Infrared spectroscopy of proteins.

Medium basis sets based upon contractions of Gaussian primitives are developed for the third-row elements Ga through Kr. The basis functions generalize the 6-31G and 6-31G* sets commonly used for atoms up to Ar. A reexamination of the 6-31G* basis set for K and Ca developed earlier leads to the inclusion of 3d orbitals into the valence space for these atoms. Now the 6-31G basis for the whole third-row K through Kr has six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split-valence pair of three and one primitives for valence orbitals, which are 4s, 4p, and 3d. The nature of the polarization functions for third-row atoms is reexamined as well. The polarization functions for K, Ca, and Ga through Kr are single set of Cartesian d-type primitives. The polarization functions for transition metals are defined to be a single 7f set of uncontracted primitives. Comparison with experimental data shows good agreement with bond lengths and angles for representative vapor-phase metal complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 976–984, 2001

6-31G* basis set for third-row atoms

Crystal polymorphism is encountered in all areas of research involving solid substances. Its occurrence introduces complications during manufacturing processes and adds another dimension to the complexity of designing materials with specific properties. Research on polymorphism is fraught with unique difficulties due to the subtlety of polymorphic transformations and the inadvertent formation of pseudopolymorphs. In this report, a summary of thermodynamic, kinetic and structural considerations of polymorphism is presented. A wide variety of techniques appropriate to the study of organic crystalline polymorphism and pseu-dopolymorphism is then surveyed, ranging from simple crystal density measurement to observation of polymorphic transformations using variable-temperature synchrotron X-ray diffraction methods. Application of newer methodology described in this report is yielding fresh insights into the nature of the crystallization process, holding promise for a deeper understanding of the phenomenon of polymorphism and its practical control.

Crystalline Polymorphism of Organic Compounds

Ab initio calculations are used to analyze the CH···O interaction between FnH3-nCH as proton donor and H2O, CH3OH, and H2CO as acceptor. The interaction is quite weak with CH4 as donor but is enhanced by 1 kcal/mol with each F added to the donor. The CH···O interaction behaves very much like a conventional OH···O H-bond in most respects, including shifts in electron density that accompany the formation of the bond and the magnitudes of the various components of the interaction energy. The two sorts of H-bonds also gravitate toward a similar equilibrium geometry and are comparably sensitive to deformations from that structure. In a quantitative sense, while both CH···O and OH···O prefer a linear configuration, the former is somewhat more easily bent and is less sensitive to stretches from its equilibrium H-bond length. Whereas the OH bond has been shown to stretch and undergo a red shift in its vibrational frequency upon formation of a H-bond, the CH bond of the molecules studied here follows the opposite ...

Fundamental Properties of the CH···O Interaction: Is It a True Hydrogen Bond?

Kraitchman has shown that a single isotopic substitution on an atom is sufficient to determine directly the coordinates of that atom with respect to the principal axes of the original molecule. Kraitchman's formulas represent exact solutions of the equations for the equilibrium moments of inertia. However, the effects of the zero‐point vibrations are such that the coordinates obtained by substitution from the ground state moments of inertia I0 are systematically less than r0. These coordinates have here been called r (substitution) or rs, and it is found that rs≃(r0+re)/2, and Is= ∑ imirsi2≃(I0+Ie)/2.In the usual method of solution, the coordinate of one atom is determined from the equation for I0, and therefore the difference I0—Is must be made up by this one coordinate. This introduces a large error in the structures normally determined from ground state constants, and results in variations of 0.01 A in structures determined from different sets of isotopic species. If instead, we obtain the structure on...

A new criterion for the determination of molecular structures from ground state rotational constants

Infrared spectra of the water clusters have been measured in the N2
				+ O2 matrix. The aggregation process of water in the matrix has been monitored by annealing the deposited samples up to 40 K and UV irradiation. The monomer, dimer, cyclic trimer and cyclic pentamer are found as water clusters in the matrix. For the hexamer, several structures such as chair, cage, prism, bag 1 and/or book 1 are likely to exist. By UV irradiation, the cyclic pentamer is predominantly formed from the monomer and dimer. On the other hand, by annealing the deposited sample, several hexamers are formed. The theoretical calculation for water clusters has revealed that the formation of one hydrogen bonding in a hydrogen-bonded chain cooperatively enhances or diminishes the strength of another hydrogen bond. Both proton donor (D) and acceptor (A) participating in a hydrogen-bonding pair DA are capable of forming hydrogen bonding with the other water molecules; D can additionally accept two protons and donate one proton, and A can additionally donate two protons and accept one proton. We have proposed the classification of hydrogen-bonding patterns considering the cooperativity, denoting as d′a′DAd″a″, where d and a are integers indicating the number of proton donors and acceptors to D (the single prime) and A (the double prime), respectively. Then, a magnitude given by MOH
				=
				−d′
				+
				a′
				+
				d″
				−
				a″ has been introduced, which is very useful for connecting the hydrogen-bonding patterns to their OH wavenumbers. As a result, it is revealed that the OH stretching bands of water clusters are characterized by eight indicators (free and MOH
				=
				−2, −1, 0, 1, 2, 3 and 4). The classification proposed here is applicable to the OH band analysis for the hydrogen-bonded water and alcohols in a condensed phase.

The effect of cooperative hydrogen bonding on the OH stretching-band shift for water clusters studied by matrix-isolation infrared spectroscopy and density functional theory.

Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding is presented. Argon matrix-isolation infrared spectra of 1-methoxy-2-(dimethylamino)ethane exhibit a band at 3016.5 cm-1. Spectral behavior with annealing indicates that this band is assigned to the most stable conformer, trans-gauche-(trans|gauche'), with an intramolecular C-H...O hydrogen bond. Density functional calculations show that this band arises from the stretching vibration of the C-H bond participating in the formation of the C-H...O hydrogen bond. The C-H bond is shortened by 0.004 A, and the C-H stretching band is blue-shifted by at least 35 cm-1 on the formation of the hydrogen bond. The (C)H...O distance is calculated as 2.38 A, which is shorter than the corresponding van der Waals separation by 0.3 A.

Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding by matrix-isolation infrared spectroscopy.

Conformational Study of 1-Butanol by the Combined Use of Vibrational Spectroscopy and ab Initio Molecular Orbital Calculations

The microwave spectra of deuterated silanes, germanes, and stannanes

The blue shift of the isolated CD stretching band of 2-butoxyethanol (C4E1), which is observed for the aqueous solution during the dilution process, has been investigated by infrared (IR) spectroscopy and quantum chemical calculations. Mono-deuterium-labeled C4E1's were employed to remove the severe overlapping among the CH stretching bands. The isolated CD stretching mode of the alpha-methylene in the butoxy group shows a large blue shift, while those of the beta-methylene and methyl groups are not largely shifted. The spectral simulation results for the C4E1/H2O complexes indicate that the large blue shift of the CD stretching band of the butoxy group arises mainly from the hydration of the ether oxygen atom.

Keiichi Ohno

Papers

The effect of cooperative hydrogen bonding on the OH stretching-band shift for water clusters studied by matrix-isolation infrared spectroscopy and density functional theory.

Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding by matrix-isolation infrared spectroscopy.

Conformational Study of 1-Butanol by the Combined Use of Vibrational Spectroscopy and ab Initio Molecular Orbital Calculations

The microwave spectra of deuterated silanes, germanes, and stannanes

Origin of the blue shift of the CH stretching band for 2-butoxyethanol in water.