We present fully geometrically optimized density functional theory calculations at the B3LYP/D95(d,p) level on antiparallel β-sheet models consisting of two or four strands glycine residues and artificial nylon-like two- four-strand separated by methylene groups. Unlike H-bonds in α-helices chains H-bonding amides, association polyglycine shows little no H-bond cooperativity. show that C5 intrastrand are either disrupted enhanced upon formation interstrand H-bonds, depending pattern (but not...

The radiofrequency and microwave spectra of H2S⋅HF deuterium substituted analogs have been studied by molecular beam electric resonance spectroscopy. Rotational constant data, dipole moments, nuclear hyperfine interactions were obtained from the spectra. structure determined this data has H2S as proton acceptor. hydrogen bond is linear to within ±10°. S⋅⋅⋅F distance 3.249 Å. plane oriented perpendicular axis conservative error limits right angle compared tetrahedral orientation acceptors in...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular beam electric deflection behavior and polarity of hydrogen-bonded complexes ROH, RSH, RNHJ. A. Odutola, R. Viswanathan, T. DykeCite this: J. Am. Chem. Soc. 1979, 101, 17, 4787–4792Publication Date (Print):August 1, 1979Publication History Published online1 May 2002Published inissue 1 August 1979https://pubs.acs.org/doi/10.1021/ja00511a002https://doi.org/10.1021/ja00511a002research-articleACS PublicationsRequest reuse permissionsArticle...

The rates and mechanism for the unimolecular decomposition of SiH4 have been investigated using quasiclassical trajectory methods to follow dynamics Metropolis sampling procedures average over initial phase space. semiempirical potential-energy surface has fitted scaled SCF calculations a variety experimental data. It gives correct equilibrium structure, reaction endothermicities, bond energies SiH4, SiH3, SiH2. All hydrogen atoms are treated in an equivalent fashion. Excellent first-order...

A classical variational phase-space procedure for the computation of microcanonical dissociation rate coefficients is presented and applied to simple bond rupture in CH4 SiH4 systems. The method replaces sum density quantum states that appear RRKM formalism with equivalent multidimensional integrals which are evaluated using a Metropolis Monte Carlo sampling procedure. computed good agreement previously reported trajectory results obtained on same potential-energy surfaces, provided dividing...

Molecular beam electric resonance spectroscopy has been used to determine the radiofrequency and microwave spectrum of H2S⋅Ar, HDS⋅Ar, D2S⋅Ar. The dipole moment nuclear hyperfine interactions reflect an angular structure in which H2S C2 axis is nearly perpendicular Ar...S axis, argon are coplanar. effective argon–H2S center-of-mass distance 3.977 Å.

The lack of a deep understanding how proteins interact remains an important roadblock in advancing efforts to identify binding partners and uncover the corresponding regulatory mechanisms functions they mediate. Understanding protein-protein interactions is also essential for designing specific chemical modifications develop new reagents therapeutics. We explored hypothesis whether protein interaction sites serve as generic biding non-cognate ligands, just it has been observed...

We present a procedure that numerically evaluates the scattering wave function. The solution to time-independent Schrödinger equation is calculated by novel combination of: (a) Mo/ller operator of theory, (b) time-dependent packets whose shape unconstrained, and (c) efficient packet propagation on dynamically-adapted grid. superposition appropriate boundary conditions yields full function, from which amplitudes are then obtained. Since does not make use basis-set expansions, its...

A previously formulated Monte Carlo transition-state theory approach to unimolecular reactions has been extended the calculation of microcanonical rate coefficients for specific angular momentum states. The method is applied a study two-center dissociation CH4 on Duchovic–Hase–Schlegel (DHS) ab initio potential-energy surface. rotationally averaged DHS surface are found be consistently less than those calculated semiempirical due principally larger C–H bond dissciation energy relatively...

Classical trajectories have been used to compute the total and individual microcanonical rate coefficients as a function of energy for CH4→CH2+H2 CH4→CH3+H. Reaction mechanisms product translational distributions both reaction channels also obtained initial CH4 internal energy. A semiempirical valence-force potential-energy surface was throughout. Averaging over phase space available accomplished by Metropolis-type Monte Carlo procedure. Excellent first-order decay plots are integration 103...

Microcanonical rate coefficients and product energy distributions are computed for the CH3+H CH2+H2 dissociation channels of CH4 by a random walk procedure. The formulation is based on Slater theory, but uses Metropolis Monte Carlo procedures to average over reactant phase space. We find that convergence rates calculations system less rapid than obtained in previous studies more simple systems involving argon clusters. found decrease as complexity process increases. Thus, two-center...

We present B3LYP/D95** calculations on the CO and N−H couplings in H-bonded chains of 4-pyridones. 14C-substitutions are used to decouple various vibrations for purposes illustration. The coupled bear analogy amide I bands proteins peptides. coupling CO's occurs primarily via cooperative H-bonds rather than transition dipole (TDC), as demonstrated by fact that (1) greater previously reported similar studies formamides despite larger distance between pyridone (TDC decreases with distance) (2)...

We report the first molecular orbital/density functional theory (DFT) calculations on vibrational frequencies involved in amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These use B3LYP/D95** level DFT. The primary means coupling occurs through H bond, rather than space, interactions, which is consistent with a previous alpha-helical polyalanines and H-bonding chains both formamides 4-pyridones. decoupled C=O...

The effects of three acidic hexapeptides on in vitro hydroxyapatite growth were characterized by pH-stat kinetic studies, adsorption isotherms, and molecular modeling. peptides, pSDEpSDE, SDESDE, DDDDDD, are equal-length model compounds for the sequences osteopontin, a protein that inhibits mineral formation both calcified noncalcified tissues. Growth rates from 1.67 mM calcium 1.00 phosphate solution measured at pH 7.4 37 °C 150 NaCl. pSDEpSDE was strong inhibitor when preadsorbed onto (HA)...

A time-dependent wave packet method for the investigation of adiabatic vibrational predissociation (VP) collinear X–BC systems is described. Discrete–discrete and discrete–continuum couplings are introduced into initial function using a first-order perturbation procedure. The system evolved in time by an explicit integration procedure reaction probabilities P(t) as computed integrating over configuration space VP products. rate coefficient given directly {−∂ ln[1−P(t)]/∂t}. has been applied...

Identifying antigen epitopes is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, costly experimental determination of epitopes. Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope further complicated by the fact that multiple may be located on same complete data often unavailable.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA valence-bond potential-energy surface for silylene dissociationR. Viswanathan, D. L. Thompson, and M. RaffCite this: J. Phys. Chem. 1985, 89, 8, 1428–1432Publication Date (Print):April 1, 1985Publication History Published online1 May 2002Published inissue 1 April 1985https://pubs.acs.org/doi/10.1021/j100254a025https://doi.org/10.1021/j100254a025research-articleACS PublicationsRequest reuse permissionsArticle Views64Altmetric-Citations17LEARN...

Abstract Background Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide development of novel therapeutic agents. A variety computational approaches have been developed for predicting a protein’s interfacial residues from its known sequence structure. Methods using three-dimensional structures be template-based or template-free. Template-based methods limited success in when...

The semiempirical valence-bond surface formulated by Viswanathan et al. [J. Phys. Chem. 89, 1428 (1985)] for the unimolecular dissociation of SiH2 has been fitted to an analytical function type suggested Murrell and co-workers 88, 4887 (1984)]. accurately represents most experimental CI results. dynamics form Si H2 have investigated classical trajectory methods on this surface. effect describing initial state molecule using normal local mode approximations studied. In spite presence heavier...

Collisional energy transfer, exchange, and complex formation mechanisms for Ar2 dimer depletion in free jet expansions have been investigated using quasiclassical trajectory methods on several different potential-energy surfaces. Computed dissociation cross sections show that V → transfer is an unimportant mechanistic pathway collisions with CO2, N2, CO. An R found to be important at translational energies of 0.03 eV. However, there very little difference among the results obtained At higher...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheoretical investigations of the reaction dynamics polyatomic gas-phase systems: ozone + nitric oxide reactionR. Viswanathan and L. M. RaffCite this: J. Phys. Chem. 1983, 87, 17, 3251–3266Publication Date (Print):August 1, 1983Publication History Published online1 May 2002Published inissue 1 August 1983https://pubs.acs.org/doi/10.1021/j100240a017https://doi.org/10.1021/j100240a017research-articleACS PublicationsRequest reuse permissionsArticle...

Functional sensitivity analysis is used to study the effect of potential structure upon elastic scattering He atoms from a one-dimensional surface. The calculations are implemented by computing total wave functions packet calculation Mo/ller operator method. functional sensitivities various diffraction probabilities for several angles incidence and surface corrugation studied. method extended examine role with adsorbed impurities. It was observed that processes draw local regions in very...