization of metal nanoparticles (NPs) to fabricate metal electrodes under mild conditions is one of the most studied topic in recent years. In this work, colloidal Au NPs were deposited on two isostructural molecular crystals, namely 1,2,3,4-tetrafluoro-7-thiomethyl-acridine (MeSAcr) and 1,2,3,4-tetrafluoro-7-methoxy-acridine (MeOAcr), exposing S atoms and O atoms, respectively, at their largest crystal faces. The depositions were carried out mainly by drop casting under ambient conditions, increasing the contact time from 1 to 120 min, and the samples were then analyzed by atomic force microscopy (AFM) to evaluate the coverage. Thanks to the affinity between S and Au atoms, Au NPs are observed to adhere on the MeSAcr surface within 1-min contact time, whereas at least 1h is required to find NPs on the MeOAcr surface. NP adsorption is also affected by the substrate surface morphology; indeed, step edges represent preferential adsorption sites even in the absence of Au-S interaction. Experiments under different conditions were performed to maximize the coverage on MeSAcr, reaching values up to 13%. AFM equipped with fluid cell was also employed to simultaneously depositing and imaging NPs, achieving a better understanding of the adsorption mechanism.     

Temperature-dependent approach to chemical reactivity concepts in density functional theory

The chemical reactivity concepts of density functional theory are studied through a unified view in the temperature-dependent approach provided by the grand canonical ensemble. This procedure leads to a more general perspective that enriches our understanding of the behavior of the average energy and its derivatives with respect to the average number of electrons, provides alternative definitions for those quantities that are “ill defined” at zero temperature, and allows one to determine the relationships among reactivity concepts at any temperature. In particular, it has been found that at high temperatures the parabolic model for reactivity indicators may be justified through the electronic entropy term in the Helmholtz free energy, and that at nonzero temperatures there is an electronic heat capacity contribution to the average energy. In summary, the unified view of the temperature-dependent approach is an important complement to the zero-temperature formulation that clarifies fundamental issues therein.     

Revealing the true crystal structure of L-phenylalanine using solid-state density functional theory

Solid-state density functional theory can be used for crystal structure determination from powder X-ray diffraction data of molecular crystals that are too large and complex for conventional refinement methods.     

Biochar-based functional materials as heterogeneous catalysts for organic reactions

The development of cheap, effective and heterogeneous catalysts remains a substantial challenge in organic synthesis. Of the extensive heterogeneous catalysis, biochar materials have attracted increasing attention to be considered as an important class of support materials in organic reactions due to their distinctive characteristics such as high porosity, large specific surface area, high adsorption ability, excellent cation exchange capacity and outstanding stability. This review highlights recent advances over the past 5 years, outlining the synthetic methods of biochar materials and their applications as catalysts or catalyst supports in a range of organic reactions including oxidation, reduction, esterification, coupling, alkylation and multi-component reactions.     

Development of a finite-temperature density functional approach to electrochemical reactions

We present a computational method to calculate the electronic states of a molecule in an electrochemical environment. The method is based on our recently developed finite-temperature density functional theory approach to calculate the electronic structures at a constant chemical potential. A solvent effect is treated at the level of the extended self-consistent reaction field model, which allows considering a nonequilibrium solvation effect. An exchange-correlation functional with a long-range correction is employed in this calculation, because the functional is adjusted so that the derivative discontinuity of energy with respect to a number of electrons could be satisfied. It has been found that the derivative discontinuity condition plays a crucial role in an electrochemical system. The computational results are presented for a reaction of NO(+) + e(-) <==> NO in chemical equilibrium. Owing to the improvement in the solvation effect and the exchange-correlation functional, the calculated activation free energy is in good agreement with experimental results.     

Desorption electrospray ionization mass spectrometry for monitoring the kinetics of Baeyer-Villiger solid-state organic reactions

Desorption electrospray ionization mass spectrometry (DESI-MS) has been used for monitoring solid-state organic reaction in ambient air, specifically the Baeyer-Villiger (BV) type reaction involving the oxidation of ketones (benzophenone or deoxybenzoin) by m-chloroperbenzoic acid (m-CPBA) in solid-state. The DESI mass spectra obtained at regular intervals during the BV reaction processes are featured, with the amount of ester products increasing as those of ketone reactants decrease. Quantitative analyses of relative intensities of the product, made to quantify the reaction degree of typical solid-state organic reaction (SSOR), show a precision with RSDs of around 5% to 12%, though the RSDs for direct analysis of intensities of the reactant or the product in the solid-state are obviously larger. The kinetics of the Baeyer-Villiger type reactions in solid-state are shown to be dramatically different, in reaction rate, kinetic curve, as well as concentration dependence, from those of the same reactions taking place in solution.     

Understanding rubredoxin redox sites by density functional theory studies of analogues

Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ～0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.     

Flexible organic crystals. Understanding the tractable co-existence of elastic and plastic bending

As an emerging class of flexible materials, mechanically bendable molecular crystals are broadly classified as elastic or plastic. Nevertheless, flexible organic crystals with mutually exclusive elastic and plastic traits, with contrasting structural requirements, co-existing under different stress settings are exceptional; hence, it is imperative to establish the concurring factors that beget this rare occurrence. We report a series of halogen-substituted benzil crystals showing elastic bending (within ∼2.45% strain), followed by elastoplastic deformation under ambient conditions. Under higher stress settings, they display exceptional plastic flexibility that one could bend, twist, or even coil around a capillary tube. X-ray diffraction, microscopy, and computational data reveal the microscopic and macroscopic basis for the exciting co-existence of elastic, elastoplastic, and plastic properties in the crystals. The layered molecular arrangement and the weak dispersive interactions sustaining the interlayer region provide considerable tolerance towards breaking and making upon engaging or releasing the external stress; it enables restoring the original state within the elastic strain. Comparative studies with oxalate compounds, wherein the twisted diketo moiety in benzil was replaced with a rigid and coplanar central oxalate moiety, enabled us to understand the effect of the anisotropy factor on the crystal packing induced by the C O⋯C tetral interactions. The enhanced anisotropy depreciated the elastic domain, making the oxalate crystals more prone to plastic deformation. Three-point bending experiments and the determined Young''s moduli further corroborate the co-existence of the elastic and plastic realm and highlight the critical role of the underlying structural elements that determine the elastic to plastic transformation. The work highlights the possible co-existence of orthogonal mechanical characteristics in molecular crystals and further construed the concurrent role of microscopic and macroscopic elements in attaining this exceptional mechanical trait.

Structural and mechanical studies of benzil and oxalate crystals highlight the microscopic and macroscopic basis for the co-existence of orthogonal mechanical traits and the elastic to plastic transformation under different stress settings.