Showing papers in "International Journal of Molecular Sciences in 2004"

Vertical Ionization Energies of α-L-Amino Acids as a Function of Their Conformation: an Ab Initio Study

Abstract: Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the 6-31G**(5d) basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF) method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO) can change a lot as a function of the nuclear structure.

Nucleic Acid Quadratic Indices of the "Macromolecular Graph's Nucleotides Adjacency Matrix". Modeling of Footprints after the Interaction of Paromomycin with the HIV-1 Ψ-RNA Packaging Region

Abstract: This report describes a new set of macromolecular descriptors of relevance to nucleic acid QSAR/QSPR studies, nucleic acids’ quadratic indices. These descriptors are calculated from the macromolecular graph’s nucleotide adjacency matrix. A study of the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV illustrates this approach. A linear discriminant function gave rise to excellent discrimination between 90.10% (91/101) and 81.82% (9/11) of interacting/noninteracting sites of nucleotides in training and test set, respectively. The LOO crossvalidation procedure was used to assess the stability and predictability of the model. Using this approach, the classification model has shown a LOO global good classification of 91.09%. In addition, the model’s overall predictability oscillates from 89.11% until 87.13%, when n varies from 2 to 3 in leave-n-out jackknife method. This value stabilizes around 88.12% when n was > 3. On the other hand, a linear regression model predicted the local binding affinity constants [log K (10-4M-1)] between a specific nucleotide and the aforementioned antibiotic. The linear model explains almost 92% of the variance of the experimental log K (R = 0.96 and s = 0.07) and LOO press statistics evidenced its predictive ability (q2 = 0.85 and scv = 0.09). These models also permit the interpretation of the driving forces of the interaction process. In this sense, developed equations involve short-reaching (k < 3), middle-reaching (4 < k < 9) and far-reaching (k = 10 or greater) nucleotide’s quadratic indices. This situation points to electronic and topologic nucleotide’s backbone interactions control of the stability profile of Paromomycin-RNA complexes. Consequently, the present approach represents a novel and rather promising way to chem & bioinformatics research.

QSAR Study of Skin Sensitization Using Local Lymph Node Assay Data

Abstract: Allergic Contact Dermatitis (ACD) is a common work-related skin disease that often develops as a result of repetitive skin exposures to a sensitizing chemical agent. A variety of experimental tests have been suggested to assess the skin sensitization potential. We applied a method of Quantitative Structure-Activity Relationship (QSAR) to relate measured and calculated physical-chemical properties of chemical compounds to their sensitization potential. Using statistical methods, each of these properties, called molecular descriptors, was tested for its propensity to predict the sensitization potential. A few of the most informative descriptors were subsequently selected to build a model of skin sensitization. In this work sensitization data for the murine Local Lymph Node Assay (LLNA) were used. In principle, LLNA provides a standardized continuous scale suitable for quantitative assessment of skin sensitization. However, at present many LLNA results are still reported on a dichotomous scale, which is consistent with the scale of guinea pig tests, which were widely used in past years. Therefore, in this study only a dichotomous version of the LLNA data was used. To the statistical end, we relied on the logistic regression approach. This approach provides a statistical tool for investigating and predicting skin sensitization that is expressed only in categorical terms of activity and non-activity. Based on the data of compounds used in this study, our results suggest a QSAR model of ACD that is based on the following descriptors: nDB (number of double bonds), C-003 (number of

Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3) and Ammonia (NH3) Donor-Acceptor Complex

Abstract: The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule’s barrier to internal rotation is very small. A rationale for the low height of the barrier has been put forward in terms of the energy partitioning analysis. On the question of origin of the barrier to internal rotation, we conclude that the conformational barrier to internal rotation does not originate from a particular region of the molecule, but rather it is a result of the subtle conjoint interplay of a number of opposing effects of one- and two-center bonded and nonbonded energy terms involving the entire skeleton of the molecule.

Density Functional Studies of the Dipole Polarizabilities of Substituted Stilbene, Azoarene and Related Push-Pull Molecules

Abstract: We report high quality B3LYP Ab Initio studies of the electric dipole polarizability of three related series of molecules: para- XC 6 H 4 Y, XC 6 H 4 CH=CHC 6 H 4 Y and XC 6 H 4 N=NC 6 H 4 Y, where X and Y represent H together with the six various activating through deactivating groups NH 2 , OH, OCH 3, CHO, CN and NO 2 . Molecules for which X is activating and Y deactivating all show an enhancement to the mean polarizability compared to the unsubstituted molecule, in accord with the order given above. A number of representative Ab Initio calculations at different levels of theory are discussed for azoarene; all subsequent Ab Initio polarizability calculations were done at the B3LYP/6-311G(2d,1p)//B3LYP/6-311++G(2d,1p) level of theory. We also consider semi-empirical polarizability and molecular volume calculations at the AM1 level of theory together with QSAR-quality empirical polarizability calculations using Miller’s scheme. Least-squares correlations between the various sets of results show that these less costly procedures are reliable predictors of for the first series of molecules, but less reliable for the larger molecules.

Exploring QSAR of Non-Nucleoside Reverse Transcriptase Inhibitors by Neural Networks: TIBO Derivatives

Abstract: Human Immunodeficiency Virus type 1 (HIV-1) reverse transcriptase is an important target for chemotherapeutic agents against the AIDS disease. 4,5,6,7-Tetrahydro-5-methylimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-ones (TIBO) derivatives are potent non-nucleoside reverse transcriptase inhibitors (NNRTIs). In the present work, quantitative structure-activity relationship (QSAR) analysis for a set of 82 TIBO derivatives has been investigated by means of a three-layered neural network (NN). It has been shown that NN can be a potential tool in the investigation of QSAR analysis compared with the models given in the literature. NN gave good statistical results both in fitting and prediction processes (0.861 ≤ r² ≤ 0.928, 0.839 ≤q² ≤ 0.845). The relevant factors controlling the anti-HIV-1 activity of TIBO derivatives have been identified. The results are along the same lines as those of our previous studies on HEPT derivatives and indicate the importance of the hydrophobic parameter in modeling the QSAR for TIBO derivatives.

Intramolecular C−H···π Interactions in Metal-Porphyrin Complexes

Abstract: Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances indicates that interactions of hydrogen atoms in positions 2 and 6 of axially coordinated pyridine are more favorable with ruffled than with planar porphyrin.

Molecular similarity of MDR inhibitors

Abstract: The molecular similarity of multidrug resistance (MDR) inhibitors was evaluated using the point centred atom charge approach in an attempt to find some common features of structurally unrelated inhibitors. A series of inhibitors of bacterial MDR were studied and there is a high similarity between these in terms of their shape, presence and orientation of aromatic ring moieties. A comparison of the lipophilic properties of these molecules has also been conducted suggesting that this factor is important in MDR inhibition.

The Interpretation of the Short Range Disorder in the Fluorene-TCNE Crystal Structure

Abstract: The interpretation of the short-range static and/or dynamic disorder in a crystal structure from X-ray data is often a rather complex problem. Recently, we synthesized and characterized three co-crystalline complexes between fluorene, showing C2v symmetry, and three electron withdrawing D2h compounds, employing FTIR and Raman spectroscopy and single crystal X-ray diffraction techniques. The crystal structures of the complexes of fluorene with the three different electron withdrawing molecules are disordered in the solid state and only approximate structures were obtained by refinement of the single crystal data. Indeed, the fluorene moiety presents a very irregular geometry, showing for example C-C bonds ranging from 1.25A to 1.75A. Graphical inspection of the solved crystal structures indicates that the fluorene molecules in these co-crystalline complexes can assume two possible positions, both with 50% population. A two-step procedure to improve the disordered models is described. At first, the two possible ordered structures, with the fluorene molecule in only one of the two populated positions, are "separated" by molecular graphic techniques and then their geometry is fully optimized employing the periodic ab initio “CRYSTAL” code to obtain a chemically sensible model with reasonable distances and angles. The main aim of this communication is to demonstrate that ordered models can be obtained, starting from a disordered crystal structure, focusing our attention on the fluorene-TCNE molecular complex.

The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases

Abstract: The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action. 4-methyl-5-β-hydroxyethylthiazole kinase (Thz kinase) was chosen as a representative model and the mechanism proposed in X-ray crystal structure paper provided the basis for calculations. In particular, the possible role of several active site residues (Arg121 and Cys198 among others) and of the two magnesium ions was examined. Static and dynamic catalytic fields for the reaction were generated revealing the most favourable environment for the preferential transition state stabilization. An attempt to model the phosphoryl transfer reaction as well as to investigate the influence of the cysteine residue on the reaction course at the semiempirical PM3 level of theory was undertaken.

Enol and Enethiol Occurrence for Some Ketones and Thioketones. Mass Spectrometry and Theoretical Calculations

Abstract: The mass spectra of ketones can provide valuable information with regards to keto-enol equilibria occurring in the gas phase. Mass spectra of selected ketones and thioketones have been analysed and specific fragmentation assignments have been done to characterised and weigh co-existing keto and enol tautomers. Thioketones are of particular interest due to their tendency to shift the tautomeric equilibrium towards the enethiol form. The predictive value of this methodology is not only supported by the influence of these compound’s nature and size of the substituent on these equilibria but also by the good correlation found between the selected fragments abundances ratio and semi-empirical calculation (AM1) of the corresponding heats of tautomerization.

State Selective Electron Capture in the Collision of S3+ Ions in Atomic Hydrogen and Helium

Abstract: : A full theoretical treatment including an ab-initio molecular calculation of the potential energy curves and couplings followed by a semi-classical collision dynamics has been performed for the one-electron capture by S 3+ ions in collision with atomic hydrogen. The present paper completes a previous letter [9] and displays the full results concerning this process in order to provide a detailed understanding of the mechanism. These calculations show evidence of the predominance of the S 2+ (3s 2 3p3d) 3 F° capture level, already pointed out by translational energy spectroscopy experiments and confirms experimental measurements. A compared study of the behaviour of the S 3+ projectile colliding both hydrogen and helium targets is also presented. Keywords : Ion-atom collisions, ab-initio molecular calculations, radial and rotational couplings. Introduction The charge transfer recombination involving low-energy multiply charged ions in collision with atomic or molecular targets is an important process in astrophysical plasmas for many low charged ions whose emission lines are used to provide direct information on the ionization structure of

Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches

Abstract: For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature and experimental data. It was demonstrated that for qualitatively correct spectra description the AO basis must include both the polarization and diffuse functions. The later play an important role in formation of Rydberg MOs. Estimated energies of the spectra transitions using the CIS method remain relatively far from the measured values. RPA method can be already considered as a quantitatively accurate method when sufficiently large basis set is used. For CASSCF approach, it was shown that even the lowest energy transitions are insufficiently described in CAS formalism and much larger active space or inclusion of more inactive orbitals in correlation treatment would be necessary for obtaining sufficient accuracy. It can be stated that without sufficiently large correlation contributions, the determined spectra are not able to reach quantitative agreement with experimental data. From the methods treated in this study, only TDDFT can be considered as a useful tool for spectra prediction, at least for calculations of lower excited states. It is relatively fast and feasible for calculation of middle-size molecules. ZINDO approximation is also relatively successful for such large systems. Acceptable predictions of experimentally observed energy transitions in the range of Q and B bands were obtained. Until higher (UV) part of spectra is examined where the excitations to Rydberg orbital will happen, it can be considered as a good candidate for electron spectra calculations.

Structure, Stability and Interaction Studies on Schiff Base Analogue Systems

Abstract: Ab initio and density functional theory methods have been applied to study the molecular structure and interaction of water with N-methyl-2-propenylidenimine and Nmethyl- 2-butenylidenimine molecules. The most possible reactive sites of the above molecules have been identified for the water interactions. The strength of the hydrogen bond is discussed using the atomic charges, which were calculated using the Mulliken population analysis and Natural population analysis schemes at MP2/6-31G* level of theory. The electron density (ρ) and laplacian of electron density (∇2ρ) have been calculated for the possible existence of the hydrogen bonds with CH and CH3 groups of molecules using the “Atoms in molecules” approach. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed for the conformational stability of these molecules.

Scalar Relativistic Study of the Structure of Rhodium Acetate

Abstract: Rhodium acetate, related rhodium carboxylates, and rhodium amide complexes are powerful catalysts for carbene chemistry. They readily promote the decomposition of diazo compounds and transfer the resulting carbene to a variety of substrates. There have been several quantum chemistry studies of these compounds, particularly of the acetate. These have all used non-relativistic methods, and all have shown optimized Rh-Rh bond lengths significantly longer than the experimental value. In this study we have surveyed several scalar relativistic DFT methods using Gaussian, Slater, and numerical basis functions (in DGAUSS, ADF, and DMOL3). Several combinations of exchange-correlation functionals with relativistic and non-relativistic effective core potentials (ECP) were investigated, as were non-relativistic and all electron scalar relativistic methods. The combination of the PW91 exchange and PW91 correlation functional with the Christiansen-Ermler ECP gave the best results: 2.3918 A compared to the experimental value of 2.3855±0.0005 A.

Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

Abstract: In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient.

Electronic Density Approaches to the Energetics of Noncovalent Interactions

Abstract: We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon the electrostatic interaction between two unperturbed molecules, the effect of the polarization of each charge distribution by the other, and the total energy of interaction. The expression for the latter is based upon the Hellmann-Feynman theorem. Applications to a number of systems are discussed; among them are dimers of uracil and interacting pairs of molecules in the crystal lattice of the energetic compound RDX.

Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics

Abstract: We have theoretically characterized the ground state and the excited state properties of wybutine, a naturally fluorescent modified base occuring in tRNAs, using configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods Both gas phase excited state properties and solvent effects, modelled through Onsager reaction field method, were considered In addition to vertical excitation energies, the fluorescence transitions were calculated, based on S1 equilibrium geometry optimized at CIS level Our computations show encouraging agreement with known experimental data either directly (TDDFT) or after applying empirical scaling (CIS) The fluorescence Stokes’ shift for the S0 A S1 transition is computed taking into account the contributions from both intramolecular and solvent reorganization processes The results suggest that intramolecular relaxation of the S1 state accounts for the major part of the magnitude of the Stokes’ shift, while the role of solvent reorganization seems to be of less importance

A GMDH Approach to Modelling Gibbsite Solubility in Bayer Process Liquors

Abstract: The most widely employed industrial process for producing alumina (Bayer process) involves the dissolution of available aluminium hydroxide minerals present in raw bauxite into high temperature sodium hydroxide solutions. On cooling of the solution, or liquor in the industrial vernacular, Al is precipitated from solution in the form of gibbsite (Al(OH)3). In order to optimise the process, a detailed knowledge of factors influencing gibbsite solubility is required, a problem that is confounded by the presence of liquor impurities. In this paper, the use of the Group Method of Data Handling (GMDH) polynomial neural network for developing a gibbsite equilibrium solubility model for Bayer process liquors is discussed. The resulting predictive model appears to correctly incorporate the effects of liquor impurities and is found to offer a level of performance comparable to the most sophisticated phenomenological model presented to date.

Visualization of the Differential Transition State Stabilization within the Active Site Environment

Abstract: Dept. of Chemistry, Jackson State UniversityCorresponding author: Pawel Kedzierski,˛ E-mail: P.Kedzierski@mml.ch.pwr.wroc.plReceived: 15 December 2003Abstract: Increasing interest in the enzymatic reaction mechanisms and in the nature ofcatalytic effects in enzymes causes the need of appropriate visualization methods. A new in-teractive method to investigate catalytic effects using differential transition state stabilizationapproach (DTSS) [1,2] is presented. The catalytic properties of the active site of cytidinedeaminase (E.C. 3.5.4.5) is visualized in the form of differential electrostatic properties. Thevisualization was implemented using scripting interface of VMD [3]. Cumulative AtomicMultipole Moments (CAMM) [4,5,6] were utilized for efficient yet accurate evaluation of theelectrostatic properties. The implementation is efficient enough for interactive presentationof catalytic effects in the active site of the enzyme due to transition state or substrate move-ment. This system of visualization of DTTS approach can be potentially used to validatehypotheses regarding the catalytic mechanism or to study binding properties of transitionstate analogues.Keywords: Differential Transition State Stabilization; Catalytic properties; Visualization;Enzymatic catalysis; Molecular electrostatic potential; Molecular Electrostatic field; Multi-pole moments.This work is dedicated to prof. Henryk Chojnacki on his 70th anniversary.c 2004 by MDPI, Basel, Switzerland. Reproduction for non-commercial purposes permitted.

Molecular Dynamics Simulations of the O-glycosylated 21-residue MUC1 Peptides

Abstract: The conformational propensities of the 21-residue peptide and its Oglycosylated analogs were studied by molecular dynamics (MD) simulations. This polypeptide motif comprises the tandem repeat of the human mucin (MUC1) protein core that is differently glycosylated in normal and cancer cells. To evaluate the structural effects of O-glycosylation on the polypeptide backbone, conformations of the nonglycosylated peptide and its glycosylated analogs were monitored during the 1 ns MD simulations. Radius gyration for whole peptide and its fragments, as well as root-meansquare-deviation between coordinate sets of the backbone atoms of starting structures and generated structures, were calculated. It was shown that O-glycosylation promotes and stabilizes the extended conformations of the whole peptide and its central PDTRP fragment. O-glycosylation of the specific Thr residues significantly affects the conformational distributions of the flanking Ser residues. It was also shown that Oglycosylation promoted backbone conformations of the immunodominant region PDTRP that were similar to the structural features of the peptides presented by the major histocompatability complex (MHC) to T-cell receptors.

Calculated Electronic Behavior and Spectrum of Mg+@C60 Using a Simple Jellium-shell Model

Abstract: We present a method for calculating the energy levels and wave functions of any atom or ion with a single valence electron encapsulated in a Fullerene cage using a jelluim-shell model. The valence electron-core interaction is represented by a one-body pseudo-potential obtained through density functional theory with strikingly accurate parameters for Mg+ and which reduces to a purely Coulombic interaction in the case of H. We find that most energy states are affected little by encapsulation. However, when either the electron in the non-encapsulated species has a high probability of being near the jellium cage, or when the cage induces a maximum electron probability density within it, the energy levels shift considerably. Mg+ shows behavior similar to that of H, but since its wave functions are broader, the changes in its energy levels from encapsulation are slightly more pronounced. Agreement with other computational work as well as experiment is excellent and the method presented here is generalizable to any encapsulated species where a one-body electronic pseudo-potential for the free atom (or ion) is available. Results are also presented for off-center hydrogen, where a ground state energy minimum of -14.01 eV is found at a nuclear displacement of around 0.1 A.

NMR-based Structural Studies of the Glycosylated MUC1 Tandem Repeat Peptide

Abstract: MUC1 is a glycoprotein that plays an important role in cancer pathogenesis. In order to study the effect of glycosylation on the conformational propensities of the tandem repeat domain of MUC1, we have determined the structure of the MUC1 tandem repeat peptide AHGVTSAPDTRPAPGSTAPP, O-glycosylated with the trisaccharide (α-Glc-1,4-β-Glc-1,4-α-GalNAc-) at Thr5. This glycopeptide was synthesized to model a heavily Oglycosylated threonine residue in the tandem repeat domain. The NMR experiments used in this study included TOCSY, NOESY, ROESY, DQF-COSY, HSQC and 1D NMR. The peak volumes determined using the program SPARKY were converted into distance constraints using the program CALIBA. The programs FiSiNOE and HABAS were used to generate angle constraints. Using conformational restraints obtained from NMR, the program DYANA was used to determine the structures of the peptide. Finally, structural refinement was performed within the SYBYL software package using GLYCAM parameters and Kollman-all atom types. The presence of strong sequential αN connectivities suggested an extended conformation of the peptide backbone. Strong sequential αδ connectivities were indicative of a trans conformation of the Ala-Pro peptide bonds. In addition, presence of sequential NN connectivities in the peptide segments Gly3-Val4-Thr5-Ser6, Asp9-Thr10-Arg11 and Gly-Ser16 were indicative of twist-like conformations of the peptide backbone in these peptide segments.

Ab initio Study of Alkyl-oxonium Cations CnH2n+1OH2+, n=1,2,3,4

Abstract: Within the framework of the itinerant radical model, the solvated electron in liquid alcohols is understood as an itinerant alkyl-oxonium ROH2. radical. As a first step in the investigation of those radicals, this study deals with the optimization of related ROH2+ alky-oxonium cations: CnH2n+1OH2+,n=1,2,3,4. The structures were optimized at the MP2/6-31G**++ level with the help of the GAMESS ab initio package. Optimized structures are reported for the following cations: MethylOxonium; EthylOxonium; 1-PropylOxonium, 2-PropylOxonium and 1-ButylOxonium, 2-ButylOxonium, IsoButylOxonium, TertButylOxonium. Optimized geometries are displayed with the help of the ChemApp Java applet. Vibrational frequencies and ZPEs have been computed, and visual depictions of expected experimental IR spectra have been simulated with the help of Lorentzian functions.

Interactions between Physics and Biodisciplines within the Framework of Molecular Sciences

Abstract: In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern biochemical reactivity, enzymatic catalysis, origin of life, experimental tools for structure elucidation and quantum chemistry methods. Additional remarks are related to ultrafast processes, experiments with individual molecules, and to symmetry considerations.