Ibon Alkorta

Bio: Ibon Alkorta is an academic researcher from Spanish National Research Council. The author has contributed to research in topics: Hydrogen bond & Ab initio. The author has an hindex of 68, co-authored 856 publications receiving 23258 citations. Previous affiliations of Ibon Alkorta include National University of Distance Education & Saint Petersburg State University.

Beryllium Bonds, Do They Exist?

Abstract: The complexes between BeX2 (X = H, F, Cl, OH) with different Lewis bases have been investigated through the use of B3LYP, MP2, and CCSD(T) approaches. This theoretical survey showed that these complexes are stabilized through the interaction between the Be atom and the basic center of the base, which are characterized by electron densities at the corresponding bond critical points larger than those found in conventional hydrogen bonds (HBs). Actually, all bonding indices indicate that, although these interactions that we named "beryllium bonds" are in general significantly stronger than HBs, they share many common features. Both interactions have a dominant electrostatic character but also some covalent contributions associated with a non-negligible electron transfer between the interacting subunits. This electron transfer, which in HBs takes place from the HB acceptor lone-pairs toward the σYH* antibonding orbital of the HB donor, in beryllium bonds goes from the lone pairs of the Lewis base toward the empty p orbital of Be and the σBeX* antibonding orbital. Accordingly, a significant distortion of the BeX2 subunit, which in the complex becomes nonlinear, takes place. Concomitantly, a significant red-shifting of the X-Be-X antisymmetric stretching frequencies and a significant lengthening of the X-Be bonds occur. The presence of the beryllium bond results in a significant blue-shifting of the X-Be-X symmetric stretch.

Theoretical Study of Strong Hydrogen Bonds between Neutral Molecules: The Case of Amine Oxides and Phosphine Oxides as Hydrogen Bond Acceptors

Abstract: A theoretical study of the ability of amine oxides and phosphine oxides as hydrogen bond (HB) acceptors has been carried out using ammonium oxide, trimethylamine oxide, and phosphine oxide as model systems. The analysis of the energetic results indicate that only small spatial preferences are observed in the HB interaction. The value of the interaction energies are in several cases within the range of strong HB (>12 kcal/mol), and in complexes between amine oxides and strong acids in the gas phase, a spontaneous proton transfer is obtained. A logarithmic correlation between the electron density at the HB critical points and the HB distance that is able to fit not only calculated data but also experimental ones has been obtained. Finally, a linear relationship has been found between the number of HBs and the 31P NMR shielding in the H3PO···(HF)n series, in good agreement with experimental reports.

Molecular polarization potential maps of the nucleic acid bases

Abstract: Ab initio calculations at the SCF level were carried out to compute the polarization potential map NM of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine For this purpose, the Dunning`s 9s5p basis set contracted to a split-valence, was selected to perform the calculations The molecular polarization potential (MPP) at each point was evaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (MEP) at that point MEPS and MPPS for the different molecules were computed with a density of 5 points/{Angstrom}{sup 2} on the van der Waals surface of each molecule, defined using the van der Waals radii Due to the symmetry of the molecules, only half the points were computed The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, and 699 for guanine The results of these calculations are analyzed in terms of their implications on the molecular interactions between pairs of nucleic acid bases 23 refs, 5 figs, 1 tab

Bond Length–Electron Density Relationships: From Covalent Bonds to Hydrogen Bond Interactions

Abstract: It is possible to treat bond distances of covalent C-H bonds and C⋯H hydrogen bonds simultaneously assuming a logarithmic relationship with the electron density at the bond critical point. Similar relationships have been found for other X-H/X⋯H bonds. The data used for obtaining these equations have been determined theoretically. All the systems have been fully optimized and their electron densities calculated at the B3LYP/6-311 + + G(d,p) level.

Pnicogen Bonded Complexes of PO2X (X = F, Cl) with Nitrogen Bases

Abstract: An ab initio MP2/aug′-cc-pVTZ study has been carried out on complexes formed between PO2X (X = F and Cl) as the Lewis acids and a series of nitrogen bases ZN, including NH3, H2C═NH, NH2F, NP, NCH, NCF, NF3, and N2. Binding energies of these complexes vary from −10 to −150 kJ/mol, and P—N distances from 1.88 to 2.72 A. Complexes ZN:PO2F have stronger P...N bonds and shorter P—N distances than the corresponding complexes ZN:PO2Cl. Charge transfer from the N lone pair through the π-hole to the P—X and P—O σ* orbitals leads to stabilization of these complexes, although charge-transfer energies can be evaluated only for complexes with binding energies less than −71 kJ/mol. Complexation of PO2X with the strongest bases leads to P···N bonds with a significant degree of covalency, and P—N distances that approach the P—N distances in the molecules PO2NC and PO2NH2. In these complexes, the PO2X molecules distort from planarity. Changes in 31P absolute chemical shieldings upon complexation do not correlate with chan...

Quantum mechanical continuum solvation models.

Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

The hydrogen bond in the solid state.

Abstract: The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

Kirk-Othmer Encyclopedia of Chemical Technology数据库介绍及实例

Abstract: 介绍了Kirk—Othmer Encyclopedia of Chemical Technology（化工技术百科全书）（第五版）电子图书网络版数据库，并对该数据库使用方法和检索途径作出了说明，且结合实例简单地介绍了该数据库的检索方法。

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

Abstract: Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.