Practical aspects of computational chemistry i an overview of the last two decades and current trends

Practical Aspects of Computational Chemistry I Jerzy Leszczynski • Manoj K Shukla Editors Practical Aspects of Computational Chemistry I An Overview of the Last Two Decades and Current Trends 123 Editors Prof Jerzy Leszczynski Department of Chemistry Jackson State University P.O Box 17910 1400 Lynch Street Jackson, MS 39217 USA jerzy@icnanotox.org Prof Manoj K Shukla Department of Chemistry Jackson State University P.O Box 17910 1400 Lynch Street Jackson, MS 39217 USA Present affiliation: Environmental Laboratory US Army Engineer Research and Development Center 3909 Halls Ferry Road Vicksburg, MS 39180 USA mshukla@icnanotox.org ISBN 978-94-007-0918-8 e-ISBN 978-94-007-0919-5 DOI 10.1007/978-94-007-0919-5 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2011940796 © Springer Science+Business Media B.V 2012 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface It is a rare event that the impressive group of leading experts is willing to share their views and reflections on development of their research areas in the last few decades The editors of this book have been very fortunate to attract such contributions, and as an effect two volumes of “Practical Aspects of Computational Chemistry: Overview of the Last Two Decades and Current Trends” are being published Astonishingly, we found that this task was not so difficult since the pool of authors was derived from a large gathering of speakers who during the last 20 years have participated in the series of meetings “Conferences on Current Trends in Computational Chemistry” (CCTCC) organized by us in Jackson, Mississippi We asked this group to prepare for the 20th CCTCC that was hold in October 2011 the reviews of the last 20 years of the progress in their research disciplines Their response to our request was overwhelming This initiative was conveyed to Springer who in collaboration with the European Academy of Sciences (EAS) invited as to edit such a book The current volume presents the compilation of splendid contributions distributed over 21 chapters The very first chapter contributed by Istvan Hargittai presents the historical account of development of structural chemistry It also depicts some historical memories of scientists presented in the form of their pictures This historical description covers a vast period of time Intruder states pose serious problem in the multireference formulation based on Rayleigh-Schrodinger expansion Ivan Hubac and Stephen Wilson discuss the current development and future prospects of Many-Body Brillouin-Wigner theories to avoid the problem of intruder states in the next chapter The third chapter written by Vladimir Ivanov and collaborators reveals the development of multireference state-specific coupled cluster theory The next chapter from Maria Barysz discusses the development and application of relativistic effects in chemical problems while the fifth chapter contributed by Manthos Papadopoulos and coworkers describes electronic, vibrational and relativistic contributions to the linear and nonlinear optical properties of molecules James Chelikowsky and collaborators discuss use of Chebyshen-filtered subspace iteration and windowing methods to solve the Kohn-Sham problem in the sixth chapter Next chapter contributed by Karlheinz Schwarz and Peter Blaha v vi Preface provides a detailed account of applications of WIEN2K program to determination of electronic structure of solids and surfaces The recent development of model core potentials during the first decade of the current century is discussed by Tao Zeng and Mariusz Klobukowski in the Chap Next two chapters discuss Monte Carlo method Chapter written by William Lester and coworkers describes practicality of Monte Carlo method to study electronic structure of molecules and Chap 10 describes the relativistic quantum Monte Carlo method and is written by Takahito Nakajima and Yutaka Nakatsuka There are two chapters presenting discussion on the various important aspects of nanoscience Chapter 11 is written by Kwang Kim and coworkers and presents description of computer aided nanomaterial design techniques applying to nanooptics, molecular electronics, spintronics and DNA sequencing Jorge Seminario and coworkers describe application of computational methods to design nanodevices and other nanosystems in the Chap 12 The problem of DNA photodimerization has always been very attractive to research communities Martin McCullagh and George Schatz discuss the application of ground state dynamics to model the thyminethymine photodimerization reaction in the Chap 13 In the next chapter A Luzanov and O Zhikol review the excited state structural analysis using the time dependent Density Functional Theory approach The next four chapters deal with molecular interactions In the Chap 15 Joanna Sadlej and coworkers reveal the application of VCD chirality transfer to study the intermolecular interactions Peter Politzer and Jane Murray review different aspects of non-hydrogen bonding intramolecular interactions in the Chap 16 The next chapter by Slawomir Grabowski describes characterization of X-H : : :   and X-H : : : ¢ interactions Chapter 18 deals with role of cation- ,  –  and hydrogen bonding interaction towards modeling of finite molecular assemblies and is written by A.S Mahadevi and G.N Sastry In the Chap 19, Oleg Shishkin and Svitlana Shishkina discuss the conformational analysis of cyclohexene, its derivatives and heterocyclic analogues The stabilization of bivalent metal cations in zeolite catalysts is reviewed by G Zhidomirov in the Chap 20 The last chapter of the current volume written by Andrea Michalkova and Jerzy Leszczynski deals with the interaction of nucleic acid bases with minerals that could shed a light on the understanding of origin of life With great pleasure, we take this opportunity to thank all authors for devoting their time and hard work enabling us to complete the current volume “Practical Aspects of Computational Chemistry I: Overview of the Last Two Decades and Current Trends” We are grateful to excellent support from the President of the EAS as well as Editors at the Springer Many thanks go to our families and friends without whom the realization of the book would be not possible Jackson, Mississippi, USA Jerzy Leszczynski Manoj K Shukla Contents Models—Experiment—Computation: A History of Ideas in Structural Chemistry Istvan Hargittai Many-Body Brillouin-Wigner Theories: Development and Prospects Ivan Hubaˇc and Stephen Wilson 33 Multireference State–Specific Coupled Cluster Theory with a Complete Active Space Reference Vladimir V Ivanov, Dmitry I Lyakh, Tatyana A Klimenko, and Ludwik Adamowicz 69 Relativistic Effects in Chemistry and a Two-Component Theory 103 Maria Barysz On the Electronic, Vibrational and Relativistic Contributions to the Linear and Nonlinear Optical Properties of Molecules 129 Aggelos Avramopoulos, Heribert Reis, and Manthos G Papadopoulos Using Chebyshev-Filtered Subspace Iteration and Windowing Methods to Solve the Kohn-Sham Problem 167 Grady Schofield, James R Chelikowsky, and Yousef Saad Electronic Structure of Solids and Surfaces with WIEN2k 191 Karlheinz Schwarz and Peter Blaha Model Core Potentials in the First Decade of the XXI Century 209 Tao Zeng and Mariusz Klobukowski vii viii Contents Practical Aspects of Quantum Monte Carlo for the Electronic Structure of Molecules 255 Dmitry Yu Zubarev, Brian M Austin, and William A Lester Jr 10 Relativistic Quantum Monte Carlo Method 293 Takahito Nakajima and Yutaka Nakatsuka 11 Computer Aided Nanomaterials Design – Self-assembly, Nanooptics, Molecular Electronics/Spintronics, and Fast DNA Sequencing 319 Yeonchoo Cho, Seung Kyu Min, Ju Young Lee, Woo Youn Kim, and Kwang S Kim 12 Computational Molecular Engineering for Nanodevices and Nanosystems 347 Norma L Rangel, Paola A Leon-Plata, and Jorge M Seminario 13 Theoretical Studies of Thymine–Thymine Photodimerization: Using Ground State Dynamics to Model Photoreaction 385 Martin McCullagh and George C Schatz 14 Excited State Structural Analysis: TDDFT and Related Models 415 A.V Luzanov and O.A Zhikol 15 VCD Chirality Transfer: A New Insight into the Intermolecular Interactions 451 Jan Cz Dobrowolski, Joanna E Rode, and Joanna Sadlej 16 Non-hydrogen-Bonding Intramolecular Interactions: Important but Often Overlooked 479 Peter Politzer and Jane S Murray 17 X –H   and X –H ¢ Interactions – Hydrogen Bonds with Multicenter Proton Acceptors 497 Sławomir J Grabowski 18 Computational Approaches Towards Modeling Finite Molecular Assemblies: Role of Cation- ,   –  and Hydrogen Bonding Interactions 517 A Subha Mahadevi and G Narahari Sastry 19 Unusual Properties of Usual Molecules Conformational Analysis of Cyclohexene, Its Derivatives and Heterocyclic Analogues 557 Oleg V Shishkin and Svitlana V Shishkina Contents ix 20 Molecular Models of the Stabilization of Bivalent Metal Cations in Zeolite Catalysts 579 G.M Zhidomirov, A.A Shubin, A.V Larin, S.E Malykhin, and A.A Rybakov 21 Towards Involvement of Interactions of Nucleic Acid Bases with Minerals in the Origin of Life: Quantum Chemical Approach 645 Andrea Michalkova and Jerzy Leszczynski Index 673 666 A Michalkova and J Leszczynski the adsorption strength, COSMO approach leads to significantly lower interaction energy These values are more than two times lower than those obtained for K(3t)NaW and K(3o)NaW This suggests an importance of performing both types of calculation instead applying only the explicit addition of water The general trend in the stabilization is also changed compared with the results obtained using the supermolecular approach Uracil appears the most strongly adsorbed on the nonhydrated octahedral surface followed by uracil adsorbed on non-hydrated tetrahedral fragment The Ecorr values of K(3o)Na-TH and K(3o)Na-U from the COSMO calculation vary by about 1.7 kcal/mol This number agrees well with the energy difference from the microsolvation The interaction energies of the most stable uracil and thymine adsorbed on large mineral fragments (K(3o)Na, K(3t)Na, K(3t)NaW and K(3o)NaW) were also calculated at the B3LYP/6-31G(d)//M05-2X/6-31G(d) level of theory and the results are presented in Table 21.6 [151] The M05-2X results confirm predictions obtained using the B3LYP functional Comparison of the Ecorr values for the most stable uracil and thymine systems obtained at B3LYP and M05-2X levels (presented in Table 21.6) reveals that dispersion term amounts to about kcal/mol for K(3t)Na, K(3t)NaW and 7–10 kcal/mol for K(3o)Na and K(3o)NaW Such difference in the energy reveals similar trend in the stability of thymine and uracil with exception of K(3o)NaW-TH (it exhibits smaller adsorption strength than K(3o)NaW found the most stable at the B3LYP level) 21.4.3.4 Implication to Origin of Life The adsorption strength of clay fragments depends on their structure and physicochemical properties since DNA bases possess different binding affinities and slightly different conformations when adsorbed to various kaolinite mineral surfaces This was found to be true also for DNA molecules adsorbed on different layered materials [161] The substitution in the mineral sheet and the presence of the counterion affect the adsorption of the nucleobases the most significantly Such a conclusion is in agreement with statement of Paget and co-workers [59] that DNA interaction with clay minerals is a charge-dependent process Structural and chemical differences of specific layered silicate mineral surfaces cause varying adsorption of DNA bases Higher affinity was predicted for the octahedral surface, which induces the changes in the conformation of DNA bases The clays ability to organize the nucleic acids (based on their orientation towards the surface and presence of the interlayer cation and water) could indicate that specifically designed clay mineral surfaces may posses a catalytic potential when used as substrates for biomolecules or to activate and concentrate the monomer building blocks in the prebiotic chemistry Furthermore, the isolated mineral fragments with well defined edges may have also played an important role in the adsorption of DNA bases and their derivatives on the early earth 21 Towards Involvement of Interactions of Nucleic Acid Bases with Minerals 667 21.5 Conclusions This chapter summarizes the results of experimental and theoretical studies on the interactions of nucleic acid bases with minerals, water and sodium cation The computational study to some extent supported experimentally proposed Wăachtershăausers cycle (the production of acetic acid from CO and CH3 SH) [9] It was shown that Fe-Ni-S surface model as catalyst can partially catalyze this reaction through the creation of different coordination complexes [138] But synthesis of formic acid from CO2 and H2 S in the presence of pyrite was shown to be endergonic under modeled conditions The simulations show that this reaction pathway does not lead to sufficient amount of the product in isolated systems and the cycle can possibly operate at low rates But to make the final conclusion about the rates, the kinetic study based on reaction rates needs to be performed and inclusion of conditions close to those that occurred on the early Earth, are required to confirm feasibility of studied prebiotic reactions The thermodynamic and kinetic parameters of the stepwise hydration of 1-methylcytosine and its imino-oxo tautomer in the presence of the NaC cation have been investigated [139] Hydration of 1-methylcytosine by one water molecule leads to an increase of the concentration of its imino-oxo tautomer in the equilibrium mixture and decrease of the barrier of the tatutomer formation (to 15.6 kcal/mol) If the sodium cation is present the tautomeric form is much less favored and tautomerization barrier increases to 25.2 kcal/mol The computationally predicted values of the rate constants suggest that the tautomerization of 1-methylcytosine to its imino-oxo form proceeds mainly due to a presence of the hydrated (MeCW) species Based on the kinetic analysis of the tautomerization process in hydrated MeC in the presence of sodium ions it was concluded that complexes of hydrated MeC with NaC are unlikely to contribute to the frequency of DNA point mutations caused by the tautomers This is due to the fact that the interactions with NaC lead to a decrease of both the rate and the equilibrium constants of the tautomerization reactions in hydrated 1-methylcytosine The calculations of the adsorption of thymine and uracil on the octahedral and tetrahedral surface of clay minerals of the kaolinite group in the presence of sodium cation and solution show that thymine and uracil interact in a very similar way with the mineral surface [147, 151] Studied clay mineral fragments posses high sorption affinity for nucleic acid bases The presence of NaC leads to a significant stabilization of these molecules on both surfaces due to the formation of strong interaction between NaC and the molecular oxygen atoms Explicit addition of water molecule has only small influence on the stabilization of the nucleic acid bases in the presence of the NaC The binding strength of thymine with the clay surface is slightly larger than of uracil, which can be explained in terms of their chemical nature This attractive interaction contributes the most to the adsorption strength, which depends on several other factors such as the type of the surface, its chemistry, position and orientation of the target molecule towards the surface Such a large 668 A Michalkova and J Leszczynski effect is suggested to be an indication of the catalytic properties that these materials may have shown also when used as substrates for biomolecules in the prebiotic chemistry The above summarized studies of the interaction of nucleic acid bases with water, cations, clay minerals and clay-based materials are only the first step in attempt to understand such adsorption To provide full details necessary for the understanding of the fate of nucleobases when interacting with soil components, simulations need to include the effects of different type of soil and nucleobase, the chemical environment (the pH of the system), and of external physical conditions (temperature) Therefore, future studies should concentrate on other types of layered minerals with considering above mentioned factors The reviewed data strongly suggest that computational 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Li H, Zhang L, Han S (2007) J Phys Chem B 111(31):9347 158 Chatterjee A, Ebina T, Iwasaki T (2001) J Phys Chem A 105(47):10694 159 Castro EAS, Martins JBL (2005) J Comput Aided Mater Des 12:121 160 Tunega D, Benco L, Haberhauer G, Gerzabek MH, Lischka H (2002) J Phys Chem B 106:11515 161 Antognozzi M, Wotherspoon A, Hayes JM, Miles MJ, Szczelkun MD, Valdre G (2006) Nanotechnology 17(15):3897 Index A ab initio model potential (AIMP), 218, 223, 226, 238, 244, 245, 247 ab initio quantum chemistry, 70, 256, 281, 466 Absorbance, 369, 455 Adsorption, 241, 242, 370, 379, 380, 547, 580, 581, 587–590, 593, 607–610, 617, 618, 621, 623, 646–649, 651–653, 659–661, 664–668 AgH, 136–139 AIM See Atoms in molecules (AIM) Algebraic approximation, 35, 39, 124 Alpha helix, 15–19 Alpha keratin, 17 Alpha-oxygen, 630, 638 Anderson, P., 19, 256 Angle contraction in Si-O-N linkages, 490 Anion-radical, 540 Arm-chair, 342, 356, 358–360 Atoms in molecules (AIM), 197, 505–510, 524, 532, 540, 564, 649 AuH, 136–139 Avery, O.T., 13, 14 B Babbage, C., 34 Backdoor, 41 Backdoor intruder states, 41, 42 Bartell, L.S., 10 Basis-free method, 168 Basis set superposition error (BSSE), 241, 256, 501, 503, 506, 512, 524, 536–538, 545, 649, 663 Becke-3-Lee-Yang-Parr (B3LYP), 130, 149–151, 154, 155, 322, 428, 429, 443, 445, 464, 465, 468, 522, 529, 530, 533, 534, 540, 545, 546, 561, 585, 587, 598–601, 603–609, 611–615, 617, 618, 620, 632, 633, 636, 637, 649, 653, 654, 658, 660–662, 665, 666 Benzene-ammonia complex, 499 Bernal, J.D., 14 Beta keratin, 17 Bishop–Kirtman perturbation theory (BKPT), 135–139, 159, 163 Blackbody infrared radiative dissociation, 533 B3LYP See Becke-3-Lee-Yang-Parr (B3LYP) Bohr, N., 5, 34, 188 Bond critical point (BCP), 506–510, 512–514, 532, 540 Bond path (BPs), 506–514 Born and Oppenheimer, 34, 136, 266, 352, 461, 548 Born, M., 21, 22 Boron hydride (BH), 87, 94, 95 B3PW91, 355 Bragg, W.H., 11 Bragg, W.L., 11 Brandow, B.H., 43 Breit–Pauli Hamiltonian, 304 Brillouin–Wigner, 38, 40, 44–51, 57, 64 Brillouin–Wigner coupled cluster singles and doubles theory (BW-CCSD), 43 Brillouin–Wigner coupled cluster theory, 43, 52 Brillouin–Wigner full configuration interaction (BW-FCI), 42 Brillouin–Wigner methods, many-body, 33–64 Brillouin–Wigner perturbation theory, 35, 39–44, 46, 48, 51–53 Brillouin–Wigner theory, 33–64 Brownian motion, 34, 259 Brown, R., 34 J Leszczynski and M.K Shukla (eds.), Practical Aspects of Computational Chemistry I: An Overview of the Last Two Decades and Current Trends, DOI 10.1007/978-94-007-0919-5, © Springer ScienceCBusiness Media B.V 2012 673 674 Brown–Ravenhall disease, 116 Brueckner, K.A., 38, 39 BSSE See Basis set superposition error (BSSE) C CADPAC, 221, 238, 466 Cambridge Structural Database (CSD), 486, 500, 527, 530, 539, 542 CaPTURE, 526 Carbon fixation cycle, 653 CASCCD, 74–78 CASPT2, 107, 112, 113, 135–140, 163, 224, 242 CASSCF, 74, 81, 94, 95, 99, 112, 113, 135, 136, 138–140, 224, 241, 242, 273, 388–392, 395, 410, 632 Cation-  interaction, 339, 340, 517–551 cc-pVDZ, 94, 95, 221, 241, 389–392, 428, 540, 559, 561 CCSD(T), 57, 81, 82, 105, 109, 130, 132–134, 136–140, 143–146, 162, 163, 241, 242, 502, 520, 534, 535, 540, 605 CdS, 131–134 Charge density distribution, 168 Charge transfer numbers, 422, 444 CHARMM27, 393, 396, 400 Chebyshev–Davidson method, 181, 182, 186, 188 Chebyshev filtered subspace iteration, 167–188 Chebyshev–Jackson approximation, 181 Chirality, 374, 451–472 Chlorotrinitromethane Cl–C(NO2 )3 , 482, 484–488 Classification of hydrogen bonds, 497–501 Clay, kaolinite, 647, 648, 652, 659, 667 Closed-shell interactions, 507, 649 CMOS See Complementary metal-oxide semiconductor (CMOS) Coester, F., 38 Coinage metal hydrides, 136–139 Collaborative research, 37, 55 Collaborative virtual environment (CVE), 37, 38, 52–57 Collectivity number, 422, 423, 428, 430, 433–436, 439, 443 Collision induced dissociation (CID), 522, 533 Complementary metal-oxide semiconductor (CMOS), 351, 362 Computer and communications technology, 35 Computing, high performance, 35, 39 Conductor-like screening model (COSMO), 459, 467, 650, 665, 666 Index Configuration interaction (CI), 38, 39, 42, 43, 52, 57, 58, 70, 75, 78, 88, 153, 163, 192, 232–234, 237, 240, 256, 263, 265, 270, 275, 416, 422, 425, 427, 431, 432, 438, 441–443, 536 Conical intersection, 388, 390, 391, 395, 411 Contemporary computers, power of, 35 Cooperativity, 521, 540–546 Core electron binding energy (CEBE), 111–114, 243, 244 Core orbital, 211, 214–216, 218, 232, 244, 273, 274 Core-valence separability, 211 Corey, R., 17 Correlating functions, 221, 238, 241, 244, 245 COSMO See Conductor-like screening model (COSMO) Coulson, C., 20, 21, 205 Counterpoise method (CP), 241, 649 Coupled cluster (CC), 33, 39, 43, 52, 57, 70–75, 78, 79, 83–88, 99, 100, 133, 134, 192, 193, 256, 270, 273, 282, 294, 416, 462, 518 Coupled cluster singles and doubles theory (CCSD), 57, 70–77, 88, 416 Coupled cluster (CC) theory, 42, 43, 58, 70, 71, 77, 79, 82, 256 Covalent interactions, 321, 507, 518, 524 CPD See Cyclobutane pyrimidine dimer (CPD) Crick, F., 14, 287 CuH, 136–139, 314, 315 Current trends in computational chemistry (CCTCC), 11 Cusp correction, 303, 309–315 CVE See Collaborative virtual environment (CVE) Cyclobutane pyrimidine dimer (CPD), 386–388, 402 Cyclohexene, 557–576 Cyclopropenone, 140–142 Cyclopropenethione, 140–142 D Dale, H., 14 Das, T.P., 39 Democritos’s maxim, deMon2K, 238 Density functional theory (DFT), 23, 130, 168, 192, 215, 256, 320, 352, 416, 458, 520, 592, 649 Density of state (DOS), 184, 196, 197, 205, 331, 336–338, 355 Index Deoxyribonucleic acid, 14 Desoxyribose, 14 Dewar, M., 23, 24, 444 DFT See Density functional theory (DFT) DFT catastrophe, 149 DFT-GF formalism, 355 Diagonalization, 119, 120, 169, 171, 173–176, 181, 185–186, 194 Diagrammatic formalism, 38 Diagrammatic techniques, 38 Dickenson, R., 15 Diffusion Monte Carlo (DMC), 256–268, 277, 282, 283, 286–288, 294, 298–301, 311, 315 1,2-Dihydro fullerenes, 149, 152 Dihydrogen bond, 479, 498, 500 Dirac density matrix, 419 Dirac Hamiltonian, 115, 116, 118–121, 123, 303, 304 Dirac, P.A.M., 34, 103 Dissociative processes, 39 Divide and conquer approach, 536 DKHn approach, 122 DNA, 14, 210, 243, 287, 341–344, 356, 361, 385–392, 396–400, 405, 410, 411, 454, 518–520, 535, 549, 647, 648, 650–653, 659, 660, 665–667 DNA sequencing, 319–344 Double-helix model, 14, 386, 394 Duplex, 387, 388, 392, 395, 398, 399, 403–405, 549 D vibrational Schroedinger equation, 262 Dynamic correlation, 126, 224, 226, 230, 234, 245, 247, 270 E Effective core potential (ECP), 158, 209, 211–215, 218, 219, 226, 241, 243, 244, 246, 266, 268, 274–275, 283, 353, 649 Effective Hamiltonian, 43, 160, 214, 275, 300, 328 Effectively unpaired electrons, 425, 426, 441 Eigenproblem, 176, 181 Einstein, A., 3, 34, 259 Electron affinity, 105, 233, 540 Electron correlation, 39, 53, 55, 69–71, 81, 112, 113, 132–134, 140, 151, 212, 215, 226, 238, 241–243, 247, 256, 267–269, 275–277, 285, 293, 294, 301, 315, 316, 354, 355, 464, 470, 522, 546, 605, 633 Electron correlation energy, 464 Electron density distribution, 7, 13, 25, 532, 564, 649 675 Electron diffraction, 12, 13, 558, 559 Electronic structure, 20, 70, 82, 83, 111, 169, 174, 181, 182, 191–206, 210, 230, 242, 244, 255–288, 331, 386, 464–465, 520, 548, 580, 582, 630–634 Electronic structure theory, 83 Electron-nucleus coalescence condition, 302–303 Electron transport, 327, 329–330, 333, 335, 342, 355, 376, 379 Electrostatic potentials, 349, 364, 480–485, 488, 493, 520, 649, 660, 662, 664 Encyclopedia of computational chemistry, 58 Endohedral fullerenes, 149–159 European metalaboratory for multireference, 52 Ewald, P.P., 393 Excitation indices, 423, 426, 438 F FCI See Full configuration interaction (FCI) FDTD simulations See Finite-difference time-domain (FDTD) simulations FeIV DO, 631–634, 638 Fermi–Dirac distribution function, 328 Feynman, R.P., 273 Fine-structure splitting, 222 Finite basis set expansion, 35, 39 Finite difference method, 172, 599 Finite-difference time-domain (FDTD) simulations, 323–325 First-order RA (FORA), 117, 305, 306 Fixed-node approximation (FNA), 261, 262, 267, 300 Fixed-node diffusion Monte Carlo, 311 Fluorine hydride (FH), 94–99 Fock space Brillouin–Wigner methods, 59–64 Fock, V.A., 23, 25, 39 FORA See First-order RA (FORA) Fragment molecular orbital method (FMO), 221, 243 Friedrich, W., 11 Full configuration interaction (FCI), 42, 79, 81, 82, 88, 94, 99, 265, 270, 442, 443 Fullerenes, 149–159, 548 G GAMESS-US, 221, 232, 242, 243, 245 Gamma helix, 18 Gauge invariant atomic orbitals (GIAO), 463, 465 GAUSSIAN, 352, 466, 584, 587, 598, 613 676 Gaussian function, 39, 126, 262, 353 Gay–Lussac, J.L., 27 Generalized bond index, 426, 427 Generalized Van Vleck perturbation theory, 161 GENIP, 355, 357, 358, 363, 378 Gillespie, R.J., 7, 10 GNR See Graphene nanoribbon (GNR) Goldstone, J., 38, 39, 43 Google sites, 54, 56 Graphene, 335, 341, 343, 356–360, 363–379 Graphene nanoribbon (GNR), 320, 335–339, 341–344, 368, 369 Green function (GF) theory, 352, 374 Green’s function, 256, 262, 299, 300, 328, 332, 336 Growth of the internet, 35 Guanine, 287, 388, 406–408, 410, 411, 522, 648, 652, 659 H Hairpin, 388, 395–402, 404, 406, 410 Harmonic vibrational analysis, 242 Hartree, D.R., 23, 25 Hartree–Fock (HF), 39, 70, 72, 90, 93, 95, 131, 145, 150, 155, 156, 158, 192, 193, 211, 214, 215, 223, 235, 238, 239, 247, 256, 261, 262, 266, 268–271, 294, 301, 303, 312, 313, 315, 353–354, 396, 416–419, 421, 427, 441, 464, 560, 633 H2 as the proton acceptor, 504 Hauptman, H., 11 Heitler and London, 15, 34 Heitler, W., 5, 15, 34 Hellman–Feynman theorem, 266 Hemoglobin, 16 Heredity, 14 HERZBERG package, 88 Hessian matrix, 463 FH–H2 complex, 500, 514 HgS, 131–134 High performance computing (HPC), 39, 286, 287 High-pressure mass spectrometry (HPMS), 533 HLG See HOMO-LUMO gap (HLG) H2 molecule, 498, 500, 501 Hoffmann, R., 20 Hohenberg–Kohn, 354, 443, 483  -Hole interactions, 482 ¢-Hole interactions, 479, 482, 492, 494 Homochirality, 454 HOMO-LUMO gap (HLG), 350, 356–359, 377 Index Hubaˇc, I., 33, 43, 52 Hubbard, J., 38 Hugenholtz, N.M., 38 Human-human communication, 37, 55 Human-machine communication, 37, 38 Hund, F., 20–22 Hund–Mulliken theory, 22 Hybrid DFT, 241, 522, 633 Hydration, 243, 532, 533, 549, 648, 656, 657, 661, 664, 667 Hydrogen bonding, 16, 17, 340, 361, 454, 459, 466, 468–470, 479, 498, 499, 502, 503, 507, 509, 512, 517, 551, 647, 649 Hydrophobic interaction, 518 Hyperpolarizabilities, 64, 108, 130–132, 134, 135, 139–153, 155, 156, 162 I Infinite order two-component approach (IOTC), 106, 112, 113, 118–122, 125, 126 Infinite-order regular approximation (IORA), 117, 305, 306, 311 Insulin, 14 Intel, 35, 186 Intermediate coupling (IC), 229, 233, 235 Internet, growth of the, 35 Internet users, number of, 35, 36 Intramolecular interactions, 479–495, 505, 562, 564, 566, 569, 570, 576 Intrinsic reaction coordinate (IRC), 558, 560, 561, 571 Intruder state problem, 38, 40, 41, 44, 52, 54 Intruder states, 40–42, 57 Inversion in NH3 , 159–163 J Jahn–Teller, 198, 205, 238 Jastrow correlation factor, 301, 302 Jastrow–Slater wave function, 268, 301, 309, 311 j-j coupling, 238 K Kaldor, U., 39 Karle, J., 11 Kelly, H.P., 39 Kepler, J., 2, Ketones, 129, 140–142 Kinetics, 121, 160, 163, 193, 246, 247, 259, 262, 297, 300, 302, 304–308, 352, 507, Index 522, 533, 539, 583, 635, 649, 654, 656, 667 Kitaura–Morokuma decomposition, 503 Knipping, P., 11 Kohn–Sham, 167–188, 192–194, 205, 215, 261, 303, 354, 443, 548 Kohn, W., 23, 193 Krylov subspace, 185 Kumar, M., 34 Kăummel, H., 38 L LandauerBăuttiker formalism, 327, 328 Large amplitude motions, 159 Laue, M., 10 LEVEL package, 92 Lewis, G.N., Li@C60 , 154–159 [Li@C 60 ]C , 154, 155, 157 Linear scaling, 53, 256, 276, 283–285, 536 Linked diagram theorem, 38, 39, 51 Lipscomb, W.N., 20 Lithium hydride (LiH), 87, 90–93, 130, 143, 144, 294 Local energy, 257, 258, 261, 264, 278–280, 282–285, 294, 295, 297, 298, 301–303, 306–307, 309, 311, 313–315 Localization operator, 423, 425 Locked nucleic acid, 388–405 London dispersion, 546 London, F.W., 5, 15, 34 L-S coupling, 235, 238 M Magic structures, 329 Magnetoresitance (MR), 57, 74, 335, 338, 344, 605 Many-body Brillouin–Wigner methods, 33, 35, 37 Many-body methods, 33, 38, 42, 52 Many-body perturbation theory (MBPT), 39, 43, 51, 57, 70, 256 M´asˇik, J., 43 Massively parallel, 172 Matrix-isolation VCD, 468 Mavridis, A., 52 McWeeny formula, 419 Medal, C., 14 Mehra, J., 34 Meissner, L., 52 Metal-cycopentadienyl (M–Cp), 534 Metal hydrides, 136–139, 500 677 Metal-oxide semiconductor, 362 Metal-sigma interactions, 500 Metropolis method, 257, 296 Mirsky, A., 16 Model core potential, 209–247 Molar extinction coefficient, 456 MOLCAS, 118, 238 Molecular biology, 13–15, 482 Molecular electrostatic potential (MEPs), 347, 349–350, 360, 361, 363–365, 367, 374, 379 Molecular engineering, 347–380 Molecular mechanics, 3–4, 558–560, 563 Molecular orbital (MO) theory, 5, 15, 22, 294, 350, 352–353, 426 Molecular tailoring approach (MTA), 194, 536, 537 Moore, G.E., 35 Moore’s law, 35 MO theory See Molecular orbital (MO) theory MRCC See Multireference coupled cluster (MRCC) Mulliken, R.S., 1, 5, 20–22, 27, 590, 600, 609, 614, 633, 634 Multicenter proton acceptors, 495–514 Multiconfiguration quasi-degenerate perturbation theory, 229 Multi-reference, 35, 37–42, 48–54, 57–59, 69–100, 238, 240 Multi-reference Brillouin–Wigner perturbation theory, 42, 52 Multireference coupled cluster (MRCC), 52, 71, 72, 82, 88 Multi-reference functions, 39, 48, 49, 58 Multi-reference RayleighSchrăodinger perturbation theory, 4042, 52 Mutation, 385, 386, 549, 550, 658, 667 M05-2X, 355, 520, 546, 649, 666 M06-2X, 444, 520 N NAMD, 393 Nanocrystal, 186, 187, 646 Nano-scale phenomena, 320 Natural spin-orbitals, 421 Natural spinors, 235, 238, 421 NEGF See Non-equilibrium Green’s function (NEGF) Neogr´ady, P., 43 NH4 C -(H2 )n clusters, 504 Ni-Fe Sulfide, 645, 653 Nobel Prize, 5, 11, 22, 23, 27 Nodeless orbitals, 212–214 678 Non-bonded interaction, 8–10, 355, 440, 518, 520, 522, 530, 537, 541, 546, 550 Noncovalent interaction, 479–482, 518–543, 546, 547, 550, 649 Non-equilibrium Green’s function (NEGF), 320, 327, 331, 342 Nonlinear eigenproblem, 170, 194 Non-linear optical properties, 129–163 Non-relativistic cusp condition, 308 Non-relativistic local energy, 294 Nuclear physics, 38, 59 Nucleic acid base, 645–668 Number of internet users, 35, 36 Numerov–Cooley (NC), 135–139, 485 Nyholm, R.J., O Oliphant–Adamowicz coupled cluster model, 72 Oppenheimer, J.R., 34, 136, 266, 352, 461, 548 Organic nanostructures, 320 Organoxenon complexes, 241 Origin of life, 645–668 Orthogonalization, 181, 186 P Paldus, J., 38, 39, 82, 91, 92 Parr, R.G., 23, 24 PARSEC See Pseudopotential algorithm for real-space electronic calculations (PARSEC) Pauli exclusion principle, Pepsin, 14 Perturbation theory (PT), 38, 39, 51, 57, 58, 69, 70, 112, 117, 161, 229, 230, 233–237, 240, 247, 633 Perturbation theory, a posteriori corrections to, 43, 52, 57 Perturbation theory, Brillouin–Wigner, 39–44, 48, 52, 53 Perturbation theory, many-body, 39, 43, 51, 256 Perturbation theory, multi-reference, 40–42, 52, 53 Perturbation theory, RayleighSchrăodinger, 4042, 52, 53 Perutz, M., 15 Phenylalanine, 520, 522, 523 Photoadduct, 386, 405 6-4 Photoadduct, 386 Photodimerization, 385–411, 437 Pittner, J., 40, 52 Index Plasmonic, 367–368, 370–374, 379, 380 Polanyi, M., 1, 28 Polarizabilities, 64, 108, 109, 123, 124, 130, 132, 133, 145, 154–156, 162, 533 Polarizable continuum model (PCMs), 467, 468, 534, 535, 540 Polarization functions, 465 Polycyclic aromatic hydrocarbons (PAHs), 428, 436 Pople, J., 1, 11, 23 Posteriori adjustments, 38 Posteriori corrections to Brillouin–Wigner perturbation theory, 43, 51–52 Powell, H.M., Power of contemporary computers, 35 Protein data bank (PDB), 520, 527, 528, 530, 539, 542, 543, 548, 550 Protein folding, 549 Pseudopotential, 160, 168, 169, 186, 205, 209–212, 215, 218, 222, 223, 234, 244, 265, 269, 311, 649 Pseudopotential algorithm for real-space electronic calculations (PARSEC), 169, 172, 181, 184–187 Pseudo-valence orbital, 211, 212, 244 Pure vibrational contribution, 132, 134–137, 142, 145, 147, 148 Pyrimidine dimer, 385–387 Pyrite, 646, 651, 653, 654, 667 Pyrrole, 145–149, 340 Q Quantum chemical methods, 34, 37, 38, 52, 54, 470, 530, 559, 560, 580, 595, 596, 632, 634 Quantum field theory, 31 Quantum many-body theories, 35 Quantum Monte Carlo (QMC), 255–288, 293–316 Quantum theory of atoms in molecules (QTAIM), 504–510, 512 Quantum yield, 388, 392, 394–402, 404–411 R Rate constants, 650, 658, 667 RayleighRitz method, 181 RayleighSchrăodinger, 38, 4047, 5153, 64, 231 RayleighSchrăodinger formalism, 40 RayleighSchrăodinger perturbation theory, 4043, 45, 51–53, 231 Real-space method, 168, 169, 172 Index Rechenberg, H., 34 Reduced density matrix (RDM), 419–421, 423–425, 442, 443 Relativistic Brillouin–Wigner methods, 59 Relativistic cusp correction, 309, 314 Relativistic effect, 103–126, 131, 136, 138, 139, 195, 211, 222–238, 245, 247, 294, 309, 316 Relativistic effects, 103–126, 131, 136, 138, 139, 195, 211, 222–238, 245, 247, 294, 309, 316 Relativistic Hamiltonian, 105, 115, 117, 247, 294, 298, 300, 307 Relativistic many-body Brillouin–Wigner methods, 59 Relativistic QMC method, 295 Renn, J., 34 Roberts, J.M., 20, 21, 35 Rockefeller, 14 Rotatory strength, 456, 461, 464, 465, 470 R4QMC program, 311, 314 Rydberg–Klein–Reese (RKR) approach, 96–99 S Sayre, D., 11, 12, 14 Scalar mass velocity (MV), 106 Scalar-relativistic effects, 211, 222–226, 245 Scanning tunneling microscope (STM), 200, 361 Schrăodinger, E., 15 SCS-CCSD, 520 SCS-MP2, 520, 546 Selenazofurin, 492, 494 Selenazoles, 493 Self consistent field, 74, 169, 270, 329, 464 Shavitt, I., 39 Sidgwick, N.V., Silver, D.M., 39 Single crystal, 12, 196 Single-reference CC theory, 70 Singular value decomposition, 421 Si-PETN, 490, 491 Snowflakes, 2, Solid state physics, 38, 464 Sommerfeld, A., 10, 15, 104 Spectrum slicing, 181–184 Spin-forbidden radiative transitions, 222 Spin orbital, 70, 72, 73, 75, 80, 81, 83, 125, 126, 268, 352, 417, 418, 421, 426 Spin-orbit coupling (SOC), 205, 211, 212, 215, 219, 222, 223, 226–235, 237, 238, 244–246 Spin-orbit effect, 212, 219 679 Spin-orbit operator, 219, 304 Spintronic, 319–344 SSMRCC See State specific MRCC (SSMRCC) Stacking interaction, 321, 343, 519, 520, 535, 537, 546, 550 Staemmler, V., 52 State specific, 35, 37, 40, 41, 47, 48, 51–53, 69–100, 237 State specific MRCC (SSMRCC), 71–77, 79 State-specific multi-reference correlation problem, 35 Statistical overlap, 417, 425 Steiner, M.M., 41 Stereochemistry, 3, 456, 557, 558, 576 Strong orthogonality constraint, 211, 214 Structural chemistry, 1–28, 422, 438 Super-magnetoresistance (SMR), 320, 335, 338 Super-refraction, 320 Surface-plasmon excitation, 323 T Tautomerism, 648 Teller, E., 19 Theory of resonance, 15–19 Thermodynamics, 597, 602, 650, 651, 653, 654, 656, 657, 667 Thiazoles, 493 Thiones, 140, 141, 566, 569 Thymine, 287, 385–411, 438, 648, 652, 653, 659, 667 Thymine-thymine dimer (TT dimer), 386–388, 394, 396, 398–400, 406–411 Tiazofurin, 492–494 Topochemical rules, 387 n *-Transition, 430–432   *-Transition, 431 Transition metal systems, 200, 220, 221, 223, 230, 239, 240, 246, 266, 288, 500, 522, 532, 549, 606, 649, 653, 654 Trinucleotide, 388, 406–411 Tryptophan, 520, 522, 523 Tsipis, C., 52 TT dimer See Thymine-thymine dimer (TT dimer) TT dimerization, 388–392, 396–399, 402 Tyrosine, 520, 522, 523 U Ultrafast DNA sequencing, 320, 344 Unlinked diagrams, 38, 58 680 V Valence-bond theory (VB theory), 15, 20, 271 Valence orbital, 124, 210–212, 214–216, 219, 226, 232, 244, 245, 274 Valence photoisomerization, 438 Valence shell electron pair repulsion (VSEPR), 5–8 van der Waals interaction, 465, 647 Variance minimization technique, 278, 279, 307, 311 Variational Monte Carlo (VMC), 256–258, 260, 263, 266, 267, 277, 282, 294, 295, 297–298, 307, 311, 313–315 VB theory See Valence-bond theory (VB theory) Vibrational contributions, 131–137, 140–143, 145–149, 153, 154, 158, 161, 163 Vibrational electronics (Vibronics), 348–349, 362, 363, 365, 367–370, 374, 379, 380 Violarite, 646, 650 Viral DNA, 518 W Walker, 258, 260–266, 274, 275, 277–279, 282, 283, 286, 297, 299–302, 307 Watson, R.E., 14, 287 Weakly coupled subsystems, 433–434 Index Weaver, W., 14 Well-tempered basis sets (WTBS), 220, 231, 232 Wenzel, W., 41 Westheimer, F., 3–4 Wheland, G., 15, 16 Wiberg bond indices, 417, 427 Wigner–Witmer rules, 28 William Astbury, 14, 17 Wilson, S., 33–64 X X-ray crystallography, 10–12, 14, 15, 17, 387 Z Zeroth order regular approximation (ZORA), 117, 295, 304–309, 311, 312, 314, 315 Zigzag, 335, 336, 356, 358–360, 373, 627 Ziman, J., 37 ZnS, 131–134 ZORA See Zeroth order regular approximation (ZORA) ZORA local energy, 307, 315 ZORA pseudo local energy, 307 ZPVA contribution, 134, 135, 163 .. .Practical Aspects of Computational Chemistry I Jerzy Leszczynski • Manoj K Shukla Editors Practical Aspects of Computational Chemistry I An Overview of the Last Two Decades and Current Trends. .. assemblies and is written by A.S Mahadevi and G.N Sastry In the Chap 19, Oleg Shishkin and Svitlana Shishkina discuss the conformational analysis of cyclohexene, its derivatives and heterocyclic analogues... , depending on the nature of the ligands X and Y This is depicted in Fig 1.5 [19] These geometrical variations and constancies could be visualized as if the two oxygen ligands were firmly attached